# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 05:41:32 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-[5-(4-carbamimidoylphenyl)thiophen-2-yl]-1H-indole-6-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)c2sc(cc2)c3[nH]c4cc(ccc4c3)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
 X8V  X8V  "2-[5-(4-carbamimidoylphenyl)thiophen-2-yl]-1H-indole-6-carboximidamide"
  ligand  43  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X8V
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
 X8V  N1   N  N     0  -0.648  10.0606  16.8567  16.6436
 X8V  N3   N  NR15  0  -0.764   9.9878  23.0070   7.8076
 X8V  C4   C  CR5   0  -0.270   8.5860  22.2801   9.7127
 X8V  C5   C  CR6   0   0.154   9.3214  20.1752  12.9394
 X8V  C6   C  CR16  0  -0.311  10.6605  20.2339  13.3291
 X8V  C7   C  CR16  0  -0.270  11.1202  19.5076  14.4154
 X8V  C8   C  CR6   0   0.034  10.2575  18.7012  15.1539
 X8V  C10  C  CR16  0  -0.317   8.4608  19.3543  13.6768
 X8V  C13  C  CR15  0  -0.453   7.9275  23.8764   7.8581
 X8V  C15  C  CR56  0   0.369   9.8907  23.8100   6.7092
 X8V  C17  C  CR16  0  -0.302   9.1778  25.5531   4.7086
 X8V  C14  C  CR56  0   0.088   8.5991  24.3810   6.7134
 X8V  C16  C  CR16  0  -0.335   8.2509  25.2667   5.6857
 X8V  C18  C  CR6   0  -0.025  10.4621  24.9696   4.7136
 X8V  N5   N  NH2   0  -0.802  12.2846  24.3373   3.2718
 X8V  N4   N  N     0  -0.640  11.5220  26.4924   3.1077
 X8V  C19  C  CR16  0  -0.348  10.8260  24.0853   5.7184
 X8V  C12  C  CR5   0   0.445   8.8044  23.0346   8.5017
 X8V  S1   S  S2    0   0.243   9.8820  21.5723  10.6040
 X8V  C3   C  CR15  0  -0.227   7.3868  22.0337  10.3302
 X8V  C2   C  CR15  0  -0.212   7.5186  21.2793  11.5138
 X8V  C1   C  CR5   0  -0.213   8.8148  20.9424  11.8068
 X8V  C11  C  C     0   0.336  10.7219  17.9014  16.3208
 X8V  N2   N  NH2   0  -0.822  11.8700  18.3446  16.9145
 X8V  C9   C  CR16  0  -0.250   8.9215  18.6333  14.7607
 X8V  H1   H  H     0   0.325  10.4520  16.4112  17.4695
 X8V  H2   H  HNR5  0   0.415  10.7828  22.4229   8.0150
 X8V  H3   H  HCR6  0   0.257  11.3637  20.8595  12.7923
 X8V  H4   H  HCR6  0   0.261  12.1706  19.5714  14.6689
 X8V  H5   H  HCR6  0   0.257   7.4197  19.2658  13.3951
 X8V  H6   H  HCR5  0   0.256   6.9283  24.1173   8.1846
 X8V  H7   H  HCR6  0   0.252   8.9051  26.2238   3.9035
 X8V  H8   H  HCR6  0   0.250   7.2665  25.7161   5.6546
 X8V  H9   H  HNH2  0   0.389  11.9584  23.3868   3.3294
 X8V  H10  H  HNH2  0   0.381  12.8594  24.5267   2.4658
 X8V  H11  H  H     0   0.328  10.8969  27.1474   3.5623
 X8V  H12  H  HCR6  0   0.267  11.8123  23.6393   5.7491
 X8V  H13  H  HCR5  0   0.267   6.4395  22.3810   9.9425
 X8V  H14  H  HCR5  0   0.269   6.6781  21.0062  12.1359
 X8V  H15  H  HNH2  0   0.391  12.1343  17.9108  17.7851
