# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:33:53 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-methyl-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2[nH]ccc2c1
#
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
 5MI  5MI  '5-methyl-1H-indole       '  ligand  19  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5MI
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
 5MI  C5    C  CR6   0   0.086  -1.8519   0.2127   0.0209
 5MI  C6    C  CR16  0  -0.318  -1.5276  -1.1601   0.0756
 5MI  C7    C  CR16  0  -0.291  -0.2232  -1.6091   0.0749
 5MI  C8    C  CR56  0   0.325   0.7895  -0.6520   0.0182
 5MI  N1    N  NR15  0  -0.677   2.1480  -0.7905   0.0034
 5MI  C4    C  CR16  0  -0.403  -0.8349   1.1476  -0.0357
 5MI  C9    C  CR56  0   0.075   0.5031   0.7285  -0.0375
 5MI  C3    C  CR15  0  -0.424   1.7601   1.4076  -0.0850
 5MI  C2    C  CR15  0  -0.031   2.7277   0.4435  -0.0578
 5MI  CAJ   C  CH3   0  -0.722  -3.2951   0.6338   0.0245
 5MI  H6    H  HCR6  0   0.241  -2.3311  -1.8860   0.1186
 5MI  H4    H  HCR6  0   0.236  -1.0704   2.2052  -0.0780
 5MI  HAJ1  H  HCH3  0   0.238  -3.8113   0.2861   0.9214
 5MI  HAJ2  H  HCH3  0   0.239  -3.3937   1.7184  -0.0129
 5MI  HAJ3  H  HCH3  0   0.238  -3.8347   0.2232  -0.8311
 5MI  H7    H  HCR6  0   0.256   0.0013  -2.6676   0.1166
 5MI  H1    H  HNR5  0   0.408   2.6501  -1.6614   0.0401
 5MI  H2    H  HCR5  0   0.279   3.8012   0.5428  -0.0738
 5MI  H3    H  HCR5  0   0.245   1.9258   2.4720  -0.1350

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
 5MI  C5   C6    aromatic  1.412  0.020  1.412
 5MI  C5   C4    aromatic  1.383  0.020  1.383
 5MI  C5   CAJ   single    1.503  0.020  1.503
 5MI  C6   C7    aromatic  1.380  0.020  1.380
 5MI  C7   C8    aromatic  1.394  0.020  1.394
 5MI  C8   N1    aromatic  1.366  0.020  1.366
 5MI  C8   C9    aromatic  1.411  0.020  1.411
 5MI  N1   C2    aromatic  1.365  0.020  1.365
 5MI  C4   C9    aromatic  1.402  0.020  1.402
 5MI  C9   C3    aromatic  1.429  0.020  1.429
 5MI  C3   C2    aromatic  1.366  0.020  1.366
 5MI  C6   H6    single    0.930  0.020  1.080
 5MI  C4   H4    single    0.930  0.020  1.080
 5MI  CAJ  HAJ1  single    0.970  0.020  1.090
 5MI  CAJ  HAJ2  single    0.970  0.020  1.090
 5MI  CAJ  HAJ3  single    0.970  0.020  1.090
 5MI  C7   H7    single    0.930  0.020  1.080
 5MI  N1   H1    single    0.860  0.020  1.020
 5MI  C2   H2    single    0.930  0.020  1.080
 5MI  C3   H3    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
 5MI  CAJ   C5   C4    121.12  3.000
 5MI  CAJ   C5   C6    119.53  3.000
 5MI  C4    C5   C6    119.35  3.000
 5MI  H6    C6   C7    118.89  3.000
 5MI  H6    C6   C5    118.86  3.000
 5MI  C7    C6   C5    122.25  3.000
 5MI  H7    C7   C8    121.46  3.000
