# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:23:43 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: (2~{S})-2-azanyl-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-[(1~{R})-3-oxidanylidene-1-phenyl-propyl]sulfanyl-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@H](CC=O)c1ccccc1)C(=O)NCC(O)=O)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
 P9H  P9H  '(2~{S})-2-azanyl-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-[(1~{R})-3-oxidanylidene-1-phenyl-propyl]sulfanyl-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid'  ligand  55  30  .  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_P9H
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
 P9H  N1   N  NH2   0  -0.799  27.9234   5.5782  13.3883
 P9H  C4   C  CR16  0  -0.299  33.6306   7.0140  14.7218
 P9H  C5   C  CR16  0  -0.241  33.8338   5.7567  14.1705
 P9H  C6   C  CR16  0  -0.264  35.0035   5.4813  13.4745
 P9H  C7   C  CR16  0  -0.238  35.9657   6.4723  13.3317
 P9H  C8   C  CR16  0  -0.291  35.7602   7.7306  13.8812
 P9H  C10  C  CH1   0  -0.224  31.7834  11.6282  15.1262
 P9H  C13  C  CH2   0  -0.453  29.3115   7.4815  13.9772
 P9H  C15  C  C     0   0.529  29.9266   6.0219  12.0621
 P9H  C17  C  CH2   0  -0.422  30.9663  14.8501  16.9154
 P9H  N    N  NH1   0  -0.617  30.9147  10.8085  14.3333
 P9H  O    O  O     0  -0.373  35.9292   9.5951  18.2555
 P9H  C1   C  CH2   0  -0.536  35.4954   9.9962  15.9309
 P9H  C11  C  C     0   0.593  30.6442   9.5230  14.6402
 P9H  C12  C  CH2   0  -0.600  30.0591   8.7171  13.5043
 P9H  C14  C  CH1   0  -0.168  28.7647   6.6192  12.8315
 P9H  C16  C  C     0   0.577  31.1320  12.9818  15.3920
 P9H  C18  C  C     0   0.539  29.4846  14.8334  17.2305
 P9H  C2   C  CH1   0  -0.492  34.3294   9.3899  15.1461
 P9H  C3   C  CR6   0   0.137  34.5920   8.0130  14.5863
 P9H  C9   C  CH2   0  -0.593  33.1328  11.8855  14.4274
 P9H  N2   N  NH1   0  -0.624  31.4610  13.5548  16.5583
 P9H  O1   O  O     0  -0.445  30.3659   6.4961  11.0424
 P9H  O2   O  OH1   0  -0.579  30.4430   4.9466  12.6406
 P9H  O3   O  O     0  -0.491  30.8853   9.0364  15.7356
 P9H  O4   O  O     0  -0.478  30.4194  13.5209  14.5625
 P9H  O5   O  OH1   0  -0.590  29.0081  16.0665  17.3207
 P9H  O6   O  O     0  -0.434  28.8302  13.8394  17.4006
 P9H  S    S  S2    0   0.050  33.8888  10.4174  13.6971
 P9H  H1   H  HNH2  0   0.354  27.1818   6.0135  13.9228
 P9H  H2   H  HNH2  0   0.354  27.4628   5.0656  12.6466
 P9H  H4   H  HCR6  0   0.257  32.7146   7.2240  15.2602
 P9H  H5   H  HCR6  0   0.255  33.0761   4.9924  14.2861
 P9H  H6   H  HCR6  0   0.259  35.1643   4.5010  13.0450
 P9H  H7   H  HCR6  0   0.259  36.8791   6.2670  12.7884
 P9H  H8   H  HCR6  0   0.259  36.5211   8.4913  13.7534
 P9H  H9   H  HCH1  0   0.294  31.9570  11.1085  16.0688
 P9H  H10  H  HCH2  0   0.256  28.4564   7.7924  14.5837
 P9H  H11  H  HCH2  0   0.249  29.9438   6.8671  14.6203
 P9H  H12  H  HCH2  0   0.317  31.5017  15.1929  17.8023
 P9H  H13  H  HCH2  0   0.292  31.1652  15.5799  16.1286
 P9H  H14  H  HNH1  0   0.401  30.7055  11.1290  13.3998
