# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:50:57 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-[4-(3-chlorobenzoyl)piperazin-1-yl]-1H-inden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)C(=O)N2CCN(CC2)c3ccc4C(=O)C=Cc4c3
#
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
 41O  41O  5-[4-(3-chlorobenzoyl)piperazin-1-yl]-1H-inden-1-one  ligand  42  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_41O
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
 41O  C7   C   CR16  0  -0.230   4.2245  -0.2095  -0.6425
 41O  C3   C   CR16  0  -0.212   5.5821  -1.4558   0.9233
 41O  C4   C   CR16  0  -0.248   4.9477  -0.8089   1.9737
 41O  C5   C   CR16  0  -0.249   3.9448   0.1170   1.7286
 41O  C30  C   CR16  0  -0.412  -3.3018  -0.6123   0.6371
 41O  C29  C   CR56  0   0.140  -4.6088  -0.8995   0.3551
 41O  C31  C   CR15  0  -0.229  -5.4849  -1.9670   0.8831
 41O  C32  C   CR15  0  -0.367  -6.7009  -1.8687   0.3336
 41O  C33  C   CR5   0   0.336  -6.7143  -0.7079  -0.6099
 41O  O34  O   O     0  -0.384  -7.6505  -0.3285  -1.2785
 41O  C28  C   CR56  0  -0.088  -5.3545  -0.1335  -0.5471
 41O  C27  C   CR16  0  -0.259  -4.7760   0.9418  -1.1779
 41O  C26  C   CR16  0  -0.382  -3.4425   1.2501  -0.9116
 41O  C25  C   CR6   0   0.413  -2.6828   0.4942  -0.0058
 41O  N22  N   NT    0  -0.523  -1.3771   0.8181   0.3003
 41O  C23  C   CH2   0  -0.311  -0.7988   2.0285  -0.2509
 41O  C24  C   CH2   0  -0.317   0.3987   2.4678   0.5761
 41O  C21  C   CH2   0  -0.295  -0.3989  -0.2488   0.4565
 41O  C20  C   CH2   0  -0.325   0.7959   0.2029   1.2806
 41O  N19  N   NT    0  -0.454   1.3739   1.4040   0.7093
 41O  O11  O   O     0  -0.479   2.9083   2.4162  -0.6127
 41O  C6   C   CR6   0  -0.081   3.5786   0.4138   0.4194
 41O  C8   C   CR6   0  -0.028   5.2062  -1.1490  -0.3758
 41O  CL9  CL  CL    0  -0.123   5.9897  -1.9493  -1.6983
 41O  H1   H   HCR6  0   0.285   3.9559   0.0263  -1.6637
 41O  H2   H   HCR6  0   0.286   6.3589  -2.1836   1.1137
 41O  H3   H   HCR6  0   0.275   5.2408  -1.0313   2.9907
 41O  H4   H   HCR6  0   0.277   3.4578   0.6130   2.5586
 41O  H5   H   HCR6  0   0.273  -2.7660  -1.2065   1.3649
 41O  H6   H   HCR5  0   0.278  -5.1623  -2.7071   1.6023
 41O  H7   H   HCR5  0   0.277  -7.5544  -2.5044   0.5166
 41O  H8   H   HCR6  0   0.263  -5.3314   1.5434  -1.8871
 41O  H9   H   HCR6  0   0.275  -3.0008   2.0810  -1.4414
 41O  H10  H   HCH2  0   0.236  -0.5008   1.8951  -1.3001
 41O  H11  H   HCH2  0   0.268  -1.5296   2.8350  -0.2133
 41O  H12  H   HCH2  0   0.277   0.8563   3.3405   0.1190
 41O  H13  H   HCH2  0   0.258   0.0609   2.7484   1.5776
 41O  H14  H   HCH2  0   0.273  -0.8380  -1.1074   0.9575
 41O  H15  H   HCH2  0   0.237  -0.0497  -0.5884  -0.5283
 41O  H16  H   HCH2  0   0.259   0.4866   0.4032   2.3098
 41O  H17  H   HCH2  0   0.284   1.5187  -0.6076   1.3019
 41O  C10  C   C     0   0.524   2.5817   1.4904   0.1160

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
 41O  O11  C10  double    1.223  0.020  1.223
 41O  CL9  C8   single    1.733  0.020  1.733
 41O  C3   C8   aromatic  1.387  0.020  1.387
 41O  C3   C4   aromatic  1.387  0.020  1.387
 41O  C8   C7   aromatic  1.385  0.020  1.385
 41O  C4   C5   aromatic  1.387  0.020  1.387
 41O  C7   C6   aromatic  1.390  0.020  1.390
 41O  C5   C6   aromatic  1.391  0.020  1.391
 41O  C6   C10  single    1.498  0.020  1.498
 41O  C10  N19  single    1.348  0.020  1.348
 41O  N19  C24  single    1.449  0.020  1.449
 41O  N19  C20  single    1.450  0.020  1.450
