# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:55:36 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: [5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)c2ccc3sc(cc3c2)C(N)N
#
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
 IYX  IYX  '[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine'  ligand  40  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IYX
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
 IYX  C1    C  CR56  0   0.260  -2.0433  -0.1932   0.0195
 IYX  C2    C  CR56  0  -0.242  -2.3571   1.1109  -0.3982
 IYX  C3    C  CR16  0  -0.401  -0.7027  -0.5813   0.0847
 IYX  C4    C  CR16  0  -0.263  -1.3616   2.0199  -0.7412
 IYX  C5    C  CR6   0   0.093   0.3038   0.3091  -0.2606
 IYX  C6    C  CR16  0  -0.329  -0.0455   1.6104  -0.6701
 IYX  C7    C  CR15  0  -0.260  -3.2195  -0.9527   0.3337
 IYX  C8    C  CR5   0  -0.173  -4.3646  -0.2541   0.1579
 IYX  S9    S  S2    0   0.204  -4.0700   1.3721  -0.3919
 IYX  C10   C  CR6   0   0.092   1.7216  -0.1003  -0.2115
 IYX  C11   C  CR16  0  -0.327   2.1159  -1.3728  -0.5935
 IYX  C12   C  CR16  0  -0.457   2.7042   0.8018   0.2205
 IYX  C13   C  CR16  0  -0.371   3.4574  -1.7458  -0.5556
 IYX  C14   C  CR6   0   0.335   4.0394   0.4438   0.2640
 IYX  C15   C  CR6   0   0.301   4.4279  -0.8527  -0.1346
 IYX  O16   O  O2    0  -0.465   5.0387   1.2473   0.6727
 IYX  C17   C  CH3   0  -0.439   4.7184   2.5658   1.0661
 IYX  O18   O  O2    0  -0.462   5.7462  -1.1119  -0.0706
 IYX  C19   C  CH3   0  -0.437   6.1950  -2.3852  -0.4883
 IYX  C20   C  CH1   0  -0.011  -5.7910  -0.7316   0.2993
 IYX  N21   N  NH2   0  -0.770  -6.3706  -1.1726  -0.9554
 IYX  N22   N  NH2   0  -0.790  -5.8167  -1.8485   1.2170
 IYX  H3    H  HCR6  0   0.253  -0.4544  -1.5783   0.4283
 IYX  H4    H  HCR6  0   0.268  -1.6074   3.0221  -1.0666
 IYX  H6    H  HCR6  0   0.255   0.7325   2.3059  -0.9591
 IYX  H7    H  HCR5  0   0.262  -3.1974  -1.9782   0.6743
 IYX  H11   H  HCR6  0   0.252   1.3860  -2.0880  -0.9507
 IYX  H12   H  HCR6  0   0.278   2.3988   1.7866   0.5481
 IYX  H13   H  HCR6  0   0.283   3.7271  -2.7430  -0.8749
 IYX  H17   H  HCH3  0   0.261   5.6567   3.0447   1.3351
 IYX  H17A  H  HCH3  0   0.227   4.2548   3.1340   0.2549
 IYX  H17B  H  HCH3  0   0.228   4.0539   2.5856   1.9342
 IYX  H19   H  HCH3  0   0.228   5.9497  -2.5810  -1.5356
 IYX  H19A  H  HCH3  0   0.260   7.2764  -2.3837  -0.3765
 IYX  H19B  H  HCH3  0   0.228   5.7803  -3.1886   0.1265
 IYX  HN21  H  HNH2  0   0.351  -6.4961  -0.3871  -1.5810
 IYX  HN2A  H  HNH2  0   0.345  -5.7379  -1.8170  -1.4154
 IYX  HN2C  H  HNH2  0   0.352  -5.5109  -1.5532   2.1353
