# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:45:44 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (5-methoxy-1~{H}-indol-2-yl)-phenyl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[nH]c(cc2c1)C(=O)c3ccccc3
#
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
 D3L  D3L  (5-methoxy-1~{H}-indol-2-yl)-phenyl-methanone  ligand  32  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D3L
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
 D3L  C10  C  C     0   0.327   1.9508  -1.2913  -0.0465
 D3L  C13  C  CR16  0  -0.271   4.1962  -0.5121   0.6663
 D3L  C15  C  CR16  0  -0.247   5.1238   1.5652  -0.1113
 D3L  C17  C  CR16  0  -0.295   2.9214   0.9011  -0.8127
 D3L  C01  C  CR16  0  -0.446  -3.0683  -1.0105  -0.3181
 D3L  C02  C  CR6   0   0.385  -3.9370   0.0287  -0.0447
 D3L  C03  C  CR16  0  -0.392  -3.4454   1.2821   0.3876
 D3L  C04  C  CR16  0  -0.291  -2.0942   1.5068   0.5468
 D3L  C05  C  CR56  0   0.334  -1.2187   0.4603   0.2669
 D3L  C06  C  CR56  0   0.079  -1.6925  -0.8015  -0.1576
 D3L  C07  C  CR15  0  -0.391  -0.5513  -1.6276  -0.3301
 D3L  C08  C  CR5   0   0.223   0.5497  -0.8608  -0.0285
 D3L  N09  N  NR15  0  -0.736   0.1398   0.4010   0.3233
 D3L  O11  O  O     0  -0.391   2.2251  -2.4770  -0.0476
 D3L  C12  C  CR6   0  -0.033   3.0262  -0.2633  -0.0523
 D3L  C14  C  CR16  0  -0.244   5.2330   0.4059   0.6485
 D3L  C16  C  CR16  0  -0.239   3.9725   1.8068  -0.8477
 D3L  C19  C  CH3   0  -0.436  -6.1881   0.8049   0.0253
 D3L  H1   H  HCR6  0   0.266   4.2865  -1.4180   1.2519
 D3L  H2   H  HCR6  0   0.268   5.9384   2.2771  -0.1316
 D3L  H3   H  HCR6  0   0.279   2.0362   1.0944  -1.4056
 D3L  H4   H  HCR6  0   0.257  -3.4500  -1.9685  -0.6494
 D3L  H5   H  HCR6  0   0.281  -4.1259   2.0951   0.5992
 D3L  H6   H  HCR6  0   0.271  -1.7351   2.4725   0.8772
 D3L  H7   H  HCR5  0   0.263  -0.5332  -2.6550  -0.6573
 D3L  H8   H  HNR5  0   0.418   0.7371   1.1347   0.6687
 D3L  H9   H  HCR6  0   0.266   6.1300   0.2162   1.2232
 D3L  H10  H  HCR6  0   0.267   3.8910   2.7006  -1.4518
 D3L  H11  H  HCH3  0   0.225  -6.0315   1.6621  -0.6353
 D3L  H12  H  HCH3  0   0.258  -7.1708   0.3853  -0.1769
 D3L  H13  H  HCH3  0   0.225  -6.1648   1.1521   1.0619
 D3L  O18  O  O2    0  -0.480  -5.2553  -0.2277  -0.2133

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
 D3L  O18  C19  single    1.412  0.020  1.412
 D3L  O18  C02  single    1.354  0.020  1.354
 D3L  C03  C02  aromatic  1.414  0.020  1.414
 D3L  C03  C04  aromatic  1.379  0.020  1.379
 D3L  C02  C01  aromatic  1.382  0.020  1.382
 D3L  C04  C05  aromatic  1.393  0.020  1.393
 D3L  C01  C06  aromatic  1.401  0.020  1.401
 D3L  C05  C06  aromatic  1.413  0.020  1.413
 D3L  C05  N09  aromatic  1.361  0.020  1.361
 D3L  C06  C07  aromatic  1.419  0.020  1.419
 D3L  N09  C08  aromatic  1.373  0.020  1.373
 D3L  C07  C08  aromatic  1.375  0.020  1.375
 D3L  C08  C10  single    1.466  0.020  1.466
 D3L  C10  O11  double    1.217  0.020  1.217