 41O  C24  C23  single    1.520  0.020  1.520
 41O  C23  N22  single    1.450  0.020  1.450
 41O  C20  C21  single    1.520  0.020  1.520
 41O  C21  N22  single    1.456  0.020  1.456
 41O  N22  C25  single    1.380  0.020  1.380
 41O  C25  C26  aromatic  1.403  0.020  1.403
 41O  C25  C30  aromatic  1.422  0.020  1.422
 41O  C26  C27  aromatic  1.394  0.020  1.394
 41O  C30  C29  aromatic  1.368  0.020  1.368
 41O  C27  C28  aromatic  1.374  0.020  1.374
 41O  C29  C28  aromatic  1.399  0.020  1.399
 41O  C29  C31  single    1.478  0.020  1.478
 41O  C28  C33  single    1.478  0.020  1.478
 41O  C31  C32  double    1.338  0.020  1.338
 41O  C33  O34  double    1.211  0.020  1.211
 41O  C33  C32  single    1.496  0.020  1.496
 41O  C7   H1   single    0.930  0.020  1.080
 41O  C3   H2   single    0.930  0.020  1.080
 41O  C4   H3   single    0.930  0.020  1.080
 41O  C5   H4   single    0.930  0.020  1.080
 41O  C30  H5   single    0.930  0.020  1.080
 41O  C31  H6   single    0.930  0.020  1.080
 41O  C32  H7   single    0.930  0.020  1.080
 41O  C27  H8   single    0.930  0.020  1.080
 41O  C26  H9   single    0.930  0.020  1.080
 41O  C23  H10  single    0.970  0.020  1.090
 41O  C23  H11  single    0.970  0.020  1.090
 41O  C24  H12  single    0.970  0.020  1.090
 41O  C24  H13  single    0.970  0.020  1.090
 41O  C21  H14  single    0.970  0.020  1.090
 41O  C21  H15  single    0.970  0.020  1.090
 41O  C20  H16  single    0.970  0.020  1.090
 41O  C20  H17  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
 41O  H1   C7   C8   120.37  3.000
 41O  H1   C7   C6   120.52  3.000
 41O  C8   C7   C6   119.10  3.000
 41O  H2   C3   C8   120.57  3.000
 41O  H2   C3   C4   120.60  3.000
 41O  C8   C3   C4   118.83  3.000
 41O  H3   C4   C5   119.96  3.000
 41O  H3   C4   C3   119.49  3.000
 41O  C5   C4   C3   120.55  3.000
 41O  H4   C5   C6   120.35  3.000
 41O  H4   C5   C4   119.72  3.000
 41O  C6   C5   C4   119.93  3.000
 41O  H5   C30  C25  121.08  3.000
 41O  H5   C30  C29  119.79  3.000
 41O  C25  C30  C29  119.10  3.000
 41O  C28  C29  C31  108.05  3.000
 41O  C31  C29  C30  130.11  3.000
 41O  C28  C29  C30  121.83  3.000
 41O  H6   C31  C32  126.48  3.000
 41O  H6   C31  C29  123.71  3.000
 41O  C32  C31  C29  109.80  3.000
 41O  H7   C32  C33  123.82  3.000
 41O  H7   C32  C31  127.26  3.000
 41O  C33  C32  C31  108.92  3.000
 41O  C28  C33  O34  127.81  3.000
 41O  O34  C33  C32  126.73  3.000
 41O  C28  C33  C32  105.46  3.000
 41O  C27  C28  C33  132.23  3.000
 41O  C33  C28  C29  107.77  3.000
 41O  C27  C28  C29  120.01  3.000
 41O  H8   C27  C26  119.51  3.000
 41O  H8   C27  C28  121.28  3.000
 41O  C26  C27  C28  119.20  3.000
 41O  H9   C26  C25  120.65  3.000
 41O  H9   C26  C27  117.88  3.000
 41O  C25  C26  C27  121.47  3.000
 41O  N22  C25  C26  121.95  3.000
 41O  C26  C25  C30  118.39  3.000
 41O  N22  C25  C30  119.64  3.000
 41O  C21  N22  C23  112.61  3.000
 41O  C21  N22  C25  119.18  3.000
 41O  C23  N22  C25  119.27  3.000
 41O  H11  C23  H10  107.75  3.000
 41O  H11  C23  C24  107.21  3.000
 41O  H10  C23  C24  109.94  3.000
 41O  H11  C23  N22  109.72  3.000
 41O  H10  C23  N22  111.70  3.000
 41O  C24  C23  N22  110.40  3.000
 41O  H13  C24  H12  108.02  3.000
 41O  H13  C24  N19  108.19  3.000
 41O  H12  C24  N19  110.17  3.000
 41O  H13  C24  C23  109.21  3.000
 41O  H12  C24  C23  109.58  3.000
 41O  N19  C24  C23  111.59  3.000
 41O  H15  C21  H14  107.30  3.000
 41O  H15  C21  C20  109.14  3.000
 41O  H14  C21  C20  107.61  3.000
 41O  H15  C21  N22  110.12  3.000
