# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:55:14 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  54  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.793  -2.3791   0.3499   2.0653
 S23  P     P  P      0   1.190  -1.1582   0.9629   1.4136
 S23  O1    O  OP    -1  -0.804   0.1944   0.7526   2.1037
 S23  C1    C  CH1    0  -0.336  -1.4531   2.7791   1.2065
 S23  N1    N  NH2    0  -0.799  -2.7148   3.0798   0.5301
 S23  C2    C  CH3    0  -0.662  -1.4197   3.4627   2.5678
 S23  C3    C  CH2    0  -0.714  -1.0264   0.3525  -0.3187
 S23  C4    C  CH1    0  -0.390  -0.7852  -1.1672  -0.4226
 S23  C6    C  CH2    0  -0.484  -1.5746  -1.7841  -1.5833
 S23  C7    C  C      0   0.130  -3.0632  -1.6052  -1.4534
 S23  C8    C  C1     0  -0.320  -3.7939  -0.9540  -2.4438
 S23  C10   C  C1     0  -0.241  -5.1718  -0.8034  -2.3404
 S23  C12   C  C1     0  -0.278  -5.8442  -1.3036  -1.2351
 S23  C11   C  C1     0  -0.242  -5.1266  -1.9530  -0.2369
 S23  C9    C  C1     0  -0.280  -3.7520  -2.0972  -0.3454
 S23  C5    C  C      0   0.566   0.7008  -1.5239  -0.5426
 S23  O3    O  O      0  -0.533   1.0989  -2.3361  -1.3774
 S23  N2    N  NH1    0  -0.649   1.5060  -0.8950   0.3111
 S23  C13   C  CH1    0  -0.186   2.9133  -1.1672   0.4169
 S23  C14   C  C      0   0.406   3.2405  -2.3435   1.3773
 S23  O4    O  O      0  -0.592   2.2921  -2.9252   1.9283
 S23  O5    O  OC    -1  -0.620   4.4558  -2.6041   1.4971
 S23  C15   C  CH2    0  -0.550   3.6491   0.1130   0.8413
 S23  C16   C  CR6    0   0.156   3.5525   1.2007  -0.1910
 S23  C17   C  CR16   0  -0.316   4.5038   1.2928  -1.2051
 S23  C19   C  CR16   0  -0.243   4.4085   2.2668  -2.1907
 S23  C21   C  CR16   0  -0.276   3.3533   3.1700  -2.1775
 S23  C20   C  CR16   0  -0.252   2.3993   3.0901  -1.1706
 S23  C18   C  CR16   0  -0.322   2.4991   2.1144  -0.1873
 S23  H1    H  HCH1   0   0.229  -0.6431   3.1920   0.5941
 S23  HN1   H  HNH2   0   0.345  -2.6687   2.7832  -0.4368
 S23  HN1A  H  HNH2   0   0.334  -3.4509   2.5243   0.9526
 S23  H2    H  HCH3   0   0.225  -0.4568   3.3209   3.0573
 S23  H2A   H  HCH3   0   0.226  -1.5973   4.5340   2.4625
 S23  H2B   H  HCH3   0   0.215  -2.1907   3.0579   3.2267
 S23  H3    H  HCH2   0   0.251  -1.9746   0.5978  -0.8025
 S23  H3A   H  HCH2   0   0.250  -0.2507   0.9053  -0.8565
 S23  H4    H  HCH1   0   0.264  -1.1378  -1.6419   0.5028
 S23  H6    H  HCH2   0   0.234  -1.2402  -1.3428  -2.5256
 S23  H6A   H  HCH2   0   0.247  -1.3489  -2.8511  -1.6455
 S23  H8    H  H      0   0.243  -3.2773  -0.5591  -3.3110
 S23  H10   H  H      0   0.248  -5.7170  -0.2943  -3.1253
 S23  H12   H  H      0   0.248  -6.9174  -1.1896  -1.1496
 S23  H11   H  H      0   0.248  -5.6409  -2.3469   0.6306
 S23  H9    H  H      0   0.236  -3.2081  -2.6027   0.4434
 S23  HN2   H  HNH1   0   0.428   1.0811  -0.2966   1.0351
 S23  H13   H  HCH1   0   0.233   3.2863  -1.4523  -0.5718
 S23  H15   H  HCH2   0   0.240   3.2422   0.4630   1.7951
