# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 10:26:03 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(2-methylphenyl)-1H-indole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2[nH]c3ccc(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
 MI2  MI2  2-(2-methylphenyl)-1H-indole-5-carboximidamide  ligand  34  19  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MI2
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
 MI2  C1    C  CR56  0   0.097  -3.6035  49.2395   1.3752
 MI2  C2    C  CR56  0   0.344  -3.6253  49.0448   2.7738
 MI2  N3    N  NR15  0  -0.727  -2.3496  49.1849   3.2256
 MI2  C4    C  CR5   0   0.310  -1.5122  49.4689   2.1751
 MI2  C5    C  CR15  0  -0.443  -2.2488  49.5091   1.0201
 MI2  C6    C  CR6   0   0.022  -0.0738  49.6967   2.3502
 MI2  C7    C  CR16  0  -0.294   0.4937  50.8101   1.7274
 MI2  C8    C  CR16  0  -0.259   1.8487  51.0778   1.8339
 MI2  C9    C  CR16  0  -0.246   2.6554  50.2266   2.5751
 MI2  C10   C  CR16  0  -0.292   2.0998  49.1126   3.1875
 MI2  C11   C  CR6   0   0.078   0.7411  48.8222   3.0878
 MI2  C12   C  CH3   0  -0.758   0.2060  47.5774   3.7386
 MI2  C13   C  CR16  0  -0.302  -4.8046  48.7650   3.4615
 MI2  C14   C  CR16  0  -0.318  -5.9641  48.6641   2.7237
 MI2  C15   C  CR6   0  -0.008  -5.9730  48.8439   1.3248
 MI2  C16   C  CR16  0  -0.393  -4.7956  49.1366   0.6534
 MI2  C17   C  C     0   0.327  -7.2563  48.6921   0.5856
 MI2  N18   N  N     0  -0.647  -8.1912  47.8782   0.9030
 MI2  N19   N  NH2   0  -0.804  -7.3783  49.4723  -0.5281
 MI2  HN3   H  HNR5  0   0.411  -2.0761  49.1620   4.1943
 MI2  H5    H  HCR5  0   0.254  -1.8578  49.6909   0.0313
 MI2  H7    H  HCR6  0   0.253  -0.1442  51.4797   1.1641
 MI2  H8    H  HCR6  0   0.258   2.2685  51.9486   1.3480
 MI2  H9    H  HCR6  0   0.258   3.7151  50.4237   2.6724
 MI2  H10   H  HCR6  0   0.252   2.7377  48.4408   3.7495
 MI2  H121  H  HCH3  0   0.248  -0.2805  47.7896   4.6929
 MI2  H122  H  HCH3  0   0.256   1.0158  46.8799   3.9482
 MI2  H123  H  HCH3  0   0.251  -0.5208  47.0659   3.1075
 MI2  H13   H  HCR6  0   0.265  -4.8153  48.6365   4.5360
 MI2  H14   H  HCR6  0   0.255  -6.8939  48.4633   3.2407
 MI2  H16   H  HCR6  0   0.255  -4.7894  49.2644  -0.4220
 MI2  HN18  H  H     0   0.329  -7.9087  47.2974   1.6836
 MI2  H191  H  HNH2  0   0.390  -6.9117  50.3639  -0.5319
 MI2  H192  H  HNH2  0   0.381  -8.2880  49.4818  -0.9617

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
 MI2  C1   C2    aromatic  1.412  0.020  1.412
 MI2  C1   C5    aromatic  1.426  0.020  1.426
 MI2  C1   C16   aromatic  1.397  0.020  1.397
 MI2  C2   N3    aromatic  1.361  0.020  1.361
 MI2  C2   C13   aromatic  1.393  0.020  1.393
 MI2  N3   C4    aromatic  1.373  0.020  1.373
 MI2  N3   HN3   single    0.860  0.020  1.020
 MI2  C4   C5    aromatic  1.370  0.020  1.370
 MI2  C4   C6    single    1.467  0.020  1.467
 MI2  C5   H5    single    0.930  0.020  1.080
 MI2  C6   C7    aromatic  1.396  0.020  1.396
 MI2  C6   C11   aromatic  1.405  0.020  1.405
 MI2  C7   C8    aromatic  1.385  0.020  1.385
 MI2  C7   H7    single    0.930  0.020  1.080
 MI2  C8   C9    aromatic  1.387  0.020  1.387
 MI2  C8   H8    single    0.930  0.020  1.080
 MI2  C9   C10   aromatic  1.387  0.020  1.387