 P9H  H15  H  H     0   0.193  36.0429   8.0994  16.9215
 P9H  H16  H  HCH2  0   0.280  36.3834  10.0563  15.2938
 P9H  H17  H  HCH2  0   0.274  35.2581  11.0095  16.2574
 P9H  H18  H  HCH2  0   0.277  30.9073   8.4494  12.8649
 P9H  H19  H  HCH2  0   0.269  29.4120   9.3478  12.8890
 P9H  H20  H  HCH1  0   0.245  28.2434   7.2775  12.1232
 P9H  H21  H  HCH1  0   0.309  33.4538   9.3358  15.7959
 P9H  H22  H  HCH2  0   0.291  33.8201  12.3812  15.1145
 P9H  H23  H  HCH2  0   0.305  32.9934  12.5625  13.5807
 P9H  H24  H  HNH1  0   0.416  31.9822  13.0348  17.2448
 P9H  H25  H  HOH1  0   0.478  31.1938   4.6276  12.1176
 P9H  H26  H  HOH1  0   0.485  28.0682  16.0458  17.5557
 P9H  C    C  C1    0   0.201  35.8469   9.1656  17.1321

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
 P9H  O1   C15  double    1.207  0.020  1.207
 P9H  O2   C15  single    1.326  0.020  1.326
 P9H  C15  C14  single    1.516  0.020  1.516
 P9H  C14  N1   single    1.450  0.020  1.450
 P9H  C14  C13  single    1.535  0.020  1.535
 P9H  C12  C13  single    1.520  0.020  1.520
 P9H  C12  C11  single    1.511  0.020  1.511
 P9H  N    C11  single    1.349  0.020  1.349
 P9H  N    C10  single    1.434  0.020  1.434
 P9H  O4   C16  double    1.219  0.020  1.219
 P9H  S    C9   single    1.806  0.020  1.806
 P9H  S    C2   single    1.830  0.020  1.830
 P9H  C9   C10  single    1.541  0.020  1.541
 P9H  C11  O3   double    1.223  0.020  1.223
 P9H  C7   C8   aromatic  1.388  0.020  1.388
 P9H  C7   C6   aromatic  1.389  0.020  1.389
 P9H  C10  C16  single    1.526  0.020  1.526
 P9H  C8   C3   aromatic  1.393  0.020  1.393
 P9H  C16  N2   single    1.340  0.020  1.340
 P9H  C6   C5   aromatic  1.389  0.020  1.389
 P9H  C3   C2   single    1.509  0.020  1.509
 P9H  C3   C4   aromatic  1.393  0.020  1.393
 P9H  C2   C1   single    1.531  0.020  1.531
 P9H  C5   C4   aromatic  1.388  0.020  1.388
 P9H  N2   C17  single    1.432  0.020  1.432
 P9H  C1   C    single    1.502  0.020  1.502
 P9H  C17  C18  single    1.515  0.020  1.515
 P9H  C    O    double    1.206  0.020  1.206
 P9H  C18  O6   double    1.202  0.020  1.202
 P9H  C18  O5   single    1.325  0.020  1.325
 P9H  N1   H1   single    0.890  0.020  1.040
 P9H  N1   H2   single    0.890  0.020  1.040
 P9H  C4   H4   single    0.930  0.020  1.080
 P9H  C5   H5   single    0.930  0.020  1.080
 P9H  C6   H6   single    0.930  0.020  1.080
 P9H  C7   H7   single    0.930  0.020  1.080
 P9H  C8   H8   single    0.930  0.020  1.080
 P9H  C10  H9   single    0.970  0.020  1.090
 P9H  C13  H10  single    0.970  0.020  1.090
 P9H  C13  H11  single    0.970  0.020  1.090
 P9H  C17  H12  single    0.970  0.020  1.090
 P9H  C17  H13  single    0.970  0.020  1.090
 P9H  N    H14  single    0.860  0.020  1.020
 P9H  C    H15  single    0.930  0.020  1.080
 P9H  C1   H16  single    0.970  0.020  1.090
 P9H  C1   H17  single    0.970  0.020  1.090
 P9H  C12  H18  single    0.970  0.020  1.090
 P9H  C12  H19  single    0.970  0.020  1.090
 P9H  C14  H20  single    0.970  0.020  1.090
