# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:46:03 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2-benzyl-1-phenyl-1H-indol-3-yl)(piperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCNCC1)c2c(Cc3ccccc3)n(c4ccccc4)c5ccccc25
#
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
 S51  S51  (2-benzyl-1-phenyl-1H-indol-3-yl)(piperazin-1-yl)methanone  ligand  55  30  .  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_S51
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
 S51  C1    C  CR16  0  -0.246  -4.9867  -0.8935  -1.2028
 S51  C2    C  CR16  0  -0.253  -4.6630  -0.7145   0.1360
 S51  C3    C  CR16  0  -0.245  -3.3357  -0.6970   0.5352
 S51  C4    C  CR6   0   0.268  -2.3323  -0.8726  -0.4086
 S51  C5    C  CR16  0  -0.270  -2.6491  -1.0690  -1.7462
 S51  C6    C  CR16  0  -0.258  -3.9795  -1.0692  -2.1423
 S51  N12   N  NR5   0  -0.680  -0.9772  -0.8391   0.0003
 S51  C13   C  CR56  0   0.323  -0.3588  -1.8022   0.7592
 S51  C14   C  CR56  0   0.127   0.9728  -1.3932   0.9677
 S51  C15   C  CR5   0  -0.257   1.1244  -0.1399   0.2965
 S51  C16   C  CR5   0   0.396  -0.0761   0.1674  -0.2767
 S51  C17   C  CR16  0  -0.300  -0.8525  -3.0026   1.2633
 S51  C18   C  CR16  0  -0.283   0.0181  -3.7903   1.9941
 S51  C19   C  CR16  0  -0.265   1.3472  -3.3982   2.2164
 S51  C20   C  CR16  0  -0.376   1.8333  -2.2091   1.7079
 S51  C26   C  CR6   0   0.137  -1.4339   2.2579  -0.2526
 S51  C29   C  CR16  0  -0.288  -1.0386   2.8415   0.9490
 S51  C30   C  CR16  0  -0.244  -1.9217   3.6277   1.6742
 S51  C31   C  CR16  0  -0.271  -3.2143   3.8382   1.2076
 S51  C32   C  CR16  0  -0.238  -3.6164   3.2545   0.0147
 S51  C33   C  CR16  0  -0.299  -2.7295   2.4685  -0.7096
 S51  C39   C  C     0   0.454   2.3340   0.7246   0.3542
 S51  N40   N  NT    0  -0.434   3.2267   0.5931  -0.6438
 S51  O41   O  O     0  -0.488   2.4867   1.5022   1.2912
 S51  C42   C  CH2   0  -0.323   4.4854   1.3224  -0.6357
 S51  C43   C  CH2   0  -0.316   5.6500   0.3364  -0.5785
 S51  N44   N  NH1   0  -0.579   5.6079  -0.6737  -1.6208
 S51  C45   C  CH2   0  -0.311   4.3182  -1.3396  -1.6591
 S51  C46   C  CH2   0  -0.314   3.1352  -0.3771  -1.7226
 S51  C60   C  CH2   0  -0.626  -0.4675   1.3939  -1.0297
 S51  H1    H  HCR6  0   0.261  -6.0235  -0.8993  -1.5128
 S51  H2    H  HCR6  0   0.263  -5.4451  -0.5755   0.8704
 S51  H3    H  HCR6  0   0.266  -3.0765  -0.5290   1.5726
 S51  H5    H  HCR6  0   0.272  -1.8609  -1.2197  -2.4732
 S51  H6    H  HCR6  0   0.264  -4.2273  -1.2164  -3.1852
 S51  H17   H  HCR6  0   0.263  -1.8762  -3.3113   1.0942
 S51  H18   H  HCR6  0   0.253  -0.3332  -4.7288   2.4025
 S51  H19   H  HCR6  0   0.250   1.9985  -4.0394   2.7958
 S51  H20   H  HCR6  0   0.240   2.8610  -1.9158   1.8853
 S51  H29   H  HCR6  0   0.248  -0.0335   2.6745   1.3206
 S51  H30   H  HCR6  0   0.252  -1.6013   4.0782   2.6050
 S51  H31   H  HCR6  0   0.252  -3.9031   4.4529   1.7726
 S51  H32   H  HCR6  0   0.251  -4.6235   3.4065  -0.3519