 5MI  H7    C7   C6    120.94  3.000
 5MI  C8    C7   C6    117.60  3.000
 5MI  C9    C8   N1    107.50  3.000
 5MI  C9    C8   C7    121.72  3.000
 5MI  N1    C8   C7    130.79  3.000
 5MI  H1    N1   C2    124.92  3.000
 5MI  H1    N1   C8    125.72  3.000
 5MI  C2    N1   C8    109.35  3.000
 5MI  H4    C4   C9    119.92  3.000
 5MI  H4    C4   C5    120.09  3.000
 5MI  C9    C4   C5    119.99  3.000
 5MI  C3    C9   C4    134.20  3.000
 5MI  C3    C9   C8    106.72  3.000
 5MI  C4    C9   C8    119.08  3.000
 5MI  H3    C3   C2    126.06  3.000
 5MI  H3    C3   C9    127.27  3.000
 5MI  C2    C3   C9    106.67  3.000
 5MI  H2    C2   C3    129.79  3.000
 5MI  H2    C2   N1    120.45  3.000
 5MI  C3    C2   N1    109.76  3.000
 5MI  HAJ3  CAJ  HAJ2  107.62  3.000
 5MI  HAJ3  CAJ  HAJ1  106.88  3.000
 5MI  HAJ2  CAJ  HAJ1  107.61  3.000
 5MI  HAJ3  CAJ  C5    111.54  3.000
 5MI  HAJ2  CAJ  C5    111.44  3.000
 5MI  HAJ1  CAJ  C5    111.51  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
 5MI  CONST_01  C8    C7   C6  C5    0.00   0.0  0
 5MI  CONST_02  C8    C9   C4  C5    0.00   0.0  0
 5MI  CONST_03  C3    C9   C4  C5  180.00   0.0  0
 5MI  CONST_04  C9    C4   C5  C6    0.00   0.0  0
 5MI  CONST_05  N1    C8   C7  C6  180.00   0.0  0
 5MI  CONST_06  C9    C8   C7  C6    0.00   0.0  0
 5MI  CONST_07  C4    C5   C6  C7    0.00   0.0  0
 5MI  CONST_08  C2    N1   C8  C7  180.00   0.0  0
 5MI  CONST_09  C4    C9   C8  C7    0.00   0.0  0
 5MI  CONST_10  C3    C9   C8  C7  180.00   0.0  0
 5MI  CONST_11  C3    C2   N1  C8    0.00   0.0  0
 5MI  CONST_12  C2    C3   C9  C8    0.00   0.0  0
 5MI  CONST_13  C4    C9   C8  N1  180.00   0.0  0
 5MI  CONST_14  C3    C9   C8  N1    0.00   0.0  0
 5MI  CONST_15  C9    C3   C2  N1    0.00   0.0  0
 5MI  CONST_16  C2    C3   C9  C4  180.00   0.0  0
 5MI  CONST_17  C2    N1   C8  C9    0.00   0.0  0
 5MI  CONST_18  CAJ   C5   C6  C7  180.00   0.0  0
 5MI  CONST_19  CAJ   C5   C4  C9  180.00   0.0  0
 5MI  CONST_20  H7    C7   C6  C5  180.00   0.0  0
 5MI  CONST_21  H4    C4   C5  C6  180.00   0.0  0
 5MI  CONST_22  H1    N1   C8  C7    0.00   0.0  0
 5MI  CONST_23  H6    C6   C7  C8  180.00   0.0  0
 5MI  CONST_24  H2    C2   N1  C8  180.00   0.0  0
 5MI  CONST_25  H3    C3   C9  C8  180.00   0.0  0
 5MI  Var_01    HAJ1  CAJ  C5  C6   59.27  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
 5MI  plan-1  C5   0.020
 5MI  plan-1  C6   0.020
 5MI  plan-1  C7   0.020
 5MI  plan-1  C8   0.020
 5MI  plan-1  N1   0.020
 5MI  plan-1  C4   0.020
 5MI  plan-1  C9   0.020
 5MI  plan-1  C3   0.020
 5MI  plan-1  C2   0.020
 5MI  plan-1  CAJ  0.020
 5MI  plan-1  H6   0.020
 5MI  plan-1  H4   0.020
 5MI  plan-1  H7   0.020
 5MI  plan-1  H1   0.020
 5MI  plan-1  H2   0.020
 5MI  plan-1  H3   0.020

