# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:01:35 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-{3-[(4-hydroxypiperidin-1-yl)acetyl]-2,5-dimethyl-1H-pyrrol-1-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(c(C)n1c2ccc(cc2)C#N)C(=O)CN3CCC(O)CC3
#
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
 A8O  A8O  4-{3-[(4-hydroxypiperidin-1-yl)acetyl]-2,5-dimethyl-1H-pyrrol-1-yl}benzonitrile  ligand  48  25  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A8O
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
 A8O  C13  C  CH2   0  -0.389  -2.7543   0.8661  -0.1777
 A8O  C12  C  C     0   0.298  -1.5992  -0.0290  -0.5958
 A8O  C17  C  CH2   0  -0.477  -5.6186  -1.4523   0.4767
 A8O  C16  C  CH2   0  -0.296  -4.2911  -0.7456   0.7025
 A8O  C11  C  CR5   0   0.327   1.4261   1.7132   0.5416
 A8O  C10  C  CR15  0  -0.443   0.0763   1.6847   0.3758
 A8O  C8   C  CR5   0   0.354   0.9084  -0.2667  -0.4252
 A8O  C22  C  CH3   0  -0.738   2.3057   2.7756   1.0963
 A8O  C5   C  CR16  0  -0.239   5.3266  -0.2515  -1.1440
 A8O  C4   C  CR16  0  -0.244   3.9861   0.0898  -1.1464
 A8O  C19  C  CH2   0  -0.461  -6.4623   0.6151  -0.6000
 A8O  C20  C  CH2   0  -0.291  -5.1049   1.2513  -0.3407
 A8O  C9   C  CR5   0  -0.118  -0.2690   0.4391  -0.2340
 A8O  C24  C  CSP   0   0.063   7.3538  -0.8512   0.0739
 A8O  O14  O  O     0  -0.420  -1.7857  -1.0634  -1.2115
 A8O  N15  N  NT    0  -0.413  -4.0479   0.2536  -0.3253
 A8O  C18  C  CH1   0   0.068  -6.7589  -0.4451   0.4449
 A8O  O21  O  OH1   0  -0.675  -8.0047  -1.0373   0.1427
 A8O  N7   N  NR5   0  -0.602   1.9198   0.5146   0.0508
 A8O  C3   C  CR6   0   0.273   3.2914   0.1666   0.0542
 A8O  C2   C  CR16  0  -0.249   3.9301  -0.0887   1.2610
 A8O  C1   C  CR16  0  -0.240   5.2729  -0.4197   1.2718
 A8O  C6   C  CR6   0   0.011   5.9691  -0.5031   0.0672
 A8O  N25  N  NS    0  -0.245   8.4712  -1.1313   0.0799
 A8O  H1   H  HCH2  0   0.228  -2.5739   1.2359   0.8462
 A8O  H2   H  HCH2  0   0.278  -2.7019   1.7527  -0.8209
 A8O  H3   H  HCH2  0   0.221  -5.5882  -2.0031  -0.4686
 A8O  H4   H  HCH2  0   0.235  -5.7737  -2.1827   1.2762
 A8O  H5   H  HCH2  0   0.190  -4.2882  -0.2866   1.7080
 A8O  H6   H  HCH2  0   0.246  -3.4866  -1.4802   0.6932
 A8O  H7   H  HCR5  0   0.252  -0.5945   2.4853   0.6465
 A8O  H8   H  HCH3  0   0.251   2.7435   2.5003   2.0573
 A8O  H9   H  HCH3  0   0.251   3.1282   3.0243   0.4232
 A8O  H10  H  HCH3  0   0.264   1.7204   3.6797   1.2521
 A8O  H11  H  HCR6  0   0.291   5.8724  -0.3161  -2.0749
 A8O  H12  H  HCR6  0   0.291   3.4823   0.3005  -2.0799
 A8O  H13  H  HCH2  0   0.238  -7.2315   1.3911  -0.5888
 A8O  H14  H  HCH2  0   0.221  -6.4653   0.1604  -1.5954
 A8O  H15  H  HCH2  0   0.242  -4.8904   1.9775  -1.1280
 A8O  H16  H  HCH2  0   0.190  -5.1426   1.8177   0.6071
 A8O  H17  H  HCH3  0   0.259   1.0350  -1.6255  -2.0751
 A8O  H18  H  HCH3  0   0.251   2.1333  -1.9983  -0.7520
