diff --git a/links_and_mods.cif b/links_and_mods.cif index 8ed65e99c..1d8cb64fb 100644 --- a/links_and_mods.cif +++ b/links_and_mods.cif @@ -5256,7 +5256,7 @@ _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd -LYS-PLP 1 NZ 2 C4A DOUBLE 1.270 0.0174 +LYS-PLP 1 NZ 2 C4A DOUBLE 1.269 0.0164 loop_ _chem_link_angle.link_id @@ -5268,9 +5268,9 @@ _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd -LYS-PLP 1 CE 1 NZ 2 C4A 118.382 1.50 -LYS-PLP 2 C4 2 C4A 1 NZ 122.438 1.52 -LYS-PLP 1 NZ 2 C4A 2 H4A 118.729 1.50 +LYS-PLP 1 CE 1 NZ 2 C4A 118.355 1.81 +LYS-PLP 2 C4 2 C4A 1 NZ 122.167 2.29 +LYS-PLP 1 NZ 2 C4A 2 H4A 118.654 1.50 loop_ _chem_link_tor.link_id @@ -5286,7 +5286,9 @@ _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period -LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.00 2 +LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.0 2 +LYS-PLP sp2_sp2_2 2 C3 2 C4 2 C4A 1 NZ 180.000 5.0 2 +LYS-PLP sp2_sp3_2 2 C4A 1 NZ 1 CE 1 CD 120.000 20.0 6 loop_ _chem_link_plane.link_id @@ -11442,7 +11444,7 @@ _chem_mod_atom.new_charge LYSmod4 delete HZ1 . H H 0 LYSmod4 delete HZ2 . H H 0 LYSmod4 delete HZ3 . H H 0 -LYSmod4 change NZ . N N 0 +LYSmod4 change NZ . N N20 0 loop_ _chem_mod_bond.mod_id @@ -11457,7 +11459,7 @@ _chem_mod_bond.new_value_dist_nucleus_esd LYSmod4 delete NZ HZ1 single . . . . LYSmod4 delete NZ HZ2 single . . . . LYSmod4 delete NZ HZ3 single . . . . -LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100 +LYSmod4 change CD CE single 1.524 0.0136 1.524 0.0136 loop_ _chem_mod_angle.mod_id @@ -11483,7 +11485,7 @@ _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd -LYSmod4 delete CD CE NZ HZ1 . . +LYSmod4 delete CD CE NZ HZ3 . . data_mod_PLPmod1 loop_ @@ -11507,8 +11509,6 @@ _chem_mod_bond.new_value_dist_esd _chem_mod_bond.new_value_dist_nucleus _chem_mod_bond.new_value_dist_nucleus_esd PLPmod1 delete C4A O4A double . . . . -PLPmod1 change C4 C4A single 1.459 0.0148 1.459 0.0148 -PLPmod1 change C4A H4A single 0.975 0.010 1.082 0.013 loop_ _chem_mod_angle.mod_id @@ -11520,7 +11520,7 @@ _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd PLPmod1 delete C4 C4A O4A . . PLPmod1 delete O4A C4A H4A . . -PLPmod1 change C4 C4A H4A 118.833 1.50 +PLPmod1 change C4 C4A H4A 119.178 1.50 loop_ _chem_mod_tor.mod_id @@ -11543,17 +11543,6 @@ PLPmod1 delete plan-2 C4 0.020 PLPmod1 delete plan-2 C4A 0.020 PLPmod1 delete plan-2 H4A 0.020 PLPmod1 delete plan-2 O4A 0.020 -PLPmod1 delete plan-1 C2 0.020 -PLPmod1 delete plan-1 C2A 0.020 -PLPmod1 