# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 10:29:37 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-{(2S)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[P@@](O)(=O)C[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)C(O)=O
#
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
 S23  S23  N-{(2S)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine  ligand  56  29  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S23
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
 S23  O2    O  O     0  -0.698  -2.3712   0.5853   1.5179
 S23  P     P  P     0   1.205  -1.2045   1.1985   0.8238
 S23  O1    O  OH1   0  -0.769   0.0913   1.1379   1.8040
 S23  C1    C  CH1   0  -0.338  -1.4768   2.9525   0.3502
 S23  N1    N  NH2   0  -0.788  -2.6131   3.0680  -0.5511
 S23  C2    C  CH3   0  -0.661  -1.6853   3.8139   1.5894
 S23  C3    C  CH2   0  -0.729  -0.6861   0.3485  -0.6942
 S23  C4    C  CH1   0  -0.370  -0.5623  -1.1839  -0.5127
 S23  C6    C  CH2   0  -0.518  -1.5162  -1.9443  -1.4421
 S23  C7    C  CR6   0   0.144  -2.9554  -1.5975  -1.1749
 S23  C8    C  CR16  0  -0.326  -3.6452  -0.7038  -1.9900
 S23  C10   C  CR16  0  -0.238  -4.9603  -0.3516  -1.7124
 S23  C12   C  CR16  0  -0.273  -5.6097  -0.9014  -0.6168
 S23  C11   C  CR16  0  -0.236  -4.9359  -1.8038   0.1972
 S23  C9    C  CR16  0  -0.281  -3.6209  -2.1430  -0.0795
 S23  C5    C  C     0   0.585   0.8838  -1.5714  -0.7735
 S23  O3    O  O     0  -0.481   1.2780  -1.9251  -1.8728
 S23  N2    N  NH1   0  -0.627   1.6990  -1.4252   0.2902
 S23  C13   C  CH1   0  -0.229   3.1228  -1.5841   0.2196
 S23  C14   C  C     0   0.560   3.5597  -2.8378   0.9597
 S23  O4    O  O     0  -0.424   2.8205  -3.5608   1.5735
 S23  O5    O  OH1   0  -0.589   4.8641  -3.0343   0.8422
 S23  C15   C  CH2   0  -0.514   3.8588  -0.3418   0.7556
 S23  C16   C  CR6   0   0.146   3.3418   0.9372   0.1536
 S23  C17   C  CR16  0  -0.290   3.1806   1.0851  -1.2229
 S23  C19   C  CR16  0  -0.241   2.6886   2.2677  -1.7574
 S23  C21   C  CR16  0  -0.262   2.3522   3.3302  -0.9270
 S23  C20   C  CR16  0  -0.255   2.5280   3.2045   0.4440
 S23  C18   C  CR16  0  -0.405   3.0177   2.0148   0.9768
 S23  HO1   H  HOH1  0   0.485   0.9110   1.5079   1.4416
 S23  H1    H  HCH1  0   0.266  -0.5872   3.3069  -0.1813
 S23  HN1   H  HNH2  0   0.360  -2.4152   2.6651  -1.4571
 S23  HN1A  H  HNH2  0   0.351  -3.4225   2.5869  -0.1773
 S23  H2    H  HCH3  0   0.235  -0.8218   3.7836   2.2531
 S23  H2A   H  HCH3  0   0.251  -1.8467   4.8486   1.2887
 S23  H2B   H  HCH3  0   0.234  -2.5582   3.4843   2.1541
 S23  H3    H  HCH2  0   0.290  -1.4232   0.5762  -1.4653
 S23  H3A   H  HCH2  0   0.295   0.2476   0.7999  -1.0434
 S23  H4    H  HCH1  0   0.287  -0.8155  -1.4630   0.5152
 S23  H6    H  HCH2  0   0.256  -1.2637  -1.7221  -2.4803
 S23  H6A   H  HCH2  0   0.261  -1.3646  -3.0171  -1.2999
 S23  H8    H  HCR6  0   0.248  -3.1527  -0.2803  -2.8582
 S23  H10   H  HCR6  0   0.250  -5.4784   0.3464  -2.3577
 S23  H12   H  HCR6  0   0.250  -6.6362  -0.6339  -0.4010
 S23  H11   H  HCR6  0   0.249  -5.4381  -2.2437   1.0495
 S23  H9    H  HCR6  0   0.239  -3.1033  -2.8455   0.5644
 S23  HN2   H  HNH1  0   0.397   1.2932  -1.1880   1.1826