 A8O  H19  H  HCH3  0   0.264   0.4117  -2.3305  -0.5971
 A8O  H21  H  HCH1  0   0.185  -6.7967   0.0512   1.4280
 A8O  H22  H  HOH1  0   0.446  -8.1915  -1.7023   0.8127
 A8O  H23  H  HCR6  0   0.292   3.3772  -0.0391   2.1895
 A8O  H24  H  HCR6  0   0.292   5.7741  -0.6224   2.2080
 A8O  C23  C  CH3   0  -0.731   1.1395  -1.6233  -0.9889

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
 A8O  N25  C24  triple    1.152  0.020  1.152
 A8O  C24  C6   single    1.428  0.020  1.428
 A8O  C6   C5   aromatic  1.394  0.020  1.394
 A8O  C6   C1   aromatic  1.394  0.020  1.394
 A8O  C5   C4   aromatic  1.383  0.020  1.383
 A8O  C1   C2   aromatic  1.383  0.020  1.383
 A8O  C4   C3   aromatic  1.389  0.020  1.389
 A8O  C2   C3   aromatic  1.389  0.020  1.389
 A8O  C3   N7   single    1.415  0.020  1.415
 A8O  C23  C8   single    1.487  0.020  1.487
 A8O  N7   C8   aromatic  1.364  0.020  1.364
 A8O  N7   C11  aromatic  1.386  0.020  1.386
 A8O  C8   C9   aromatic  1.386  0.020  1.386
 A8O  C11  C22  single    1.487  0.020  1.487
 A8O  C11  C10  aromatic  1.360  0.020  1.360
 A8O  C9   C10  aromatic  1.429  0.020  1.429
 A8O  C9   C12  single    1.456  0.020  1.456
 A8O  O14  C12  double    1.218  0.020  1.218
 A8O  C12  C13  single    1.520  0.020  1.520
 A8O  C20  C19  single    1.521  0.020  1.521
 A8O  C20  N15  single    1.454  0.020  1.454
 A8O  C19  C18  single    1.518  0.020  1.518
 A8O  C13  N15  single    1.439  0.020  1.439
 A8O  N15  C16  single    1.454  0.020  1.454
 A8O  C18  O21  single    1.412  0.020  1.412
 A8O  C18  C17  single    1.522  0.020  1.522
 A8O  C16  C17  single    1.521  0.020  1.521
 A8O  C13  H1   single    0.970  0.020  1.090
 A8O  C13  H2   single    0.970  0.020  1.090
 A8O  C17  H3   single    0.970  0.020  1.090
 A8O  C17  H4   single    0.970  0.020  1.090
 A8O  C16  H5   single    0.970  0.020  1.090
 A8O  C16  H6   single    0.970  0.020  1.090
 A8O  C10  H7   single    0.930  0.020  1.080
 A8O  C22  H8   single    0.970  0.020  1.090
 A8O  C22  H9   single    0.970  0.020  1.090
 A8O  C22  H10  single    0.970  0.020  1.090
 A8O  C5   H11  single    0.930  0.020  1.080
 A8O  C4   H12  single    0.930  0.020  1.080
 A8O  C19  H13  single    0.970  0.020  1.090
 A8O  C19  H14  single    0.970  0.020  1.090
 A8O  C20  H15  single    0.970  0.020  1.090
 A8O  C20  H16  single    0.970  0.020  1.090
 A8O  C23  H17  single    0.970  0.020  1.090
 A8O  C23  H18  single    0.970  0.020  1.090
 A8O  C23  H19  single    0.970  0.020  1.090
 A8O  C18  H21  single    0.970  0.020  1.090
 A8O  O21  H22  single    0.850  0.020  0.980
 A8O  C2   H23  single    0.930  0.020  1.080
 A8O  C1   H24  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
 A8O  H2   C13  H1   105.40  3.000
 A8O  H2   C13  N15  109.09  3.000
 A8O  H1   C13  N15  112.64  3.000
 A8O  H2   C13  C12  106.16  3.000
 A8O  H1   C13  C12  109.17  3.000