 X8V  H16  H  HNH2  0   0.394  12.0776  19.3294  16.8809
 X8V  H17  H  HCR6  0   0.258   8.2372  18.0047  15.3138
 X8V  C20  C  C     0   0.327  11.4290  25.3344   3.6426

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
 X8V  N4   C20  double    1.279  0.020  1.279
 X8V  N5   C20  single    1.365  0.020  1.365
 X8V  C20  C18  single    1.488  0.020  1.488
 X8V  C18  C17  aromatic  1.411  0.020  1.411
 X8V  C18  C19  aromatic  1.387  0.020  1.387
 X8V  C17  C16  aromatic  1.377  0.020  1.377
 X8V  C19  C15  aromatic  1.390  0.020  1.390
 X8V  C16  C14  aromatic  1.401  0.020  1.401
 X8V  C15  C14  aromatic  1.412  0.020  1.412
 X8V  C15  N3   aromatic  1.364  0.020  1.364
 X8V  C14  C13  aromatic  1.420  0.020  1.420
 X8V  N3   C12  aromatic  1.372  0.020  1.372
 X8V  C13  C12  aromatic  1.375  0.020  1.375
 X8V  C12  C4   single    1.443  0.020  1.443
 X8V  C4   C3   aromatic  1.371  0.020  1.371
 X8V  C4   S1   aromatic  1.725  0.020  1.725
 X8V  C3   C2   aromatic  1.410  0.020  1.410
 X8V  S1   C1   aromatic  1.727  0.020  1.727
 X8V  C2   C1   aromatic  1.371  0.020  1.371
 X8V  C1   C5   single    1.459  0.020  1.459
 X8V  C5   C6   aromatic  1.396  0.020  1.396
 X8V  C5   C10  aromatic  1.399  0.020  1.399
 X8V  C6   C7   aromatic  1.385  0.020  1.385
 X8V  C10  C9   aromatic  1.381  0.020  1.381
 X8V  C7   C8   aromatic  1.393  0.020  1.393
 X8V  C9   C8   aromatic  1.394  0.020  1.394
 X8V  C8   C11  single    1.489  0.020  1.489
 X8V  C11  N1   double    1.278  0.020  1.278
 X8V  C11  N2   single    1.366  0.020  1.366
 X8V  N1   H1   single    0.890  0.020  1.040
 X8V  N3   H2   single    0.860  0.020  1.020
 X8V  C6   H3   single    0.930  0.020  1.080
 X8V  C7   H4   single    0.930  0.020  1.080
 X8V  C10  H5   single    0.930  0.020  1.080
 X8V  C13  H6   single    0.930  0.020  1.080
 X8V  C17  H7   single    0.930  0.020  1.080
 X8V  C16  H8   single    0.930  0.020  1.080
 X8V  N5   H9   single    0.890  0.020  1.040
 X8V  N5   H10  single    0.890  0.020  1.040
 X8V  N4   H11  single    0.890  0.020  1.040
 X8V  C19  H12  single    0.930  0.020  1.080
 X8V  C3   H13  single    0.930  0.020  1.080
 X8V  C2   H14  single    0.930  0.020  1.080
 X8V  N2   H15  single    0.890  0.020  1.040
 X8V  N2   H16  single    0.890  0.020  1.040
 X8V  C9   H17  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
 X8V  H1   N1   C11  111.35  3.000
 X8V  H2   N3   C12  125.99  3.000
 X8V  H2   N3   C15  124.26  3.000
 X8V  C12  N3   C15  109.52  3.000
 X8V  C3   C4   S1   110.53  3.000
 X8V  S1   C4   C12  122.30  3.000
 X8V  C3   C4   C12  127.17  3.000
 X8V  C1   C5   C10  120.27  3.000
 X8V  C10  C5   C6   117.87  3.000
 X8V  C1   C5   C6   121.86  3.000
 X8V  H3   C6   C7   118.42  3.000