 S23  H15A  H  HCH2   0   0.249   4.6945  -0.1407   1.0153
 S23  H17   H  HCR6   0   0.241   5.3329   0.5940  -1.2245
 S23  H19   H  HCR6   0   0.249   5.1604   2.3221  -2.9677
 S23  H21   H  HCR6   0   0.249   3.2769   3.9311  -2.9432
 S23  H20   H  HCR6   0   0.246   1.5734   3.7906  -1.1497
 S23  H18   H  HCR6   0   0.253   1.7489   2.0496   0.5918

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     deloc     1.514  0.020  1.514
 S23  C3   P     single    1.841  0.020  1.841
 S23  P    O1    deloc     1.533  0.020  1.533
 S23  P    C1    single    1.852  0.020  1.852
 S23  C1   N1    single    1.463  0.020  1.463
 S23  C1   C2    single    1.524  0.020  1.524
 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    1.542  0.020  1.542
 S23  C3   H3    single    0.970  0.020  1.090
 S23  C3   H3A   single    0.970  0.020  1.090
 S23  C6   C4    single    1.533  0.020  1.533
 S23  C4   C5    single    1.533  0.020  1.533
 S23  C4   H4    single    0.970  0.020  1.090
 S23  C7   C6    single    1.505  0.020  1.505
 S23  C6   H6    single    0.970  0.020  1.090
 S23  C6   H6A   single    0.970  0.020  1.090
 S23  C9   C7    aromatic  1.394  0.020  1.394
 S23  C8   C7    aromatic  1.392  0.020  1.392
 S23  C10  C8    aromatic  1.390  0.020  1.390
 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    1.231  0.020  1.231
 S23  C5   N2    single    1.331  0.020  1.331
 S23  C13  N2    single    1.437  0.020  1.437
 S23  N2   HN2   single    0.860  0.020  1.020
 S23  C14  C13   single    1.553  0.020  1.553
 S23  C13  C15   single    1.536  0.020  1.536
 S23  C13  H13   single    0.970  0.020  1.090
 S23  O4   C14   deloc     1.242  0.020  1.242
 S23  C14  O5    deloc     1.249  0.020  1.249
 S23  C15  C16   single    1.503  0.020  1.503
 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  1.389  0.020  1.389
 S23  C17  H17   single    0.930  0.020  1.080
 S23  C19  C21   aromatic  1.389  0.020  1.389
 S23  C19  H19   single    0.930  0.020  1.080
 S23  C21  C20   aromatic  1.389  0.020  1.389
 S23  C21  H21   single    0.930  0.020  1.080
 S23  C18  C20   aromatic  1.389  0.020  1.389
 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   103.38  3.000
 S23  C1    P    O1   108.99  3.000
 S23  C3    P    O1   108.36  3.000
 S23  C1    P    O2   108.47  3.000
 S23  O1    P    O2   117.54  3.000
 S23  C3    P    O2   109.18  3.000
 S23  H1    C1   C2   108.30  3.000
 S23  H1    C1   N1   107.55  3.000
 S23  C2    C1   N1   109.87  3.000
 S23  H1    C1   P    108.31  3.000
 S23  C2    C1   P    109.67  3.000
 S23  N1    C1   P    113.00  3.000
 S23  HN1A  N1   HN1  105.69  3.000
 S23  HN1A  N1   C1   108.70  3.000
 S23  HN1   N1   C1   110.00  3.000
 S23  H2B   C2   H2A  107.90  3.000
 S23  H2B   C2   H2   107.74  3.000
 S23  H2A   C2   H2   108.36  3.000
 S23  H2B   C2   C1   110.93  3.000
 S23  H2A   C2   C1   110.53  3.000
 S23  H2    C2   C1   111.25  3.000
 S23  H3A   C3   H3   106.52  3.000
