# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 00:25:04 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (5S)-7-oxo-6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NC(=O)c2c1c3c([nH]c4ccccc34)c5[nH]c6ccccc6c25
#
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
 KCT  KCT  '(5S)-7-oxo-6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5-carboxylic acid'  ligand  40  27  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KCT
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
 KCT  O27  O  OH1   0  -0.578  -3.2854   2.9600   0.5292
 KCT  C25  C  C     0   0.564  -2.0244   2.6421   0.7621
 KCT  O26  O  O     0  -0.415  -1.4979   2.6776   1.8413
 KCT  C7   C  CR15  0  -0.271  -1.2831   2.2398  -0.5156
 KCT  N6   N  NR15  0  -0.654  -0.1512   3.1066  -0.6972
 KCT  C22  C  CR56  0   0.014  -0.6196   0.9022  -0.3347
 KCT  C21  C  CR56  0   0.068  -1.2000  -0.3616  -0.1938
 KCT  C20  C  CR56  0   0.046  -2.5420  -0.8862  -0.2070
 KCT  C8   C  CR16  0  -0.410  -3.8095  -0.3306  -0.3898
 KCT  C9   C  CR16  0  -0.262  -4.9170  -1.1578  -0.3514
 KCT  C10  C  CR16  0  -0.275  -4.7807  -2.5344  -0.1320
 KCT  C11  C  CR16  0  -0.317  -3.5378  -3.1138   0.0456
 KCT  C19  C  CR56  0   0.342  -2.4275  -2.2769   0.0025
 KCT  N12  N  NR15  0  -0.786  -1.1010  -2.5966   0.1337
 KCT  C18  C  CR56  0   0.317  -0.3505  -1.4653   0.0134
 KCT  C17  C  CR56  0   0.292   1.0359  -1.2981   0.0574
 KCT  C16  C  CR56  0   0.096   1.6118  -0.0253  -0.1052
 KCT  C23  C  CR56  0  -0.236   0.7487   1.0702  -0.3002
 KCT  C5   C  CR5   0   0.505   1.0487   2.4999  -0.5130
 KCT  O24  O  O     0  -0.465   2.1324   3.0565  -0.5457
 KCT  N13  N  NR15  0  -0.785   2.0197  -2.2280   0.2391
 KCT  C14  C  CR56  0   0.340   3.2362  -1.6049   0.2002
 KCT  C15  C  CR56  0   0.024   3.0367  -0.2224  -0.0128
 KCT  C1   C  CR16  0  -0.320   4.5056  -2.1605   0.3401
 KCT  C2   C  CR16  0  -0.274   5.5880  -1.3056   0.2639
 KCT  C3   C  CR16  0  -0.262   5.4146   0.0696   0.0529
 KCT  C4   C  CR16  0  -0.401   4.1532   0.6166  -0.0849
 KCT  H1   H  HOH1  0   0.490  -3.7340   3.2002   1.3555
 KCT  H2   H  HCR5  0   0.312  -1.9550   2.2647  -1.3780
 KCT  H3   H  HNR5  0   0.410  -0.2439   4.1033  -0.8145
 KCT  H4   H  HCR6  0   0.249  -3.9399   0.7281  -0.5644
 KCT  H5   H  HCR6  0   0.255  -5.9033  -0.7368  -0.4941
 KCT  H6   H  HCR6  0   0.259  -5.6637  -3.1592  -0.1035
 KCT  H7   H  HCR6  0   0.267  -3.4322  -4.1787   0.2071
 KCT  H8   H  HNR5  0   0.416  -0.7483  -3.5271   0.2854
 KCT  H9   H  HNR5  0   0.414   1.8841  -3.2178   0.3604
 KCT  H10  H  HCR6  0   0.264   4.6378  -3.2224   0.5020
 KCT  H11  H  HCR6  0   0.257   6.5879  -1.7060   0.3704
 KCT  H12  H  HCR6  0   0.251   6.2834   0.7121  -0.0027
 KCT  H13  H  HCR6  0   0.262   4.0283   1.6772  -0.2445

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
 KCT  C2   C1   aromatic  1.381  0.020  1.381
 KCT  C2   C3   aromatic  1.402  0.020  1.402
 KCT  C1   C14  aromatic  1.393  0.020  1.393
 KCT  C3   C4   aromatic  1.382  0.020  1.382
 KCT  C14  C15  aromatic  1.413  0.020  1.413
