# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:49:53 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: (3S)-3-{3-[(6-bromo-2-oxo-2,3-dihydro-1H-indol-4-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](CC(O)=O)N1C(=O)N(Cc2cc(Br)cc3NC(=O)Cc23)c4ccccc14
#
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
 1P9  1P9  '(3S)-3-{3-[(6-bromo-2-oxo-2,3-dihydro-1H-indol-4-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}hexanoic acid'  ligand  52  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 (reasonable std)
;

data_comp_1P9
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
 1P9  O22  O   O     0  -0.447  60.3872  59.2809   0.6042
 1P9  C21  C   CR5   0   0.527  61.0789  59.5023  -0.3647
 1P9  N20  N   NR15  0  -0.746  61.4541  60.7380  -0.8103
 1P9  C23  C   CH2   0  -0.641  61.6980  58.4847  -1.3108
 1P9  C24  C   CR56  0  -0.027  62.4297  59.3357  -2.2970
 1P9  C19  C   CR56  0   0.445  62.2488  60.6707  -1.9416
 1P9  C18  C   CR16  0  -0.297  62.8124  61.7129  -2.6548
 1P9  C16  C   CR6   0  -0.105  63.5727  61.3530  -3.7608
 1P9  BR1  BR  BR    0  -0.037  64.3900  62.7136  -4.7865
 1P9  C15  C   CR16  0  -0.282  63.7652  60.0348  -4.1424
 1P9  C14  C   CR6   0   0.041  63.1898  59.0027  -3.3997
 1P9  C13  C   CH2   0  -0.374  63.4070  57.5504  -3.7478
 1P9  N12  N   NR5   0  -0.603  64.0502  57.3553  -5.0156
 1P9  C10  C   CR5   0   0.689  65.4145  57.2672  -5.1753
 1P9  O11  O   O     0  -0.491  66.2412  57.2219  -4.2849
 1P9  C25  C   CR56  0   0.325  63.4306  57.3983  -6.2486
 1P9  C30  C   CR56  0   0.327  64.4382  57.3103  -7.2150
 1P9  C29  C   CR16  0  -0.309  64.1210  57.3157  -8.5619
 1P9  C28  C   CR16  0  -0.270  62.7766  57.4186  -8.9122
 1P9  C27  C   CR16  0  -0.274  61.7817  57.5157  -7.9463
 1P9  C26  C   CR16  0  -0.317  62.0975  57.5088  -6.5902
 1P9  N9   N   NR5   0  -0.608  65.6435  57.2419  -6.5337
 1P9  C4   C   CH1   0  -0.122  66.9794  57.1960  -7.1042
 1P9  C5   C   CH2   0  -0.574  67.2448  58.4008  -8.0146
 1P9  C6   C   C     0   0.538  66.7657  59.7245  -7.4823
 1P9  O8   O   O     0  -0.429  66.1845  60.5515  -8.1369
 1P9  O7   O   OH1   0  -0.589  67.0757  59.9028  -6.2009
 1P9  C3   C   CH2   0  -0.412  67.2380  55.8840  -7.8430
 1P9  C2   C   CH2   0  -0.426  67.1403  54.6528  -6.9524
 1P9  C1   C   CH3   0  -0.662  67.4144  53.3678  -7.7214
 1P9  H1   H   HNR5  0   0.418  61.1892  61.5960  -0.3496
 1P9  H2   H   HCH2  0   0.309  60.9169  57.8678  -1.7639
 1P9  H3   H   HCH2  0   0.312  62.3521  57.8097  -0.7519
 1P9  H4   H   HCR6  0   0.292  62.6678  62.7441  -2.3633
 1P9  H5   H   HCR6  0   0.250  64.3569  59.8107  -5.0183