 X8V  H3   C6   C5   120.57  3.000
 X8V  C7   C6   C5   121.01  3.000
 X8V  H4   C7   C8   120.73  3.000
 X8V  H4   C7   C6   118.35  3.000
 X8V  C8   C7   C6   120.92  3.000
 X8V  C9   C8   C11  119.59  3.000
 X8V  C11  C8   C7   122.23  3.000
 X8V  C9   C8   C7   118.18  3.000
 X8V  H5   C10  C9   118.85  3.000
 X8V  H5   C10  C5   120.16  3.000
 X8V  C9   C10  C5   120.98  3.000
 X8V  H6   C13  C12  125.86  3.000
 X8V  H6   C13  C14  127.08  3.000
 X8V  C12  C13  C14  107.05  3.000
 X8V  C19  C15  C14  122.51  3.000
 X8V  C14  C15  N3   107.50  3.000
 X8V  C19  C15  N3   129.99  3.000
 X8V  H7   C17  C18  119.22  3.000
 X8V  H7   C17  C16  119.14  3.000
 X8V  C18  C17  C16  121.62  3.000
 X8V  C16  C14  C15  118.74  3.000
 X8V  C15  C14  C13  106.93  3.000
 X8V  C16  C14  C13  134.32  3.000
 X8V  H8   C16  C14  120.64  3.000
 X8V  H8   C16  C17  120.36  3.000
 X8V  C14  C16  C17  119.00  3.000
 X8V  C19  C18  C20  120.47  3.000
 X8V  C19  C18  C17  120.34  3.000
 X8V  C20  C18  C17  119.18  3.000
 X8V  H10  N5   H9   114.08  3.000
 X8V  H10  N5   C20  115.94  3.000
 X8V  H9   N5   C20  118.10  3.000
 X8V  H11  N4   C20  110.66  3.000
 X8V  H12  C19  C18  121.47  3.000
 X8V  H12  C19  C15  120.73  3.000
 X8V  C18  C19  C15  117.78  3.000
 X8V  C13  C12  C4   128.02  3.000
 X8V  C4   C12  N3   122.98  3.000
 X8V  C13  C12  N3   108.99  3.000
 X8V  C1   S1   C4    92.59  3.000
 X8V  H13  C3   C2   123.71  3.000
 X8V  H13  C3   C4   123.18  3.000
 X8V  C2   C3   C4   113.11  3.000
 X8V  H14  C2   C1   123.38  3.000
 X8V  H14  C2   C3   123.08  3.000
 X8V  C1   C2   C3   113.54  3.000
 X8V  C2   C1   S1   110.23  3.000
 X8V  C2   C1   C5   128.57  3.000
 X8V  S1   C1   C5   121.20  3.000
 X8V  N2   C11  C8   115.36  3.000
 X8V  N2   C11  N1   126.18  3.000
 X8V  C8   C11  N1   118.40  3.000
 X8V  H16  N2   H15  113.30  3.000
 X8V  H16  N2   C11  118.43  3.000
 X8V  H15  N2   C11  117.13  3.000
 X8V  H17  C9   C10  119.60  3.000
 X8V  H17  C9   C8   119.37  3.000
 X8V  C10  C9   C8   121.04  3.000
 X8V  N4   C20  N5   120.14  3.000
 X8V  N5   C20  C18  115.06  3.000
 X8V  N4   C20  C18  124.76  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
 X8V  CONST_01  C18  C19  C15  N3    180.00   0.0  0
 X8V  CONST_02  C16  C14  C15  N3    180.00   0.0  0
 X8V  CONST_03  C13  C14  C15  N3      0.00   0.0  0
 X8V  CONST_04  C14  C13  C12  N3      0.00   0.0  0
 X8V  CONST_05  C3   C4   C12  N3    180.00   0.0  0
 X8V  CONST_06  S1   C4   C12  N3      0.00   0.0  0
 X8V  CONST_07  C15  N3   C12  C4    180.00   0.0  0
 X8V  CONST_08  C14  C13  C12  C4    180.00   0.0  0
 X8V  CONST_09  C1   C2   C3   C4      0.00   0.0  0
 X8V  CONST_10  C2   C1   S1   C4      0.00   0.0  0
 X8V  CONST_11  C5   C1   S1   C4    180.00   0.0  0
