# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 21:24:44 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: [4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN)c1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PMP  PMP  "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE"  ligand  29  16  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PMP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PMP  N1    N  N     0  -0.407  22.2382  10.6103  29.1247
 PMP  C2    C  CR6   0   0.129  23.3733  11.2602  29.3279
 PMP  C2A   C  CH3   0  -0.719  24.0439  11.9002  28.1522
 PMP  C3    C  CR6   0   0.273  23.9563  11.3463  30.6042
 PMP  O3    O  OH1   0  -0.647  25.1143  12.0037  30.7245
 PMP  C4    C  CR6   0   0.028  23.3229  10.7378  31.6925
 PMP  C4A   C  CH2   0  -0.340  23.9565  10.7765  33.0622
 PMP  N4A   N  NH2   0  -0.833  24.7103  12.0134  33.2661
 PMP  C5    C  CR6   0  -0.016  22.1251  10.0595  31.4472
 PMP  C6    C  CR16  0  -0.150  21.6350  10.0272  30.1525
 PMP  C5A   C  CH2   0  -0.292  21.3760   9.3481  32.5287
 PMP  O4P   O  O2    0  -0.582  22.1704   8.2284  32.9553
 PMP  P     P  P     0   1.470  21.8386   7.3737  34.2591
 PMP  O1P   O  O     0  -0.689  22.6724   6.1613  34.3313
 PMP  O2P   O  OH1   0  -0.746  20.2543   7.1402  34.2780
 PMP  O3P   O  OH1   0  -0.745  22.0123   8.4634  35.4121
 PMP  H2A1  H  HCH3  0   0.244  25.0256  11.4622  27.9607
 PMP  H2A2  H  HCH3  0   0.243  23.4343  11.7687  27.2607
 PMP  H2A3  H  HCH3  0   0.243  24.2001  12.9688  28.3091
 PMP  HO3   H  HOH1  0   0.474  25.2429  12.1609  31.7121
 PMP  H4A1  H  HCH2  0   0.251  23.2063  10.6260  33.8416
 PMP  H4A2  H  HCH2  0   0.273  24.6558   9.9411  33.1466
 PMP  HNA1  H  HNH2  0   0.387  25.3604  11.9086  34.0338
 PMP  HNA2  H  HNH2  0   0.379  24.0866  12.7743  33.5064
 PMP  H6    H  HCR6  0   0.250  20.7079   9.5044  29.9379
 PMP  H5A1  H  HCH2  0   0.255  21.1705  10.0166  33.3690
 PMP  H5A2  H  HCH2  0   0.269  20.4175   8.9913  32.1465
 PMP  HOP2  H  HOH1  0   0.496  19.9607   6.3661  33.7779
 PMP  HOP3  H  HOH1  0   0.500  21.9172   8.1282  36.3144

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.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PMP  N1   C2    aromatic  1.324  0.020  1.324
 PMP  N1   C6    aromatic  1.327  0.020  1.327
 PMP  C2   C2A   single    1.497  0.020  1.497
 PMP  C2   C3    aromatic  1.406  0.020  1.406
 PMP  C2A  H2A1  single    0.970  0.020  1.090
 PMP  C2A  H2A2  single    0.970  0.020  1.090
 PMP  C2A  H2A3  single    0.970  0.020  1.090
 PMP  C3   O3    single    1.337  0.020  1.337
 PMP  C3   C4    aromatic  1.399  0.020  1.399
 PMP  O3   HO3   single    0.850  0.020  0.980
 PMP  C4   C4A   single    1.510  0.020  1.510
 PMP  C4   C5    aromatic  1.398  0.020  1.398
 PMP  C4A  N4A   single    1.463  0.020  1.463
 PMP  C4A  H4A1  single    0.970  0.020  1.090
 PMP  C4A  H4A2  single    0.970  0.020  1.090
 PMP  N4A  HNA1  single    0.890  0.020  1.040
 PMP  N4A  HNA2  single    0.890  0.020  1.040
 PMP  C5   C6    aromatic  1.385  0.020  1.385
 PMP  C5   C5A   single    1.496  0.020  1.496
 PMP  C6   H6    single    0.930  0.020  1.080
 PMP  C5A  O4P   single    1.438  0.020  1.438
 PMP  C5A  H5A1  single    0.970  0.020  1.090
 PMP  C5A  H5A2  single    0.970  0.020  1.090
 PMP  O4P  P     single    1.594  0.020  1.594
 PMP  P    O1P   double    1.473  0.020  1.473
 PMP  P    O2P   single    1.602  0.020  1.602
 PMP  P    O3P   single    1.596  0.020  1.596
 PMP  O2P  HOP2  single    0.850  0.020  0.980
 PMP  O3P  HOP3  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PMP  C6    N1   C2    119.13  3.000
 PMP  C3    C2   C2A   120.06  3.000
 PMP  C3    C2   N1    121.68  3.000
 PMP  C2A   C2   N1    118.26  3.000
 PMP  H2A3  C2A  H2A2  108.45  3.000
 PMP  H2A3  C2A  H2A1  106.82  3.000
 PMP  H2A2  C2A  H2A1  108.15  3.000
 PMP  H2A3  C2A  C2    111.70  3.000
 PMP  H2A2  C2A  C2    109.92  3.000
 PMP  H2A1  C2A  C2    111.65  3.000
 PMP  C4    C3   O3    122.43  3.000