 KCT  C14  N13  aromatic  1.367  0.020  1.367
 KCT  C4   C15  aromatic  1.398  0.020  1.398
 KCT  C15  C16  aromatic  1.441  0.020  1.441
 KCT  N13  C17  aromatic  1.366  0.020  1.366
 KCT  C16  C17  aromatic  1.406  0.020  1.406
 KCT  C16  C23  aromatic  1.408  0.020  1.408
 KCT  C17  C18  aromatic  1.397  0.020  1.397
 KCT  O24  C5   double    1.219  0.020  1.219
 KCT  C18  N12  aromatic  1.363  0.020  1.363
 KCT  C18  C21  aromatic  1.408  0.020  1.408
 KCT  N12  C19  aromatic  1.371  0.020  1.371
 KCT  C23  C5   single    1.476  0.020  1.476
 KCT  C23  C22  aromatic  1.379  0.020  1.379
 KCT  C5   N6   single    1.357  0.020  1.357
 KCT  C21  C22  aromatic  1.398  0.020  1.398
 KCT  C21  C20  aromatic  1.441  0.020  1.441
 KCT  C22  C7   single    1.504  0.020  1.504
 KCT  C19  C11  aromatic  1.391  0.020  1.391
 KCT  C19  C20  aromatic  1.411  0.020  1.411
 KCT  N6   C7   single    1.437  0.020  1.437
 KCT  C11  C10  aromatic  1.383  0.020  1.383
 KCT  C20  C8   aromatic  1.396  0.020  1.396
 KCT  C7   C25  single    1.531  0.020  1.531
 KCT  O26  C25  double    1.201  0.020  1.201
 KCT  C25  O27  single    1.321  0.020  1.321
 KCT  C10  C9   aromatic  1.401  0.020  1.401
 KCT  C8   C9   aromatic  1.383  0.020  1.383
 KCT  O27  H1   single    0.850  0.020  0.980
 KCT  C7   H2   single    0.970  0.020  1.090
 KCT  N6   H3   single    0.860  0.020  1.020
 KCT  C8   H4   single    0.930  0.020  1.080
 KCT  C9   H5   single    0.930  0.020  1.080
 KCT  C10  H6   single    0.930  0.020  1.080
 KCT  C11  H7   single    0.930  0.020  1.080
 KCT  N12  H8   single    0.860  0.020  1.020
 KCT  N13  H9   single    0.860  0.020  1.020
 KCT  C1   H10  single    0.930  0.020  1.080
 KCT  C2   H11  single    0.930  0.020  1.080
 KCT  C3   H12  single    0.930  0.020  1.080
 KCT  C4   H13  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
 KCT  H1   O27  C25  110.53  3.000
 KCT  C7   C25  O26  123.05  3.000
 KCT  O26  C25  O27  124.72  3.000
 KCT  C7   C25  O27  112.22  3.000
 KCT  H2   C7   C22  112.72  3.000
 KCT  H2   C7   N6   111.75  3.000
 KCT  C22  C7   N6   101.78  3.000
 KCT  H2   C7   C25  110.78  3.000
 KCT  N6   C7   C25  109.17  3.000
 KCT  C22  C7   C25  110.30  3.000
 KCT  H3   N6   C5   122.64  3.000
 KCT  H3   N6   C7   122.59  3.000
 KCT  C5   N6   C7   114.18  3.000
 KCT  C23  C22  C21  121.31  3.000
 KCT  C21  C22  C7   129.27  3.000
 KCT  C23  C22  C7   109.41  3.000
 KCT  C18  C21  C20  106.13  3.000
 KCT  C20  C21  C22  135.64  3.000
 KCT  C18  C21  C22  118.23  3.000
 KCT  C19  C20  C8   119.04  3.000
 KCT  C8   C20  C21  134.58  3.000
 KCT  C19  C20  C21  106.38  3.000
 KCT  H4   C8   C9   119.58  3.000
 KCT  H4   C8   C20  121.37  3.000
 KCT  C9   C8   C20  119.04  3.000
 KCT  H5   C9   C10  119.47  3.000
 KCT  H5   C9   C8   119.58  3.000
 KCT  C10  C9   C8   120.95  3.000
 KCT  H6   C10  C11  119.22  3.000
 KCT  H6   C10  C9   119.48  3.000
 KCT  C11  C10  C9   121.29  3.000
 KCT  H7   C11  C19  121.25  3.000
 KCT  H7   C11  C10  121.27  3.000
 KCT  C19  C11  C10  117.48  3.000
 KCT  N12  C19  C11  128.99  3.000