 MI2  C9   H9    single    0.930  0.020  1.080
 MI2  C10  C11   aromatic  1.393  0.020  1.393
 MI2  C10  H10   single    0.930  0.020  1.080
 MI2  C11  C12   single    1.503  0.020  1.503
 MI2  C12  H121  single    0.970  0.020  1.090
 MI2  C12  H122  single    0.970  0.020  1.090
 MI2  C12  H123  single    0.970  0.020  1.090
 MI2  C13  C14   aromatic  1.378  0.020  1.378
 MI2  C13  H13   single    0.930  0.020  1.080
 MI2  C14  C15   aromatic  1.410  0.020  1.410
 MI2  C14  H14   single    0.930  0.020  1.080
 MI2  C15  C16   aromatic  1.387  0.020  1.387
 MI2  C15  C17   single    1.489  0.020  1.489
 MI2  C16  H16   single    0.930  0.020  1.080
 MI2  C17  N18   double    1.280  0.020  1.280
 MI2  C17  N19   single    1.365  0.020  1.365
 MI2  N18  HN18  single    0.890  0.020  1.040
 MI2  N19  H191  single    0.890  0.020  1.040
 MI2  N19  H192  single    0.890  0.020  1.040

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
 MI2  C16   C1   C5    134.08  3.000
 MI2  C16   C1   C2    119.22  3.000
 MI2  C5    C1   C2    106.69  3.000
 MI2  C13   C2   N3    130.56  3.000
 MI2  C13   C2   C1    121.97  3.000
 MI2  N3    C2   C1    107.47  3.000
 MI2  HN3   N3   C4    125.11  3.000
 MI2  HN3   N3   C2    124.88  3.000
 MI2  C4    N3   C2    109.82  3.000
 MI2  C6    C4   C5    128.54  3.000
 MI2  C6    C4   N3    122.61  3.000
 MI2  C5    C4   N3    108.85  3.000
 MI2  H5    C5   C4    125.64  3.000
 MI2  H5    C5   C1    127.18  3.000
 MI2  C4    C5   C1    107.17  3.000
 MI2  C11   C6   C7    119.66  3.000
 MI2  C11   C6   C4    122.34  3.000
 MI2  C7    C6   C4    117.98  3.000
 MI2  H7    C7   C8    119.78  3.000
 MI2  H7    C7   C6    119.06  3.000
 MI2  C8    C7   C6    121.16  3.000
 MI2  H8    C8   C9    120.54  3.000
 MI2  H8    C8   C7    120.04  3.000
 MI2  C9    C8   C7    119.42  3.000
 MI2  H9    C9   C10   119.91  3.000
 MI2  H9    C9   C8    120.37  3.000
 MI2  C10   C9   C8    119.72  3.000
 MI2  H10   C10  C11   118.83  3.000
 MI2  H10   C10  C9    119.41  3.000
 MI2  C11   C10  C9    121.76  3.000
 MI2  C12   C11  C10   119.27  3.000
 MI2  C12   C11  C6    122.44  3.000
 MI2  C10   C11  C6    118.28  3.000
 MI2  H123  C12  H122  107.86  3.000
 MI2  H123  C12  H121  107.46  3.000
 MI2  H122  C12  H121  106.71  3.000
 MI2  H123  C12  C11   112.05  3.000
 MI2  H122  C12  C11   110.42  3.000
 MI2  H121  C12  C11   112.09  3.000
 MI2  H13   C13  C14   120.97  3.000
 MI2  H13   C13  C2    121.48  3.000
 MI2  C14   C13  C2    117.55  3.000
 MI2  H14   C14  C15   119.47  3.000
 MI2  H14   C14  C13   118.72  3.000
 MI2  C15   C14  C13   121.80  3.000
 MI2  C17   C15  C16   120.87  3.000
 MI2  C17   C15  C14   119.00  3.000
 MI2  C16   C15  C14   120.12  3.000
 MI2  H16   C16  C15   120.70  3.000
 MI2  H16   C16  C1    119.96  3.000
 MI2  C15   C16  C1    119.33  3.000
 MI2  N19   C17  N18   120.04  3.000
 MI2  N19   C17  C15   115.07  3.000
 MI2  N18   C17  C15   124.86  3.000
 MI2  HN18  N18  C17   110.61  3.000
 MI2  H192  N19  H191  114.11  3.000
 MI2  H192  N19  C17   115.91  3.000
 MI2  H191  N19  C17   117.91  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
 MI2  CONST_01  C4    N3   C2   C1     0.00   0.0  0
 MI2  CONST_02  C14   C13  C2   C1     0.00   0.0  0
