# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:42:38 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2-phenoxy-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(Oc3ccccc3)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
 S52  S52  (2-phenoxy-1-phenyl-1H-indol-3-yl)(piperazin-1-yl)methanone  ligand  53  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_S52
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
 S52  C1    C  CR16  0  -0.243   4.9830   0.4740  -1.4524
 S52  O1    O  O2    0  -0.500   0.2048   1.4720  -0.5366
 S52  C2    C  CR16  0  -0.259   3.9544   0.3587  -2.3780
 S52  C3    C  CR16  0  -0.252   2.6874  -0.0286  -1.9667
 S52  C4    C  CR6   0   0.256   2.4580  -0.2875  -0.6228
 S52  C5    C  CR16  0  -0.243   3.4805  -0.1750   0.3088
 S52  C6    C  CR16  0  -0.253   4.7466   0.2007  -0.1116
 S52  N12   N  NR5   0  -0.668   1.1561  -0.6452  -0.1903
 S52  C13   C  CR56  0   0.345   0.7411  -1.8925   0.2229
 S52  C14   C  CR56  0   0.088  -0.6389  -1.8190   0.4971
 S52  C15   C  CR5   0  -0.239  -1.0479  -0.4638   0.2491
 S52  C16   C  CR5   0   0.528   0.0785   0.1972  -0.1506
 S52  C17   C  CR16  0  -0.293   1.4704  -3.0663   0.3661
 S52  C18   C  CR16  0  -0.283   0.7896  -4.1865   0.8095
 S52  C19   C  CR16  0  -0.260  -0.5795  -4.1339   1.1033
 S52  C20   C  CR16  0  -0.372  -1.2992  -2.9627   0.9530
 S52  C26   C  CR6   0   0.331   1.0406   2.2762   0.2190
 S52  C29   C  CR16  0  -0.293   1.8983   3.1215  -0.4644
 S52  C30   C  CR16  0  -0.249   2.7461   3.9476   0.2584
 S52  C31   C  CR16  0  -0.259   2.7403   3.9199   1.6470
 S52  C32   C  CR16  0  -0.251   1.8692   3.0689   2.3134
 S52  C33   C  CR16  0  -0.298   1.0073   2.2432   1.6042
 S52  C39   C  C     0   0.490  -2.3376   0.1935   0.5449
 S52  N40   N  NT    0  -0.455  -3.4595  -0.4370   0.1285
 S52  O41   O  O     0  -0.486  -2.3630   1.2385   1.1870
 S52  C42   C  CH2   0  -0.324  -4.7706   0.0773   0.4932
 S52  C43   C  CH2   0  -0.316  -5.4447   0.7220  -0.7140
 S52  N44   N  NH1   0  -0.579  -5.5081  -0.1574  -1.8695
 S52  C45   C  CH2   0  -0.305  -4.2053  -0.7183  -2.1787
 S52  C46   C  CH2   0  -0.328  -3.5101  -1.3726  -0.9853
 S52  H1    H  HCR6  0   0.263   5.9697   0.7764  -1.7769
 S52  H2    H  HCR6  0   0.265   4.1384   0.5670  -3.4235
 S52  H3    H  HCR6  0   0.269   1.8821  -0.1244  -2.6834
 S52  H5    H  HCR6  0   0.269   3.2818  -0.3676   1.3550
 S52  H6    H  HCR6  0   0.264   5.5455   0.2906   0.6121
 S52  H17   H  HCR6  0   0.266   2.5292  -3.1074   0.1446
 S52  H18   H  HCR6  0   0.255   1.3258  -5.1182   0.9332
 S52  H19   H  HCR6  0   0.252  -1.0802  -5.0268   1.4539
 S52  H20   H  HCR6  0   0.248  -2.3562  -2.9351   1.1859
 S52  H29   H  HCR6  0   0.265   1.9125   3.1211  -1.5464
 S52  H30   H  HCR6  0   0.260   3.4222   4.6066  -0.2704
 S52  H31   H  HCR6  0   0.257   3.4085   4.5597   2.2078