 1P9  H6   H   HCH2  0   0.284  62.4567  57.0120  -3.7528
 1P9  H7   H   HCH2  0   0.304  64.0163  57.0766  -2.9763
 1P9  H8   H   HCR6  0   0.268  64.8744  57.2449  -9.3326
 1P9  H9   H   HCR6  0   0.260  62.5089  57.4255  -9.9602
 1P9  H10  H   HCR6  0   0.260  60.7464  57.5993  -8.2480
 1P9  H11  H   HCR6  0   0.271  61.3231  57.5878  -5.8386
 1P9  H12  H   HCH1  0   0.282  67.6601  57.2462  -6.2539
 1P9  H13  H   HCH2  0   0.273  66.8132  58.2611  -9.0051
 1P9  H14  H   HCH2  0   0.310  68.3266  58.4727  -8.1616
 1P9  H15  H   HOH1  0   0.473  66.7902  60.7834  -5.9120
 1P9  H16  H   HCH2  0   0.228  66.5458  55.7865  -8.6843
 1P9  H17  H   HCH2  0   0.242  68.2393  55.9404  -8.2799
 1P9  H18  H   HCH2  0   0.222  67.8494  54.7459  -6.1249
 1P9  H19  H   HCH2  0   0.222  66.1460  54.5983  -6.5015
 1P9  H20  H   HCH3  0   0.231  67.3542  52.4954  -7.0704
 1P9  H21  H   HCH3  0   0.220  66.6919  53.2294  -8.5277
 1P9  H22  H   HCH3  0   0.220  68.4099  53.3786  -8.1687

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
 1P9  C28  C29  aromatic  1.393  0.020  1.393
 1P9  C28  C27  aromatic  1.390  0.020  1.390
 1P9  C29  C30  aromatic  1.384  0.020  1.384
 1P9  O8   C6   double    1.204  0.020  1.204
 1P9  C5   C6   single    1.505  0.020  1.505
 1P9  C5   C4   single    1.533  0.020  1.533
 1P9  C3   C4   single    1.528  0.020  1.528
 1P9  C3   C2   single    1.523  0.020  1.523
 1P9  C27  C26  aromatic  1.392  0.020  1.392
 1P9  C1   C2   single    1.522  0.020  1.522
 1P9  C6   O7   single    1.330  0.020  1.330
 1P9  C30  N9   single    1.386  0.020  1.386
 1P9  C30  C25  aromatic  1.399  0.020  1.399
 1P9  C4   N9   single    1.453  0.020  1.453
 1P9  C26  C25  aromatic  1.381  0.020  1.381
 1P9  N9   C10  single    1.378  0.020  1.378
 1P9  C25  N12  single    1.381  0.020  1.381
 1P9  C10  N12  single    1.376  0.020  1.376
 1P9  C10  O11  double    1.216  0.020  1.216
 1P9  N12  C13  single    1.435  0.020  1.435
 1P9  BR1  C16  single    1.890  0.020  1.890
 1P9  C15  C16  aromatic  1.386  0.020  1.386
 1P9  C15  C14  aromatic  1.396  0.020  1.396
 1P9  C16  C18  aromatic  1.390  0.020  1.390
 1P9  C13  C14  single    1.509  0.020  1.509
 1P9  C14  C24  aromatic  1.380  0.020  1.380
 1P9  C18  C19  aromatic  1.383  0.020  1.383
 1P9  C24  C19  aromatic  1.393  0.020  1.393
 1P9  C24  C23  single    1.494  0.020  1.494
 1P9  C19  N20  single    1.384  0.020  1.384
 1P9  C23  C21  single    1.521  0.020  1.521
 1P9  N20  C21  single    1.366  0.020  1.366
 1P9  C21  O22  double    1.211  0.020  1.211
 1P9  N20  H1   single    0.860  0.020  1.020
