# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:28:39 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-[(4-oxidanylidenecyclohexyl)amino]-4-(3,6,6-trimethyl-4-oxidanylidene-5,7-dihydroindol-1-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cn(c2CC(C)(C)CC(=O)c12)c3ccc(C(N)=O)c(NC4CCC(=O)CC4)c3
#
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
 73Z  73Z  2-[(4-oxidanylidenecyclohexyl)amino]-4-(3,6,6-trimethyl-4-oxidanylidene-5,7-dihydroindol-1-yl)benzamide  ligand  59  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_73Z
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
 73Z  C4   C  C     0   0.317  -4.6375  -1.6643  -0.0126
 73Z  C5   C  CR5   0  -0.180  -3.4191  -1.2586  -0.6753
 73Z  C6   C  CR5   0   0.397  -2.6502  -0.2187  -0.1850
 73Z  C8   C  CR15  0  -0.125  -1.6393  -1.0416  -1.9999
 73Z  C9   C  CR5   0   0.036  -2.7742  -1.7781  -1.8444
 73Z  C13  C  CH3   0  -0.738  -3.2343  -2.8910  -2.7235
 73Z  C14  C  CR6   0   0.330  -0.5177   0.8406  -0.8556
 73Z  C15  C  CR16  0  -0.317  -0.7773   2.2030  -0.9319
 73Z  C1   C  CH2   0  -0.541  -4.9159  -0.9615   1.3009
 73Z  C2   C  CT    0  -0.133  -4.4308   0.4936   1.3856
 73Z  C3   C  CH2   0  -0.478  -2.9300   0.5532   1.0535
 73Z  N7   N  NR5   0  -0.607  -1.5743  -0.0915  -0.9946
 73Z  O10  O  O     0  -0.434  -5.3762  -2.5389  -0.4377
 73Z  C16  C  CR16  0  -0.287   0.2906   3.0702  -0.8081
 73Z  C17  C  CR6   0  -0.142   1.5999   2.6300  -0.6206
 73Z  C18  C  CR6   0   0.403   1.8544   1.2349  -0.5139
 73Z  C19  C  CR16  0  -0.388   0.7595   0.3611  -0.6489
 73Z  C20  C  C     0   0.520   2.7060   3.6203  -0.4998
 73Z  N21  N  NH1   0  -0.710   3.1092   0.7534  -0.3257
 73Z  C22  C  CH1   0  -0.088   3.4198  -0.6241  -0.0175
 73Z  C23  C  CH2   0  -0.452   4.9073  -0.8650  -0.2545
 73Z  C24  C  CH2   0  -0.564   5.2951  -2.3141   0.0449
 73Z  C25  C  C     0   0.413   4.8514  -2.7523   1.4176
 73Z  C26  C  CH2   0  -0.563   3.4088  -2.4537   1.7357
 73Z  C27  C  CH2   0  -0.452   3.0498  -1.0006   1.4195
 73Z  O28  O  O     0  -0.403   5.5896  -3.3193   2.1923
 73Z  N29  N  NH2   0  -0.805   2.5129   4.8129  -1.0823
 73Z  O30  O  O     0  -0.502   3.7454   3.3687   0.1108
 73Z  H1   H  HCR5  0   0.285  -0.8729  -1.0882  -2.7572
 73Z  H2   H  HCH3  0   0.232  -6.2951   1.2895   0.6130
 73Z  H3   H  HCH3  0   0.231  -4.9479   2.4222   0.5336
 73Z  H4   H  HCH3  0   0.232  -5.0590   1.1040  -0.6281
 73Z  H5   H  HCH3  0   0.232  -5.7075   0.9811   3.0726
 73Z  H6   H  HCH3  0   0.228  -4.1083   0.3990   3.5368
 73Z  H7   H  HCH3  0   0.232  -4.3054   2.0366   2.9097
 73Z  H8   H  HCH3  0   0.237  -3.3335  -3.8254  -2.1701
 73Z  H9   H  HCH3  0   0.237  -4.2096  -2.6792  -3.1624
 73Z  H10  H  HCH3  0   0.235  -2.5296  -3.0573  -3.5374
 73Z  H11  H  HCR6  0   0.270  -1.7791   2.5734  -1.0991
 73Z  H12  H  HCH2  0   0.256  -5.9864  -1.0176   1.5145