 X8V  CONST_12  C3   C2   C1   C5    180.00   0.0  0
 X8V  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 X8V  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 X8V  CONST_17  C9   C10  C5   C6      0.00   0.0  0
 X8V  CONST_18  C9   C8   C7   C6      0.00   0.0  0
 X8V  CONST_19  C1   C5   C6   C7    180.00   0.0  0
 X8V  CONST_20  C10  C5   C6   C7      0.00   0.0  0
 X8V  CONST_21  C10  C9   C8   C7      0.00   0.0  0
 X8V  CONST_24  C17  C16  C14  C13   180.00   0.0  0
 X8V  CONST_25  C19  C15  C14  C13   180.00   0.0  0
 X8V  CONST_26  C15  N3   C12  C13     0.00   0.0  0
 X8V  CONST_27  C3   C4   C12  C13     0.00   0.0  0
 X8V  CONST_29  C17  C18  C19  C15     0.00   0.0  0
 X8V  CONST_30  C17  C16  C14  C15     0.00   0.0  0
 X8V  CONST_31  C12  C13  C14  C15     0.00   0.0  0
 X8V  CONST_32  C18  C17  C16  C14     0.00   0.0  0
 X8V  CONST_33  C18  C19  C15  C14     0.00   0.0  0
 X8V  CONST_34  C12  N3   C15  C14     0.00   0.0  0
 X8V  CONST_35  C19  C18  C17  C16     0.00   0.0  0
 X8V  CONST_36  C19  C15  C14  C16     0.00   0.0  0
 X8V  CONST_37  C12  C13  C14  C16   180.00   0.0  0
 X8V  CONST_38  C12  N3   C15  C19   180.00   0.0  0
 X8V  CONST_39  C2   C3   C4   C12   180.00   0.0  0
 X8V  CONST_40  C1   S1   C4   C12   180.00   0.0  0
 X8V  CONST_41  C2   C3   C4   S1      0.00   0.0  0
 X8V  CONST_42  C3   C2   C1   S1      0.00   0.0  0
 X8V  CONST_43  C1   S1   C4   C3      0.00   0.0  0
 X8V  CONST_44  C9   C10  C5   C1    180.00   0.0  0
 X8V  CONST_45  C11  C8   C7   C6    180.00   0.0  0
 X8V  CONST_46  C11  C8   C9   C10   180.00   0.0  0
 X8V  CONST_47  C20  C18  C19  C15   180.00   0.0  0
 X8V  CONST_48  C16  C17  C18  C20   180.00   0.0  0
 X8V  CONST_49  H12  C19  C15  N3      0.00   0.0  0
 X8V  CONST_50  H6   C13  C12  N3    180.00   0.0  0
 X8V  CONST_51  H2   N3   C12  C4      0.00   0.0  0
 X8V  CONST_52  H6   C13  C12  C4      0.00   0.0  0
 X8V  CONST_53  H14  C2   C3   C4    180.00   0.0  0
 X8V  CONST_54  H14  C2   C1   C5      0.00   0.0  0
 X8V  CONST_55  H4   C7   C6   C5    180.00   0.0  0
 X8V  CONST_56  H17  C9   C10  C5    180.00   0.0  0
 X8V  CONST_57  H5   C10  C5   C6    180.00   0.0  0
 X8V  CONST_58  H17  C9   C8   C7    180.00   0.0  0
 X8V  CONST_59  H3   C6   C7   C8    180.00   0.0  0
 X8V  CONST_60  H5   C10  C9   C8    180.00   0.0  0
 X8V  CONST_61  H3   C6   C5   C10   180.00   0.0  0
 X8V  CONST_62  H8   C16  C14  C13     0.00   0.0  0
 X8V  CONST_63  H2   N3   C12  C13   180.00   0.0  0
 X8V  CONST_64  H8   C16  C14  C15   180.00   0.0  0
 X8V  CONST_65  H6   C13  C14  C15   180.00   0.0  0
 X8V  CONST_66  H12  C19  C18  C17   180.00   0.0  0
 X8V  CONST_67  H7   C17  C16  C14   180.00   0.0  0
 X8V  CONST_68  H12  C19  C15  C14   180.00   0.0  0
 X8V  CONST_69  H2   N3   C15  C14   180.00   0.0  0