 1P9  C23  H2   single    0.970  0.020  1.090
 1P9  C23  H3   single    0.970  0.020  1.090
 1P9  C18  H4   single    0.930  0.020  1.080
 1P9  C15  H5   single    0.930  0.020  1.080
 1P9  C13  H6   single    0.970  0.020  1.090
 1P9  C13  H7   single    0.970  0.020  1.090
 1P9  C29  H8   single    0.930  0.020  1.080
 1P9  C28  H9   single    0.930  0.020  1.080
 1P9  C27  H10  single    0.930  0.020  1.080
 1P9  C26  H11  single    0.930  0.020  1.080
 1P9  C4   H12  single    0.970  0.020  1.090
 1P9  C5   H13  single    0.970  0.020  1.090
 1P9  C5   H14  single    0.970  0.020  1.090
 1P9  O7   H15  single    0.850  0.020  0.980
 1P9  C3   H16  single    0.970  0.020  1.090
 1P9  C3   H17  single    0.970  0.020  1.090
 1P9  C2   H18  single    0.970  0.020  1.090
 1P9  C2   H19  single    0.970  0.020  1.090
 1P9  C1   H20  single    0.970  0.020  1.090
 1P9  C1   H21  single    0.970  0.020  1.090
 1P9  C1   H22  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
 1P9  C23  C21  N20  106.88  3.000
 1P9  N20  C21  O22  125.68  3.000
 1P9  C23  C21  O22  127.43  3.000
 1P9  H1   N20  C19  124.42  3.000
 1P9  H1   N20  C21  123.22  3.000
 1P9  C19  N20  C21  112.35  3.000
 1P9  H3   C23  H2   106.90  3.000
 1P9  H3   C23  C24  113.33  3.000
 1P9  H2   C23  C24  113.43  3.000
 1P9  H3   C23  C21  109.79  3.000
 1P9  H2   C23  C21  110.14  3.000
 1P9  C24  C23  C21  103.23  3.000
 1P9  C14  C24  C19  120.43  3.000
 1P9  C19  C24  C23  108.29  3.000
 1P9  C14  C24  C23  131.28  3.000
 1P9  C18  C19  C24  122.52  3.000
 1P9  C24  C19  N20  109.25  3.000
 1P9  C18  C19  N20  128.23  3.000
 1P9  H4   C18  C16  122.33  3.000
 1P9  H4   C18  C19  121.68  3.000
 1P9  C16  C18  C19  115.99  3.000
 1P9  C15  C16  BR1  118.39  3.000
 1P9  C15  C16  C18  122.79  3.000
 1P9  BR1  C16  C18  118.82  3.000
 1P9  H5   C15  C14  120.25  3.000
 1P9  H5   C15  C16  119.77  3.000
 1P9  C14  C15  C16  119.98  3.000
 1P9  C13  C14  C15  121.98  3.000
 1P9  C13  C14  C24  119.72  3.000
 1P9  C15  C14  C24  118.28  3.000
 1P9  H7   C13  H6   105.96  3.000
 1P9  H7   C13  N12  108.38  3.000
 1P9  H6   C13  N12  108.60  3.000
 1P9  H7   C13  C14  109.58  3.000
 1P9  H6   C13  C14  110.50  3.000
 1P9  N12  C13  C14  113.52  3.000
 1P9  C25  N12  C10  110.07  3.000
 1P9  C10  N12  C13  123.74  3.000
 1P9  C25  N12  C13  125.71  3.000
 1P9  N9   C10  O11  127.47  3.000
 1P9  O11  C10  N12  126.25  3.000
 1P9  N9   C10  N12  106.28  3.000
 1P9  C26  C25  C30  121.98  3.000
 1P9  C26  C25  N12  131.06  3.000
 1P9  C30  C25  N12  106.96  3.000
 1P9  N9   C30  C29  132.68  3.000
 1P9  N9   C30  C25  106.85  3.000
