# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:40:44 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(C#N)c(C)c1
#
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
 M2H  M2H  3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile  ligand  17  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M2H
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
 M2H  C01  C  CH3   0  -0.738   3.0551   0.7446   0.0122
 M2H  C02  C  CR5   0   0.343   1.6646   0.2200   0.0218
 M2H  C03  C  CR15  0  -0.421   1.2072  -1.0845   0.0572
 M2H  C04  C  CR5   0   0.065  -0.2013  -1.0620   0.0628
 M2H  C05  C  CH3   0  -0.739  -1.1273  -2.2284   0.0946
 M2H  C06  C  CR5   0   0.229  -0.5581   0.2758   0.0296
 M2H  N07  N  NR15  0  -0.653   0.5876   1.0312   0.0049
 M2H  C08  C  CSP   0  -0.012  -1.8429   0.8426   0.0152
 M2H  N09  N  NS    0  -0.267  -2.9098   1.2878   0.0063
 M2H  H1   H  HCH3  0   0.257   3.2252   1.4171  -0.8298
 M2H  H2   H  HCH3  0   0.258   3.2801   1.2989   0.9249
 M2H  H3   H  HCH3  0   0.259   3.7636  -0.0770  -0.0639
 M2H  H4   H  HCR5  0   0.254   1.8349  -1.9623   0.0764
 M2H  H5   H  HCH3  0   0.251  -0.9749  -2.8763  -0.7693
 M2H  H6   H  HCH3  0   0.251  -0.9650  -2.8371   0.9847
 M2H  H7   H  HCH3  0   0.242  -2.1713  -1.9174   0.0939
 M2H  H8   H  HNR5  0   0.422   0.6166   2.0384  -0.0178

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
 M2H  C05  C04  single    1.490  0.020  1.490
 M2H  N09  C08  triple    1.156  0.020  1.156
 M2H  C08  C06  single    1.404  0.020  1.404
 M2H  C04  C06  aromatic  1.385  0.020  1.385
 M2H  C04  C03  aromatic  1.409  0.020  1.409
 M2H  C06  N07  aromatic  1.373  0.020  1.373
 M2H  C03  C02  aromatic  1.383  0.020  1.383
 M2H  N07  C02  aromatic  1.348  0.020  1.348
 M2H  C02  C01  single    1.486  0.020  1.486
 M2H  C01  H1   single    0.970  0.020  1.090
 M2H  C01  H2   single    0.970  0.020  1.090
 M2H  C01  H3   single    0.970  0.020  1.090
 M2H  C03  H4   single    0.930  0.020  1.080
 M2H  C05  H5   single    0.970  0.020  1.090
 M2H  C05  H6   single    0.970  0.020  1.090
 M2H  C05  H7   single    0.970  0.020  1.090
 M2H  N07  H8   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
 M2H  H3   C01  H2   107.93  3.000
 M2H  H3   C01  H1   108.07  3.000
 M2H  H2   C01  H1   107.47  3.000
 M2H  H3   C01  C02  110.08  3.000
 M2H  H2   C01  C02  111.52  3.000
 M2H  H1   C01  C02  111.62  3.000
 M2H  N07  C02  C03  107.68  3.000
 M2H  N07  C02  C01  122.33  3.000
 M2H  C03  C02  C01  129.99  3.000
 M2H  H4   C03  C04  126.47  3.000
 M2H  H4   C03  C02  125.13  3.000
 M2H  C04  C03  C02  108.41  3.000
 M2H  C06  C04  C05  126.63  3.000
 M2H  C06  C04  C03  105.84  3.000
 M2H  C05  C04  C03  127.53  3.000
 M2H  H7   C05  H6   107.62  3.000
 M2H  H7   C05  H5   107.64  3.000
 M2H  H6   C05  H5   107.11  3.000
 M2H  H7   C05  C04  111.85  3.000
 M2H  H6   C05  C04  111.22  3.000
 M2H  H5   C05  C04  111.18  3.000
 M2H  C08  C06  N07  122.78  3.000
 M2H  N07  C06  C04  108.48  3.000
 M2H  C08  C06  C04  128.75  3.000
 M2H  H8   N07  C06  125.06  3.000
 M2H  H8   N07  C02  125.34  3.000
 M2H  C06  N07  C02  109.60  3.000
 M2H  N09  C08  C06  180.00  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
 M2H  CONST_01  C06  C04  C03  C02    0.00   0.0  0
 M2H  CONST_02  C04  C06  N07  C02    0.00   0.0  0
 M2H  CONST_03  N07  C06  C04  C03    0.00   0.0  0
 M2H  CONST_04  C06  N07  C02  C03    0.00   0.0  0
 M2H  CONST_05  N07  C02  C03  C04    0.00   0.0  0
 M2H  CONST_06  C04  C03  C02  C01  180.00   0.0  0
 M2H  CONST_07  C06  N07  C02  C01  180.00   0.0  0
 M2H  CONST_08  C05  C04  C03  C02  180.00   0.0  0
 M2H  CONST_09  C08  C06  N07  C02  180.00   0.0  0
 M2H  CONST_10  C08  C06  C04  C03  180.00   0.0  0
 M2H  CONST_11  N07  C06  C04  C05  180.00   0.0  0
 M2H  CONST_12  H8   N07  C02  C03  180.00   0.0  0
 M2H  CONST_13  H4   C03  C04  C06  180.00   0.0  0
 M2H  Var_01    H5   C05  C04  C03  -59.74  30.0  2
 M2H  Var_02    H1   C01  C02  C03  125.74  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
 M2H  plan-1  C01  0.020
 M2H  plan-1  C02  0.020
 M2H  plan-1  C03  0.020
 M2H  plan-1  C04  0.020
 M2H  plan-1  C05  0.020
 M2H  plan-1  C06  0.020
 M2H  plan-1  N07  0.020
 M2H  plan-1  C08  0.020
 M2H  plan-1  N09  0.020
 M2H  plan-1  H4   0.020
 M2H  plan-1  H8   0.020