 73Z  H13  H  HCH2  0   0.268  -4.4132  -1.5504   2.0798
 73Z  H14  H  HCH2  0   0.267  -2.3547   0.1209   1.8818
 73Z  H15  H  HCH2  0   0.265  -2.6065   1.5931   0.9699
 73Z  H16  H  HCR6  0   0.263   0.0842   4.1316  -0.8466
 73Z  H17  H  HCR6  0   0.282   0.8979  -0.7080  -0.5710
 73Z  H18  H  HNH1  0   0.396   3.7822   1.4452  -0.0251
 73Z  H19  H  HCH1  0   0.242   2.8702  -1.2715  -0.7099
 73Z  H20  H  HCH2  0   0.262   5.1649  -0.6252  -1.2873
 73Z  H21  H  HCH2  0   0.239   5.4895  -0.1936   0.3848
 73Z  H22  H  HCH2  0   0.267   4.8020  -2.9738  -0.6789
 73Z  H23  H  HCH2  0   0.269   6.3699  -2.4602  -0.0649
 73Z  H24  H  HCH2  0   0.265   2.7970  -3.1194   1.1157
 73Z  H25  H  HCH2  0   0.268   3.1966  -2.6947   2.7775
 73Z  H26  H  HCH2  0   0.239   3.5782  -0.3306   2.1047
 73Z  H27  H  HCH2  0   0.258   1.9828  -0.8498   1.5938
 73Z  H28  H  HNH2  0   0.414   1.7538   4.9984  -1.7138
 73Z  H29  H  HNH2  0   0.406   3.2351   5.5119  -1.0198
 73Z  C11  C  CH3   0  -0.638  -5.2245   1.3726   0.4164
 73Z  C12  C  CH3   0  -0.644  -4.6486   1.0050   2.8070

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
 73Z  O28  C25  double    1.211  0.020  1.211
 73Z  C26  C25  single    1.507  0.020  1.507
 73Z  C26  C27  single    1.530  0.020  1.530
 73Z  C25  C24  single    1.508  0.020  1.508
 73Z  C27  C22  single    1.531  0.020  1.531
 73Z  C24  C23  single    1.530  0.020  1.530
 73Z  C22  C23  single    1.525  0.020  1.525
 73Z  C22  N21  single    1.445  0.020  1.445
 73Z  N21  C18  single    1.357  0.020  1.357
 73Z  C13  C9   single    1.491  0.020  1.491
 73Z  C18  C19  aromatic  1.407  0.020  1.407
 73Z  C18  C17  aromatic  1.422  0.020  1.422
 73Z  C19  C14  aromatic  1.380  0.020  1.380
 73Z  C8   C9   aromatic  1.362  0.020  1.362
 73Z  C8   N7   aromatic  1.385  0.020  1.385
 73Z  O30  C20  double    1.231  0.020  1.231
 73Z  C9   C5   aromatic  1.433  0.020  1.433
 73Z  C20  C17  single    1.489  0.020  1.489
 73Z  C20  N29  single    1.341  0.020  1.341
 73Z  C17  C16  aromatic  1.394  0.020  1.394
 73Z  C14  N7   single    1.416  0.020  1.416
 73Z  C14  C15  aromatic  1.389  0.020  1.389
 73Z  N7   C6   aromatic  1.352  0.020  1.352
 73Z  C5   C6   aromatic  1.383  0.020  1.383
 73Z  C5   C4   single    1.445  0.020  1.445
 73Z  C16  C15  aromatic  1.381  0.020  1.381
 73Z  C6   C3   single    1.486  0.020  1.486
 73Z  O10  C4   double    1.221  0.020  1.221
 73Z  C4   C1   single    1.515  0.020  1.515
 73Z  C3   C2   single    1.538  0.020  1.538
 73Z  C11  C2   single    1.530  0.020  1.530
 73Z  C1   C2   single    1.536  0.020  1.536
 73Z  C2   C12  single    1.526  0.020  1.526
 73Z  C8   H1   single    0.930  0.020  1.080
 73Z  C11  H2   single    0.970  0.020  1.090
 73Z  C11  H3   single    0.970  0.020  1.090
 73Z  C11  H4   single    0.970  0.020  1.090
 73Z  C12  H5   single    0.970  0.020  1.090
