# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:25:01 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-methyl-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ccccc2c1
#
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
 2MI  2MI  '2-methyl-1H-indole       '  ligand  19  10  .  2022-07-22  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_2MI
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
 2MI  CAJ   C  CH3   0  -0.740   3.4426   0.0397  -0.0328
 2MI  CAG   C  CR5   0   0.335   1.9618  -0.0832  -0.0254
 2MI  CAC   C  CR15  0  -0.460   1.1732  -1.2004  -0.0637
 2MI  CAA   C  CR56  0   0.075  -0.1871  -0.7619  -0.0317
 2MI  CAD   C  CR16  0  -0.352  -1.4271  -1.4104  -0.0481
 2MI  CAH   C  CR16  0  -0.273  -2.5821  -0.6517  -0.0091
 2MI  CAI   C  CR16  0  -0.287  -2.5264   0.7499   0.0476
 2MI  CAF   C  CR16  0  -0.313  -1.3157   1.4188   0.0661
 2MI  CAB   C  CR56  0   0.333  -0.1551   0.6499   0.0266
 2MI  NAE   N  NR15  0  -0.716   1.1581   1.0254   0.0301
 2MI  HAJ1  H  HCH3  0   0.253   3.8119   0.4892   0.8909
 2MI  HAJ2  H  HCH3  0   0.256   3.9028  -0.9403  -0.1374
 2MI  HAJ3  H  HCH3  0   0.252   3.7879   0.6643  -0.8587
 2MI  HAC   H  HCR5  0   0.244   1.5279  -2.2184  -0.1130
 2MI  HAD   H  HCR6  0   0.242  -1.4820  -2.4914  -0.0904
 2MI  HAH   H  HCR6  0   0.243  -3.5470  -1.1426  -0.0231
 2MI  HAI   H  HCR6  0   0.246  -3.4469   1.3187   0.0766
 2MI  HAF   H  HCR6  0   0.256  -1.2739   2.4999   0.1089
 2MI  HAE   H  HNR5  0   0.405   1.4897   1.9755   0.0639

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
 2MI  CAJ  CAG   single    1.486  0.020  1.486
 2MI  CAJ  HAJ1  single    0.970  0.020  1.090
 2MI  CAJ  HAJ2  single    0.970  0.020  1.090
 2MI  CAJ  HAJ3  single    0.970  0.020  1.090
 2MI  CAG  CAC   aromatic  1.368  0.020  1.368
 2MI  CAG  NAE   aromatic  1.370  0.020  1.370
 2MI  CAC  CAA   aromatic  1.430  0.020  1.430
 2MI  CAC  HAC   single    0.930  0.020  1.080
 2MI  CAA  CAD   aromatic  1.399  0.020  1.399
 2MI  CAA  CAB   aromatic  1.413  0.020  1.413
 2MI  CAD  CAH   aromatic  1.382  0.020  1.382
 2MI  CAD  HAD   single    0.930  0.020  1.080
 2MI  CAH  CAI   aromatic  1.404  0.020  1.404
 2MI  CAH  HAH   single    0.930  0.020  1.080
 2MI  CAI  CAF   aromatic  1.383  0.020  1.383
 2MI  CAI  HAI   single    0.930  0.020  1.080
 2MI  CAF  CAB   aromatic  1.393  0.020  1.393
 2MI  CAF  HAF   single    0.930  0.020  1.080
 2MI  CAB  NAE   aromatic  1.366  0.020  1.366
 2MI  NAE  HAE   single    0.860  0.020  1.020

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
 2MI  HAJ3  CAJ  HAJ2  107.99  3.000
 2MI  HAJ3  CAJ  HAJ1  107.32  3.000
 2MI  HAJ2  CAJ  HAJ1  108.01  3.000
 2MI  HAJ3  CAJ  CAG   111.49  3.000
 2MI  HAJ2  CAJ  CAG   110.34  3.000
 2MI  HAJ1  CAJ  CAG   111.53  3.000
 2MI  NAE   CAG  CAC   108.89  3.000