delete plan-1 C3 0.020 -PLPmod1 delete plan-1 C4 0.020 -PLPmod1 delete plan-1 C4A 0.020 -PLPmod1 delete plan-1 C5 0.020 -PLPmod1 delete plan-1 C5A 0.020 -PLPmod1 delete plan-1 C6 0.020 -PLPmod1 delete plan-1 H6 0.020 -PLPmod1 delete plan-1 N1 0.020 -PLPmod1 delete plan-1 O3 0.020 data_mod_TRPmod1 loop_ diff --git a/list/mon_lib_list.cif b/list/mon_lib_list.cif index a49cb2b58..1ee519b44 100644 --- a/list/mon_lib_list.cif +++ b/list/mon_lib_list.cif @@ -41597,7 +41597,7 @@ _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd -LYS-PLP 1 NZ 2 C4A DOUBLE 1.270 0.0174 +LYS-PLP 1 NZ 2 C4A DOUBLE 1.269 0.0164 loop_ _chem_link_angle.link_id @@ -41609,9 +41609,9 @@ _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd -LYS-PLP 1 CE 1 NZ 2 C4A 118.382 1.50 -LYS-PLP 2 C4 2 C4A 1 NZ 122.438 1.52 -LYS-PLP 1 NZ 2 C4A 2 H4A 118.729 1.50 +LYS-PLP 1 CE 1 NZ 2 C4A 118.355 1.81 +LYS-PLP 2 C4 2 C4A 1 NZ 122.167 2.29 +LYS-PLP 1 NZ 2 C4A 2 H4A 118.654 1.50 loop_ _chem_link_tor.link_id @@ -41627,7 +41627,9 @@ _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period -LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.00 2 +LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.0 2 +LYS-PLP sp2_sp2_2 2 C3 2 C4 2 C4A 1 NZ 180.000 5.0 2 +LYS-PLP sp2_sp3_2 2 C4A 1 NZ 1 CE 1 CD 120.000 20.0 6 loop_ _chem_link_plane.link_id @@ -47783,7 +47785,7 @@ _chem_mod_atom.new_charge LYSmod4 delete HZ1 . H H 0 LYSmod4 delete HZ2 . H H 0 LYSmod4 delete HZ3 . H H 0 -LYSmod4 change NZ . N N 0 +LYSmod4 change NZ . N N20 0 loop_ _chem_mod_bond.mod_id @@ -47798,7 +47800,7 @@ _chem_mod_bond.new_value_dist_nucleus_esd LYSmod4 delete NZ HZ1 single . . . . LYSmod4 delete NZ HZ2 single . . . . LYSmod4 delete NZ HZ3 single . . . . -LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100 +LYSmod4 change CD CE single 1.524 0.0136 1.524 0.0136 loop_ _chem_mod_angle.mod_id @@ -47824,7 +47826,7 @@ _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd -LYSmod4 delete CD CE NZ HZ1 . . +LYSmod4 delete CD CE NZ HZ3 . . data_mod_PLPmod1 loop_ @@ -47848,8 +47850,6 @@ _chem_mod_bond.new_value_dist_esd _chem_mod_bond.new_value_dist_nucleus _chem_mod_bond.new_value_dist_nucleus_esd PLPmod1 delete C4A O4A double . . . . -PLPmod1 change C4 C4A single 1.459 0.0148 1.459 0.0148 -PLPmod1 change C4A H4A single 0.975 0.010 1.082 0.013 loop_ _chem_mod_angle.mod_id @@ -47861,7 +47861,7 @@ _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd PLPmod1 delete C4 C4A O4A . . PLPmod1 delete O4A C4A H4A . . -PLPmod1 