 S52  H32   H  HCR6  0   0.262   1.8513   3.0483   3.3954
 S52  H33   H  HCR6  0   0.275   0.3135   1.5948   2.1245
 S52  H42   H  HCH2  0   0.243  -5.3764  -0.7634   0.8476
 S52  H42A  H  HCH2  0   0.259  -4.6740   0.7849   1.3127
 S52  H43   H  HCH2  0   0.244  -6.4551   1.0351  -0.4457
 S52  H43A  H  HCH2  0   0.228  -4.8914   1.6247  -0.9921
 S52  HN44  H  HNH1  0   0.345  -6.1595  -0.9105  -1.6795
 S52  H45   H  HCH2  0   0.246  -4.3105  -1.4525  -2.9793
 S52  H45A  H  HCH2  0   0.225  -3.5631   0.0834  -2.5584
 S52  H46   H  HCH2  0   0.273  -2.5079  -1.6828  -1.2704
 S52  H46A  H  HCH2  0   0.241  -4.0564  -2.2687  -0.6743

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
 S52  C1   C2    aromatic  1.389  0.020  1.389
 S52  C1   C6    aromatic  1.389  0.020  1.389
 S52  O1   C16   single    1.338  0.020  1.338
 S52  O1   C26   single    1.384  0.020  1.384
 S52  C2   C3    aromatic  1.387  0.020  1.387
 S52  C3   C4    aromatic  1.388  0.020  1.388
 S52  C4   C5    aromatic  1.388  0.020  1.388
 S52  C4   N12   single    1.418  0.020  1.418
 S52  C5   C6    aromatic  1.386  0.020  1.386
 S52  N12  C13   aromatic  1.378  0.020  1.378
 S52  N12  C16   aromatic  1.368  0.020  1.368
 S52  C13  C14   aromatic  1.409  0.020  1.409
 S52  C13  C17   aromatic  1.389  0.020  1.389
 S52  C14  C15   aromatic  1.437  0.020  1.437
 S52  C14  C20   aromatic  1.397  0.020  1.397
 S52  C15  C16   aromatic  1.366  0.020  1.366
 S52  C15  C39   single    1.477  0.020  1.477
 S52  C17  C18   aromatic  1.384  0.020  1.384
 S52  C18  C19   aromatic  1.401  0.020  1.401
 S52  C19  C20   aromatic  1.383  0.020  1.383
 S52  C26  C29   aromatic  1.385  0.020  1.385
 S52  C26  C33   aromatic  1.386  0.020  1.386
 S52  C29  C30   aromatic  1.387  0.020  1.387
 S52  C30  C31   aromatic  1.389  0.020  1.389
 S52  C31  C32   aromatic  1.388  0.020  1.388
 S52  C32  C33   aromatic  1.388  0.020  1.388
 S52  C39  N40   single    1.353  0.020  1.353
 S52  C39  O41   double    1.227  0.020  1.227
 S52  N40  C42   single    1.455  0.020  1.455
 S52  N40  C46   single    1.456  0.020  1.456
 S52  C42  C43   single    1.526  0.020  1.526
 S52  C43  N44   single    1.453  0.020  1.453
 S52  N44  C45   single    1.452  0.020  1.452
 S52  C45  C46   single    1.528  0.020  1.528
 S52  C1   H1    single    0.930  0.020  1.080
 S52  C2   H2    single    0.930  0.020  1.080
 S52  C3   H3    single    0.930  0.020  1.080
 S52  C5   H5    single    0.930  0.020  1.080
 S52  C6   H6    single    0.930  0.020  1.080
 S52  C17  H17   single    0.930  0.020  1.080
 S52  C18  H18   single    0.930  0.020  1.080
 S52  C19  H19   single    0.930  0.020  1.080
 S52  C20  H20   single    0.930  0.020  1.080
 S52  C29  H29   single    0.930  0.020  1.080
 S52  C30  H30   single    0.930  0.020  1.080
 S52  C31  H31   single    0.930  0.020  1.080
 S52  C32  H32   single    0.930  0.020  1.080