 S51  H33   H  HCR6  0   0.246  -3.0526   2.0023  -1.6326
 S51  H42   H  HCH2  0   0.244   4.5470   1.9217  -1.5506
 S51  H42A  H  HCH2  0   0.264   4.5105   2.0044   0.2102
 S51  H43   H  HCH2  0   0.246   6.5924   0.8829  -0.6439
 S51  H43A  H  HCH2  0   0.228   5.6369  -0.1674   0.3938
 S51  HN44  H  HNH1  0   0.345   5.7839  -0.2368  -2.5183
 S51  H45   H  HCH2  0   0.247   4.2844  -2.0099  -2.5194
 S51  H45A  H  HCH2  0   0.223   4.2201  -1.9610  -0.7624
 S51  H46   H  HCH2  0   0.273   2.1960  -0.9220  -1.6604
 S51  H46A  H  HCH2  0   0.243   3.1432   0.1603  -2.6771
 S51  H60   H  HCH2  0   0.282   0.4408   1.9570  -1.2565
 S51  H60A  H  HCH2  0   0.283  -0.9030   1.1312  -1.9961

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
 S51  C1   C2    aromatic  1.389  0.020  1.389
 S51  C1   C6    aromatic  1.388  0.020  1.388
 S51  C2   C3    aromatic  1.386  0.020  1.386
 S51  C3   C4    aromatic  1.389  0.020  1.389
 S51  C4   C5    aromatic  1.389  0.020  1.389
 S51  C4   N12   single    1.416  0.020  1.416
 S51  C5   C6    aromatic  1.388  0.020  1.388
 S51  N12  C13   aromatic  1.373  0.020  1.373
 S51  N12  C16   aromatic  1.379  0.020  1.379
 S51  C13  C14   aromatic  1.408  0.020  1.408
 S51  C13  C17   aromatic  1.392  0.020  1.392
 S51  C14  C15   aromatic  1.430  0.020  1.430
 S51  C14  C20   aromatic  1.398  0.020  1.398
 S51  C15  C16   aromatic  1.365  0.020  1.365
 S51  C15  C39   single    1.488  0.020  1.488
 S51  C16  C60   single    1.491  0.020  1.491
 S51  C17  C18   aromatic  1.383  0.020  1.383
 S51  C18  C19   aromatic  1.403  0.020  1.403
 S51  C19  C20   aromatic  1.382  0.020  1.382
 S51  C26  C29   aromatic  1.393  0.020  1.393
 S51  C26  C33   aromatic  1.390  0.020  1.390
 S51  C26  C60   single    1.511  0.020  1.511
 S51  C29  C30   aromatic  1.387  0.020  1.387
 S51  C30  C31   aromatic  1.390  0.020  1.390
 S51  C31  C32   aromatic  1.388  0.020  1.388
 S51  C32  C33   aromatic  1.389  0.020  1.389
 S51  C39  N40   single    1.345  0.020  1.345
 S51  C39  O41   double    1.227  0.020  1.227
 S51  N40  C42   single    1.455  0.020  1.455
 S51  N40  C46   single    1.454  0.020  1.454
 S51  C42  C43   single    1.527  0.020  1.527
 S51  C43  N44   single    1.452  0.020  1.452
 S51  N44  C45   single    1.452  0.020  1.452
 S51  C45  C46   single    1.526  0.020  1.526
 S51  C1   H1    single    0.930  0.020  1.080
 S51  C2   H2    single    0.930  0.020  1.080
 S51  C3   H3    single    0.930  0.020  1.080
 S51  C5   H5    single    0.930  0.020  1.080
 S51  C6   H6    single    0.930  0.020  1.080
 S51  C17  H17   single    0.930  0.020  1.080
 S51  C18  H18   single    0.930  0.020  1.080
 S51  C19  H19   single    0.930  0.020  1.080
 S51  C20  H20   single    0.930  0.020  1.080
 S51  C29  H29   single    0.930  0.020  1.080
 S51  C30  H30   single    0.930  0.020  1.080
 S51  C31  H31   single    0.930  0.020  1.080
 S51  C32  H32   single    0.930  0.020  1.080
 S51  C33  H33   single    0.930  0.020  1.080
 S51  C42  H42   single    0.970  0.020  1.090
