# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:57:44 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(3-methylphenyl)-1H-indole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)c2[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
 23M  23M  2-(3-methylphenyl)-1H-indole-5-carboximidamide  ligand  34  19  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_23M
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
 23M  C1    C  CR56  0   0.108  -1.1951  -0.4987   0.0070
 23M  C2    C  CR56  0   0.342  -0.9068   0.8594   0.2705
 23M  N3    N  NR15  0  -0.750   0.4470   0.9925   0.2972
 23M  C4    C  CR5   0   0.368   1.0396  -0.2275   0.0781
 23M  C5    C  CR15  0  -0.457   0.0587  -1.1680  -0.1099
 23M  C6    C  CR6   0   0.078   2.4912  -0.3801   0.0465
 23M  C7    C  CR16  0  -0.340   3.0689  -1.6245   0.2987
 23M  C8    C  CR16  0  -0.222   4.4467  -1.7702   0.2611
 23M  C9    C  CR16  0  -0.306   5.2624  -0.6834  -0.0184
 23M  C10   C  CR6   0   0.119   4.7087   0.5706  -0.2729
 23M  C11   C  CR16  0  -0.370   3.3255   0.7041  -0.2396
 23M  C12   C  CH3   0  -0.724   5.5888   1.7436  -0.5934
 23M  C13   C  CR16  0  -0.299  -1.9134   1.8028   0.4562
 23M  C14   C  CR16  0  -0.317  -3.2200   1.3710   0.3539
 23M  C15   C  CR6   0   0.031  -3.5394   0.0251   0.0759
 23M  C16   C  CR16  0  -0.390  -2.5265  -0.9068  -0.0878
 23M  C17   C  C     0   0.333  -4.9553  -0.4186  -0.0338
 23M  N18   N  N     0  -0.659  -5.2468  -1.6392   0.2143
 23M  N19   N  NH2   0  -0.824  -5.8520   0.5623  -0.3578
 23M  HN3   H  HNR5  0   0.414   0.9365   1.8367   0.5456
 23M  H5    H  HCR5  0   0.253   0.2156  -2.2113  -0.3349
 23M  H7    H  HCR6  0   0.252   2.4440  -2.4743   0.5417
 23M  H8    H  HCR6  0   0.258   4.8879  -2.7375   0.4640
 23M  H9    H  HCR6  0   0.251   6.3386  -0.8088  -0.0377
 23M  H11   H  HCR6  0   0.245   2.8968   1.6747  -0.4630
 23M  H121  H  HCH3  0   0.250   6.0794   1.6143  -1.5597
 23M  H122  H  HCH3  0   0.244   5.0211   2.6723  -0.6326
 23M  H123  H  HCH3  0   0.247   6.3760   1.8620   0.1519
 23M  H13   H  HCR6  0   0.263  -1.6855   2.8377   0.6759
 23M  H14   H  HCR6  0   0.253  -4.0106   2.0915   0.5164
 23M  H16   H  HCR6  0   0.246  -2.7739  -1.9396  -0.2964
 23M  HN18  H  H     0   0.319  -6.2358  -1.8167   0.0594
 23M  H191  H  HNH2  0   0.392  -5.5327   1.3351  -0.9186
 23M  H192  H  HNH2  0   0.388  -6.7897   0.2691  -0.5822

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
 23M  C1   C2    aromatic  1.413  0.020  1.413
 23M  C1   C5    aromatic  1.426  0.020  1.426
 23M  C1   C16   aromatic  1.396  0.020  1.396
 23M  C2   N3    aromatic  1.361  0.020  1.361
 23M  C2   C13   aromatic  1.392  0.020  1.392
 23M  N3   C4    aromatic  1.374  0.020  1.374
 23M  N3   HN3   single    0.860  0.020  1.020
 23M  C4   C5    aromatic  1.372  0.020  1.372
 23M  C4   C6    single    1.460  0.020  1.460
 23M  C5   H5    single    0.930  0.020  1.080
 23M  C6   C7    aromatic  1.395  0.020  1.395
 23M  C6   C11   aromatic  1.398  0.020  1.398
 23M  C7   C8    aromatic  1.386  0.020  1.386
 23M  C7   H7    single    0.930  0.020  1.080
 23M  C8   C9    aromatic  1.387  0.020  1.387
 23M  C8   H8    single    0.930  0.020  1.080