 2MI  NAE   CAG  CAJ   121.18  3.000
 2MI  CAC   CAG  CAJ   129.93  3.000
 2MI  HAC   CAC  CAA   127.10  3.000
 2MI  HAC   CAC  CAG   125.60  3.000
 2MI  CAA   CAC  CAG   107.30  3.000
 2MI  CAB   CAA  CAD   118.91  3.000
 2MI  CAB   CAA  CAC   106.61  3.000
 2MI  CAD   CAA  CAC   134.49  3.000
 2MI  HAD   CAD  CAH   120.43  3.000
 2MI  HAD   CAD  CAA   120.52  3.000
 2MI  CAH   CAD  CAA   119.06  3.000
 2MI  HAH   CAH  CAI   119.25  3.000
 2MI  HAH   CAH  CAD   119.70  3.000
 2MI  CAI   CAH  CAD   121.06  3.000
 2MI  HAI   CAI  CAF   119.33  3.000
 2MI  HAI   CAI  CAH   119.47  3.000
 2MI  CAF   CAI  CAH   121.20  3.000
 2MI  HAF   CAF  CAB   121.34  3.000
 2MI  HAF   CAF  CAI   121.14  3.000
 2MI  CAB   CAF  CAI   117.52  3.000
 2MI  NAE   CAB  CAF   130.49  3.000
 2MI  NAE   CAB  CAA   107.25  3.000
 2MI  CAF   CAB  CAA   122.26  3.000
 2MI  HAE   NAE  CAB   125.18  3.000
 2MI  HAE   NAE  CAG   124.86  3.000
 2MI  CAB   NAE  CAG   109.96  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
 2MI  CONST_01  CAD   CAA  CAC  CAG   180.00   0.0  0
 2MI  CONST_02  CAB   CAA  CAC  CAG     0.00   0.0  0
 2MI  CONST_03  CAA   CAB  NAE  CAG     0.00   0.0  0
 2MI  CONST_04  CAF   CAB  NAE  CAG   180.00   0.0  0
 2MI  CONST_05  CAB   NAE  CAG  CAC     0.00   0.0  0
 2MI  CONST_06  CAH   CAD  CAA  CAC   180.00   0.0  0
 2MI  CONST_07  CAF   CAB  CAA  CAC   180.00   0.0  0
 2MI  CONST_08  NAE   CAB  CAA  CAC     0.00   0.0  0
 2MI  CONST_09  NAE   CAG  CAC  CAA     0.00   0.0  0
 2MI  CONST_10  CAI   CAH  CAD  CAA     0.00   0.0  0
 2MI  CONST_11  CAI   CAF  CAB  CAA     0.00   0.0  0
 2MI  CONST_12  CAF   CAB  CAA  CAD     0.00   0.0  0
 2MI  CONST_13  NAE   CAB  CAA  CAD   180.00   0.0  0
 2MI  CONST_14  CAF   CAI  CAH  CAD     0.00   0.0  0
 2MI  CONST_15  CAB   CAA  CAD  CAH     0.00   0.0  0
 2MI  CONST_16  CAB   CAF  CAI  CAH     0.00   0.0  0
 2MI  CONST_17  NAE   CAB  CAF  CAI   180.00   0.0  0
 2MI  CONST_18  CAA   CAC  CAG  CAJ   180.00   0.0  0
 2MI  CONST_19  CAB   NAE  CAG  CAJ   180.00   0.0  0
 2MI  CONST_20  HAE   NAE  CAG  CAC   180.00   0.0  0
 2MI  CONST_21  HAD   CAD  CAA  CAC     0.00   0.0  0
 2MI  CONST_22  HAH   CAH  CAD  CAA   180.00   0.0  0
 2MI  CONST_23  HAF   CAF  CAB  CAA   180.00   0.0  0
 2MI  CONST_24  HAC   CAC  CAA  CAD     0.00   0.0  0
 2MI  CONST_25  HAI   CAI  CAH  CAD   180.00   0.0  0
 2MI  Var_01    HAJ1  CAJ  CAG  CAC  -116.60  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
 2MI  plan-1  CAJ  0.020
 2MI  plan-1  CAG  0.020
 2MI  plan-1  CAC  0.020
 2MI  plan-1  CAA  0.020
 2MI  plan-1  CAD  0.020
 2MI  plan-1  CAH  0.020
 2MI  plan-1  CAI  0.020
 2MI  plan-1  CAF  0.020
 2MI  plan-1  CAB  0.020
 2MI  plan-1  NAE  0.020
 2MI  plan-1  HAC  0.020
 2MI  plan-1  HAD  0.020
 2MI  plan-1  HAH  0.020
 2MI  plan-1  HAI  0.020
 2MI  plan-1  HAF  0.020
 2MI  plan-1  HAE  0.020

