# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:54:12 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopropanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNC2(CC2)C(O)=O)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
 5PA  5PA  '1-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopropanecarboxylic acid'  ligand  39  22  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5PA
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
 5PA  C4    C  CR6   0   0.021   0.8811  -0.0789  -0.4570
 5PA  C4A   C  CH2   0  -0.332  -0.4445  -0.4095  -1.1001
 5PA  P     P  P     0   1.456  -0.7035  -0.4550   4.3487
 5PA  O1P   O  O     0  -0.706  -1.9766  -1.1818   4.1950
 5PA  O2P   O  OH1   0  -0.727   0.2752  -0.8816   5.5294
 5PA  O3P   O  OH1   0  -0.737  -0.9902   1.1102   4.4866
 5PA  O4P   O  O2    0  -0.592   0.3552  -0.6280   3.1639
 5PA  C5A   C  CH2   0  -0.217  -0.0854  -0.5371   1.8136
 5PA  C5    C  CR6   0  -0.069   1.0684  -0.1565   0.9271
 5PA  N1    N  N     0  -0.408   3.3654   0.4477   0.6729
 5PA  C6    C  CR16  0  -0.143   2.3272   0.1177   1.4360
 5PA  C2    C  CR6   0   0.129   3.2152   0.5311  -0.6373
 5PA  C2A   C  CH3   0  -0.720   4.4010   0.9049  -1.4723
 5PA  C3    C  CR6   0   0.263   1.9770   0.2726  -1.2469
 5PA  O3    O  OH1   0  -0.645   1.9070   0.3661  -2.5808
 5PA  N     N  NH1   0  -0.681  -0.7080   0.4588  -2.2460
 5PA  C8    C  CT    0   0.023  -1.8388   0.0740  -3.0399
 5PA  C7    C  C     0   0.562  -1.5882  -0.9379  -4.1072
 5PA  O7    O  O     0  -0.450  -2.4532  -1.3813  -4.8239
 5PA  O8    O  OH1   0  -0.587  -0.3176  -1.2993  -4.1897
 5PA  C9    C  CH2   0  -0.466  -3.2282   0.0495  -2.4364
 5PA  C10   C  CH2   0  -0.480  -2.8602   1.1256  -3.3897
 5PA  H4A1  H  HCH2  0   0.281  -0.4119  -1.4445  -1.4524
 5PA  H4A2  H  HCH2  0   0.254  -1.2596  -0.3611  -0.3729
 5PA  HOP2  H  HOH1  0   0.506  -0.1405  -0.9000   6.4022
 5PA  HOP3  H  HOH1  0   0.497  -0.2168   1.6678   4.6468
 5PA  H5A1  H  HCH2  0   0.254  -0.8837   0.2064   1.7098
 5PA  H5A2  H  HCH2  0   0.266  -0.5020  -1.5014   1.5115
 5PA  H6    H  HCR6  0   0.254   2.5178   0.0750   2.5003
 5PA  H2A1  H  HCH3  0   0.244   4.6238   0.1439  -2.2222
 5PA  H2A2  H  HCH3  0   0.245   4.2331   1.8397  -2.0109
 5PA  H2A3  H  HCH3  0   0.244   5.2776   1.0282  -0.8397
 5PA  HO3   H  HOH1  0   0.484   0.9454   0.3907  -2.8230
 5PA  HN    H  HNH1  0   0.388  -0.8121   1.4165  -1.9317
 5PA  HO8   H  HOH1  0   0.486  -0.2073  -1.9589  -4.8913
 5PA  H91   H  HCH2  0   0.272  -3.9111  -0.7240  -2.7605
 5PA  H92   H  HCH2  0   0.276  -3.2964   0.3022  -1.3857
 5PA  H101  H  HCH2  0   0.279  -2.6766   2.1189  -2.9992
 5PA  H102  H  HCH2  0   0.278  -3.2783   1.1072  -4.3869

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
 5PA  C4   C4A   single    1.510  0.020  1.510
 5PA  C4   C5    aromatic  1.399  0.020  1.399
 5PA  C4   C3    aromatic  1.396  0.020  1.396
 5PA  C4A  N     single    1.462  0.020  1.462
 5PA  C4A  H4A1  single    0.970  0.020  1.090
 5PA  C4A  H4A2  single    0.970  0.020  1.090