 S52  C33  H33   single    0.930  0.020  1.080
 S52  C42  H42   single    0.970  0.020  1.090
 S52  C42  H42A  single    0.970  0.020  1.090
 S52  C43  H43   single    0.970  0.020  1.090
 S52  C43  H43A  single    0.970  0.020  1.090
 S52  N44  HN44  single    0.890  0.020  1.040
 S52  C45  H45   single    0.970  0.020  1.090
 S52  C45  H45A  single    0.970  0.020  1.090
 S52  C46  H46   single    0.970  0.020  1.090
 S52  C46  H46A  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
 S52  H1    C1   C6   119.99  3.000
 S52  H1    C1   C2   119.93  3.000
 S52  C6    C1   C2   120.08  3.000
 S52  C26   O1   C16  116.94  3.000
 S52  H2    C2   C3   119.71  3.000
 S52  H2    C2   C1   120.15  3.000
 S52  C3    C2   C1   120.14  3.000
 S52  H3    C3   C4   120.11  3.000
 S52  H3    C3   C2   120.53  3.000
 S52  C4    C3   C2   119.36  3.000
 S52  N12   C4   C5   119.49  3.000
 S52  N12   C4   C3   119.63  3.000
 S52  C5    C4   C3   120.87  3.000
 S52  H5    C5   C6   120.61  3.000
 S52  H5    C5   C4   119.95  3.000
 S52  C6    C5   C4   119.44  3.000
 S52  H6    C6   C5   119.62  3.000
 S52  H6    C6   C1   120.26  3.000
 S52  C5    C6   C1   120.11  3.000
 S52  C16   N12  C13  108.14  3.000
 S52  C16   N12  C4   125.22  3.000
 S52  C13   N12  C4   126.62  3.000
 S52  C17   C13  C14  122.56  3.000
 S52  C17   C13  N12  129.61  3.000
 S52  C14   C13  N12  107.83  3.000
 S52  C20   C14  C15  133.93  3.000
 S52  C20   C14  C13  118.93  3.000
 S52  C15   C14  C13  107.12  3.000
 S52  C39   C15  C16  124.27  3.000
 S52  C39   C15  C14  129.30  3.000
 S52  C16   C15  C14  105.79  3.000
 S52  C15   C16  N12  111.10  3.000
 S52  C15   C16  O1   128.57  3.000
 S52  N12   C16  O1   120.25  3.000
 S52  H17   C17  C18  121.07  3.000
 S52  H17   C17  C13  121.63  3.000
 S52  C18   C17  C13  117.30  3.000
 S52  H18   C18  C19  119.50  3.000
 S52  H18   C18  C17  119.33  3.000
 S52  C19   C18  C17  121.17  3.000
 S52  H19   C19  C20  119.55  3.000
 S52  H19   C19  C18  119.28  3.000
 S52  C20   C19  C18  121.17  3.000
 S52  H20   C20  C19  120.42  3.000
 S52  H20   C20  C14  120.71  3.000
 S52  C19   C20  C14  118.87  3.000
 S52  C33   C26  C29  121.51  3.000
 S52  C33   C26  O1   121.14  3.000
 S52  C29   C26  O1   117.34  3.000
 S52  H29   C29  C30  120.88  3.000
 S52  H29   C29  C26  120.10  3.000
 S52  C30   C29  C26  119.01  3.000
 S52  H30   C30  C31  120.22  3.000
 S52  H30   C30  C29  119.33  3.000
 S52  C31   C30  C29  120.44  3.000
 S52  H31   C31  C32  120.09  3.000
 S52  H31   C31  C30  120.26  3.000
 S52  C32   C31  C30  119.65  3.000
 S52  H32   C32  C33  119.28  3.000
 S52  H32   C32  C31  120.13  3.000
 S52  C33   C32  C31  120.59  3.000
 S52  H33   C33  C32  120.56  3.000
 S52  H33   C33  C26  120.65  3.000
 S52  C32   C33  C26  118.78  3.000
 S52  O41   C39  N40  122.75  3.000
 S52  O41   C39  C15  120.12  3.000
 S52  N40   C39  C15  117.07  3.000