 S23  H3A   C3   C4   110.72  3.000
 S23  H3    C3   C4   109.10  3.000
 S23  H3A   C3   P    110.23  3.000
 S23  H3    C3   P    106.27  3.000
 S23  C4    C3   P    113.65  3.000
 S23  H4    C4   C5   106.06  3.000
 S23  H4    C4   C6   107.38  3.000
 S23  C5    C4   C6   110.26  3.000
 S23  H4    C4   C3   108.59  3.000
 S23  C5    C4   C3   112.72  3.000
 S23  C6    C4   C3   111.53  3.000
 S23  H6A   C6   H6   106.38  3.000
 S23  H6A   C6   C7   108.99  3.000
 S23  H6    C6   C7   109.21  3.000
 S23  H6A   C6   C4   109.25  3.000
 S23  H6    C6   C4   109.44  3.000
 S23  C7    C6   C4   113.34  3.000
 S23  C9    C7   C8   118.11  3.000
 S23  C8    C7   C6   120.88  3.000
 S23  C9    C7   C6   121.01  3.000
 S23  H8    C8   C10  119.50  3.000
 S23  H8    C8   C7   119.30  3.000
 S23  C10   C8   C7   121.20  3.000
 S23  H10   C10  C12  120.21  3.000
 S23  H10   C10  C8   119.75  3.000
 S23  C12   C10  C8   120.05  3.000
 S23  H12   C12  C11  120.28  3.000
 S23  H12   C12  C10  120.36  3.000
 S23  C11   C12  C10  119.36  3.000
 S23  H11   C11  C9   119.72  3.000
 S23  H11   C11  C12  120.00  3.000
 S23  C9    C11  C12  120.28  3.000
 S23  H9    C9   C11  119.30  3.000
 S23  H9    C9   C7   119.69  3.000
 S23  C11   C9   C7   121.01  3.000
 S23  N2    C5   O3   123.43  3.000
 S23  N2    C5   C4   115.22  3.000
 S23  O3    C5   C4   121.35  3.000
 S23  HN2   N2   C13  117.50  3.000
 S23  HN2   N2   C5   118.38  3.000
 S23  C13   N2   C5   123.36  3.000
 S23  H13   C13  C15  107.65  3.000
 S23  H13   C13  C14  106.83  3.000
 S23  C15   C13  C14  111.06  3.000
 S23  H13   C13  N2   108.45  3.000
 S23  C15   C13  N2   109.36  3.000
 S23  C14   C13  N2   113.28  3.000
 S23  O5    C14  O4   127.10  3.000
 S23  O5    C14  C13  114.98  3.000
 S23  O4    C14  C13  117.92  3.000
 S23  H15A  C15  H15  106.98  3.000
 S23  H15A  C15  C16  109.87  3.000
 S23  H15   C15  C16  110.07  3.000
 S23  H15A  C15  C13  108.04  3.000
 S23  H15   C15  C13  109.22  3.000
 S23  C16   C15  C13  112.50  3.000
 S23  C18   C16  C17  118.32  3.000
 S23  C18   C16  C15  121.40  3.000
 S23  C17   C16  C15  120.25  3.000
 S23  H17   C17  C19  119.45  3.000
 S23  H17   C17  C16  119.49  3.000
 S23  C19   C17  C16  121.05  3.000
 S23  H19   C19  C21  120.08  3.000
 S23  H19   C19  C17  119.83  3.000
 S23  C21   C19  C17  120.09  3.000
 S23  H21   C21  C20  120.31  3.000
 S23  H21   C21  C19  120.28  3.000
 S23  C20   C21  C19  119.42  3.000
 S23  H20   C20  C18  119.70  3.000
 S23  H20   C20  C21  120.03  3.000
 S23  C18   C20  C21  120.27  3.000
 S23  H18   C18  C20  120.09  3.000
 S23  H18   C18  C16  119.06  3.000
 S23  C20   C18  C16  120.85  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  Var_01    C9   C7   C6   C4   -58.65  30.0  2
 S23  Var_02    C17  C16  C15  C13  -89.16  30.0  2
 S23  Var_03    C4   C3   P    O2   -64.27  30.0  1

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

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

