# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:01:43 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (1-benzyl-5-methoxy-2-methyl-1H-indol-3-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2n(Cc3ccccc3)c(C)c(CC(O)=O)c2c1
#
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
 I3N  I3N  '(1-benzyl-5-methoxy-2-methyl-1H-indol-3-yl)acetic acid'  ligand  41  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I3N
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
 I3N  C1    C  CH3    0  -0.459   3.6560  -0.4053   4.2087
 I3N  O2    O  O2     0  -0.470   2.2738  -0.4611   3.9687
 I3N  C3    C  CR6    0   0.372   1.8040  -0.0122   2.7856
 I3N  C4    C  CR16   0  -0.448   0.4195  -0.0048   2.6364
 I3N  C5    C  CR56   0   0.064  -0.1295   0.4542   1.4328
 I3N  C6    C  CR56   0   0.447   0.7252   0.9167   0.4090
 I3N  C7    C  CR16   0  -0.383   2.1028   0.8793   0.5413
 I3N  C8    C  CR16   0  -0.434   2.6392   0.4134   1.7345
 I3N  N9    N  NR5    0  -0.527  -0.0604   1.3229  -0.6413
 I3N  C10   C  CR5    0   0.253  -1.3849   1.1199  -0.3059
 I3N  C11   C  CR5    0   0.020  -1.4699   0.5661   0.9418
 I3N  C12   C  CH2    0  -0.737  -2.6934   0.2113   1.7157
 I3N  C13   C  C      0   0.399  -2.9093  -1.2951   1.9038
 I3N  O14   O  OC    -1  -0.611  -3.8901  -1.5497   2.6121
 I3N  O15   O  O      0  -0.504  -2.0945  -2.0999   1.4150
 I3N  C16   C  CH3    0  -0.721  -2.4630   1.4179  -1.2857
 I3N  C17   C  CH2    0  -0.467   0.4404   1.7004  -1.9359
 I3N  C18   C  CR6    0   0.086   0.6780   0.5357  -2.8718
 I3N  C19   C  CR16   0  -0.222   1.2282   0.7891  -4.1288
 I3N  C20   C  CR16   0  -0.301   1.4191  -0.2373  -5.0403
 I3N  C21   C  CR16   0  -0.229   1.0694  -1.5404  -4.7033
 I3N  C22   C  CR16   0  -0.251   0.5634  -1.8044  -3.4416
 I3N  C23   C  CR16   0  -0.285   0.3569  -0.7721  -2.5334
 I3N  H11   H  HCH3   0   0.228   4.0399   0.6179   4.1769
 I3N  H12   H  HCH3   0   0.242   3.8152  -0.8029   5.2095
 I3N  H13   H  HCH3   0   0.251   4.2253  -1.0165   3.5028
 I3N  H4    H  HCR6   0   0.241  -0.2119  -0.3447   3.4487
 I3N  H7    H  HCR6   0   0.209   2.7636   1.1955  -0.2580
 I3N  H8    H  HCR6   0   0.276   3.7147   0.3924   1.8399
 I3N  H121  H  HCH2   0   0.170  -2.6227   0.6516   2.7162
 I3N  H122  H  HCH2   0   0.222  -3.5916   0.6483   1.2745
 I3N  H161  H  HCH3   0   0.276  -2.3800   0.8053  -2.1866
 I3N  H162  H  HCH3   0   0.252  -3.4379   1.2207  -0.8424
 I3N  H163  H  HCH3   0   0.275  -2.4595   2.4661  -1.5938
 I3N  H171  H  HCH2   0   0.278  -0.2609   2.4069  -2.3848
 I3N  H172  H  HCH2   0   0.255   1.3756   2.2517  -1.8068
 I3N  H19   H  HCR6   0   0.261   1.4510   1.8096  -4.4194
 I3N  H20   H  HCR6   0   0.226   1.8228  -0.0154  -6.0200
 I3N  H21   H  HCR6   0   0.271   1.2353  -2.3483  -5.4044
 I3N  H22   H  HCR6   0   0.242   0.2832  -2.8142  -3.1701