 23M  C9   C10   aromatic  1.394  0.020  1.394
 23M  C9   H9    single    0.930  0.020  1.080
 23M  C10  C11   aromatic  1.390  0.020  1.390
 23M  C10  C12   single    1.501  0.020  1.501
 23M  C11  H11   single    0.930  0.020  1.080
 23M  C12  H121  single    0.970  0.020  1.090
 23M  C12  H122  single    0.970  0.020  1.090
 23M  C12  H123  single    0.970  0.020  1.090
 23M  C13  C14   aromatic  1.380  0.020  1.380
 23M  C13  H13   single    0.930  0.020  1.080
 23M  C14  C15   aromatic  1.411  0.020  1.411
 23M  C14  H14   single    0.930  0.020  1.080
 23M  C15  C16   aromatic  1.386  0.020  1.386
 23M  C15  C17   single    1.488  0.020  1.488
 23M  C16  H16   single    0.930  0.020  1.080
 23M  C17  N18   double    1.279  0.020  1.279
 23M  C17  N19   single    1.368  0.020  1.368
 23M  N18  HN18  single    0.890  0.020  1.040
 23M  N19  H191  single    0.890  0.020  1.040
 23M  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
 23M  C16   C1   C5    134.10  3.000
 23M  C16   C1   C2    119.23  3.000
 23M  C5    C1   C2    106.68  3.000
 23M  C13   C2   N3    130.59  3.000
 23M  C13   C2   C1    121.92  3.000
 23M  N3    C2   C1    107.50  3.000
 23M  HN3   N3   C4    125.04  3.000
 23M  HN3   N3   C2    124.79  3.000
 23M  C4    N3   C2    109.82  3.000
 23M  C6    C4   C5    129.51  3.000
 23M  C6    C4   N3    121.67  3.000
 23M  C5    C4   N3    108.80  3.000
 23M  H5    C5   C4    125.99  3.000
 23M  H5    C5   C1    126.79  3.000
 23M  C4    C5   C1    107.19  3.000
 23M  C11   C6   C7    118.80  3.000
 23M  C11   C6   C4    121.12  3.000
 23M  C7    C6   C4    120.07  3.000
 23M  H7    C7   C8    119.83  3.000
 23M  H7    C7   C6    120.12  3.000
 23M  C8    C7   C6    120.04  3.000
 23M  H8    C8   C9    119.87  3.000
 23M  H8    C8   C7    119.61  3.000
 23M  C9    C8   C7    120.51  3.000
 23M  H9    C9   C10   119.69  3.000
 23M  H9    C9   C8    119.79  3.000
 23M  C10   C9   C8    120.52  3.000
 23M  C12   C10  C11   120.89  3.000
 23M  C12   C10  C9    120.60  3.000
 23M  C11   C10  C9    118.51  3.000
 23M  H11   C11  C10   118.33  3.000
 23M  H11   C11  C6    120.04  3.000
 23M  C10   C11  C6    121.62  3.000
 23M  H123  C12  H122  107.96  3.000
 23M  H123  C12  H121  107.06  3.000
 23M  H122  C12  H121  107.67  3.000
 23M  H123  C12  C10   111.23  3.000
 23M  H122  C12  C10   111.62  3.000
 23M  H121  C12  C10   111.10  3.000
 23M  H13   C13  C14   120.91  3.000
 23M  H13   C13  C2    121.53  3.000
 23M  C14   C13  C2    117.57  3.000
 23M  H14   C14  C15   119.96  3.000
 23M  H14   C14  C13   118.19  3.000
 23M  C15   C14  C13   121.83  3.000
 23M  C17   C15  C16   119.09  3.000
 23M  C17   C15  C14   120.96  3.000
 23M  C16   C15  C14   119.95  3.000
 23M  H16   C16  C15   119.82  3.000
 23M  H16   C16  C1    120.68  3.000
 23M  C15   C16  C1    119.50  3.000
 23M  N19   C17  N18   125.51  3.000
 23M  N19   C17  C15   115.31  3.000
 23M  N18   C17  C15   119.15  3.000
 23M  HN18  N18  C17   111.02  3.000
 23M  H192  N19  H191  113.23  3.000
 23M  H192  N19  C17   117.00  3.000
 23M  H191  N19  C17   118.32  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
 23M  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 23M  CONST_02  C14   C13  C2   C1      0.00   0.0  0