 73Z  C12  H6   single    0.970  0.020  1.090
 73Z  C12  H7   single    0.970  0.020  1.090
 73Z  C13  H8   single    0.970  0.020  1.090
 73Z  C13  H9   single    0.970  0.020  1.090
 73Z  C13  H10  single    0.970  0.020  1.090
 73Z  C15  H11  single    0.930  0.020  1.080
 73Z  C1   H12  single    0.970  0.020  1.090
 73Z  C1   H13  single    0.970  0.020  1.090
 73Z  C3   H14  single    0.970  0.020  1.090
 73Z  C3   H15  single    0.970  0.020  1.090
 73Z  C16  H16  single    0.930  0.020  1.080
 73Z  C19  H17  single    0.930  0.020  1.080
 73Z  N21  H18  single    0.890  0.020  1.040
 73Z  C22  H19  single    0.970  0.020  1.090
 73Z  C23  H20  single    0.970  0.020  1.090
 73Z  C23  H21  single    0.970  0.020  1.090
 73Z  C24  H22  single    0.970  0.020  1.090
 73Z  C24  H23  single    0.970  0.020  1.090
 73Z  C26  H24  single    0.970  0.020  1.090
 73Z  C26  H25  single    0.970  0.020  1.090
 73Z  C27  H26  single    0.970  0.020  1.090
 73Z  C27  H27  single    0.970  0.020  1.090
 73Z  N29  H28  single    0.860  0.020  1.020
 73Z  N29  H29  single    0.860  0.020  1.020

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
 73Z  O10  C4   C1   121.52  3.000
 73Z  C1   C4   C5   114.97  3.000
 73Z  O10  C4   C5   123.46  3.000
 73Z  C9   C5   C6   108.16  3.000
 73Z  C6   C5   C4   121.15  3.000
 73Z  C9   C5   C4   130.69  3.000
 73Z  N7   C6   C3   126.86  3.000
 73Z  C3   C6   C5   125.54  3.000
 73Z  N7   C6   C5   107.51  3.000
 73Z  H1   C8   N7   120.40  3.000
 73Z  H1   C8   C9   130.48  3.000
 73Z  N7   C8   C9   109.10  3.000
 73Z  C13  C9   C8   126.40  3.000
 73Z  C8   C9   C5   105.80  3.000
 73Z  C13  C9   C5   127.80  3.000
 73Z  H10  C13  H9   107.91  3.000
 73Z  H10  C13  H8   107.89  3.000
 73Z  H9   C13  H8   106.82  3.000
 73Z  H10  C13  C9   110.78  3.000
 73Z  H9   C13  C9   111.62  3.000
 73Z  H8   C13  C9   111.62  3.000
 73Z  C19  C14  N7   118.47  3.000
 73Z  N7   C14  C15  120.06  3.000
 73Z  C19  C14  C15  121.47  3.000
 73Z  H11  C15  C16  121.01  3.000
 73Z  H11  C15  C14  121.18  3.000
 73Z  C16  C15  C14  117.80  3.000
 73Z  H13  C1   H12  106.39  3.000
 73Z  H13  C1   C2   108.93  3.000
 73Z  H12  C1   C2   110.31  3.000
 73Z  H13  C1   C4   106.37  3.000
 73Z  H12  C1   C4   108.99  3.000
 73Z  C2   C1   C4   115.41  3.000
 73Z  C3   C2   C1   109.44  3.000
 73Z  C1   C2   C12  108.88  3.000
 73Z  C3   C2   C12  109.10  3.000
 73Z  C12  C2   C11  108.87  3.000
 73Z  C1   C2   C11  110.21  3.000
 73Z  C3   C2   C11  110.31  3.000
 73Z  H15  C3   H14  106.12  3.000
 73Z  H15  C3   C2   110.02  3.000
 73Z  H14  C3   C2   109.47  3.000
 73Z  H15  C3   C6   112.02  3.000
 73Z  H14  C3   C6   109.01  3.000
 73Z  C2   C3   C6   110.09  3.000
 73Z  C14  N7   C8   123.92  3.000
 73Z  C14  N7   C6   126.65  3.000
 73Z  C8   N7   C6   109.43  3.000
 73Z  H16  C16  C17  119.58  3.000