change C4 C4A H4A 118.833 1.50 +PLPmod1 change C4 C4A H4A 119.178 1.50 loop_ _chem_mod_tor.mod_id @@ -47884,17 +47884,6 @@ PLPmod1 delete plan-2 C4 0.020 PLPmod1 delete plan-2 C4A 0.020 PLPmod1 delete plan-2 H4A 0.020 PLPmod1 delete plan-2 O4A 0.020 -PLPmod1 delete plan-1 C2 0.020 -PLPmod1 delete plan-1 C2A 0.020 -PLPmod1 delete plan-1 C3 0.020 -PLPmod1 delete plan-1 C4 0.020 -PLPmod1 delete plan-1 C4A 0.020 -PLPmod1 delete plan-1 C5 0.020 -PLPmod1 delete plan-1 C5A 0.020 -PLPmod1 delete plan-1 C6 0.020 -PLPmod1 delete plan-1 H6 0.020 -PLPmod1 delete plan-1 N1 0.020 -PLPmod1 delete plan-1 O3 0.020 data_mod_TRPmod1 loop_ diff --git a/p/PLP.cif b/p/PLP.cif index e073b1b69..2e29b1a26 100644 --- a/p/PLP.cif +++ b/p/PLP.cif @@ -1,4 +1,3 @@ -# data_comp_list loop_ _chem_comp.id @@ -8,77 +7,109 @@ _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level -PLP PLP "PYRIDOXAL-5'-PHOSPHATE" NON-POLYMER 24 16 . -# +PLP PLP "PYRIDOXAL-5'-PHOSPHATE" NON-POLYMER 24 16 . + data_comp_PLP -# + loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id +_chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z -PLP N1 N NRD6 0 -14.349 14.133 -7.922 -PLP C2 C CR6 0 -13.036 14.180 -7.687 -PLP C2A C CH3 0 -12.425 15.509 -7.369 -PLP C3 C CR6 0 -12.261 13.000 -7.741 -PLP O3 O OH1 0 -10.904 13.013 -7.504 -PLP C4 C CR6 0 -12.891 11.771 -8.047 -PLP C4A C C1 0 -12.092 10.543 -8.105 -PLP O4A O O 0 -11.093 10.379 -8.767 -PLP C5 C CR6 0 -14.279 11.764 -8.290 -PLP C6 C CR16 0 -14.950 12.958 -8.215 -PLP C5A C CH2 0 -15.027 10.500 -8.621 -PLP O4P O O2 0 -15.090 9.616 -7.458 -PLP P P P 0 -15.802 8.170 -7.537 -PLP O1P O O 0 -14.929 7.329 -8.450 -PLP O2P O OP -1 -15.838 7.649 -6.113 -PLP O3P O OP -1 -17.184 8.420 -8.109 -PLP H2A1 H H 0 -11.473 15.414 -7.212 -PLP H2A2 H H 0 -12.846 15.874 -6.573 -PLP H2A3 H H 0 -12.568 16.115 -8.113 -PLP HO3 H H 0 -10.588 12.646 -6.792 -PLP H4A H H 0 -12.388 9.814 -7.573 -PLP H6 H H 0 -15.872 12.966 -8.373 -PLP H5A1 H H 0 -14.580 10.029 -9.357 -PLP H5A2 H H 0 -15.942 10.714 -8.906 +PLP N1 N1 N N20 0 -1.750 1.637 0.279 +PLP C2 C2 C CR6 0 -2.365 0.534 -0.126 +PLP C2A C2A C CH3 0 -3.814 0.625 -0.493 +PLP C3 C3 C CR6 0 -1.688 -0.696 -0.202 +PLP O3 O3 O OH1 0 -2.463 -1.730 -0.630 +PLP C4 C4 C CR6 0 -0.321 -0.764 0.152 +PLP C4A C4A C C1 0 0.377 -2.058 0.064 +PLP O4A O4A O O 0 -0.125 -3.102 -0.294 +PLP C5 C5 C CR6 0 0.311 0.426 0.576 +PLP C6 C6 C CR16 0 -0.448 1.585 0.616 +PLP C5A C5A C CH2 0 1.763 0.495 0.980 +PLP O4P O4P O O2 0 2.637 0.324 -0.180 +PLP P P P