 S51  C42  H42A  single    0.970  0.020  1.090
 S51  C43  H43   single    0.970  0.020  1.090
 S51  C43  H43A  single    0.970  0.020  1.090
 S51  N44  HN44  single    0.890  0.020  1.040
 S51  C45  H45   single    0.970  0.020  1.090
 S51  C45  H45A  single    0.970  0.020  1.090
 S51  C46  H46   single    0.970  0.020  1.090
 S51  C46  H46A  single    0.970  0.020  1.090
 S51  C60  H60   single    0.970  0.020  1.090
 S51  C60  H60A  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
 S51  H1    C1   C6   120.03  3.000
 S51  H1    C1   C2   120.00  3.000
 S51  C6    C1   C2   119.96  3.000
 S51  H2    C2   C3   119.68  3.000
 S51  H2    C2   C1   120.16  3.000
 S51  C3    C2   C1   120.16  3.000
 S51  H3    C3   C4   119.87  3.000
 S51  H3    C3   C2   120.48  3.000
 S51  C4    C3   C2   119.64  3.000
 S51  N12   C4   C5   119.99  3.000
 S51  N12   C4   C3   119.49  3.000
 S51  C5    C4   C3   120.52  3.000
 S51  H5    C5   C6   120.40  3.000
 S51  H5    C5   C4   120.03  3.000
 S51  C6    C5   C4   119.57  3.000
 S51  H6    C6   C5   119.64  3.000
 S51  H6    C6   C1   120.22  3.000
 S51  C5    C6   C1   120.14  3.000
 S51  C16   N12  C13  109.18  3.000
 S51  C16   N12  C4   125.78  3.000
 S51  C13   N12  C4   125.03  3.000
 S51  C17   C13  C14  122.14  3.000
 S51  C17   C13  N12  130.17  3.000
 S51  C14   C13  N12  107.69  3.000
 S51  C20   C14  C15  134.02  3.000
 S51  C20   C14  C13  119.40  3.000
 S51  C15   C14  C13  106.58  3.000
 S51  C39   C15  C16  126.90  3.000
 S51  C39   C15  C14  125.26  3.000
 S51  C16   C15  C14  107.52  3.000
 S51  C60   C16  C15  128.88  3.000
 S51  C60   C16  N12  122.02  3.000
 S51  C15   C16  N12  109.02  3.000
 S51  H17   C17  C18  121.03  3.000
 S51  H17   C17  C13  121.64  3.000
 S51  C18   C17  C13  117.34  3.000
 S51  H18   C18  C19  119.33  3.000
 S51  H18   C18  C17  119.28  3.000
 S51  C19   C18  C17  121.38  3.000
 S51  H19   C19  C20  119.69  3.000
 S51  H19   C19  C18  119.29  3.000
 S51  C20   C19  C18  121.02  3.000
 S51  H20   C20  C19  120.43  3.000
 S51  H20   C20  C14  120.84  3.000
 S51  C19   C20  C14  118.73  3.000
 S51  C60   C26  C33  120.91  3.000
 S51  C60   C26  C29  120.10  3.000
 S51  C33   C26  C29  118.99  3.000
 S51  H29   C29  C30  119.88  3.000
 S51  H29   C29  C26  119.61  3.000
 S51  C30   C29  C26  120.52  3.000
 S51  H30   C30  C31  120.05  3.000
 S51  H30   C30  C29  119.80  3.000
 S51  C31   C30  C29  120.15  3.000
 S51  H31   C31  C32  120.21  3.000
 S51  H31   C31  C30  120.16  3.000
 S51  C32   C31  C30  119.62  3.000
 S51  H32   C32  C33  119.80  3.000
 S51  H32   C32  C31  120.12  3.000
 S51  C33   C32  C31  120.09  3.000
 S51  H33   C33  C32  119.83  3.000
 S51  H33   C33  C26  119.53  3.000
 S51  C32   C33  C26  120.64  3.000
 S51  O41   C39  N40  123.08  3.000
 S51  O41   C39  C15  119.93  3.000
 S51  N40   C39  C15  116.99  3.000
 S51  C46   N40  C42  113.15  3.000
 S51  C46   N40  C39  125.02  3.000
 S51  C42   N40  C39  121.40  3.000
 S51  H42A  C42  H42  107.79  3.000