 PMP  C4    C3   C2    119.47  3.000
 PMP  O3    C3   C2    118.10  3.000
 PMP  HO3   O3   C3    105.97  3.000
 PMP  C5    C4   C4A   122.08  3.000
 PMP  C5    C4   C3    117.55  3.000
 PMP  C4A   C4   C3    120.32  3.000
 PMP  H4A2  C4A  H4A1  106.21  3.000
 PMP  H4A2  C4A  N4A   107.82  3.000
 PMP  H4A1  C4A  N4A   111.78  3.000
 PMP  H4A2  C4A  C4    108.60  3.000
 PMP  H4A1  C4A  C4    110.83  3.000
 PMP  N4A   C4A  C4    111.37  3.000
 PMP  HNA2  N4A  HNA1  107.07  3.000
 PMP  HNA2  N4A  C4A   110.55  3.000
 PMP  HNA1  N4A  C4A   110.45  3.000
 PMP  C5A   C5   C6    119.19  3.000
 PMP  C5A   C5   C4    122.21  3.000
 PMP  C6    C5   C4    118.59  3.000
 PMP  H6    C6   C5    119.89  3.000
 PMP  H6    C6   N1    116.53  3.000
 PMP  C5    C6   N1    123.58  3.000
 PMP  H5A2  C5A  H5A1  107.69  3.000
 PMP  H5A2  C5A  O4P   109.54  3.000
 PMP  H5A1  C5A  O4P   110.61  3.000
 PMP  H5A2  C5A  C5    110.00  3.000
 PMP  H5A1  C5A  C5    111.05  3.000
 PMP  O4P   C5A  C5    107.96  3.000
 PMP  P     O4P  C5A   123.05  3.000
 PMP  O3P   P    O2P   101.46  3.000
 PMP  O3P   P    O1P   117.70  3.000
 PMP  O2P   P    O1P   116.06  3.000
 PMP  O3P   P    O4P   101.66  3.000
 PMP  O2P   P    O4P   107.08  3.000
 PMP  O1P   P    O4P   111.32  3.000
 PMP  HOP2  O2P  P     114.26  3.000
 PMP  HOP3  O3P  P     115.26  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PMP  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PMP  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PMP  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PMP  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PMP  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PMP  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PMP  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PMP  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PMP  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PMP  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PMP  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PMP  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PMP  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PMP  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PMP  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PMP  CONST_16  H6    C6   C5   C4    180.00   0.0  0
 PMP  Var_01    N4A   C4A  C4   C3     32.65  30.0  2
 PMP  Var_02    O4P   C5A  C5   C4    -67.20  30.0  2
 PMP  Var_03    C5    C4   C4A  N4A  -149.89  30.0  3
 PMP  Var_04    O4P   C5A  C5   C6    111.51  30.0  2
 PMP  Var_05    H2A1  C2A  C2   N1   -117.05  30.0  2
 PMP  Var_06    H2A2  C2A  C2   N1      2.97  30.0  2
 PMP  Var_07    H2A3  C2A  C2   N1    123.40  30.0  2
 PMP  Var_08    H2A1  C2A  C2   C3     62.30  30.0  2
 PMP  Var_09    H2A2  C2A  C2   C3   -177.67  30.0  2
 PMP  Var_10    H2A3  C2A  C2   C3    -57.24  30.0  2
 PMP  Var_11    H4A1  C4A  C4   C3    157.77  30.0  2
 PMP  Var_12    H4A2  C4A  C4   C3    -85.92  30.0  2
 PMP  Var_13    H5A1  C5A  C5   C4     54.21  30.0  2
 PMP  Var_14    H5A2  C5A  C5   C4    173.32  30.0  2
 PMP  Var_15    H4A1  C4A  C4   C5    -24.77  30.0  2
 PMP  Var_16    H4A2  C4A  C4   C5     91.53  30.0  2
 PMP  Var_17    H5A1  C5A  C5   C6   -127.08  30.0  2
 PMP  Var_18    H5A2  C5A  C5   C6     -7.97  30.0  2
 PMP  Var_19    P     O4P  C5A  C5    168.99  30.0  3
 PMP  Var_20    HNA1  N4A  C4A  C4   -161.71  30.0  3
 PMP  Var_21    HNA2  N4A  C4A  C4     79.97  30.0  3
 PMP  Var_22    O1P   P    O4P  C5A   170.43  30.0  3
 PMP  Var_23    O2P   P    O4P  C5A    42.60  30.0  3
 PMP  Var_24    O3P   P    O4P  C5A   -63.41  30.0  3
 PMP  Var_25    H5A1  C5A  O4P  P      47.31  30.0  1
 PMP  Var_26    H5A2  C5A  O4P  P     -71.24  30.0  1

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
 PMP  plan-1  N1   0.020
 PMP  plan-1  C2   0.020
 PMP  plan-1  C2A  0.020
 PMP  plan-1  C3   0.020
 PMP  plan-1  O3   0.020
 PMP  plan-1  C4   0.020
 PMP  plan-1  C4A  0.020
 PMP  plan-1  C5   0.020
 PMP  plan-1  C6   0.020
 PMP  plan-1  C5A  0.020
 PMP  plan-1  H6   0.020