P 0 4.250 0.217 -0.059 +PLP O1P O1P O O 0 4.532 -1.002 0.807 +PLP O2P O2P O OP -1 4.754 0.050 -1.484 +PLP O3P O3P O OP -1 4.718 1.517 0.578 +PLP H2A1 H2A1 H H 0 -3.947 0.318 -1.402 +PLP H2A2 H2A2 H H 0 -4.121 1.543 -0.425 +PLP H2A3 H2A3 H H 0 -4.338 0.074 0.108 +PLP HO3 HO3 H H 0 -2.057 -2.480 -0.678 +PLP H4A H4A H H 0 1.290 -2.090 0.303 +PLP H6 H6 H H 0 -0.040 2.384 0.896 +PLP H5A1 H5A1 H H 0 1.965 -0.210 1.640 +PLP H5A2 H5A2 H H 0 1.968 1.368 1.392 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +PLP N1 N[6a](C[6a]C[6a]C)(C[6a]C[6a]H){1|C<3>,1|C<4>,1|O<2>} +PLP C2 C[6a](C[6a]C[6a]O)(N[6a]C[6a])(CH3){1|H<1>,2|C<3>} +PLP C2A C(C[6a]C[6a]N[6a])(H)3 +PLP C3 C[6a](C[6a]C[6a]C)(C[6a]N[6a]C)(OH){1|C<3>,1|C<4>} +PLP O3 O(C[6a]C[6a]2)(H) +PLP C4 C[6a](C[6a]C[6a]C)(C[6a]C[6a]O)(CHO){1|C<4>,1|H<1>,1|N<2>} +PLP C4A C(C[6a]C[6a]2)(H)(O) +PLP O4A O(CC[6a]H) +PLP C5 C[6a](C[6a]C[6a]C)(C[6a]N[6a]H)(CHHO){1|C<3>,1|O<2>} +PLP C6 C[6a](C[6a]C[6a]C)(N[6a]C[6a])(H){1|C<4>,2|C<3>} +PLP C5A C(C[6a]C[6a]2)(OP)(H)2 +PLP O4P O(CC[6a]HH)(PO3) +PLP P P(OC)(O)3 +PLP O1P O(PO3) +PLP O2P O(PO3) +PLP O3P O(PO3) +PLP H2A1 H(CC[6a]HH) +PLP H2A2 H(CC[6a]HH) +PLP H2A3 H(CC[6a]HH) +PLP HO3 H(OC[6a]) +PLP H4A H(CC[6a]O) +PLP H6 H(C[6a]C[6a]N[6a]) +PLP H5A1 H(CC[6a]HO) +PLP H5A2 H(CC[6a]HO) + loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 -_chem_comp_bond.type -_chem_comp_bond.aromatic +_chem_comp_bond.value_order +_chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd -PLP N1 C2 DOUBLE y 1.330 0.0101 1.330 0.0101 -PLP N1 C6 SINGLE y 1.349 0.0100 1.349 0.0100 -PLP C2 C2A SINGLE n 1.494 0.0100 1.494 0.0100 -PLP C2 C3 SINGLE y 1.400 0.0136 1.400 0.0136 -PLP C3 O3 SINGLE n 1.374 0.0155 1.374 0.0155 -PLP C3 C4 DOUBLE y 1.409 0.0100 1.409 0.0100 -PLP C4 C4A SINGLE n 1.464 0.0111 1.464 0.0111 -PLP C4 C5 SINGLE y 1.403 0.0100 1.403 0.0100 -PLP C4A O4A DOUBLE n 1.210 0.0148 1.210 0.0148 -PLP C5 C6 DOUBLE y 1.368 0.0100 1.368 0.0100 -PLP C5 C5A SINGLE n 1.503 0.0100 1.503 0.0100 -PLP C5A O4P SINGLE n 1.462 0.0104 1.462 0.0104 -PLP O4P P SINGLE n 1.614 0.0178 1.614 0.0178 -PLP P O1P DOUBLE n 1.517 0.0192 1.517 0.0192 -PLP P O2P SINGLE n 1.517 0.0192 1.517 0.0192 -PLP P O3P SINGLE n 1.517 0.0192 1.517 0.0192 -PLP C2A H2A1 SINGLE n 1.089 0.0100 0.971 0.0138 -PLP C2A H2A2 SINGLE n 1.089 0.0100 0.971 0.0138 -PLP C2A H2A3 SINGLE n 1.089 0.0100 0.971 0.0138 -PLP O3 HO3 SINGLE n 0.966 0.0059 0.861 0.0200 -PLP C4A H4A SINGLE n 1.082 0.0130 0.949 0.0200 -PLP C6 H6 SINGLE n 1.082 0.0130 0.935 