 KCT  C11  C19  C20  122.19  3.000
 KCT  N12  C19  C20  108.82  3.000
 KCT  H8   N12  C18  125.99  3.000
 KCT  H8   N12  C19  124.69  3.000
 KCT  C18  N12  C19  109.32  3.000
 KCT  C17  C18  N12  130.01  3.000
 KCT  N12  C18  C21  109.35  3.000
 KCT  C17  C18  C21  120.63  3.000
 KCT  N13  C17  C16  109.67  3.000
 KCT  C16  C17  C18  120.72  3.000
 KCT  N13  C17  C18  129.61  3.000
 KCT  C15  C16  C23  136.15  3.000
 KCT  C23  C16  C17  117.98  3.000
 KCT  C15  C16  C17  105.87  3.000
 KCT  C5   C23  C16  130.45  3.000
 KCT  C5   C23  C22  108.42  3.000
 KCT  C16  C23  C22  121.12  3.000
 KCT  O24  C5   C23  128.82  3.000
 KCT  C23  C5   N6   105.83  3.000
 KCT  O24  C5   N6   125.34  3.000
 KCT  H9   N13  C14  124.86  3.000
 KCT  H9   N13  C17  126.05  3.000
 KCT  C14  N13  C17  109.07  3.000
 KCT  C1   C14  C15  122.29  3.000
 KCT  C15  C14  N13  108.94  3.000
 KCT  C1   C14  N13  128.77  3.000
 KCT  C4   C15  C14  118.82  3.000
 KCT  C4   C15  C16  134.74  3.000
 KCT  C14  C15  C16  106.44  3.000
 KCT  H10  C1   C2   121.31  3.000
 KCT  H10  C1   C14  121.19  3.000
 KCT  C2   C1   C14  117.50  3.000
 KCT  H11  C2   C3   119.47  3.000
 KCT  H11  C2   C1   119.31  3.000
 KCT  C3   C2   C1   121.22  3.000
 KCT  H12  C3   C4   119.52  3.000
 KCT  H12  C3   C2   119.40  3.000
 KCT  C4   C3   C2   121.08  3.000
 KCT  H13  C4   C3   120.61  3.000
 KCT  H13  C4   C15  120.30  3.000
 KCT  C3   C4   C15  119.09  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
 KCT  CONST_01  C15  C16  C23  C22  180.00  0.0  0
 KCT  CONST_02  C17  C16  C23  C22    0.00  0.0  0
 KCT  CONST_03  C17  C18  C21  C22    0.00  0.0  0
 KCT  CONST_04  N12  C18  C21  C22  180.00  0.0  0
 KCT  CONST_05  C19  C20  C21  C22  180.00  0.0  0
 KCT  CONST_06  C8   C20  C21  C22    0.00  0.0  0
 KCT  CONST_07  N13  C17  C18  C21  180.00  0.0  0
 KCT  CONST_08  C16  C17  C18  C21    0.00  0.0  0
 KCT  CONST_09  C19  N12  C18  C21    0.00  0.0  0
 KCT  CONST_10  C16  C23  C22  C21    0.00  0.0  0
 KCT  CONST_11  N12  C19  C20  C21    0.00  0.0  0
 KCT  CONST_12  C11  C19  C20  C21  180.00  0.0  0
 KCT  CONST_13  C9   C8   C20  C21  180.00  0.0  0
 KCT  CONST_14  C17  C18  C21  C20  180.00  0.0  0
 KCT  CONST_15  N12  C18  C21  C20    0.00  0.0  0
 KCT  CONST_16  C23  C22  C21  C20  180.00  0.0  0
 KCT  CONST_17  C18  N12  C19  C20    0.00  0.0  0
 KCT  CONST_18  C10  C11  C19  C20    0.00  0.0  0
 KCT  CONST_19  C10  C9   C8   C20    0.00  0.0  0
 KCT  CONST_20  C18  C21  C20  C8   180.00  0.0  0
 KCT  CONST_21  N12  C19  C20  C8   180.00  0.0  0
 KCT  CONST_22  C11  C19  C20  C8     0.00  0.0  0
 KCT  CONST_23  C11  C10  C9   C8     0.00  0.0  0
 KCT  CONST_24  C19  C11  C10  C9     0.00  0.0  0
 KCT  CONST_25  C19  C20  C8   C9     0.00  0.0  0
 KCT  CONST_26  N12  C19  C11  C10  180.00  0.0  0
 KCT  CONST_27  C18  N12  C19  C11  180.00  0.0  0
 KCT  CONST_28  C17  C18  N12  C19  180.00  0.0  0
 KCT  CONST_29  C18  C21  C20  C19    0.00  0.0  0
 KCT  CONST_30  N13  C17  C18  N12    0.00  0.0  0
 KCT  CONST_31  C16  C17  C18  N12  180.00  0.0  0