 S51  H42A  C42  C43  111.01  3.000
 S51  H42   C42  C43  109.98  3.000
 S51  H42A  C42  N40  109.81  3.000
 S51  H42   C42  N40  108.55  3.000
 S51  C43   C42  N40  109.65  3.000
 S51  H43A  C43  H43  107.10  3.000
 S51  H43A  C43  N44  108.48  3.000
 S51  H43   C43  N44  109.29  3.000
 S51  H43A  C43  C42  108.73  3.000
 S51  H43   C43  C42  109.44  3.000
 S51  N44   C43  C42  113.59  3.000
 S51  HN44  N44  C45  109.18  3.000
 S51  HN44  N44  C43  109.31  3.000
 S51  C45   N44  C43  111.33  3.000
 S51  H45A  C45  H45  107.11  3.000
 S51  H45A  C45  C46  108.80  3.000
 S51  H45   C45  C46  109.30  3.000
 S51  H45A  C45  N44  108.56  3.000
 S51  H45   C45  N44  109.27  3.000
 S51  C46   C45  N44  113.59  3.000
 S51  H46A  C46  H46  107.57  3.000
 S51  H46A  C46  C45  109.87  3.000
 S51  H46   C46  C45  110.54  3.000
 S51  H46A  C46  N40  108.59  3.000
 S51  H46   C46  N40  110.26  3.000
 S51  C45   C46  N40  109.95  3.000
 S51  H60A  C60  H60  105.78  3.000
 S51  H60A  C60  C26  109.72  3.000
 S51  H60   C60  C26  110.11  3.000
 S51  H60A  C60  C16  110.71  3.000
 S51  H60   C60  C16  108.09  3.000
 S51  C26   C60  C16  112.23  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
 S51  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 S51  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 S51  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 S51  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 S51  CONST_05  N12  C4   C3   C2   180.00   0.0  0
 S51  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 S51  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 S51  CONST_10  C14  C13  N12  C4   180.00   0.0  0
 S51  CONST_11  C17  C13  N12  C4     0.00   0.0  0
 S51  CONST_12  C15  C16  N12  C4   180.00   0.0  0
 S51  CONST_15  N12  C4   C5   C6   180.00   0.0  0
 S51  CONST_16  C15  C14  C13  N12    0.00   0.0  0
 S51  CONST_17  C20  C14  C13  N12  180.00   0.0  0
 S51  CONST_18  C18  C17  C13  N12  180.00   0.0  0
 S51  CONST_19  C14  C15  C16  N12    0.00   0.0  0
 S51  CONST_20  C15  C16  N12  C13    0.00   0.0  0
 S51  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 S51  CONST_22  C19  C20  C14  C13    0.00   0.0  0
 S51  CONST_23  C19  C18  C17  C13    0.00   0.0  0
 S51  CONST_24  C16  N12  C13  C14    0.00   0.0  0
 S51  CONST_25  C18  C17  C13  C14    0.00   0.0  0
 S51  CONST_26  C18  C19  C20  C14    0.00   0.0  0
 S51  CONST_27  C17  C13  C14  C15  180.00   0.0  0
 S51  CONST_28  C19  C20  C14  C15  180.00   0.0  0
 S51  CONST_29  C17  C13  N12  C16  180.00   0.0  0
 S51  CONST_30  C20  C14  C15  C16  180.00   0.0  0
 S51  CONST_31  C20  C14  C13  C17    0.00   0.0  0
 S51  CONST_32  C20  C19  C18  C17    0.00   0.0  0
 S51  CONST_33  C31  C30  C29  C26    0.00   0.0  0
 S51  CONST_34  C31  C32  C33  C26    0.00   0.0  0
 S51  CONST_35  C32  C33  C26  C29    0.00   0.0  0
 S51  CONST_36  C32  C31  C30  C29    0.00   0.0  0
 S51  CONST_37  C33  C26  C29  C30    0.00   0.0  0
 S51  CONST_38  C33  C32  C31  C30    0.00   0.0  0