0.0200 -PLP C5A H5A1 SINGLE n 1.089 0.0100 0.982 0.0107 -PLP C5A H5A2 SINGLE n 1.089 0.0100 0.982 0.0107 +PLP N1 C2 DOUBLE y 1.328 0.0100 1.328 0.0100 +PLP N1 C6 SINGLE y 1.348 0.0100 1.348 0.0100 +PLP C2 C2A SINGLE n 1.496 0.0100 1.496 0.0100 +PLP C2 C3 SINGLE y 1.405 0.0100 1.405 0.0100 +PLP C3 O3 SINGLE n 1.355 0.0122 1.355 0.0122 +PLP C3 C4 DOUBLE y 1.404 0.0113 1.404 0.0113 +PLP C4 C4A SINGLE n 1.467 0.0100 1.467 0.0100 +PLP C4 C5 SINGLE y 1.405 0.0100 1.405 0.0100 +PLP C4A O4A DOUBLE n 1.210 0.0167 1.210 0.0167 +PLP C5 C6 DOUBLE y 1.384 0.0145 1.384 0.0145 +PLP C5 C5A SINGLE n 1.503 0.0100 1.503 0.0100 +PLP C5A O4P SINGLE n 1.462 0.0100 1.462 0.0100 +PLP O4P P SINGLE n 1.620 0.0143 1.620 0.0143 +PLP P O1P DOUBLE n 1.521 0.0200 1.521 0.0200 +PLP P O2P SINGLE n 1.521 0.0200 1.521 0.0200 +PLP P O3P SINGLE n 1.521 0.0200 1.521 0.0200 +PLP C2A H2A1 SINGLE n 1.092 0.0100 0.969 0.0191 +PLP C2A H2A2 SINGLE n 1.092 0.0100 0.969 0.0191 +PLP C2A H2A3 SINGLE n 1.092 0.0100 0.969 0.0191 +PLP O3 HO3 SINGLE n 0.966 0.0059 0.858 0.0200 +PLP C4A H4A SINGLE n 1.085 0.0150 0.948 0.0200 +PLP C6 H6 SINGLE n 1.085 0.0150 0.940 0.0200 +PLP C5A H5A1 SINGLE n 1.092 0.0100 0.986 0.0200 +PLP C5A H5A2 SINGLE n 1.092 0.0100 0.986 0.0200 + loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 @@ -86,45 +117,46 @@ _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd -PLP C2 N1 C6 119.423 1.60 -PLP N1 C2 C2A 119.020 1.50 -PLP N1 C2 C3 120.363 1.50 -PLP C2A C2 C3 120.617 1.50 -PLP C2 C2A H2A1 109.484 1.50 -PLP C2 C2A H2A2 109.484 1.50 -PLP C2 C2A H2A3 109.484 1.50 -PLP H2A1 C2A H2A2 109.339 1.66 -PLP H2A1 C2A H2A3 109.339 1.66 -PLP H2A2 C2A H2A3 109.339 1.66 -PLP C2 C3 O3 120.185 3.00 -PLP C2 C3 C4 119.630 1.50 -PLP O3 C3 C4 120.185 3.00 -PLP C3 O3 HO3 120.000 3.00 -PLP C3 C4 C4A 119.703 1.50 -PLP C3 C4 C5 118.922 1.50 -PLP C4A C4 C5 121.375 2.22 -PLP C4 C4A O4A 125.762 1.85 -PLP C4 C4A H4A 116.796 1.55 -PLP O4A C4A H4A 117.442 1.69 -PLP C4 C5 C6 118.395 1.50 -PLP C4 C5 C5A 121.689 1.50 -PLP C6 C5 C5A 119.916 1.59 -PLP N1 C6 C5 123.267 1.50 -PLP N1 C6 H6 118.102 1.50 -PLP C5 C6 H6 118.631 1.50 -PLP C5 C5A O4P 110.538 2.24 -PLP C5 C5A H5A1 109.800 1.50 -PLP C5 C5A H5A2 109.800 1.50 -PLP O4P C5A H5A1 108.933 1.90 -PLP O4P C5A H5A2 108.933 1.90 -PLP H5A1 C5A H5A2 108.248 1.50 -PLP C5A O4P P 121.496 2.55 -PLP O4P P O1P 105.808 2.07 -PLP O4P P O2P 105.808 2.07 -PLP O4P P O3P 105.808 2.07 -PLP O1P P O2P 112.864 1.69 -PLP O1P P O3P 112.864 1.69 -PLP O2P P O3P 112.864 1.69 +PLP C2 N1 