 MI2  CONST_03  N3    C4   C5   C1     0.00   0.0  0
 MI2  CONST_04  C6    C4   C5   C1   180.00   0.0  0
 MI2  CONST_05  C14   C15  C16  C1     0.00   0.0  0
 MI2  CONST_06  C4    C5   C1   C2     0.00   0.0  0
 MI2  CONST_07  C15   C16  C1   C2     0.00   0.0  0
 MI2  CONST_08  C5    C4   N3   C2     0.00   0.0  0
 MI2  CONST_09  C6    C4   N3   C2   180.00   0.0  0
 MI2  CONST_10  C15   C14  C13  C2     0.00   0.0  0
 MI2  CONST_11  C5    C1   C2   N3     0.00   0.0  0
 MI2  CONST_12  C16   C1   C2   N3   180.00   0.0  0
 MI2  CONST_13  C14   C13  C2   N3   180.00   0.0  0
 MI2  CONST_16  C13   C2   N3   C4   180.00   0.0  0
 MI2  CONST_17  C16   C1   C5   C4   180.00   0.0  0
 MI2  CONST_18  C8    C7   C6   C4   180.00   0.0  0
 MI2  CONST_19  C10   C11  C6   C4   180.00   0.0  0
 MI2  CONST_20  C13   C2   C1   C5   180.00   0.0  0
 MI2  CONST_21  C15   C16  C1   C5   180.00   0.0  0
 MI2  CONST_24  C9    C8   C7   C6     0.00   0.0  0
 MI2  CONST_25  C9    C10  C11  C6     0.00   0.0  0
 MI2  CONST_26  C10   C11  C6   C7     0.00   0.0  0
 MI2  CONST_27  C10   C9   C8   C7     0.00   0.0  0
 MI2  CONST_28  C11   C6   C7   C8     0.00   0.0  0
 MI2  CONST_29  C11   C10  C9   C8     0.00   0.0  0
 MI2  CONST_30  C16   C1   C2   C13    0.00   0.0  0
 MI2  CONST_31  C16   C15  C14  C13    0.00   0.0  0
 MI2  CONST_32  C17   C15  C16  C1   180.00   0.0  0
 MI2  CONST_33  C12   C11  C6   C4     0.00   0.0  0
 MI2  CONST_34  C12   C11  C6   C7   180.00   0.0  0
 MI2  CONST_35  C12   C11  C10  C9   180.00   0.0  0
 MI2  CONST_36  C17   C15  C14  C13  180.00   0.0  0
 MI2  CONST_37  HN3   N3   C2   C1   180.00   0.0  0
 MI2  CONST_38  H13   C13  C2   C1   180.00   0.0  0
 MI2  CONST_39  H5    C5   C1   C2   180.00   0.0  0
 MI2  CONST_40  H16   C16  C1   C2   180.00   0.0  0
 MI2  CONST_41  H14   C14  C13  C2   180.00   0.0  0
 MI2  CONST_42  H7    C7   C6   C4     0.00   0.0  0
 MI2  CONST_43  H8    C8   C7   C6   180.00   0.0  0
 MI2  CONST_44  H10   C10  C11  C6   180.00   0.0  0
 MI2  CONST_45  H9    C9   C8   C7   180.00   0.0  0
 MI2  CONST_46  HN18  N18  C17  C15    0.00   0.0  0
 MI2  CONST_48  H192  N19  C17  C15  180.00   0.0  0
 MI2  Var_01    N18   C17  C15  C14  -33.33  30.0  2
 MI2  Var_02    H121  C12  C11  C6   -81.00  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
 MI2  plan-1  C4    0.020
 MI2  plan-1  C6    0.020
 MI2  plan-1  C7    0.020
 MI2  plan-1  C8    0.020
 MI2  plan-1  C9    0.020
 MI2  plan-1  C10   0.020
 MI2  plan-1  C11   0.020
 MI2  plan-1  C12   0.020
 MI2  plan-1  H7    0.020
 MI2  plan-1  H8    0.020
 MI2  plan-1  H9    0.020
 MI2  plan-1  H10   0.020
 MI2  plan-2  C1    0.020
 MI2  plan-2  C2    0.020
 MI2  plan-2  N3    0.020
 MI2  plan-2  C4    0.020
 MI2  plan-2  C5    0.020
 MI2  plan-2  C6    0.020
 MI2  plan-2  C13   0.020
 MI2  plan-2  C14   0.020
 MI2  plan-2  C15   0.020
 MI2  plan-2  C16   0.020
 MI2  plan-2  C17   0.020
 MI2  plan-2  HN3   0.020
 MI2  plan-2  H5    0.020
 MI2  plan-2  H13   0.020
 MI2  plan-2  H14   0.020
 MI2  plan-2  H16   0.020
 MI2  plan-3  C15   0.020
 MI2  plan-3  C17   0.020
 MI2  plan-3  N18   0.020
 MI2  plan-3  N19   0.020
 MI2  plan-3  HN18  0.020
 MI2  plan-3  H191  0.020
 MI2  plan-3  H192  0.020