 D3L  C10  C12  single    1.488  0.020  1.488
 D3L  C17  C12  aromatic  1.395  0.020  1.395
 D3L  C17  C16  aromatic  1.388  0.020  1.388
 D3L  C12  C13  aromatic  1.395  0.020  1.395
 D3L  C16  C15  aromatic  1.388  0.020  1.388
 D3L  C13  C14  aromatic  1.385  0.020  1.385
 D3L  C15  C14  aromatic  1.390  0.020  1.390
 D3L  C13  H1   single    0.930  0.020  1.080
 D3L  C15  H2   single    0.930  0.020  1.080
 D3L  C17  H3   single    0.930  0.020  1.080
 D3L  C01  H4   single    0.930  0.020  1.080
 D3L  C03  H5   single    0.930  0.020  1.080
 D3L  C04  H6   single    0.930  0.020  1.080
 D3L  C07  H7   single    0.930  0.020  1.080
 D3L  N09  H8   single    0.860  0.020  1.020
 D3L  C14  H9   single    0.930  0.020  1.080
 D3L  C16  H10  single    0.930  0.020  1.080
 D3L  C19  H11  single    0.970  0.020  1.090
 D3L  C19  H12  single    0.970  0.020  1.090
 D3L  C19  H13  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
 D3L  C12  C10  O11  120.68  3.000
 D3L  C12  C10  C08  119.21  3.000
 D3L  O11  C10  C08  120.11  3.000
 D3L  H1   C13  C14  119.95  3.000
 D3L  H1   C13  C12  119.85  3.000
 D3L  C14  C13  C12  120.19  3.000
 D3L  H2   C15  C16  120.00  3.000
 D3L  H2   C15  C14  119.98  3.000
 D3L  C16  C15  C14  120.02  3.000
 D3L  H3   C17  C16  119.26  3.000
 D3L  H3   C17  C12  120.60  3.000
 D3L  C16  C17  C12  120.11  3.000
 D3L  H4   C01  C06  120.87  3.000
 D3L  H4   C01  C02  120.28  3.000
 D3L  C06  C01  C02  118.85  3.000
 D3L  O18  C02  C03  122.99  3.000
 D3L  C03  C02  C01  120.57  3.000
 D3L  O18  C02  C01  116.44  3.000
 D3L  H5   C03  C04  118.14  3.000
 D3L  H5   C03  C02  120.50  3.000
 D3L  C04  C03  C02  121.36  3.000
 D3L  H6   C04  C05  121.55  3.000
 D3L  H6   C04  C03  120.40  3.000
 D3L  C05  C04  C03  118.05  3.000
 D3L  N09  C05  C06  107.95  3.000
 D3L  N09  C05  C04  130.68  3.000
 D3L  C06  C05  C04  121.37  3.000
 D3L  C07  C06  C05  106.65  3.000
 D3L  C07  C06  C01  133.55  3.000
 D3L  C05  C06  C01  119.80  3.000
 D3L  H7   C07  C08  125.75  3.000
 D3L  H7   C07  C06  127.22  3.000
 D3L  C08  C07  C06  107.01  3.000
 D3L  N09  C08  C07  109.25  3.000
 D3L  C07  C08  C10  126.78  3.000
 D3L  N09  C08  C10  123.96  3.000
 D3L  H8   N09  C08  125.48  3.000
 D3L  H8   N09  C05  125.06  3.000
 D3L  C08  N09  C05  109.12  3.000
 D3L  C17  C12  C13  119.52  3.000
 D3L  C13  C12  C10  118.74  3.000
 D3L  C17  C12  C10  121.65  3.000
 D3L  H9   C14  C15  120.10  3.000
 D3L  H9   C14  C13  119.84  3.000
 D3L  C15  C14  C13  120.06  3.000
 D3L  H10  C16  C17  119.75  3.000
 D3L  H10  C16  C15  120.17  3.000
 D3L  C17  C16  C15  120.08  3.000
 D3L  H13  C19  H12  108.54  3.000
 D3L  H13  C19  H11  108.71  3.000
 D3L  H12  C19  H11  108.63  3.000
 D3L  H13  C19  O18  112.23  3.000
 D3L  H12  C19  O18  106.46  3.000
 D3L  H11  C19  O18  112.13  3.000
 D3L  C19  O18  C02  118.94  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
 D3L  CONST_01  C16  C17  C12  C13    0.00   0.0  0