 5PA  P    O1P   double    1.474  0.020  1.474
 5PA  P    O2P   single    1.592  0.020  1.592
 5PA  P    O3P   single    1.597  0.020  1.597
 5PA  P    O4P   single    1.598  0.020  1.598
 5PA  O2P  HOP2  single    0.850  0.020  0.980
 5PA  O3P  HOP3  single    0.850  0.020  0.980
 5PA  O4P  C5A   single    1.423  0.020  1.423
 5PA  C5A  C5    single    1.504  0.020  1.504
 5PA  C5A  H5A1  single    0.970  0.020  1.090
 5PA  C5A  H5A2  single    0.970  0.020  1.090
 5PA  C5   C6    aromatic  1.385  0.020  1.385
 5PA  N1   C6    aromatic  1.330  0.020  1.330
 5PA  N1   C2    aromatic  1.321  0.020  1.321
 5PA  C6   H6    single    0.930  0.020  1.080
 5PA  C2   C2A   single    1.498  0.020  1.498
 5PA  C2   C3    aromatic  1.404  0.020  1.404
 5PA  C2A  H2A1  single    0.970  0.020  1.090
 5PA  C2A  H2A2  single    0.970  0.020  1.090
 5PA  C2A  H2A3  single    0.970  0.020  1.090
 5PA  C3   O3    single    1.339  0.020  1.339
 5PA  O3   HO3   single    0.850  0.020  0.980
 5PA  N    C8    single    1.434  0.020  1.434
 5PA  N    HN    single    0.890  0.020  1.040
 5PA  C8   C7    single    1.492  0.020  1.492
 5PA  C8   C9    single    1.515  0.020  1.515
 5PA  C8   C10   single    1.507  0.020  1.507
 5PA  C7   O7    double    1.208  0.020  1.208
 5PA  C7   O8    single    1.324  0.020  1.324
 5PA  O8   HO8   single    0.850  0.020  0.980
 5PA  C9   C10   single    1.484  0.020  1.484
 5PA  C9   H91   single    0.970  0.020  1.090
 5PA  C9   H92   single    0.970  0.020  1.090
 5PA  C10  H101  single    0.970  0.020  1.090
 5PA  C10  H102  single    0.970  0.020  1.090

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
 5PA  C3    C4   C5    117.95  3.000
 5PA  C3    C4   C4A   120.22  3.000
 5PA  C5    C4   C4A   121.79  3.000
 5PA  H4A2  C4A  H4A1  106.16  3.000
 5PA  H4A2  C4A  N     111.14  3.000
 5PA  H4A1  C4A  N     108.36  3.000
 5PA  H4A2  C4A  C4    111.19  3.000
 5PA  H4A1  C4A  C4    108.55  3.000
 5PA  N     C4A  C4    111.23  3.000
 5PA  O4P   P    O3P   106.80  3.000
 5PA  O4P   P    O2P    96.52  3.000
 5PA  O3P   P    O2P   108.00  3.000
 5PA  O4P   P    O1P   116.20  3.000
 5PA  O3P   P    O1P   109.71  3.000
 5PA  O2P   P    O1P   118.44  3.000
 5PA  HOP2  O2P  P     114.22  3.000
 5PA  HOP3  O3P  P     115.84  3.000
 5PA  C5A   O4P  P     119.43  3.000
 5PA  H5A2  C5A  H5A1  107.15  3.000
 5PA  H5A2  C5A  C5    110.65  3.000
 5PA  H5A1  C5A  C5    109.35  3.000
 5PA  H5A2  C5A  O4P   108.90  3.000
 5PA  H5A1  C5A  O4P   111.02  3.000
 5PA  C5    C5A  O4P   109.75  3.000
 5PA  C6    C5   C5A   122.06  3.000
 5PA  C6    C5   C4    118.31  3.000
 5PA  C5A   C5   C4    119.63  3.000
 5PA  C2    N1   C6    119.72  3.000
 5PA  H6    C6   N1    115.89  3.000
 5PA  H6    C6   C5    120.90  3.000
 5PA  N1    C6   C5    123.21  3.000
 5PA  C3    C2   C2A   120.14  3.000
 5PA  C3    C2   N1    121.27  3.000
 5PA  C2A   C2   N1    118.59  3.000
 5PA  H2A3  C2A  H2A2  108.28  3.000
 5PA  H2A3  C2A  H2A1  108.31  3.000
 5PA  H2A2  C2A  H2A1  106.82  3.000
 5PA  H2A3  C2A  C2    109.99  3.000