 1P9  C29  C30  C25  120.47  3.000
 1P9  H8   C29  C28  119.90  3.000
 1P9  H8   C29  C30  122.30  3.000
 1P9  C28  C29  C30  117.79  3.000
 1P9  H9   C28  C27  119.71  3.000
 1P9  H9   C28  C29  118.88  3.000
 1P9  C27  C28  C29  121.41  3.000
 1P9  H10  C27  C26  119.28  3.000
 1P9  H10  C27  C28  119.78  3.000
 1P9  C26  C27  C28  120.94  3.000
 1P9  H11  C26  C27  120.92  3.000
 1P9  H11  C26  C25  121.68  3.000
 1P9  C27  C26  C25  117.41  3.000
 1P9  C4   N9   C30  127.44  3.000
 1P9  C4   N9   C10  122.71  3.000
 1P9  C30  N9   C10  109.82  3.000
 1P9  H12  C4   C3   108.12  3.000
 1P9  H12  C4   C5   108.59  3.000
 1P9  C3   C4   C5   111.00  3.000
 1P9  H12  C4   N9   105.44  3.000
 1P9  C3   C4   N9   111.88  3.000
 1P9  C5   C4   N9   111.55  3.000
 1P9  H14  C5   H13  106.14  3.000
 1P9  H14  C5   C6   107.72  3.000
 1P9  H13  C5   C6   107.95  3.000
 1P9  H14  C5   C4   107.61  3.000
 1P9  H13  C5   C4   111.75  3.000
 1P9  C6   C5   C4   115.22  3.000
 1P9  O7   C6   O8   122.95  3.000
 1P9  O7   C6   C5   112.61  3.000
 1P9  O8   C6   C5   124.43  3.000
 1P9  H15  O7   C6   109.88  3.000
 1P9  H17  C3   H16  106.06  3.000
 1P9  H17  C3   C2   109.51  3.000
 1P9  H16  C3   C2   109.71  3.000
 1P9  H17  C3   C4   107.69  3.000
 1P9  H16  C3   C4   109.96  3.000
 1P9  C2   C3   C4   113.62  3.000
 1P9  H19  C2   H18  106.37  3.000
 1P9  H19  C2   C1   109.27  3.000
 1P9  H18  C2   C1   109.71  3.000
 1P9  H19  C2   C3   109.87  3.000
 1P9  H18  C2   C3   109.40  3.000
 1P9  C1   C2   C3   112.06  3.000
 1P9  H22  C1   H21  107.60  3.000
 1P9  H22  C1   H20  107.63  3.000
 1P9  H21  C1   H20  107.65  3.000
 1P9  H22  C1   C2   111.28  3.000
 1P9  H21  C1   C2   111.16  3.000
 1P9  H20  C1   C2   111.34  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
 1P9  CONST_01  C16  C15  C14  C24     0.00   0.0  0
 1P9  CONST_02  C16  C18  C19  C24     0.00   0.0  0
 1P9  CONST_03  C15  C16  C18  C19     0.00   0.0  0
 1P9  CONST_04  C15  C14  C24  C19     0.00   0.0  0
 1P9  CONST_05  C14  C15  C16  C18     0.00   0.0  0
 1P9  CONST_06  C14  C24  C19  C18     0.00   0.0  0
 1P9  CONST_07  C28  C29  C30  C25     0.00   0.0  0
 1P9  CONST_08  C28  C27  C26  C25     0.00   0.0  0
 1P9  CONST_09  C27  C28  C29  C30     0.00   0.0  0
 1P9  CONST_10  C27  C26  C25  C30     0.00   0.0  0
 1P9  CONST_11  C26  C27  C28  C29     0.00   0.0  0
 1P9  CONST_12  C26  C25  C30  C29     0.00   0.0  0
 1P9  CONST_13  C19  N20  C21  C23     0.00   0.0  0
 1P9  CONST_14  N9   C30  C25  N12     0.00   0.0  0
 1P9  CONST_15  C30  N9   C10  N12     0.00   0.0  0
 1P9  CONST_16  C25  C30  N9   C10     0.00   0.0  0