 D3L  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 D3L  CONST_03  C12  C17  C16  C15    0.00   0.0  0
 D3L  CONST_04  C12  C13  C14  C15    0.00   0.0  0
 D3L  CONST_05  C14  C13  C12  C17    0.00   0.0  0
 D3L  CONST_06  C14  C15  C16  C17    0.00   0.0  0
 D3L  CONST_07  C04  C03  C02  C01    0.00   0.0  0
 D3L  CONST_08  C04  C05  C06  C01    0.00   0.0  0
 D3L  CONST_09  N09  C05  C06  C01  180.00   0.0  0
 D3L  CONST_10  C08  C07  C06  C01  180.00   0.0  0
 D3L  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 D3L  CONST_12  C05  C06  C01  C02    0.00   0.0  0
 D3L  CONST_13  C07  C06  C01  C02  180.00   0.0  0
 D3L  CONST_14  C06  C01  C02  C03    0.00   0.0  0
 D3L  CONST_15  C06  C05  C04  C03    0.00   0.0  0
 D3L  CONST_16  N09  C05  C04  C03  180.00   0.0  0
 D3L  CONST_17  C07  C06  C05  C04  180.00   0.0  0
 D3L  CONST_18  C08  N09  C05  C04  180.00   0.0  0
 D3L  CONST_19  C08  C07  C06  C05    0.00   0.0  0
 D3L  CONST_20  C07  C08  N09  C05    0.00   0.0  0
 D3L  CONST_21  C08  N09  C05  C06    0.00   0.0  0
 D3L  CONST_22  N09  C08  C07  C06    0.00   0.0  0
 D3L  CONST_23  N09  C05  C06  C07    0.00   0.0  0
 D3L  CONST_24  C05  N09  C08  C10  180.00   0.0  0
 D3L  CONST_25  C06  C07  C08  C10  180.00   0.0  0
 D3L  CONST_26  C16  C17  C12  C10  180.00   0.0  0
 D3L  CONST_27  C14  C13  C12  C10  180.00   0.0  0
 D3L  CONST_28  O18  C02  C03  C04  180.00   0.0  0
 D3L  CONST_29  O18  C02  C01  C06  180.00   0.0  0
 D3L  CONST_30  H3   C17  C12  C13  180.00   0.0  0
 D3L  CONST_31  H2   C15  C14  C13  180.00   0.0  0
 D3L  CONST_32  H1   C13  C14  C15  180.00   0.0  0
 D3L  CONST_33  H5   C03  C02  C01  180.00   0.0  0
 D3L  CONST_34  H7   C07  C06  C01    0.00   0.0  0
 D3L  CONST_35  H6   C04  C03  C02  180.00   0.0  0
 D3L  CONST_36  H4   C01  C02  C03  180.00   0.0  0
 D3L  CONST_37  H8   N09  C05  C04    0.00   0.0  0
 D3L  CONST_38  H10  C16  C17  C12  180.00   0.0  0
 D3L  CONST_39  H9   C14  C13  C12  180.00   0.0  0
 D3L  Var_01    C08  C10  C12  C13  143.19  30.0  2
 D3L  Var_02    C12  C10  C08  C07  163.70  30.0  2
 D3L  Var_03    H11  C19  O18  C02   60.84  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
 D3L  plan-1  C10  0.020
 D3L  plan-1  C13  0.020
 D3L  plan-1  C15  0.020
 D3L  plan-1  C17  0.020
 D3L  plan-1  C12  0.020
 D3L  plan-1  C14  0.020
 D3L  plan-1  C16  0.020
 D3L  plan-1  H1   0.020
 D3L  plan-1  H2   0.020
 D3L  plan-1  H3   0.020
 D3L  plan-1  H9   0.020
 D3L  plan-1  H10  0.020
 D3L  plan-2  C10  0.020
 D3L  plan-2  C01  0.020
 D3L  plan-2  C02  0.020
 D3L  plan-2  C03  0.020
 D3L  plan-2  C04  0.020
 D3L  plan-2  C05  0.020
 D3L  plan-2  C06  0.020
 D3L  plan-2  C07  0.020
 D3L  plan-2  C08  0.020
 D3L  plan-2  N09  0.020
 D3L  plan-2  H4   0.020
 D3L  plan-2  H5   0.020
 D3L  plan-2  H6   0.020
 D3L  plan-2  H7   0.020
 D3L  plan-2  H8   0.020
 D3L  plan-2  O18  0.020
 D3L  plan-3  C10  0.020
 D3L  plan-3  C08  0.020
 D3L  plan-3  O11  0.020
 D3L  plan-3  C12  0.020