 S23  H13   H  HCH1  0   0.307   3.3847  -1.7270  -0.8310
 S23  HO5   H  HOH1  0   0.488   5.1311  -3.8285   1.3296
 S23  H15   H  HCH2  0   0.268   3.7592  -0.2952   1.8430
 S23  H15A  H  HCH2  0   0.286   4.9247  -0.4459   0.5447
 S23  H17   H  HCR6  0   0.259   3.4356   0.2725  -1.8928
 S23  H19   H  HCR6  0   0.265   2.5633   2.3582  -2.8286
 S23  H21   H  HCR6  0   0.267   1.9621   4.2485  -1.3452
 S23  H20   H  HCR6  0   0.272   2.2843   4.0275   1.1038
 S23  H18   H  HCR6  0   0.283   3.1627   1.9286   2.0485

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
 S23  O2   P     double    1.490  0.020  1.490
 S23  C3   P     single    1.815  0.020  1.815
 S23  P    O1    single    1.626  0.020  1.626
 S23  P    C1    single    1.837  0.020  1.837
 S23  O1   HO1   single    0.850  0.020  0.980
 S23  C1   N1    single    1.455  0.020  1.455
 S23  C1   C2    single    1.523  0.020  1.523
 S23  C1   H1    single    0.970  0.020  1.090
 S23  N1   HN1   single    0.890  0.020  1.040
 S23  N1   HN1A  single    0.890  0.020  1.040
 S23  C2   H2    single    0.970  0.020  1.090
 S23  C2   H2A   single    0.970  0.020  1.090
 S23  C2   H2B   single    0.970  0.020  1.090
 S23  C4   C3    single    1.548  0.020  1.548
 S23  C3   H3    single    0.970  0.020  1.090
 S23  C3   H3A   single    0.970  0.020  1.090
 S23  C6   C4    single    1.534  0.020  1.534
 S23  C4   C5    single    1.520  0.020  1.520
 S23  C4   H4    single    0.970  0.020  1.090
 S23  C7   C6    single    1.504  0.020  1.504
 S23  C6   H6    single    0.970  0.020  1.090
 S23  C6   H6A   single    0.970  0.020  1.090
 S23  C9   C7    aromatic  1.393  0.020  1.393
 S23  C8   C7    aromatic  1.392  0.020  1.392
 S23  C10  C8    aromatic  1.389  0.020  1.389
 S23  C8   H8    single    0.930  0.020  1.080
 S23  C12  C10   aromatic  1.387  0.020  1.387
 S23  C10  H10   single    0.930  0.020  1.080
 S23  C12  C11   aromatic  1.390  0.020  1.390
 S23  C12  H12   single    0.930  0.020  1.080
 S23  C11  C9    aromatic  1.386  0.020  1.386
 S23  C11  H11   single    0.930  0.020  1.080
 S23  C9   H9    single    0.930  0.020  1.080
 S23  O3   C5    double    1.220  0.020  1.220
 S23  C5   N2    single    1.348  0.020  1.348
 S23  C13  N2    single    1.434  0.020  1.434
 S23  N2   HN2   single    0.860  0.020  1.020
 S23  C14  C13   single    1.520  0.020  1.520
 S23  C13  C15   single    1.540  0.020  1.540
 S23  C13  H13   single    0.970  0.020  1.090
 S23  O4   C14   double    1.202  0.020  1.202
 S23  C14  O5    single    1.324  0.020  1.324
 S23  O5   HO5   single    0.850  0.020  0.980
 S23  C15  C16   single    1.505  0.020  1.505
 S23  C15  H15   single    0.970  0.020  1.090
 S23  C15  H15A  single    0.970  0.020  1.090
 S23  C17  C16   aromatic  1.394  0.020  1.394
 S23  C16  C18   aromatic  1.394  0.020  1.394
 S23  C17  C19   aromatic  1.388  0.020  1.388
 S23  C17  H17   single    0.930  0.020  1.080
 S23  C19  C21   aromatic  1.390  0.020  1.390
 S23  C19  H19   single    0.930  0.020  1.080
 S23  C21  C20   aromatic  1.388  0.020  1.388
 S23  C21  H21   single    0.930  0.020  1.080
 S23  C18  C20   aromatic  1.392  0.020  1.392
 S23  C20  H20   single    0.930  0.020  1.080
 S23  C18  H18   single    0.930  0.020  1.080