 S51  CONST_39  C60  C16  N12  C4     0.00   0.0  0
 S51  CONST_40  C39  C15  C16  N12  180.00   0.0  0
 S51  CONST_41  C60  C16  N12  C13  180.00   0.0  0
 S51  CONST_42  C39  C15  C14  C13  180.00   0.0  0
 S51  CONST_43  C60  C16  C15  C14  180.00   0.0  0
 S51  CONST_44  C39  C15  C14  C20    0.00   0.0  0
 S51  CONST_45  C60  C26  C29  C30  180.00   0.0  0
 S51  CONST_46  C60  C26  C33  C32  180.00   0.0  0
 S51  CONST_47  C42  N40  C39  C15  180.00   0.0  0
 S51  CONST_48  C46  N40  C39  C15    0.00   0.0  0
 S51  CONST_49  H3   C3   C2   C1   180.00   0.0  0
 S51  CONST_50  H5   C5   C6   C1   180.00   0.0  0
 S51  CONST_51  H6   C6   C1   C2   180.00   0.0  0
 S51  CONST_52  H1   C1   C2   C3   180.00   0.0  0
 S51  CONST_53  H2   C2   C3   C4   180.00   0.0  0
 S51  CONST_54  H17  C17  C13  N12    0.00   0.0  0
 S51  CONST_55  H20  C20  C14  C13  180.00   0.0  0
 S51  CONST_56  H18  C18  C17  C13  180.00   0.0  0
 S51  CONST_57  H19  C19  C20  C14  180.00   0.0  0
 S51  CONST_58  H30  C30  C29  C26  180.00   0.0  0
 S51  CONST_59  H32  C32  C33  C26  180.00   0.0  0
 S51  CONST_60  H33  C33  C26  C29  180.00   0.0  0
 S51  CONST_61  H31  C31  C30  C29  180.00   0.0  0
 S51  CONST_62  H29  C29  C30  C31  180.00   0.0  0
 S51  CONST_63  C42  N40  C39  O41    0.00   0.0  0
 S51  CONST_64  C46  N40  C39  O41  180.00   0.0  0
 S51  Var_01    N44  C43  C42  N40   53.58  30.0  1
 S51  Var_02    N44  C45  C46  N40  -53.03  30.0  1
 S51  Var_03    C45  C46  N40  C42   55.56  30.0  1
 S51  Var_04    C45  N44  C43  C42  -51.81  30.0  1
 S51  Var_05    C46  N40  C42  C43  -55.75  30.0  1
 S51  Var_06    C46  C45  N44  C43   51.46  30.0  1
 S51  Var_07    C26  C60  C16  N12   67.18  30.0  2
 S51  Var_08    N40  C39  C15  C14   95.59  30.0  2
 S51  Var_09    C29  C26  C60  C16   63.68  30.0  3

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
 S51  plan-1  C1   0.020
 S51  plan-1  C2   0.020
 S51  plan-1  C3   0.020
 S51  plan-1  C4   0.020
 S51  plan-1  C5   0.020
 S51  plan-1  C6   0.020
 S51  plan-1  N12  0.020
 S51  plan-1  H1   0.020
 S51  plan-1  H2   0.020
 S51  plan-1  H3   0.020
 S51  plan-1  H5   0.020
 S51  plan-1  H6   0.020
 S51  plan-2  C26  0.020
 S51  plan-2  C29  0.020
 S51  plan-2  C30  0.020
 S51  plan-2  C31  0.020
 S51  plan-2  C32  0.020
 S51  plan-2  C33  0.020
 S51  plan-2  C60  0.020
 S51  plan-2  H29  0.020
 S51  plan-2  H30  0.020
 S51  plan-2  H31  0.020
 S51  plan-2  H32  0.020
 S51  plan-2  H33  0.020
 S51  plan-3  C4   0.020
 S51  plan-3  N12  0.020
 S51  plan-3  C13  0.020
 S51  plan-3  C14  0.020
 S51  plan-3  C15  0.020
 S51  plan-3  C16  0.020
 S51  plan-3  C17  0.020
 S51  plan-3  C18  0.020
 S51  plan-3  C19  0.020
 S51  plan-3  C20  0.020
 S51  plan-3  C39  0.020
 S51  plan-3  C60  0.020
 S51  plan-3  H17  0.020
 S51  plan-3  H18  0.020
 S51  plan-3  H19  0.020
 S51  plan-3  H20  0.020
 S51  plan-4  C15  0.020
 S51  plan-4  C39  0.020
 S51  plan-4  N40  0.020
 S51  plan-4  O41  0.020
 S51  plan-4  C42  0.020
 S51  plan-4  C46  0.020