 X8V  CONST_70  H6   C13  C14  C16     0.00   0.0  0
 X8V  CONST_71  H8   C16  C17  C18   180.00   0.0  0
 X8V  CONST_72  H7   C17  C18  C19   180.00   0.0  0
 X8V  CONST_73  H2   N3   C15  C19     0.00   0.0  0
 X8V  CONST_74  H13  C3   C4   C12     0.00   0.0  0
 X8V  CONST_75  H13  C3   C4   S1    180.00   0.0  0
 X8V  CONST_76  H14  C2   C1   S1    180.00   0.0  0
 X8V  CONST_77  H13  C3   C2   C1    180.00   0.0  0
 X8V  CONST_78  H3   C6   C5   C1      0.00   0.0  0
 X8V  CONST_79  H5   C10  C5   C1      0.00   0.0  0
 X8V  CONST_80  H4   C7   C8   C9    180.00   0.0  0
 X8V  CONST_81  H1   N1   C11  C8    180.00   0.0  0
 X8V  CONST_82  H15  N2   C11  C8    180.00   0.0  0
 X8V  CONST_84  H11  N4   C20  C18     0.00   0.0  0
 X8V  CONST_86  H10  N5   C20  C18   180.00   0.0  0
 X8V  CONST_87  H15  N2   C11  N1      0.00   0.0  0
 X8V  CONST_89  H11  N4   C20  N5    180.00   0.0  0
 X8V  CONST_91  H10  N5   C20  N4      0.00   0.0  0
 X8V  CONST_92  H1   N1   C11  N2      0.00   0.0  0
 X8V  Var_01    C7   C8   C11  N1   -154.95  30.0  2
 X8V  Var_02    C9   C8   C11  N1     23.90  30.0  2
 X8V  Var_03    N2   C11  C8   C7     22.48  30.0  2
 X8V  Var_04    N4   C20  C18  C17    34.97  30.0  3
 X8V  Var_05    N5   C20  C18  C17  -147.26  30.0  3
 X8V  Var_06    C19  C18  C20  N5     33.89  30.0  2
 X8V  Var_07    C19  C18  C20  N4   -143.88  30.0  2
 X8V  Var_08    C9   C8   C11  N2   -158.66  30.0  2

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
 X8V  plan-1  C4   0.020
 X8V  plan-1  C5   0.020
 X8V  plan-1  C12  0.020
 X8V  plan-1  S1   0.020
 X8V  plan-1  C3   0.020
 X8V  plan-1  C2   0.020
 X8V  plan-1  C1   0.020
 X8V  plan-1  H13  0.020
 X8V  plan-1  H14  0.020
 X8V  plan-2  C5   0.020
 X8V  plan-2  C6   0.020
 X8V  plan-2  C7   0.020
 X8V  plan-2  C8   0.020
 X8V  plan-2  C10  0.020
 X8V  plan-2  C1   0.020
 X8V  plan-2  C11  0.020
 X8V  plan-2  C9   0.020
 X8V  plan-2  H3   0.020
 X8V  plan-2  H4   0.020
 X8V  plan-2  H5   0.020
 X8V  plan-2  H17  0.020
 X8V  plan-3  N3   0.020
 X8V  plan-3  C4   0.020
 X8V  plan-3  C13  0.020
 X8V  plan-3  C15  0.020
 X8V  plan-3  C17  0.020
 X8V  plan-3  C14  0.020
 X8V  plan-3  C16  0.020
 X8V  plan-3  C18  0.020
 X8V  plan-3  C19  0.020
 X8V  plan-3  C12  0.020
 X8V  plan-3  H2   0.020
 X8V  plan-3  H6   0.020
 X8V  plan-3  H7   0.020
 X8V  plan-3  H8   0.020
 X8V  plan-3  H12  0.020
 X8V  plan-3  C20  0.020
 X8V  plan-4  N1   0.020
 X8V  plan-4  C8   0.020
 X8V  plan-4  C11  0.020
 X8V  plan-4  N2   0.020
 X8V  plan-4  H1   0.020
 X8V  plan-4  H15  0.020
 X8V  plan-4  H16  0.020
 X8V  plan-5  C18  0.020
 X8V  plan-5  N5   0.020
 X8V  plan-5  N4   0.020
 X8V  plan-5  H9   0.020
 X8V  plan-5  H10  0.020
 X8V  plan-5  H11  0.020
 X8V  plan-5  C20  0.020