 KCT  CONST_32  C14  N13  C17  C18  180.00  0.0  0
 KCT  CONST_33  C15  C16  C17  C18  180.00  0.0  0
 KCT  CONST_34  C23  C16  C17  C18    0.00  0.0  0
 KCT  CONST_35  C23  C22  C21  C18    0.00  0.0  0
 KCT  CONST_36  C1   C14  N13  C17  180.00  0.0  0
 KCT  CONST_37  C15  C14  N13  C17    0.00  0.0  0
 KCT  CONST_38  C14  C15  C16  C17    0.00  0.0  0
 KCT  CONST_39  C4   C15  C16  C17  180.00  0.0  0
 KCT  CONST_40  C1   C14  C15  C16  180.00  0.0  0
 KCT  CONST_41  N13  C14  C15  C16    0.00  0.0  0
 KCT  CONST_42  C3   C4   C15  C16  180.00  0.0  0
 KCT  CONST_43  C14  N13  C17  C16    0.00  0.0  0
 KCT  CONST_44  C14  C15  C16  C23  180.00  0.0  0
 KCT  CONST_45  C4   C15  C16  C23    0.00  0.0  0
 KCT  CONST_46  N13  C17  C16  C23  180.00  0.0  0
 KCT  CONST_47  C2   C1   C14  N13  180.00  0.0  0
 KCT  CONST_48  C4   C15  C14  N13  180.00  0.0  0
 KCT  CONST_49  C15  C16  C17  N13    0.00  0.0  0
 KCT  CONST_50  C3   C2   C1   C14    0.00  0.0  0
 KCT  CONST_51  C3   C4   C15  C14    0.00  0.0  0
 KCT  CONST_52  C2   C1   C14  C15    0.00  0.0  0
 KCT  CONST_53  C2   C3   C4   C15    0.00  0.0  0
 KCT  CONST_54  C4   C3   C2   C1     0.00  0.0  0
 KCT  CONST_55  C4   C15  C14  C1     0.00  0.0  0
 KCT  CONST_56  C23  C5   N6   C7     0.00  0.0  0
 KCT  CONST_57  O24  C5   N6   C7   180.00  0.0  0
 KCT  CONST_58  H8   N12  C18  C21  180.00  0.0  0
 KCT  CONST_59  H4   C8   C20  C21    0.00  0.0  0
 KCT  CONST_60  H7   C11  C19  C20  180.00  0.0  0
 KCT  CONST_61  H5   C9   C8   C20  180.00  0.0  0
 KCT  CONST_62  H6   C10  C9   C8   180.00  0.0  0
 KCT  CONST_63  H9   N13  C17  C18    0.00  0.0  0
 KCT  CONST_64  H13  C4   C15  C16    0.00  0.0  0
 KCT  CONST_65  H10  C1   C14  N13    0.00  0.0  0
 KCT  CONST_66  H11  C2   C1   C14  180.00  0.0  0
 KCT  CONST_67  H12  C3   C4   C15  180.00  0.0  0
 KCT  CONST_68  H3   N6   C5   C23  180.00  0.0  0
 KCT  CONST_69  H1   O27  C25  C7   180.00  0.0  0

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
 KCT  chir_01  C7  C22  N6  C25  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
 KCT  plan-1  C7   0.020
 KCT  plan-1  N6   0.020
 KCT  plan-1  C22  0.020
 KCT  plan-1  C21  0.020
 KCT  plan-1  C20  0.020
 KCT  plan-1  C8   0.020
 KCT  plan-1  C9   0.020
 KCT  plan-1  C10  0.020
 KCT  plan-1  C11  0.020
 KCT  plan-1  C19  0.020
 KCT  plan-1  N12  0.020
 KCT  plan-1  C18  0.020
 KCT  plan-1  C17  0.020
 KCT  plan-1  C16  0.020
 KCT  plan-1  C23  0.020
 KCT  plan-1  C5   0.020
 KCT  plan-1  O24  0.020
 KCT  plan-1  N13  0.020
 KCT  plan-1  C14  0.020
 KCT  plan-1  C15  0.020
 KCT  plan-1  C1   0.020
 KCT  plan-1  C2   0.020
 KCT  plan-1  C3   0.020
 KCT  plan-1  C4   0.020
 KCT  plan-1  H3   0.020
 KCT  plan-1  H4   0.020
 KCT  plan-1  H5   0.020
 KCT  plan-1  H6   0.020
 KCT  plan-1  H7   0.020
 KCT  plan-1  H8   0.020
 KCT  plan-1  H9   0.020
 KCT  plan-1  H10  0.020
 KCT  plan-1  H11  0.020
 KCT  plan-1  H12  0.020
 KCT  plan-1  H13  0.020
 KCT  plan-2  O27  0.020
 KCT  plan-2  C25  0.020
 KCT  plan-2  O26  0.020
 KCT  plan-2  C7   0.020
 KCT  plan-2  H1   0.020