 P9H  C2   H21  single    0.970  0.020  1.090
 P9H  C9   H22  single    0.970  0.020  1.090
 P9H  C9   H23  single    0.970  0.020  1.090
 P9H  N2   H24  single    0.860  0.020  1.020
 P9H  O2   H25  single    0.850  0.020  0.980
 P9H  O5   H26  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
 P9H  H2   N1   H1   105.73  3.000
 P9H  H2   N1   C14  110.26  3.000
 P9H  H1   N1   C14  108.61  3.000
 P9H  H4   C4   C3   119.54  3.000
 P9H  H4   C4   C5   119.80  3.000
 P9H  C3   C4   C5   120.66  3.000
 P9H  H5   C5   C6   120.21  3.000
 P9H  H5   C5   C4   119.66  3.000
 P9H  C6   C5   C4   120.14  3.000
 P9H  H6   C6   C7   120.17  3.000
 P9H  H6   C6   C5   120.24  3.000
 P9H  C7   C6   C5   119.59  3.000
 P9H  H7   C7   C8   119.70  3.000
 P9H  H7   C7   C6   120.07  3.000
 P9H  C8   C7   C6   120.23  3.000
 P9H  H8   C8   C3   120.41  3.000
 P9H  H8   C8   C7   119.05  3.000
 P9H  C3   C8   C7   120.54  3.000
 P9H  H9   C10  C9   109.40  3.000
 P9H  H9   C10  C16  109.89  3.000
 P9H  C9   C10  C16  107.74  3.000
 P9H  H9   C10  N    107.59  3.000
 P9H  C16  C10  N    110.18  3.000
 P9H  C9   C10  N    112.04  3.000
 P9H  H11  C13  H10  106.63  3.000
 P9H  H11  C13  C14  109.27  3.000
 P9H  H10  C13  C14  107.17  3.000
 P9H  H11  C13  C12  110.87  3.000
 P9H  H10  C13  C12  109.03  3.000
 P9H  C14  C13  C12  113.57  3.000
 P9H  O2   C15  O1   123.05  3.000
 P9H  O2   C15  C14  113.36  3.000
 P9H  O1   C15  C14  123.56  3.000
 P9H  H13  C17  H12  106.65  3.000
 P9H  H13  C17  N2   111.24  3.000
 P9H  H12  C17  N2   108.51  3.000
 P9H  H13  C17  C18  109.60  3.000
 P9H  H12  C17  C18  108.31  3.000
 P9H  N2   C17  C18  112.32  3.000
 P9H  H14  N    C11  118.14  3.000
 P9H  H14  N    C10  117.12  3.000
 P9H  C11  N    C10  122.72  3.000
 P9H  H17  C1   H16  107.44  3.000
 P9H  H17  C1   C2   110.84  3.000
 P9H  H16  C1   C2   109.96  3.000
 P9H  H17  C1   C    108.98  3.000
 P9H  H16  C1   C    107.82  3.000
 P9H  C2   C1   C    111.66  3.000
 P9H  O3   C11  C12  122.53  3.000
 P9H  O3   C11  N    122.92  3.000
 P9H  C12  C11  N    114.52  3.000
 P9H  H19  C12  H18  105.71  3.000
 P9H  H19  C12  C11  110.16  3.000
 P9H  H18  C12  C11  105.63  3.000
 P9H  H19  C12  C13  110.67  3.000
 P9H  H18  C12  C13  111.34  3.000
 P9H  C11  C12  C13  112.97  3.000
 P9H  H20  C14  C15  105.82  3.000
 P9H  H20  C14  C13  108.28  3.000
 P9H  C15  C14  C13  109.10  3.000
 P9H  H20  C14  N1   113.74  3.000
 P9H  C13  C14  N1   108.88  3.000
 P9H  C15  C14  N1   110.90  3.000
 P9H  O4   C16  N2   123.12  3.000
 P9H  N2   C16  C10  115.22  3.000
 P9H  O4   C16  C10  121.55  3.000
 P9H  O6   C18  O5   124.34  3.000
 P9H  O5   C18  C17  110.83  3.000
 P9H  O6   C18  C17  124.81  3.000
 P9H  H21  C2   S    107.81  3.000
 P9H  H21  C2   C3   108.37  3.000
 P9H  S    C2   C3   105.09  3.000
 P9H  H21  C2   C1   109.00  3.000
 P9H  C3   C2   C1   114.77  3.000
 P9H  S    C2   C1   111.52  3.000
 P9H  C2   C3   C8   121.23  3.000
 P9H  C2   C3   C4   119.87  3.000
 P9H  C8   C3   C4   118.85  3.000
 P9H  H23  C9   H22  106.67  3.000