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
 S23  C3    P    C1   105.89  3.000
 S23  C1    P    O1   108.01  3.000
 S23  C3    P    O1   105.01  3.000
 S23  C1    P    O2   113.39  3.000
 S23  O1    P    O2   109.14  3.000
 S23  C3    P    O2   114.87  3.000
 S23  HO1   O1   P    115.73  3.000
 S23  H1    C1   C2   108.84  3.000
 S23  H1    C1   N1   107.94  3.000
 S23  C2    C1   N1   110.62  3.000
 S23  H1    C1   P    108.28  3.000
 S23  C2    C1   P    110.51  3.000
 S23  N1    C1   P    110.56  3.000
 S23  HN1A  N1   HN1  107.32  3.000
 S23  HN1A  N1   C1   110.95  3.000
 S23  HN1   N1   C1   111.76  3.000
 S23  H2B   C2   H2A  108.14  3.000
 S23  H2B   C2   H2   108.09  3.000
 S23  H2A   C2   H2   108.18  3.000
 S23  H2B   C2   C1   111.09  3.000
 S23  H2A   C2   C1   109.43  3.000
 S23  H2    C2   C1   111.79  3.000
 S23  H3A   C3   H3   105.36  3.000
 S23  H3A   C3   C4   112.18  3.000
 S23  H3    C3   C4   110.09  3.000
 S23  H3A   C3   P    108.51  3.000
 S23  H3    C3   P    107.48  3.000
 S23  C4    C3   P    112.85  3.000
 S23  H4    C4   C5   108.43  3.000
 S23  H4    C4   C6   107.38  3.000
 S23  C5    C4   C6   111.19  3.000
 S23  H4    C4   C3   110.11  3.000
 S23  C5    C4   C3   107.96  3.000
 S23  C6    C4   C3   111.72  3.000
 S23  H6A   C6   H6   106.96  3.000
 S23  H6A   C6   C7   109.63  3.000
 S23  H6    C6   C7   110.08  3.000
 S23  H6A   C6   C4   108.76  3.000
 S23  H6    C6   C4   109.37  3.000
 S23  C7    C6   C4   111.91  3.000
 S23  C9    C7   C8   118.36  3.000
 S23  C8    C7   C6   121.19  3.000
 S23  C9    C7   C6   120.43  3.000
 S23  H8    C8   C10  119.40  3.000
 S23  H8    C8   C7   119.62  3.000
 S23  C10   C8   C7   120.97  3.000
 S23  H10   C10  C12  120.15  3.000
 S23  H10   C10  C8   119.82  3.000
 S23  C12   C10  C8   120.03  3.000
 S23  H12   C12  C11  120.24  3.000
 S23  H12   C12  C10  120.23  3.000
 S23  C11   C12  C10  119.54  3.000
 S23  H11   C11  C9   119.86  3.000
 S23  H11   C11  C12  120.00  3.000
 S23  C9    C11  C12  120.14  3.000
 S23  H9    C9   C11  119.53  3.000
 S23  H9    C9   C7   119.51  3.000
 S23  C11   C9   C7   120.96  3.000
 S23  N2    C5   O3   123.15  3.000
 S23  N2    C5   C4   114.36  3.000
 S23  O3    C5   C4   122.41  3.000
 S23  HN2   N2   C13  117.96  3.000
 S23  HN2   N2   C5   118.71  3.000
 S23  C13   N2   C5   123.33  3.000
 S23  H13   C13  C15  109.01  3.000
 S23  H13   C13  C14  106.95  3.000
 S23  C15   C13  C14  111.01  3.000
 S23  H13   C13  N2   107.45  3.000
 S23  C15   C13  N2   111.58  3.000
 S23  C14   C13  N2   110.65  3.000
 S23  O5    C14  O4   124.17  3.000
 S23  O5    C14  C13  111.24  3.000
 S23  O4    C14  C13  124.60  3.000
 S23  HO5   O5   C14  110.38  3.000
 S23  H15A  C15  H15  106.57  3.000
 S23  H15A  C15  C16  109.83  3.000
 S23  H15   C15  C16  109.29  3.000
 S23  H15A  C15  C13  108.81  3.000
 S23  H15   C15  C13  109.70  3.000
 S23  C16   C15  C13  112.46  3.000
 S23  C18   C16  C17  118.31  3.000
 S23  C18   C16  C15  120.03  3.000
 S23  C17   C16  C15  121.66  3.000
 S23  H17   C17  C19  118.97  3.000
 S23  H17   C17  C16  120.25  3.000
 S23  C19   C17  C16  120.78  3.000
 S23  H19   C19  C21  119.97  3.000
 S23  H19   C19  C17  119.56  3.000
 S23  C21   C19  C17  120.47  3.000