 73Z  H16  C16  C15  117.73  3.000
 73Z  C17  C16  C15  122.68  3.000
 73Z  C20  C17  C18  120.88  3.000
 73Z  C20  C17  C16  119.90  3.000
 73Z  C18  C17  C16  119.20  3.000
 73Z  N21  C18  C19  120.82  3.000
 73Z  C19  C18  C17  117.56  3.000
 73Z  N21  C18  C17  121.59  3.000
 73Z  H17  C19  C18  120.51  3.000
 73Z  H17  C19  C14  118.23  3.000
 73Z  C18  C19  C14  121.25  3.000
 73Z  O30  C20  N29  121.23  3.000
 73Z  N29  C20  C17  116.68  3.000
 73Z  O30  C20  C17  122.08  3.000
 73Z  H18  N21  C22  116.47  3.000
 73Z  H18  N21  C18  114.46  3.000
 73Z  C22  N21  C18  124.50  3.000
 73Z  H19  C22  C27  109.06  3.000
 73Z  H19  C22  C23  107.32  3.000
 73Z  C27  C22  C23  110.04  3.000
 73Z  H19  C22  N21  108.69  3.000
 73Z  C23  C22  N21  109.08  3.000
 73Z  C27  C22  N21  112.49  3.000
 73Z  H21  C23  H20  107.00  3.000
 73Z  H21  C23  C24  109.38  3.000
 73Z  H20  C23  C24  109.49  3.000
 73Z  H21  C23  C22  109.33  3.000
 73Z  H20  C23  C22  110.04  3.000
 73Z  C24  C23  C22  111.49  3.000
 73Z  H23  C24  H22  107.23  3.000
 73Z  H23  C24  C25  110.05  3.000
 73Z  H22  C24  C25  107.08  3.000
 73Z  H23  C24  C23  110.93  3.000
 73Z  H22  C24  C23  109.08  3.000
 73Z  C25  C24  C23  112.27  3.000
 73Z  O28  C25  C26  122.77  3.000
 73Z  C26  C25  C24  114.60  3.000
 73Z  O28  C25  C24  122.62  3.000
 73Z  H25  C26  H24  107.32  3.000
 73Z  H25  C26  C27  111.22  3.000
 73Z  H24  C26  C27  109.20  3.000
 73Z  H25  C26  C25  110.13  3.000
 73Z  H24  C26  C25  107.12  3.000
 73Z  C27  C26  C25  111.66  3.000
 73Z  H27  C27  H26  106.70  3.000
 73Z  H27  C27  C26  109.12  3.000
 73Z  H26  C27  C26  109.80  3.000
 73Z  H27  C27  C22  110.62  3.000
 73Z  H26  C27  C22  108.69  3.000
 73Z  C26  C27  C22  111.77  3.000
 73Z  H29  N29  H28  116.92  3.000
 73Z  H29  N29  C20  119.15  3.000
 73Z  H28  N29  C20  123.09  3.000
 73Z  H4   C11  H3   107.52  3.000
 73Z  H4   C11  H2   107.60  3.000
 73Z  H3   C11  H2   107.59  3.000
 73Z  H4   C11  C2   112.72  3.000
 73Z  H3   C11  C2   110.66  3.000
 73Z  H2   C11  C2   110.54  3.000
 73Z  H7   C12  H6   107.82  3.000
 73Z  H7   C12  H5   107.61  3.000
 73Z  H6   C12  H5   107.77  3.000
 73Z  H7   C12  C2   111.05  3.000
 73Z  H6   C12  C2   111.47  3.000
 73Z  H5   C12  C2   110.95  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
 73Z  CONST_01  N7   C8   C9   C5     0.00   0.0  0
 73Z  CONST_02  C8   N7   C6   C5     0.00   0.0  0
 73Z  CONST_03  C14  N7   C6   C5   180.00   0.0  0
 73Z  CONST_04  C9   C8   N7   C6     0.00   0.0  0
 73Z  CONST_07  C8   C9   C5   C6     0.00   0.0  0
 73Z  CONST_10  C14  N7   C8   C9   180.00   0.0  0
 73Z  CONST_11  N7   C6   C5   C9     0.00   0.0  0
 73Z  CONST_12  C17  C18  C19  C14    0.00   0.0  0
 73Z  CONST_13  C17  C16  C15  C14    0.00   0.0  0
 73Z  CONST_14  C18  C19  C14  C15    0.00   0.0  0