 P9H  H23  C9   S    104.10  3.000
 P9H  H22  C9   S    111.13  3.000
 P9H  H23  C9   C10  110.06  3.000
 P9H  H22  C9   C10  109.99  3.000
 P9H  S    C9   C10  114.47  3.000
 P9H  H24  N2   C16  119.98  3.000
 P9H  H24  N2   C17  118.43  3.000
 P9H  C16  N2   C17  121.26  3.000
 P9H  H25  O2   C15  109.47  3.000
 P9H  H26  O5   C18  110.21  3.000
 P9H  C9   S    C2   103.71  3.000
 P9H  H15  C    C1   115.02  3.000
 P9H  H15  C    O    120.63  3.000
 P9H  C1   C    O    124.35  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
 P9H  CONST_01  C7   C8   C3   C4      0.00   0.0  0
 P9H  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 P9H  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 P9H  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 P9H  CONST_05  C3   C8   C7   C6      0.00   0.0  0
 P9H  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 P9H  CONST_07  C2   C3   C4   C5    180.00   0.0  0
 P9H  CONST_08  C2   C3   C8   C7    180.00   0.0  0
 P9H  CONST_09  H8   C8   C3   C4    180.00   0.0  0
 P9H  CONST_10  H6   C6   C5   C4    180.00   0.0  0
 P9H  CONST_11  H7   C7   C6   C5    180.00   0.0  0
 P9H  CONST_12  H4   C4   C5   C6    180.00   0.0  0
 P9H  CONST_13  H5   C5   C6   C7    180.00   0.0  0
 P9H  CONST_16  C17  N2   C16  C10   180.00   0.0  0
 P9H  CONST_17  O4   C16  N2   C17     0.00   0.0  0
 P9H  CONST_18  H24  N2   C16  C10     0.00   0.0  0
 P9H  CONST_19  H14  N    C11  C12     0.00   0.0  0
 P9H  CONST_20  H26  O5   C18  C17   180.00   0.0  0
 P9H  CONST_21  H25  O2   C15  C14   180.00   0.0  0
 P9H  Var_01    N    C11  C12  C13  -159.05  30.0  3
 P9H  Var_02    C2   C1   C    O    -127.07  30.0  2
 P9H  Var_03    C14  C13  C12  C11  -177.43  30.0  3
 P9H  Var_04    C18  C17  N2   C16    70.74  30.0  3
 P9H  Var_05    O6   C18  C17  N2     12.47  30.0  3
 P9H  Var_06    H22  C9   S    C2     57.97  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
 P9H  chir_01  C10  N   C9   C16  negativ
 P9H  chir_02  C14  N1  C15  C13  positiv
 P9H  chir_03  C2   S   C3   C1   negativ

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
 P9H  plan-1  C4   0.020
 P9H  plan-1  C5   0.020
 P9H  plan-1  C6   0.020
 P9H  plan-1  C7   0.020
 P9H  plan-1  C8   0.020
 P9H  plan-1  C2   0.020
 P9H  plan-1  C3   0.020
 P9H  plan-1  H4   0.020
 P9H  plan-1  H5   0.020
 P9H  plan-1  H6   0.020
 P9H  plan-1  H7   0.020
 P9H  plan-1  H8   0.020
 P9H  plan-2  O    0.020
 P9H  plan-2  C1   0.020
 P9H  plan-2  H15  0.020
 P9H  plan-2  C    0.020
 P9H  plan-3  C10  0.020
 P9H  plan-3  N    0.020
 P9H  plan-3  C11  0.020
 P9H  plan-3  C12  0.020
 P9H  plan-3  O3   0.020
 P9H  plan-3  H14  0.020
 P9H  plan-4  C10  0.020
 P9H  plan-4  C17  0.020
 P9H  plan-4  C16  0.020
 P9H  plan-4  N2   0.020
 P9H  plan-4  O4   0.020
 P9H  plan-4  H24  0.020
 P9H  plan-5  C15  0.020
 P9H  plan-5  C14  0.020
 P9H  plan-5  O1   0.020
 P9H  plan-5  O2   0.020
 P9H  plan-5  H25  0.020
 P9H  plan-6  C17  0.020
 P9H  plan-6  C18  0.020
 P9H  plan-6  O5   0.020
 P9H  plan-6  O6   0.020
 P9H  plan-6  H26  0.020