 A8O  N15  C13  C12  113.85  3.000
 A8O  O14  C12  C9   122.58  3.000
 A8O  O14  C12  C13  121.52  3.000
 A8O  C9   C12  C13  115.89  3.000
 A8O  H4   C17  H3   107.40  3.000
 A8O  H4   C17  C18  110.54  3.000
 A8O  H3   C17  C18  109.62  3.000
 A8O  H4   C17  C16  109.00  3.000
 A8O  H3   C17  C16  109.75  3.000
 A8O  C18  C17  C16  110.47  3.000
 A8O  H6   C16  H5   106.61  3.000
 A8O  H6   C16  N15  109.50  3.000
 A8O  H5   C16  N15  110.93  3.000
 A8O  H6   C16  C17  109.27  3.000
 A8O  H5   C16  C17  109.29  3.000
 A8O  N15  C16  C17  111.13  3.000
 A8O  N7   C11  C22  122.64  3.000
 A8O  C22  C11  C10  130.35  3.000
 A8O  N7   C11  C10  106.99  3.000
 A8O  H7   C10  C9   127.13  3.000
 A8O  H7   C10  C11  124.81  3.000
 A8O  C9   C10  C11  108.05  3.000
 A8O  N7   C8   C23  122.66  3.000
 A8O  N7   C8   C9   106.86  3.000
 A8O  C23  C8   C9   130.45  3.000
 A8O  H10  C22  H9   107.72  3.000
 A8O  H10  C22  H8   107.41  3.000
 A8O  H9   C22  H8   107.35  3.000
 A8O  H10  C22  C11  109.20  3.000
 A8O  H9   C22  C11  112.25  3.000
 A8O  H8   C22  C11  112.68  3.000
 A8O  H11  C5   C6   120.31  3.000
 A8O  H11  C5   C4   120.17  3.000
 A8O  C6   C5   C4   119.52  3.000
 A8O  H12  C4   C3   120.15  3.000
 A8O  H12  C4   C5   120.07  3.000
 A8O  C3   C4   C5   119.78  3.000
 A8O  H14  C19  H13  107.60  3.000
 A8O  H14  C19  C18  109.60  3.000
 A8O  H13  C19  C18  110.58  3.000
 A8O  H14  C19  C20  109.34  3.000
 A8O  H13  C19  C20  109.23  3.000
 A8O  C18  C19  C20  110.44  3.000
 A8O  H16  C20  H15  106.51  3.000
 A8O  H16  C20  N15  111.57  3.000
 A8O  H15  C20  N15  108.73  3.000
 A8O  H16  C20  C19  109.28  3.000
 A8O  H15  C20  C19  109.29  3.000
 A8O  N15  C20  C19  111.32  3.000
 A8O  C8   C9   C10  107.30  3.000
 A8O  C10  C9   C12  127.37  3.000
 A8O  C8   C9   C12  125.33  3.000
 A8O  N25  C24  C6   180.00  3.000
 A8O  C20  N15  C16  110.95  3.000
 A8O  C16  N15  C13  111.74  3.000
 A8O  C20  N15  C13  111.26  3.000
 A8O  H21  C18  O21  110.46  3.000
 A8O  H21  C18  C19  107.83  3.000
 A8O  O21  C18  C19  108.54  3.000
 A8O  H21  C18  C17  107.77  3.000
 A8O  O21  C18  C17  112.83  3.000
 A8O  C19  C18  C17  109.28  3.000
 A8O  H22  O21  C18  108.18  3.000
 A8O  C3   N7   C8   125.36  3.000
 A8O  C8   N7   C11  110.79  3.000
 A8O  C3   N7   C11  123.85  3.000
 A8O  C2   C3   N7   119.54  3.000
 A8O  N7   C3   C4   119.75  3.000
 A8O  C2   C3   C4   120.71  3.000
 A8O  H23  C2   C1   120.03  3.000
 A8O  H23  C2   C3   120.15  3.000
 A8O  C1   C2   C3   119.82  3.000
 A8O  H24  C1   C6   120.37  3.000
 A8O  H24  C1   C2   120.12  3.000
 A8O  C6   C1   C2   119.50  3.000
 A8O  C1   C6   C24  119.66  3.000
 A8O  C1   C6   C5   120.66  3.000
 A8O  C24  C6   C5   119.68  3.000
 A8O  H19  C23  H18  107.97  3.000
 A8O  H19  C23  H17  107.05  3.000
 A8O  H18  C23  H17  107.67  3.000
 A8O  H19  C23  C8   110.64  3.000
 A8O  H18  C23  C8   111.94  3.000