 IYX  HN2D  H  HNH2  0   0.355  -6.7733  -2.1662   1.3134
 IYX  H20   H  HCH1  0   0.226  -6.4017   0.1194   0.6349

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
 IYX  C3   C1    aromatic  1.397  0.020  1.397
 IYX  C1   C7    aromatic  1.435  0.020  1.435
 IYX  C1   C2    aromatic  1.405  0.020  1.405
 IYX  C2   C4    aromatic  1.391  0.020  1.391
 IYX  C2   S9    aromatic  1.733  0.020  1.733
 IYX  C5   C3    aromatic  1.387  0.020  1.387
 IYX  C3   H3    single    0.930  0.020  1.080
 IYX  C6   C4    aromatic  1.380  0.020  1.380
 IYX  C4   H4    single    0.930  0.020  1.080
 IYX  C10  C5    single    1.477  0.020  1.477
 IYX  C5   C6    aromatic  1.408  0.020  1.408
 IYX  C6   H6    single    0.930  0.020  1.080
 IYX  C7   C8    aromatic  1.353  0.020  1.353
 IYX  C7   H7    single    0.930  0.020  1.080
 IYX  C8   C20   single    1.511  0.020  1.511
 IYX  C8   S9    aromatic  1.742  0.020  1.742
 IYX  C12  C10   aromatic  1.402  0.020  1.402
 IYX  C10  C11   aromatic  1.386  0.020  1.386
 IYX  C13  C11   aromatic  1.393  0.020  1.393
 IYX  C11  H11   single    0.930  0.020  1.080
 IYX  C14  C12   aromatic  1.383  0.020  1.383
 IYX  C12  H12   single    0.930  0.020  1.080
 IYX  C15  C13   aromatic  1.384  0.020  1.384
 IYX  C13  H13   single    0.930  0.020  1.080
 IYX  O16  C14   single    1.346  0.020  1.346
 IYX  C14  C15   aromatic  1.411  0.020  1.411
 IYX  O18  C15   single    1.345  0.020  1.345
 IYX  C17  O16   single    1.413  0.020  1.413
 IYX  C17  H17   single    0.970  0.020  1.090
 IYX  C17  H17A  single    0.970  0.020  1.090
 IYX  C17  H17B  single    0.970  0.020  1.090
 IYX  C19  O18   single    1.413  0.020  1.413
 IYX  C19  H19   single    0.970  0.020  1.090
 IYX  C19  H19A  single    0.970  0.020  1.090
 IYX  C19  H19B  single    0.970  0.020  1.090
 IYX  N22  C20   single    1.446  0.020  1.446
 IYX  C20  N21   single    1.451  0.020  1.451
 IYX  N21  HN21  single    0.890  0.020  1.040
 IYX  N21  HN2A  single    0.890  0.020  1.040
 IYX  N22  HN2C  single    0.890  0.020  1.040
 IYX  N22  HN2D  single    0.890  0.020  1.040
 IYX  C20  H20   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
 IYX  C7    C1   C3    128.99  3.000
 IYX  C7    C1   C2    111.92  3.000
 IYX  C3    C1   C2    119.08  3.000
 IYX  S9    C2   C4    127.58  3.000
 IYX  S9    C2   C1    111.08  3.000
 IYX  C4    C2   C1    121.34  3.000
 IYX  H3    C3   C5    120.22  3.000
 IYX  H3    C3   C1    119.36  3.000
 IYX  C5    C3   C1    120.41  3.000
 IYX  H4    C4   C6    120.46  3.000
 IYX  H4    C4   C2    121.12  3.000
 IYX  C6    C4   C2    118.41  3.000
 IYX  C10   C5   C6    120.27  3.000