 I3N  H23   H  HCR6   0   0.234  -0.1021  -0.9964  -1.5782

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
 I3N  C1   O2    single    1.404  0.020  1.404
 I3N  C1   H11   single    0.970  0.020  1.090
 I3N  C1   H12   single    0.970  0.020  1.090
 I3N  C1   H13   single    0.970  0.020  1.090
 I3N  O2   C3    single    1.350  0.020  1.350
 I3N  C3   C4    aromatic  1.393  0.020  1.393
 I3N  C3   C8    aromatic  1.408  0.020  1.408
 I3N  C4   C5    aromatic  1.400  0.020  1.400
 I3N  C4   H4    single    0.930  0.020  1.080
 I3N  C5   C6    aromatic  1.412  0.020  1.412
 I3N  C5   C11   aromatic  1.432  0.020  1.432
 I3N  C6   C7    aromatic  1.384  0.020  1.384
 I3N  C6   N9    aromatic  1.373  0.020  1.373
 I3N  C7   C8    aromatic  1.389  0.020  1.389
 I3N  C7   H7    single    0.930  0.020  1.080
 I3N  C8   H8    single    0.930  0.020  1.080
 I3N  N9   C10   aromatic  1.381  0.020  1.381
 I3N  N9   C17   single    1.439  0.020  1.439
 I3N  C10  C11   aromatic  1.368  0.020  1.368
 I3N  C10  C16   single    1.487  0.020  1.487
 I3N  C11  C12   single    1.491  0.020  1.491
 I3N  C12  C13   single    1.533  0.020  1.533
 I3N  C12  H121  single    0.970  0.020  1.090
 I3N  C12  H122  single    0.970  0.020  1.090
 I3N  C13  O14   deloc     1.236  0.020  1.236
 I3N  C13  O15   deloc     1.245  0.020  1.245
 I3N  C16  H161  single    0.970  0.020  1.090
 I3N  C16  H162  single    0.970  0.020  1.090
 I3N  C16  H163  single    0.970  0.020  1.090
 I3N  C17  C18   single    1.513  0.020  1.513
 I3N  C17  H171  single    0.970  0.020  1.090
 I3N  C17  H172  single    0.970  0.020  1.090
 I3N  C18  C19   aromatic  1.395  0.020  1.395
 I3N  C18  C23   aromatic  1.388  0.020  1.388
 I3N  C19  C20   aromatic  1.386  0.020  1.386
 I3N  C19  H19   single    0.930  0.020  1.080
 I3N  C20  C21   aromatic  1.391  0.020  1.391
 I3N  C20  H20   single    0.930  0.020  1.080
 I3N  C21  C22   aromatic  1.385  0.020  1.385
 I3N  C21  H21   single    0.930  0.020  1.080
 I3N  C22  C23   aromatic  1.390  0.020  1.390
 I3N  C22  H22   single    0.930  0.020  1.080
 I3N  C23  H23   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
 I3N  H13   C1   H12   108.25  3.000
 I3N  H13   C1   H11   108.76  3.000
 I3N  H12   C1   H11   108.50  3.000
 I3N  H13   C1   O2    112.33  3.000
 I3N  H12   C1   O2    106.65  3.000
 I3N  H11   C1   O2    112.20  3.000
 I3N  C3    O2   C1    118.63  3.000
 I3N  C8    C3   C4    120.53  3.000
 I3N  C8    C3   O2    123.25  3.000
 I3N  C4    C3   O2    116.21  3.000
 I3N  H4    C4   C5    121.25  3.000
 I3N  H4    C4   C3    119.83  3.000
 I3N  C5    C4   C3    118.92  3.000
 I3N  C11   C5   C6    107.01  3.000
 I3N  C11   C5   C4    133.42  3.000
 I3N  C6    C5   C4    119.57  3.000
 I3N  N9    C6   C7    130.57  3.000
 I3N  N9    C6   C5    107.78  3.000