 73Z  CONST_15  C18  C17  C16  C15    0.00   0.0  0
 73Z  CONST_16  C18  C19  C14  N7   180.00   0.0  0
 73Z  CONST_17  C16  C15  C14  N7   180.00   0.0  0
 73Z  CONST_18  C19  C18  C17  C16    0.00   0.0  0
 73Z  CONST_19  C19  C14  C15  C16    0.00   0.0  0
 73Z  CONST_20  C3   C6   N7   C14    0.00   0.0  0
 73Z  CONST_21  C13  C9   C5   C4     0.00   0.0  0
 73Z  CONST_22  C13  C9   C5   C6   180.00   0.0  0
 73Z  CONST_23  N7   C8   C9   C13  180.00   0.0  0
 73Z  CONST_24  N21  C18  C19  C14  180.00   0.0  0
 73Z  CONST_25  C20  C17  C16  C15  180.00   0.0  0
 73Z  CONST_26  N21  C18  C17  C16  180.00   0.0  0
 73Z  CONST_27  C20  C17  C18  C19  180.00   0.0  0
 73Z  CONST_28  C22  N21  C18  C17  180.00   0.0  0
 73Z  CONST_29  C22  N21  C18  C19    0.00   0.0  0
 73Z  CONST_30  H1   C8   C9   C5   180.00   0.0  0
 73Z  CONST_31  H16  C16  C15  C14  180.00   0.0  0
 73Z  CONST_32  H17  C19  C14  C15  180.00   0.0  0
 73Z  CONST_33  H11  C15  C14  N7     0.00   0.0  0
 73Z  CONST_35  H28  N29  C20  C17    0.00   0.0  0
 73Z  CONST_36  H29  N29  C20  C17  180.00   0.0  0
 73Z  Var_01    C3   C2   C1   C4   -54.79  30.0  1
 73Z  Var_02    C2   C3   C6   C5   -24.61  30.0  1
 73Z  Var_03    C2   C1   C4   C5    32.84  30.0  1
 73Z  Var_04    C1   C4   C5   C6    -5.59  30.0  1
 73Z  Var_05    C1   C2   C3   C6    47.97  30.0  1
 73Z  Var_06    C25  C26  C27  C22   53.14  30.0  1
 73Z  Var_07    C25  C24  C23  C22  -52.74  30.0  1
 73Z  Var_08    C26  C25  C24  C23   49.48  30.0  1
 73Z  Var_09    C27  C26  C25  C24  -49.49  30.0  1
 73Z  Var_10    O30  C20  C17  C16  153.83  30.0  2
 73Z  Var_11    H8   C13  C9   C5   -59.75  30.0  2
 73Z  Var_12    H2   C11  C2   C1    55.87  30.0  3
 73Z  Var_13    H5   C12  C2   C1   -60.94  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
 73Z  chir_01  C22  C27  C23  N21  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
 73Z  plan-1  C14  0.020
 73Z  plan-1  C15  0.020
 73Z  plan-1  N7   0.020
 73Z  plan-1  C16  0.020
 73Z  plan-1  C17  0.020
 73Z  plan-1  C18  0.020
 73Z  plan-1  C19  0.020
 73Z  plan-1  C20  0.020
 73Z  plan-1  N21  0.020
 73Z  plan-1  H11  0.020
 73Z  plan-1  H16  0.020
 73Z  plan-1  H17  0.020
 73Z  plan-2  C4   0.020
 73Z  plan-2  C5   0.020
 73Z  plan-2  C6   0.020
 73Z  plan-2  C8   0.020
 73Z  plan-2  C9   0.020
 73Z  plan-2  C13  0.020
 73Z  plan-2  C14  0.020
 73Z  plan-2  C3   0.020
 73Z  plan-2  N7   0.020
 73Z  plan-2  H1   0.020
 73Z  plan-3  C17  0.020
 73Z  plan-3  C20  0.020
 73Z  plan-3  N29  0.020
 73Z  plan-3  O30  0.020
 73Z  plan-3  H28  0.020
 73Z  plan-3  H29  0.020
 73Z  plan-4  C18  0.020
 73Z  plan-4  N21  0.020
 73Z  plan-4  C22  0.020
 73Z  plan-4  H18  0.020
 73Z  plan-5  C4   0.020
 73Z  plan-5  C5   0.020
 73Z  plan-5  C1   0.020
 73Z  plan-5  O10  0.020
 73Z  plan-6  C24  0.020
 73Z  plan-6  C25  0.020
 73Z  plan-6  C26  0.020
 73Z  plan-6  O28  0.020