 IYX  C6    C5   C3    119.04  3.000
 IYX  C10   C5   C3    120.68  3.000
 IYX  H6    C6   C5    119.53  3.000
 IYX  H6    C6   C4    118.74  3.000
 IYX  C5    C6   C4    121.71  3.000
 IYX  H7    C7   C8    123.24  3.000
 IYX  H7    C7   C1    123.67  3.000
 IYX  C8    C7   C1    113.08  3.000
 IYX  C20   C8   S9    118.97  3.000
 IYX  S9    C8   C7    112.33  3.000
 IYX  C20   C8   C7    128.59  3.000
 IYX  C8    S9   C2     91.58  3.000
 IYX  C12   C10  C11   118.44  3.000
 IYX  C11   C10  C5    121.24  3.000
 IYX  C12   C10  C5    120.31  3.000
 IYX  H11   C11  C13   118.78  3.000
 IYX  H11   C11  C10   120.38  3.000
 IYX  C13   C11  C10   120.82  3.000
 IYX  H12   C12  C14   119.91  3.000
 IYX  H12   C12  C10   118.76  3.000
 IYX  C14   C12  C10   121.31  3.000
 IYX  H13   C13  C15   120.65  3.000
 IYX  H13   C13  C11   118.63  3.000
 IYX  C15   C13  C11   120.71  3.000
 IYX  O16   C14  C15   115.46  3.000
 IYX  C15   C14  C12   119.66  3.000
 IYX  O16   C14  C12   124.88  3.000
 IYX  O18   C15  C14   115.69  3.000
 IYX  O18   C15  C13   125.26  3.000
 IYX  C14   C15  C13   119.05  3.000
 IYX  C17   O16  C14   118.26  3.000
 IYX  H17B  C17  H17A  108.78  3.000
 IYX  H17B  C17  H17   108.67  3.000
 IYX  H17A  C17  H17   108.70  3.000
 IYX  H17B  C17  O16   112.07  3.000
 IYX  H17A  C17  O16   111.99  3.000
 IYX  H17   C17  O16   106.52  3.000
 IYX  C19   O18  C15   118.08  3.000
 IYX  H19B  C19  H19A  108.69  3.000
 IYX  H19B  C19  H19   108.78  3.000
 IYX  H19A  C19  H19   108.78  3.000
 IYX  H19B  C19  O18   112.05  3.000
 IYX  H19A  C19  O18   106.51  3.000
 IYX  H19   C19  O18   111.92  3.000
 IYX  H20   C20  N22   113.21  3.000
 IYX  H20   C20  N21   106.09  3.000
 IYX  N22   C20  N21   107.88  3.000
 IYX  H20   C20  C8    107.95  3.000
 IYX  N21   C20  C8    113.10  3.000
 IYX  N22   C20  C8    108.69  3.000
 IYX  HN2A  N21  HN21  106.88  3.000
 IYX  HN2A  N21  C20   109.66  3.000
 IYX  HN21  N21  C20   110.38  3.000
 IYX  HN2D  N22  HN2C  106.90  3.000
 IYX  HN2D  N22  C20   108.64  3.000
 IYX  HN2C  N22  C20   110.19  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
 IYX  CONST_01  C10   C5   C3   C1    180.00   0.0  0
 IYX  CONST_02  C6    C5   C3   C1      0.00   0.0  0
 IYX  CONST_03  S9    C8   C7   C1      0.00   0.0  0
 IYX  CONST_04  C6    C4   C2   C1      0.00   0.0  0
 IYX  CONST_05  C8    S9   C2   C1      0.00   0.0  0
 IYX  CONST_06  C5    C3   C1   C2      0.00   0.0  0
 IYX  CONST_07  C8    C7   C1   C2      0.00   0.0  0
 IYX  CONST_08  C5    C6   C4   C2      0.00   0.0  0
 IYX  CONST_09  C7    C8   S9   C2      0.00   0.0  0