 S52  C46   N40  C42  112.81  3.000
 S52  C46   N40  C39  124.33  3.000
 S52  C42   N40  C39  120.36  3.000
 S52  H42A  C42  H42  107.75  3.000
 S52  H42A  C42  C43  111.15  3.000
 S52  H42   C42  C43  109.64  3.000
 S52  H42A  C42  N40  109.82  3.000
 S52  H42   C42  N40  107.95  3.000
 S52  C43   C42  N40  110.44  3.000
 S52  H43A  C43  H43  107.09  3.000
 S52  H43A  C43  N44  108.60  3.000
 S52  H43   C43  N44  109.18  3.000
 S52  H43A  C43  C42  109.04  3.000
 S52  H43   C43  C42  109.62  3.000
 S52  N44   C43  C42  113.12  3.000
 S52  HN44  N44  C45  109.24  3.000
 S52  HN44  N44  C43  109.18  3.000
 S52  C45   N44  C43  111.34  3.000
 S52  H45A  C45  H45  107.13  3.000
 S52  H45A  C45  C46  108.51  3.000
 S52  H45   C45  C46  109.19  3.000
 S52  H45A  C45  N44  108.50  3.000
 S52  H45   C45  N44  109.25  3.000
 S52  C46   C45  N44  114.04  3.000
 S52  H46A  C46  H46  107.52  3.000
 S52  H46A  C46  C45  110.21  3.000
 S52  H46   C46  C45  109.68  3.000
 S52  H46A  C46  N40  109.03  3.000
 S52  H46   C46  N40  110.61  3.000
 S52  C45   C46  N40  109.77  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
 S52  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 S52  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 S52  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 S52  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 S52  CONST_05  N12  C4   C3   C2   180.00   0.0  0
 S52  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 S52  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 S52  CONST_10  C14  C13  N12  C4   180.00   0.0  0
 S52  CONST_11  C17  C13  N12  C4     0.00   0.0  0
 S52  CONST_12  C15  C16  N12  C4   180.00   0.0  0
 S52  CONST_15  N12  C4   C5   C6   180.00   0.0  0
 S52  CONST_16  C15  C14  C13  N12    0.00   0.0  0
 S52  CONST_17  C20  C14  C13  N12  180.00   0.0  0
 S52  CONST_18  C18  C17  C13  N12  180.00   0.0  0
 S52  CONST_19  C14  C15  C16  N12    0.00   0.0  0
 S52  CONST_20  C15  C16  N12  C13    0.00   0.0  0
 S52  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 S52  CONST_22  C19  C20  C14  C13    0.00   0.0  0
 S52  CONST_23  C19  C18  C17  C13    0.00   0.0  0
 S52  CONST_24  C16  N12  C13  C14    0.00   0.0  0
 S52  CONST_25  C18  C17  C13  C14    0.00   0.0  0
 S52  CONST_26  C18  C19  C20  C14    0.00   0.0  0
 S52  CONST_27  C17  C13  C14  C15  180.00   0.0  0
 S52  CONST_28  C19  C20  C14  C15  180.00   0.0  0
 S52  CONST_29  C17  C13  N12  C16  180.00   0.0  0
 S52  CONST_30  C20  C14  C15  C16  180.00   0.0  0
 S52  CONST_31  C20  C14  C13  C17    0.00   0.0  0
 S52  CONST_32  C20  C19  C18  C17    0.00   0.0  0
 S52  CONST_33  C31  C30  C29  C26    0.00   0.0  0
 S52  CONST_34  C31  C32  C33  C26    0.00   0.0  0
 S52  CONST_35  C32  C33  C26  C29    0.00   0.0  0
 S52  CONST_36  C32  C31  C30  C29    0.00   0.0  0
 S52  CONST_37  C33  C26  C29  C30    0.00   0.0  0