 41O  H14  C21  N22  110.92  3.000
 41O  C20  C21  N22  111.63  3.000
 41O  H17  C20  H16  107.85  3.000
 41O  H17  C20  N19  111.13  3.000
 41O  H16  C20  N19  109.39  3.000
 41O  H17  C20  C21  108.18  3.000
 41O  H16  C20  C21  110.02  3.000
 41O  N19  C20  C21  110.24  3.000
 41O  C10  N19  C20  125.69  3.000
 41O  C20  N19  C24  112.08  3.000
 41O  C10  N19  C24  121.02  3.000
 41O  C10  C6   C5   121.25  3.000
 41O  C10  C6   C7   118.46  3.000
 41O  C5   C6   C7   120.05  3.000
 41O  CL9  C8   C3   119.35  3.000
 41O  C3   C8   C7   121.52  3.000
 41O  CL9  C8   C7   119.13  3.000
 41O  C6   C10  O11  119.15  3.000
 41O  C6   C10  N19  117.44  3.000
 41O  O11  C10  N19  123.37  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
 41O  CONST_01  C4   C3   C8   C7      0.00   0.0  0
 41O  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 41O  CONST_03  C6   C7   C8   C3      0.00   0.0  0
 41O  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 41O  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 41O  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 41O  CONST_07  C27  C26  C25  C30     0.00   0.0  0
 41O  CONST_08  C27  C28  C29  C30     0.00   0.0  0
 41O  CONST_09  C26  C25  C30  C29     0.00   0.0  0
 41O  CONST_10  C26  C27  C28  C29     0.00   0.0  0
 41O  CONST_11  C25  C26  C27  C28     0.00   0.0  0
 41O  CONST_12  C25  C30  C29  C28     0.00   0.0  0
 41O  CONST_13  N22  C25  C30  C29   180.00   0.0  0
 41O  CONST_14  N22  C25  C26  C27   180.00   0.0  0
 41O  CONST_15  CL9  C8   C3   C4    180.00   0.0  0
 41O  CONST_16  C10  C6   C5   C4    180.00   0.0  0
 41O  CONST_17  C8   C7   C6   C10   180.00   0.0  0
 41O  CONST_18  CL9  C8   C7   C6    180.00   0.0  0
 41O  CONST_19  C6   C10  N19  C24   180.00   0.0  0
 41O  CONST_21  H2   C3   C8   C7    180.00   0.0  0
 41O  CONST_22  H4   C5   C6   C7    180.00   0.0  0
 41O  CONST_23  H1   C7   C8   C3    180.00   0.0  0
 41O  CONST_24  H9   C26  C25  C30   180.00   0.0  0
 41O  CONST_25  H8   C27  C28  C29   180.00   0.0  0
 41O  CONST_26  H5   C30  C29  C31     0.00   0.0  0
 41O  CONST_27  H3   C4   C5   C6    180.00   0.0  0
 41O  CONST_28  O11  C10  N19  C24     0.00   0.0  0
 41O  Var_01    C23  N22  C25  C30  -173.53  30.0  1
 41O  Var_02    C24  C23  N22  C25   159.07  30.0  1
 41O  Var_03    C20  C21  N22  C25  -158.33  30.0  1
 41O  Var_04    N19  C24  C23  N22    54.40  30.0  1
 41O  Var_05    N19  C20  C21  N22   -54.31  30.0  1
 41O  Var_06    C20  N19  C24  C23   -56.36  30.0  1
 41O  Var_07    C21  C20  N19  C24    55.65  30.0  1
 41O  Var_08    N19  C10  C6   C7    130.22  30.0  2

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
 41O  plan-1  C7   0.020
 41O  plan-1  C3   0.020
 41O  plan-1  C4   0.020
 41O  plan-1  C5   0.020
 41O  plan-1  C6   0.020
 41O  plan-1  C8   0.020
 41O  plan-1  CL9  0.020
 41O  plan-1  H1   0.020
 41O  plan-1  H2   0.020
 41O  plan-1  H3   0.020
 41O  plan-1  H4   0.020
 41O  plan-1  C10  0.020
 41O  plan-2  C24  0.020
 41O  plan-2  C20  0.020
 41O  plan-2  N19  0.020
 41O  plan-2  O11  0.020
 41O  plan-2  C6   0.020
 41O  plan-2  C10  0.020
 41O  plan-3  C30  0.020
 41O  plan-3  C29  0.020
 41O  plan-3  C31  0.020
 41O  plan-3  C32  0.020
 41O  plan-3  C33  0.020
 41O  plan-3  O34  0.020
 41O  plan-3  C28  0.020
 41O  plan-3  C27  0.020
 41O  plan-3  C26  0.020
 41O  plan-3  C25  0.020
 41O  plan-3  N22  0.020
 41O  plan-3  H5   0.020
 41O  plan-3  H6   0.020
 41O  plan-3  H7   0.020
 41O  plan-3  H8   0.020
 41O  plan-3  H9   0.020