 5PA  H2A2  C2A  C2    111.53  3.000
 5PA  H2A1  C2A  C2    111.76  3.000
 5PA  O3    C3   C2    117.76  3.000
 5PA  O3    C3   C4    122.70  3.000
 5PA  C2    C3   C4    119.54  3.000
 5PA  HO3   O3   C3    107.19  3.000
 5PA  HN    N    C8    110.13  3.000
 5PA  HN    N    C4A   109.68  3.000
 5PA  C8    N    C4A   114.63  3.000
 5PA  C10   C8   C9     58.82  3.000
 5PA  C10   C8   C7    114.90  3.000
 5PA  C9    C8   C7    115.34  3.000
 5PA  C10   C8   N     118.40  3.000
 5PA  C9    C8   N     120.46  3.000
 5PA  C7    C8   N     116.46  3.000
 5PA  O8    C7   O7    123.39  3.000
 5PA  O8    C7   C8    113.02  3.000
 5PA  O7    C7   C8    123.59  3.000
 5PA  HO8   O8   C7    109.88  3.000
 5PA  H92   C9   H91   114.71  3.000
 5PA  H92   C9   C10   118.01  3.000
 5PA  H91   C9   C10   118.87  3.000
 5PA  H92   C9   C8    116.13  3.000
 5PA  H91   C9   C8    118.12  3.000
 5PA  C10   C9   C8     60.33  3.000
 5PA  H102  C10  H101  114.43  3.000
 5PA  H102  C10  C9    118.96  3.000
 5PA  H101  C10  C9    118.40  3.000
 5PA  H102  C10  C8    117.66  3.000
 5PA  H101  C10  C8    116.20  3.000
 5PA  C9    C10  C8     60.86  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
 5PA  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 5PA  CONST_02  N1    C2   C3   C4      0.00   0.0  0
 5PA  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 5PA  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 5PA  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 5PA  CONST_06  C3    C2   N1   C6      0.00   0.0  0
 5PA  CONST_07  C2A   C2   C3   C4    180.00   0.0  0
 5PA  CONST_08  C6    C5   C4   C4A   180.00   0.0  0
 5PA  CONST_09  C2    C3   C4   C4A   180.00   0.0  0
 5PA  CONST_10  C3    C4   C5   C5A   180.00   0.0  0
 5PA  CONST_11  N1    C6   C5   C5A   180.00   0.0  0
 5PA  CONST_12  O3    C3   C4   C5    180.00   0.0  0
 5PA  CONST_13  O3    C3   C2   N1    180.00   0.0  0
 5PA  CONST_14  C2A   C2   N1   C6    180.00   0.0  0
 5PA  CONST_15  H6    C6   C5   C4    180.00   0.0  0
 5PA  CONST_16  HO8   O8   C7   C8    180.00   0.0  0
 5PA  Var_01    C10   C9   C8   N     106.80  30.0  1
 5PA  Var_02    H101  C10  C9   C8   -105.85  30.0  1
 5PA  Var_03    C8    N    C4A  C4    170.51  30.0  3
 5PA  Var_04    O4P   C5A  C5   C4    176.61  30.0  2
 5PA  Var_05    C9    C8   N    C4A    62.00  30.0  3
 5PA  Var_06    N     C4A  C4   C5    144.13  30.0  2
 5PA  Var_07    H2A1  C2A  C2   N1    122.38  30.0  2
 5PA  Var_08    C5    C5A  O4P  P     156.49  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5PA  chir_01  C8  C7  C9  C10  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
 5PA  plan-1  C4   0.020
 5PA  plan-1  C4A  0.020
 5PA  plan-1  C5A  0.020
 5PA  plan-1  C5   0.020
 5PA  plan-1  N1   0.020
 5PA  plan-1  C6   0.020
 5PA  plan-1  C2   0.020
 5PA  plan-1  C2A  0.020
 5PA  plan-1  C3   0.020
 5PA  plan-1  O3   0.020
 5PA  plan-1  H6   0.020
 5PA  plan-2  C8   0.020
 5PA  plan-2  C7   0.020
 5PA  plan-2  O7   0.020
 5PA  plan-2  O8   0.020
 5PA  plan-2  HO8  0.020