 1P9  CONST_17  C30  C25  N12  C10     0.00   0.0  0
 1P9  CONST_18  N9   C10  N12  C25     0.00   0.0  0
 1P9  CONST_19  C13  C14  C24  C23     0.00   0.0  0
 1P9  CONST_20  BR1  C16  C18  C19   180.00   0.0  0
 1P9  CONST_21  C13  C14  C24  C19   180.00   0.0  0
 1P9  CONST_22  C13  C14  C15  C16   180.00   0.0  0
 1P9  CONST_23  C14  C15  C16  BR1   180.00   0.0  0
 1P9  CONST_24  C19  N20  C21  O22   180.00   0.0  0
 1P9  CONST_25  C30  C25  N12  C13   180.00   0.0  0
 1P9  CONST_26  N9   C10  N12  C13   180.00   0.0  0
 1P9  CONST_27  C4   N9   C10  N12   180.00   0.0  0
 1P9  CONST_28  C30  N9   C10  O11   180.00   0.0  0
 1P9  CONST_29  C25  N12  C10  O11   180.00   0.0  0
 1P9  CONST_30  C4   N9   C30  C25   180.00   0.0  0
 1P9  CONST_31  H4   C18  C19  N20     0.00   0.0  0
 1P9  CONST_32  H5   C15  C14  C24   180.00   0.0  0
 1P9  CONST_33  H11  C26  C25  N12     0.00   0.0  0
 1P9  CONST_34  H8   C29  C30  C25   180.00   0.0  0
 1P9  CONST_35  H10  C27  C26  C25   180.00   0.0  0
 1P9  CONST_36  H9   C28  C29  C30   180.00   0.0  0
 1P9  CONST_37  H1   N20  C21  C23   180.00   0.0  0
 1P9  CONST_38  O11  C10  N12  C13     0.00   0.0  0
 1P9  CONST_39  C4   N9   C10  O11     0.00   0.0  0
 1P9  CONST_40  H15  O7   C6   C5    180.00   0.0  0
 1P9  Var_01    N12  C13  C14  C24   171.61  30.0  1
 1P9  Var_02    C25  N12  C13  C14   -80.61  30.0  2
 1P9  Var_03    H2   C23  C21  N20  -121.64  30.0  1
 1P9  Var_04    O8   C6   C5   C4   -136.13  30.0  3
 1P9  Var_05    C1   C2   C3   C4   -179.57  30.0  3
 1P9  Var_06    H20  C1   C2   C3    179.26  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
 1P9  chir_01  C4  C5  C3  N9  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
 1P9  plan-1  C13  0.020
 1P9  plan-1  N12  0.020
 1P9  plan-1  C10  0.020
 1P9  plan-1  O11  0.020
 1P9  plan-1  C25  0.020
 1P9  plan-1  C30  0.020
 1P9  plan-1  C29  0.020
 1P9  plan-1  C28  0.020
 1P9  plan-1  C27  0.020
 1P9  plan-1  C26  0.020
 1P9  plan-1  N9   0.020
 1P9  plan-1  C4   0.020
 1P9  plan-1  H8   0.020
 1P9  plan-1  H9   0.020
 1P9  plan-1  H10  0.020
 1P9  plan-1  H11  0.020
 1P9  plan-2  O22  0.020
 1P9  plan-2  C21  0.020
 1P9  plan-2  N20  0.020
 1P9  plan-2  C23  0.020
 1P9  plan-2  C24  0.020
 1P9  plan-2  C19  0.020
 1P9  plan-2  C18  0.020
 1P9  plan-2  C16  0.020
 1P9  plan-2  BR1  0.020
 1P9  plan-2  C15  0.020
 1P9  plan-2  C14  0.020
 1P9  plan-2  C13  0.020
 1P9  plan-2  H1   0.020
 1P9  plan-2  H4   0.020
 1P9  plan-2  H5   0.020
 1P9  plan-3  C5   0.020
 1P9  plan-3  C6   0.020
 1P9  plan-3  O8   0.020
 1P9  plan-3  O7   0.020
 1P9  plan-3  H15  0.020