 S52  CONST_38  C33  C32  C31  C30    0.00   0.0  0
 S52  CONST_39  C4   N12  C16  O1     0.00   0.0  0
 S52  CONST_40  C13  N12  C16  O1   180.00   0.0  0
 S52  CONST_41  C14  C15  C16  O1   180.00   0.0  0
 S52  CONST_42  C30  C29  C26  O1   180.00   0.0  0
 S52  CONST_43  C32  C33  C26  O1   180.00   0.0  0
 S52  CONST_44  C39  C15  C16  N12  180.00   0.0  0
 S52  CONST_45  C39  C15  C14  C13  180.00   0.0  0
 S52  CONST_46  C39  C15  C14  C20    0.00   0.0  0
 S52  CONST_47  C42  N40  C39  C15  180.00   0.0  0
 S52  CONST_49  H3   C3   C2   C1   180.00   0.0  0
 S52  CONST_50  H5   C5   C6   C1   180.00   0.0  0
 S52  CONST_51  H6   C6   C1   C2   180.00   0.0  0
 S52  CONST_52  H1   C1   C2   C3   180.00   0.0  0
 S52  CONST_53  H2   C2   C3   C4   180.00   0.0  0
 S52  CONST_54  H17  C17  C13  N12    0.00   0.0  0
 S52  CONST_55  H20  C20  C14  C13  180.00   0.0  0
 S52  CONST_56  H18  C18  C17  C13  180.00   0.0  0
 S52  CONST_57  H19  C19  C20  C14  180.00   0.0  0
 S52  CONST_58  H30  C30  C29  C26  180.00   0.0  0
 S52  CONST_59  H32  C32  C33  C26  180.00   0.0  0
 S52  CONST_60  H33  C33  C26  C29  180.00   0.0  0
 S52  CONST_61  H31  C31  C30  C29  180.00   0.0  0
 S52  CONST_62  H29  C29  C30  C31  180.00   0.0  0
 S52  CONST_63  C42  N40  C39  O41    0.00   0.0  0
 S52  Var_01    N44  C43  C42  N40   53.63  30.0  1
 S52  Var_02    N44  C45  C46  N40  -52.95  30.0  1
 S52  Var_03    C45  C46  N40  C42   55.07  30.0  1
 S52  Var_04    C45  N44  C43  C42  -51.42  30.0  1
 S52  Var_05    C46  N40  C42  C43  -55.86  30.0  1
 S52  Var_06    C46  C45  N44  C43   51.47  30.0  1
 S52  Var_07    N40  C39  C15  C14  -50.46  30.0  2
 S52  Var_08    C29  C26  O1   C16  136.51  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
 S52  plan-1  C1   0.020
 S52  plan-1  C2   0.020
 S52  plan-1  C3   0.020
 S52  plan-1  C4   0.020
 S52  plan-1  C5   0.020
 S52  plan-1  C6   0.020
 S52  plan-1  N12  0.020
 S52  plan-1  H1   0.020
 S52  plan-1  H2   0.020
 S52  plan-1  H3   0.020
 S52  plan-1  H5   0.020
 S52  plan-1  H6   0.020
 S52  plan-2  O1   0.020
 S52  plan-2  C26  0.020
 S52  plan-2  C29  0.020
 S52  plan-2  C30  0.020
 S52  plan-2  C31  0.020
 S52  plan-2  C32  0.020
 S52  plan-2  C33  0.020
 S52  plan-2  H29  0.020
 S52  plan-2  H30  0.020
 S52  plan-2  H31  0.020
 S52  plan-2  H32  0.020
 S52  plan-2  H33  0.020
 S52  plan-3  O1   0.020
 S52  plan-3  C4   0.020
 S52  plan-3  N12  0.020
 S52  plan-3  C13  0.020
 S52  plan-3  C14  0.020
 S52  plan-3  C15  0.020
 S52  plan-3  C16  0.020
 S52  plan-3  C17  0.020
 S52  plan-3  C18  0.020
 S52  plan-3  C19  0.020
 S52  plan-3  C20  0.020
 S52  plan-3  C39  0.020
 S52  plan-3  H17  0.020
 S52  plan-3  H18  0.020
 S52  plan-3  H19  0.020
 S52  plan-3  H20  0.020
 S52  plan-4  C15  0.020
 S52  plan-4  C39  0.020
 S52  plan-4  N40  0.020
 S52  plan-4  O41  0.020
 S52  plan-4  C42  0.020
 S52  plan-4  C46  0.020