 23M  CONST_03  N3    C4   C5   C1      0.00   0.0  0
 23M  CONST_04  C6    C4   C5   C1    180.00   0.0  0
 23M  CONST_05  C14   C15  C16  C1      0.00   0.0  0
 23M  CONST_06  C4    C5   C1   C2      0.00   0.0  0
 23M  CONST_07  C15   C16  C1   C2      0.00   0.0  0
 23M  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 23M  CONST_09  C6    C4   N3   C2    180.00   0.0  0
 23M  CONST_10  C15   C14  C13  C2      0.00   0.0  0
 23M  CONST_11  C5    C1   C2   N3      0.00   0.0  0
 23M  CONST_12  C16   C1   C2   N3    180.00   0.0  0
 23M  CONST_13  C14   C13  C2   N3    180.00   0.0  0
 23M  CONST_16  C13   C2   N3   C4    180.00   0.0  0
 23M  CONST_17  C16   C1   C5   C4    180.00   0.0  0
 23M  CONST_18  C8    C7   C6   C4    180.00   0.0  0
 23M  CONST_19  C10   C11  C6   C4    180.00   0.0  0
 23M  CONST_20  C13   C2   C1   C5    180.00   0.0  0
 23M  CONST_21  C15   C16  C1   C5    180.00   0.0  0
 23M  CONST_24  C9    C8   C7   C6      0.00   0.0  0
 23M  CONST_25  C9    C10  C11  C6      0.00   0.0  0
 23M  CONST_26  C10   C11  C6   C7      0.00   0.0  0
 23M  CONST_27  C10   C9   C8   C7      0.00   0.0  0
 23M  CONST_28  C11   C6   C7   C8      0.00   0.0  0
 23M  CONST_29  C11   C10  C9   C8      0.00   0.0  0
 23M  CONST_30  C16   C1   C2   C13     0.00   0.0  0
 23M  CONST_31  C16   C15  C14  C13     0.00   0.0  0
 23M  CONST_32  C17   C15  C16  C1    180.00   0.0  0
 23M  CONST_33  C12   C10  C11  C6    180.00   0.0  0
 23M  CONST_34  C12   C10  C9   C8    180.00   0.0  0
 23M  CONST_35  C17   C15  C14  C13   180.00   0.0  0
 23M  CONST_36  HN3   N3   C2   C1    180.00   0.0  0
 23M  CONST_37  H13   C13  C2   C1    180.00   0.0  0
 23M  CONST_38  H5    C5   C1   C2    180.00   0.0  0
 23M  CONST_39  H16   C16  C1   C2    180.00   0.0  0
 23M  CONST_40  H14   C14  C13  C2    180.00   0.0  0
 23M  CONST_41  H7    C7   C6   C4      0.00   0.0  0
 23M  CONST_42  H11   C11  C6   C4      0.00   0.0  0
 23M  CONST_43  H8    C8   C7   C6    180.00   0.0  0
 23M  CONST_44  H9    C9   C8   C7    180.00   0.0  0
 23M  CONST_45  HN18  N18  C17  C15   180.00   0.0  0
 23M  CONST_47  H192  N19  C17  C15   180.00   0.0  0
 23M  Var_01    N18   C17  C15  C14  -153.98  30.0  2
 23M  Var_02    H121  C12  C10  C9     67.54  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
 23M  plan-1  C4    0.020
 23M  plan-1  C6    0.020
 23M  plan-1  C7    0.020
 23M  plan-1  C8    0.020
 23M  plan-1  C9    0.020
 23M  plan-1  C10   0.020
 23M  plan-1  C11   0.020
 23M  plan-1  C12   0.020
 23M  plan-1  H7    0.020
 23M  plan-1  H8    0.020
 23M  plan-1  H9    0.020
 23M  plan-1  H11   0.020
 23M  plan-2  C1    0.020
 23M  plan-2  C2    0.020
 23M  plan-2  N3    0.020
 23M  plan-2  C4    0.020
 23M  plan-2  C5    0.020
 23M  plan-2  C6    0.020
 23M  plan-2  C13   0.020
 23M  plan-2  C14   0.020
 23M  plan-2  C15   0.020
 23M  plan-2  C16   0.020
 23M  plan-2  C17   0.020
 23M  plan-2  HN3   0.020
 23M  plan-2  H5    0.020
 23M  plan-2  H13   0.020
 23M  plan-2  H14   0.020
 23M  plan-2  H16   0.020
 23M  plan-3  C15   0.020
 23M  plan-3  C17   0.020
 23M  plan-3  N18   0.020
 23M  plan-3  N19   0.020
 23M  plan-3  HN18  0.020
 23M  plan-3  H191  0.020
 23M  plan-3  H192  0.020