 S23  H21   C21  C20  120.29  3.000
 S23  H21   C21  C19  120.34  3.000
 S23  C20   C21  C19  119.37  3.000
 S23  H20   C20  C18  119.70  3.000
 S23  H20   C20  C21  120.31  3.000
 S23  C18   C20  C21  119.99  3.000
 S23  H18   C18  C20  119.53  3.000
 S23  H18   C18  C16  119.39  3.000
 S23  C20   C18  C16  121.08  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
 S23  CONST_01  C12  C11  C9   C7     0.00   0.0  0
 S23  CONST_02  C12  C10  C8   C7     0.00   0.0  0
 S23  CONST_03  C11  C9   C7   C8     0.00   0.0  0
 S23  CONST_04  C11  C12  C10  C8     0.00   0.0  0
 S23  CONST_05  C9   C7   C8   C10    0.00   0.0  0
 S23  CONST_06  C9   C11  C12  C10    0.00   0.0  0
 S23  CONST_07  C21  C19  C17  C16    0.00   0.0  0
 S23  CONST_08  C21  C20  C18  C16    0.00   0.0  0
 S23  CONST_09  C20  C18  C16  C17    0.00   0.0  0
 S23  CONST_10  C20  C21  C19  C17    0.00   0.0  0
 S23  CONST_11  C18  C16  C17  C19    0.00   0.0  0
 S23  CONST_12  C18  C20  C21  C19    0.00   0.0  0
 S23  CONST_13  C11  C9   C7   C6   180.00   0.0  0
 S23  CONST_14  C10  C8   C7   C6   180.00   0.0  0
 S23  CONST_15  C19  C17  C16  C15  180.00   0.0  0
 S23  CONST_16  C20  C18  C16  C15  180.00   0.0  0
 S23  CONST_17  H11  C11  C9   C7   180.00   0.0  0
 S23  CONST_18  H10  C10  C8   C7   180.00   0.0  0
 S23  CONST_19  H9   C9   C7   C8   180.00   0.0  0
 S23  CONST_20  H12  C12  C10  C8   180.00   0.0  0
 S23  CONST_21  H8   C8   C10  C12  180.00   0.0  0
 S23  CONST_22  H19  C19  C17  C16  180.00   0.0  0
 S23  CONST_23  H20  C20  C18  C16  180.00   0.0  0
 S23  CONST_24  H18  C18  C16  C17  180.00   0.0  0
 S23  CONST_25  H21  C21  C19  C17  180.00   0.0  0
 S23  CONST_26  H17  C17  C19  C21  180.00   0.0  0
 S23  CONST_27  C13  N2   C5   C4   180.00   0.0  0
 S23  CONST_28  C13  N2   C5   O3     0.00   0.0  0
 S23  CONST_29  HN2  N2   C5   C4     0.00   0.0  0
 S23  CONST_30  HO5  O5   C14  C13  180.00   0.0  0
 S23  Var_01    C9   C7   C6   C4   -77.42  30.0  2
 S23  Var_02    C17  C16  C15  C13  -49.21  30.0  2
 S23  Var_03    C4   C3   P    O2   -47.69  30.0  2

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
 S23  chir_02  C1   P   N1   C2   negativ
 S23  chir_03  C4   C3  C6   C5   negativ
 S23  chir_04  C13  N2  C14  C15  positiv
 S23  chir_05  P    C3  O1   C1   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
 S23  plan-1  C6   0.020
 S23  plan-1  C7   0.020
 S23  plan-1  C8   0.020
 S23  plan-1  C10  0.020
 S23  plan-1  C12  0.020
 S23  plan-1  C11  0.020
 S23  plan-1  C9   0.020
 S23  plan-1  H8   0.020
 S23  plan-1  H10  0.020
 S23  plan-1  H12  0.020
 S23  plan-1  H11  0.020
 S23  plan-1  H9   0.020
 S23  plan-2  C15  0.020
 S23  plan-2  C16  0.020
 S23  plan-2  C17  0.020
 S23  plan-2  C19  0.020
 S23  plan-2  C21  0.020
 S23  plan-2  C20  0.020
 S23  plan-2  C18  0.020
 S23  plan-2  H17  0.020
 S23  plan-2  H19  0.020
 S23  plan-2  H21  0.020
 S23  plan-2  H20  0.020
 S23  plan-2  H18  0.020
 S23  plan-3  C4   0.020
 S23  plan-3  C5   0.020
 S23  plan-3  O3   0.020
 S23  plan-3  N2   0.020
 S23  plan-3  C13  0.020
 S23  plan-3  HN2  0.020
 S23  plan-4  C13  0.020
 S23  plan-4  C14  0.020
 S23  plan-4  O4   0.020
 S23  plan-4  O5   0.020
 S23  plan-4  HO5  0.020