 I3N  C7    C6   C5    121.63  3.000
 I3N  H7    C7   C8    119.72  3.000
 I3N  H7    C7   C6    121.89  3.000
 I3N  C8    C7   C6    118.39  3.000
 I3N  H8    C8   C7    118.34  3.000
 I3N  H8    C8   C3    120.76  3.000
 I3N  C7    C8   C3    120.90  3.000
 I3N  C17   N9   C10   126.22  3.000
 I3N  C17   N9   C6    124.53  3.000
 I3N  C10   N9   C6    108.63  3.000
 I3N  C16   C10  C11   129.58  3.000
 I3N  C16   C10  N9    120.38  3.000
 I3N  C11   C10  N9    109.92  3.000
 I3N  C12   C11  C10   128.39  3.000
 I3N  C12   C11  C5    124.87  3.000
 I3N  C10   C11  C5    106.64  3.000
 I3N  H122  C12  H121  105.14  3.000
 I3N  H122  C12  C13   109.09  3.000
 I3N  H121  C12  C13   106.98  3.000
 I3N  H122  C12  C11   111.73  3.000
 I3N  H121  C12  C11   108.99  3.000
 I3N  C13   C12  C11   114.40  3.000
 I3N  O15   C13  O14   127.66  3.000
 I3N  O15   C13  C12   119.65  3.000
 I3N  O14   C13  C12   112.60  3.000
 I3N  H163  C16  H162  106.94  3.000
 I3N  H163  C16  H161  107.76  3.000
 I3N  H162  C16  H161  107.58  3.000
 I3N  H163  C16  C10   112.08  3.000
 I3N  H162  C16  C10   110.16  3.000
 I3N  H161  C16  C10   112.08  3.000
 I3N  H172  C17  H171  105.76  3.000
 I3N  H172  C17  C18   109.08  3.000
 I3N  H171  C17  C18   110.16  3.000
 I3N  H172  C17  N9    108.90  3.000
 I3N  H171  C17  N9    108.43  3.000
 I3N  C18   C17  N9    114.17  3.000
 I3N  C23   C18  C19   118.81  3.000
 I3N  C23   C18  C17   122.54  3.000
 I3N  C19   C18  C17   118.65  3.000
 I3N  H19   C19  C20   119.50  3.000
 I3N  H19   C19  C18   119.57  3.000
 I3N  C20   C19  C18   120.82  3.000
 I3N  H20   C20  C21   120.34  3.000
 I3N  H20   C20  C19   119.66  3.000
 I3N  C21   C20  C19   119.99  3.000
 I3N  H21   C21  C22   120.26  3.000
 I3N  H21   C21  C20   120.25  3.000
 I3N  C22   C21  C20   119.43  3.000
 I3N  H22   C22  C23   119.36  3.000
 I3N  H22   C22  C21   120.06  3.000
 I3N  C23   C22  C21   120.53  3.000
 I3N  H23   C23  C22   119.03  3.000
 I3N  H23   C23  C18   120.53  3.000
 I3N  C22   C23  C18   120.38  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
 I3N  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 I3N  CONST_02  C11   C5   C4   C3    180.00   0.0  0
 I3N  CONST_03  C6    C7   C8   C3      0.00   0.0  0
 I3N  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 I3N  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 I3N  CONST_06  N9    C6   C5   C4    180.00   0.0  0
 I3N  CONST_07  C10   C11  C5   C4    180.00   0.0  0
 I3N  CONST_08  C8    C3   C4   C5      0.00   0.0  0
 I3N  CONST_09  C8    C7   C6   C5      0.00   0.0  0
 I3N  CONST_10  C10   N9   C6   C5      0.00   0.0  0
 I3N  CONST_11  N9    C10  C11  C5      0.00   0.0  0
 I3N  CONST_12  C10   C11  C5   C6      0.00   0.0  0
 I3N  CONST_13  C11   C10  N9   C6      0.00   0.0  0
 I3N  CONST_14  C11   C5   C6   C7    180.00   0.0  0