 IYX  CONST_10  C8    C7   C1   C3    180.00   0.0  0
 IYX  CONST_11  C4    C2   C1   C3      0.00   0.0  0
 IYX  CONST_12  S9    C2   C1   C3    180.00   0.0  0
 IYX  CONST_15  C4    C6   C5   C3      0.00   0.0  0
 IYX  CONST_16  C7    C1   C2   C4    180.00   0.0  0
 IYX  CONST_17  C8    S9   C2   C4    180.00   0.0  0
 IYX  CONST_18  C10   C5   C6   C4    180.00   0.0  0
 IYX  CONST_19  C7    C1   C3   C5    180.00   0.0  0
 IYX  CONST_20  C14   C12  C10  C5    180.00   0.0  0
 IYX  CONST_21  C13   C11  C10  C5    180.00   0.0  0
 IYX  CONST_22  S9    C2   C4   C6    180.00   0.0  0
 IYX  CONST_25  S9    C2   C1   C7      0.00   0.0  0
 IYX  CONST_26  C15   C14  C12  C10     0.00   0.0  0
 IYX  CONST_27  C15   C13  C11  C10     0.00   0.0  0
 IYX  CONST_28  C14   C12  C10  C11     0.00   0.0  0
 IYX  CONST_29  C14   C15  C13  C11     0.00   0.0  0
 IYX  CONST_30  C13   C11  C10  C12     0.00   0.0  0
 IYX  CONST_31  C13   C15  C14  C12     0.00   0.0  0
 IYX  CONST_32  C20   C8   C7   C1    180.00   0.0  0
 IYX  CONST_33  C20   C8   S9   C2    180.00   0.0  0
 IYX  CONST_34  O16   C14  C12  C10   180.00   0.0  0
 IYX  CONST_35  O18   C15  C13  C11   180.00   0.0  0
 IYX  CONST_36  O18   C15  C14  C12   180.00   0.0  0
 IYX  CONST_37  O16   C14  C15  C13   180.00   0.0  0
 IYX  CONST_38  H4    C4   C2   C1    180.00   0.0  0
 IYX  CONST_39  H3    C3   C1   C2    180.00   0.0  0
 IYX  CONST_40  H7    C7   C1   C2    180.00   0.0  0
 IYX  CONST_41  H6    C6   C4   C2    180.00   0.0  0
 IYX  CONST_42  H12   C12  C10  C5      0.00   0.0  0
 IYX  CONST_43  H11   C11  C10  C5      0.00   0.0  0
 IYX  CONST_44  H13   C13  C11  C10   180.00   0.0  0
 IYX  Var_01    N22   C20  C8   C7     25.87  30.0  2
 IYX  Var_02    HN2C  N22  C20  C8     63.03  30.0  3
 IYX  Var_03    HN21  N21  C20  C8    -68.02  30.0  3
 IYX  Var_04    H17   C17  O16  C14  -178.81  30.0  3
 IYX  Var_05    H19   C19  O18  C15    60.21  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
 IYX  plan-1  C5   0.020
 IYX  plan-1  C10  0.020
 IYX  plan-1  C11  0.020
 IYX  plan-1  C12  0.020
 IYX  plan-1  C13  0.020
 IYX  plan-1  C14  0.020
 IYX  plan-1  C15  0.020
 IYX  plan-1  O16  0.020
 IYX  plan-1  O18  0.020
 IYX  plan-1  H11  0.020
 IYX  plan-1  H12  0.020
 IYX  plan-1  H13  0.020
 IYX  plan-2  C1   0.020
 IYX  plan-2  C2   0.020
 IYX  plan-2  C3   0.020
 IYX  plan-2  C4   0.020
 IYX  plan-2  C5   0.020
 IYX  plan-2  C6   0.020
 IYX  plan-2  C7   0.020
 IYX  plan-2  C8   0.020
 IYX  plan-2  S9   0.020
 IYX  plan-2  C10  0.020
 IYX  plan-2  C20  0.020
 IYX  plan-2  H3   0.020
 IYX  plan-2  H4   0.020
 IYX  plan-2  H6   0.020
 IYX  plan-2  H7   0.020