 A8O  H17  C23  C8   111.36  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
 A8O  CONST_03  C9   C8   N7   C11     0.00   0.0  0
 A8O  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 A8O  CONST_05  C3   N7   C11  C10   180.00   0.0  0
 A8O  CONST_06  C8   N7   C11  C10     0.00   0.0  0
 A8O  CONST_07  N7   C8   C9   C10     0.00   0.0  0
 A8O  CONST_10  C2   C1   C6   C5      0.00   0.0  0
 A8O  CONST_11  C2   C3   C4   C5      0.00   0.0  0
 A8O  CONST_12  N7   C3   C4   C5    180.00   0.0  0
 A8O  CONST_13  C1   C6   C5   C4      0.00   0.0  0
 A8O  CONST_14  C1   C2   C3   C4      0.00   0.0  0
 A8O  CONST_15  C3   N7   C8   C9    180.00   0.0  0
 A8O  CONST_16  N7   C11  C10  C9      0.00   0.0  0
 A8O  CONST_17  C1   C2   C3   N7    180.00   0.0  0
 A8O  CONST_18  C6   C5   C4   C3      0.00   0.0  0
 A8O  CONST_19  C6   C1   C2   C3      0.00   0.0  0
 A8O  CONST_20  N7   C8   C9   C12   180.00   0.0  0
 A8O  CONST_21  C11  C10  C9   C12   180.00   0.0  0
 A8O  CONST_22  C23  C8   N7   C11   180.00   0.0  0
 A8O  CONST_23  C23  C8   C9   C10   180.00   0.0  0
 A8O  CONST_24  C22  C11  N7   C8    180.00   0.0  0
 A8O  CONST_25  C3   N7   C11  C22     0.00   0.0  0
 A8O  CONST_26  C9   C10  C11  C22   180.00   0.0  0
 A8O  CONST_27  C24  C6   C5   C4    180.00   0.0  0
 A8O  CONST_28  C3   N7   C8   C23     0.00   0.0  0
 A8O  CONST_29  C2   C1   C6   C24   180.00   0.0  0
 A8O  CONST_30  H7   C10  C9   C8    180.00   0.0  0
 A8O  CONST_31  H24  C1   C6   C5    180.00   0.0  0
 A8O  CONST_32  H23  C2   C3   C4    180.00   0.0  0
 A8O  CONST_33  H12  C4   C3   N7      0.00   0.0  0
 A8O  CONST_34  H11  C5   C4   C3    180.00   0.0  0
 A8O  Var_01    C20  N15  C16  C17    59.18  30.0  1
 A8O  Var_02    C19  C20  N15  C16   -59.15  30.0  1
 A8O  Var_03    C18  C19  C20  N15    57.30  30.0  1
 A8O  Var_04    C18  C17  C16  N15   -57.44  30.0  1
 A8O  Var_05    C8   C9   C12  C13   174.76  30.0  2
 A8O  Var_06    N15  C13  C12  C9   -168.85  30.0  3
 A8O  Var_07    H8   C22  C11  C10   110.87  30.0  2
 A8O  Var_08    H17  C23  C8   C9     75.34  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
 A8O  chir_01  C18  C19  O21  C17  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
 A8O  plan-1  C12  0.020
 A8O  plan-1  C11  0.020
 A8O  plan-1  C10  0.020
 A8O  plan-1  C8   0.020
 A8O  plan-1  C22  0.020
 A8O  plan-1  C9   0.020
 A8O  plan-1  N7   0.020
 A8O  plan-1  C3   0.020
 A8O  plan-1  H7   0.020
 A8O  plan-1  C23  0.020
 A8O  plan-2  C5   0.020
 A8O  plan-2  C4   0.020
 A8O  plan-2  C24  0.020
 A8O  plan-2  N7   0.020
 A8O  plan-2  C3   0.020
 A8O  plan-2  C2   0.020
 A8O  plan-2  C1   0.020
 A8O  plan-2  C6   0.020
 A8O  plan-2  N25  0.020
 A8O  plan-2  H11  0.020
 A8O  plan-2  H12  0.020
 A8O  plan-2  H23  0.020
 A8O  plan-2  H24  0.020
 A8O  plan-3  C13  0.020
 A8O  plan-3  C12  0.020
 A8O  plan-3  C9   0.020
 A8O  plan-3  O14  0.020