 I3N  CONST_15  C10   N9   C6   C7    180.00   0.0  0
 I3N  CONST_16  N9    C6   C7   C8    180.00   0.0  0
 I3N  CONST_17  C11   C5   C6   N9      0.00   0.0  0
 I3N  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 I3N  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 I3N  CONST_20  C22   C23  C18  C19     0.00   0.0  0
 I3N  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 I3N  CONST_22  C23   C18  C19  C20     0.00   0.0  0
 I3N  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 I3N  CONST_24  C5    C4   C3   O2    180.00   0.0  0
 I3N  CONST_25  C7    C8   C3   O2    180.00   0.0  0
 I3N  CONST_26  C12   C11  C5   C4      0.00   0.0  0
 I3N  CONST_27  C17   N9   C6   C5    180.00   0.0  0
 I3N  CONST_28  C16   C10  C11  C5    180.00   0.0  0
 I3N  CONST_29  C12   C11  C5   C6    180.00   0.0  0
 I3N  CONST_30  C16   C10  N9   C6    180.00   0.0  0
 I3N  CONST_31  C17   N9   C6   C7      0.00   0.0  0
 I3N  CONST_32  C12   C11  C10  N9    180.00   0.0  0
 I3N  CONST_33  C17   N9   C10  C11   180.00   0.0  0
 I3N  CONST_34  C20   C19  C18  C17   180.00   0.0  0
 I3N  CONST_35  C22   C23  C18  C17   180.00   0.0  0
 I3N  CONST_36  H7    C7   C8   C3    180.00   0.0  0
 I3N  CONST_37  H8    C8   C3   C4    180.00   0.0  0
 I3N  CONST_38  H4    C4   C5   C6    180.00   0.0  0
 I3N  CONST_39  H20   C20  C19  C18   180.00   0.0  0
 I3N  CONST_40  H22   C22  C23  C18   180.00   0.0  0
 I3N  CONST_41  H23   C23  C18  C19   180.00   0.0  0
 I3N  CONST_42  H21   C21  C20  C19   180.00   0.0  0
 I3N  CONST_43  H19   C19  C20  C21   180.00   0.0  0
 I3N  Var_01    C18   C17  N9   C6     84.16  30.0  2
 I3N  Var_02    C19   C18  C17  N9   -176.77  30.0  2
 I3N  Var_03    C4    C3   O2   C1   -175.71  30.0  2
 I3N  Var_04    C13   C12  C11  C5    -72.61  30.0  2
 I3N  Var_05    H161  C16  C10  N9     61.56  30.0  2
 I3N  Var_06    O14   C13  C12  C11   176.21  30.0  3
 I3N  Var_07    H11   C1   O2   C3     60.86  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
 I3N  plan-1  C17  0.020
 I3N  plan-1  C18  0.020
 I3N  plan-1  C19  0.020
 I3N  plan-1  C20  0.020
 I3N  plan-1  C21  0.020
 I3N  plan-1  C22  0.020
 I3N  plan-1  C23  0.020
 I3N  plan-1  H19  0.020
 I3N  plan-1  H20  0.020
 I3N  plan-1  H21  0.020
 I3N  plan-1  H22  0.020
 I3N  plan-1  H23  0.020
 I3N  plan-2  O2   0.020
 I3N  plan-2  C3   0.020
 I3N  plan-2  C4   0.020
 I3N  plan-2  C5   0.020
 I3N  plan-2  C6   0.020
 I3N  plan-2  C7   0.020
 I3N  plan-2  C8   0.020
 I3N  plan-2  N9   0.020
 I3N  plan-2  C10  0.020
 I3N  plan-2  C11  0.020
 I3N  plan-2  C12  0.020
 I3N  plan-2  C16  0.020
 I3N  plan-2  C17  0.020
 I3N  plan-2  H4   0.020
 I3N  plan-2  H7   0.020
 I3N  plan-2  H8   0.020
 I3N  plan-3  C12  0.020
 I3N  plan-3  C13  0.020
 I3N  plan-3  O14  0.020
 I3N  plan-3  O15  0.020