C6 119.145 3.00 +PLP N1 C2 C2A 118.422 1.50 +PLP N1 C2 C3 121.162 1.50 +PLP C2A C2 C3 120.415 1.50 +PLP C2 C2A H2A1 109.858 2.49 +PLP C2 C2A H2A2 109.858 2.49 +PLP C2 C2A H2A3 109.858 2.49 +PLP H2A1 C2A H2A2 109.327 3.00 +PLP H2A1 C2A H2A3 109.327 3.00 +PLP H2A2 C2A H2A3 109.327 3.00 +PLP C2 C3 O3 118.314 2.74 +PLP C2 C3 C4 119.252 1.50 +PLP O3 C3 C4 122.433 2.39 +PLP C3 O3 HO3 108.013 3.00 +PLP C3 C4 C4A 119.391 1.59 +PLP C3 C4 C5 118.809 1.50 +PLP C4A C4 C5 121.800 3.00 +PLP C4 C4A O4A 125.098 2.92 +PLP C4 C4A H4A 117.258 1.50 +PLP O4A C4A H4A 117.644 2.17 +PLP C4 C5 C6 118.248 3.00 +PLP C4 C5 C5A 121.638 1.63 +PLP C6 C5 C5A 120.115 2.42 +PLP N1 C6 C5 123.384 1.78 +PLP N1 C6 H6 117.901 1.50 +PLP C5 C6 H6 118.715 1.50 +PLP C5 C5A O4P 110.300 3.00 +PLP C5 C5A H5A1 109.826 1.50 +PLP C5 C5A H5A2 109.826 1.50 +PLP O4P C5A H5A1 108.466 3.00 +PLP O4P C5A H5A2 108.466 3.00 +PLP H5A1 C5A H5A2 108.241 1.50 +PLP C5A O4P P 121.760 3.00 +PLP O4P P O1P 105.737 3.00 +PLP O4P P O2P 105.737 3.00 +PLP O4P P O3P 105.737 3.00 +PLP O1P P O2P 112.951 3.00 +PLP O1P P O3P 112.951 3.00 +PLP O2P P O3P 112.951 3.00 + loop_ _chem_comp_tor.comp_id _chem_comp_tor.id @@ -135,18 +167,19 @@ _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period -PLP const_sp2_sp2_2 C2A C2 N1 C6 180.000 5.0 2 -PLP const_19 C5 C6 N1 C2 0.000 10.0 2 -PLP sp3_sp3_1 C5 C5A O4P P 180.000 10.0 3 -PLP sp3_sp3_6 C5A O4P P O1P 60.000 10.0 3 -PLP sp2_sp3_1 N1 C2 C2A H2A1 150.000 10.0 6 -PLP const_sp2_sp2_6 C2A C2 C3 O3 0.000 5.0 2 -PLP sp2_sp2_1 C2 C3 O3 HO3 180.000 5.0 2 -PLP const_10 O3 C3 C4 C4A 0.000 10.0 2 -PLP sp2_sp2_3 C3 C4 C4A O4A 180.000 5.0 2 -PLP const_14 C4A C4 C5 C5A 0.000 10.0 2 -PLP sp2_sp3_8 C4 C5 C5A O4P -90.000 10.0 6 -PLP const_17 C5A C5 C6 N1 180.000 10.0 2 +PLP const_0 C2A C2 N1 C6 180.000 0.0 1 +PLP const_1 C5 C6 N1 C2 0.000 0.0 1 +PLP sp3_sp3_1 C5 C5A O4P P 180.000 10.0 3 +PLP sp3_sp3_2 C5A O4P P O1P 60.000 10.0 3 +PLP sp2_sp3_1 N1 C2 C2A H2A1 150.000 20.0 6 +PLP const_2 C2A C2 C3 O3 0.000 0.0 1 +PLP sp2_sp2_1 C2 C3 O3 HO3 180.000 5.0 2 +PLP const_3 O3 C3 C4 C4A 0.000 0.0 1 +PLP sp2_sp2_2 C3 C4 C4A O4A 180.000 5.0 2 +PLP const_4 C4A C4 C5 C5A 0.000 0.0 1 +PLP sp2_sp3_2 C4 C5 C5A O4P -90.000 20.0 6 +PLP const_5 C5A C5 C6 N1 180.000 0.0 1 + loop_ _chem_comp_chir.comp_id _chem_comp_chir.id @@ -155,46 +188,61 @@ _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign -PLP chir_1 P O4P O2P O3P both +PLP chir_1 P O4P O2P O3P both + loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd -PLP plan-1 C2 0.020 -PLP plan-1 C2A 0.020 -PLP plan-1 C3 0.020 -PLP plan-1 C4 0.020 -PLP plan-1 C4A 0.020 -PLP plan-1 C5 0.020 -PLP plan-1 C5A 0.020 -PLP plan-1 C6 0.020 -PLP plan-1 H6 0.020 -PLP plan-1 N1 0.020 -PLP plan-1 O3 0.020 -PLP plan-2 C4 0.020 -PLP plan-2 C4A 0.020 -PLP plan-2 H4A 0.020 -PLP plan-2 O4A 0.020 +PLP plan-1 C2 0.020 +PLP plan-1 C2A 0.020 +PLP plan-1 C3 0.020 +PLP plan-1 C4 0.020 +PLP plan-1 C4A 0.020 +PLP plan-1 C5 0.020 +PLP plan-1 C5A 0.020 +PLP plan-1 C6 0.020 +PLP plan-1 H6 0.020 +PLP plan-1 N1 0.020 +PLP plan-1 O3 0.020 +PLP plan-2 C4 0.020 +PLP plan-2 C4A 0.020 +PLP plan-2 H4A 0.020 +PLP plan-2 O4A 0.020 + +loop_ +_chem_comp_ring_atom.comp_id +_chem_comp_ring_atom.ring_serial_number +_chem_comp_ring_atom.atom_id +_chem_comp_ring_atom.is_aromatic_ring +PLP ring-1 N1 YES +PLP ring-1 C2 YES +PLP ring-1 C3 YES +PLP ring-1 C4 YES +PLP ring-1 C5 YES +PLP ring-1 C6 YES + loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor -PLP SMILES ACDLabs 10.04 O=P(O)(O)OCc1cnc(c(O)c1C=O)C -PLP SMILES_CANONICAL CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O -PLP SMILES CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O -PLP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O -PLP SMILES "OpenEye OEToolkits" 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O -PLP InChI InChI 1.03 InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14) -PLP InChIKey InChI 1.03 NGVDGCNFYWLIFO-UHFFFAOYSA-N +PLP SMILES ACDLabs 10.04 "O=P(O)(O)OCc1cnc(c(O)c1C=O)C" +PLP SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O" +PLP SMILES CACTVS 3.341 "Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O" +PLP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O" +PLP SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O" +PLP InChI InChI 1.03 "InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)" +PLP InChIKey InChI 1.03 NGVDGCNFYWLIFO-UHFFFAOYSA-N + loop_ -_pdbx_chem_comp_description_generator.comp_id -_pdbx_chem_comp_description_generator.program_name -_pdbx_chem_comp_description_generator.program_version -_pdbx_chem_comp_description_generator.descriptor -PLP acedrg 243 "dictionary generator" -PLP acedrg_database 11 "data source" -PLP rdkit 2017.03.2 "Chemoinformatics tool" -PLP refmac5 5.8.0238 "optimization tool" +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +PLP acedrg 331 "dictionary generator" +PLP acedrg_database 12 "data source" +PLP rdkit 2023.03.3 "Chemoinformatics tool" +PLP servalcat 0.4.146 'optimization tool'