# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:10:18 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-[1-methyl-3-(1H-pyrrol-1-yl)-1H-pyrazol-4-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2ccccn2)c(n1)n3cccc3
#
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
 8SM  8SM  2-[1-methyl-3-(1H-pyrrol-1-yl)-1H-pyrazol-4-yl]pyridine  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SM
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
 8SM  N1   N  NR5   0  -0.270   2.2172  -1.7722  -0.0794
 8SM  N3   N  N     0  -0.290   2.3747  -0.4541  -0.0132
 8SM  C4   C  CR6   0   0.186  -1.2845  -0.8872  -0.0681
 8SM  C5   C  CR16  0  -0.336  -2.0752  -1.8995   0.4788
 8SM  C6   C  CR16  0  -0.158  -3.4524  -1.7975   0.3872
 8SM  C7   C  CR16  0  -0.324  -4.0034  -0.6840  -0.2304
 8SM  C8   C  CR16  0  -0.085  -3.1361   0.2745  -0.7326
 8SM  C10  C  CR15  0  -0.059   1.7172   2.3463  -0.6023
 8SM  C13  C  CR15  0  -0.048   0.0991   2.0708   0.9145
 8SM  C1   C  CH3   0  -0.505   3.3716  -2.6352  -0.1547
 8SM  C2   C  CR15  0   0.040   0.9300  -2.1327  -0.0728
 8SM  C3   C  CR5   0  -0.173   0.1747  -0.9752  -0.0243
 8SM  N2   N  N     0  -0.412  -1.8155   0.1794  -0.6640
 8SM  C9   C  CR5   0   0.477   1.1545   0.0409   0.0116
 8SM  N4   N  NR5   0  -0.509   0.9805   1.4221   0.0929
 8SM  C11  C  CR15  0  -0.375   1.2970   3.5917  -0.2256
 8SM  C12  C  CR15  0  -0.362   0.2693   3.4163   0.7420
 8SM  H1   H  HCR6  0   0.268  -1.6182  -2.7455   0.9748
 8SM  H2   H  HCR6  0   0.273  -4.0850  -2.5715   0.8012
 8SM  H3   H  HCR6  0   0.270  -5.0732  -0.5566  -0.3201
 8SM  H4   H  HCR6  0   0.260  -3.5277   1.1607  -1.2200
 8SM  H6   H  HCR5  0   0.274  -0.5672   1.5253   1.5613
 8SM  H7   H  HCH3  0   0.265   3.9381  -2.4305  -1.0606
 8SM  H8   H  HCH3  0   0.265   4.0114  -2.4860   0.7123
 8SM  H9   H  HCH3  0   0.262   3.0350  -3.6673  -0.1728
 8SM  H10  H  HCR5  0   0.304   0.6279  -3.1661  -0.1349
 8SM  H11  H  HCR5  0   0.245   1.6797   4.5269  -0.6026
 8SM  H12  H  HCR5  0   0.244  -0.2805   4.1905   1.2534
 8SM  H5   H  HCR5  0   0.274   2.4683   2.0369  -1.3101

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
 8SM  C1   N1   single    1.443  0.020  1.443
 8SM  N1   C2   aromatic  1.337  0.020  1.337
 8SM  N1   N3   aromatic  1.329  0.020  1.329
 8SM  C2   C3   aromatic  1.383  0.020  1.383
 8SM  N3   C9   aromatic  1.317  0.020  1.317
 8SM  C3   C4   single    1.463  0.020  1.463
 8SM  C3   C9   aromatic  1.412  0.020  1.412
 8SM  N2   C4   aromatic  1.332  0.020  1.332
 8SM  N2   C8   aromatic  1.326  0.020  1.326
 8SM  C4   C5   aromatic  1.396  0.020  1.396
 8SM  C8   C7   aromatic  1.387  0.020  1.387
 8SM  C9   N4   single    1.395  0.020  1.395
 8SM  C5   C6   aromatic  1.384  0.020  1.384
 8SM  C7   C6   aromatic  1.387  0.020  1.387
 8SM  N4   C13  aromatic  1.368  0.020  1.368
 8SM  N4   C10  aromatic  1.371  0.020  1.371
 8SM  C13  C12  aromatic  1.367  0.020  1.367
 8SM  C10  C11  aromatic  1.367  0.020  1.367
 8SM  C12  C11  aromatic  1.422  0.020  1.422
 8SM  C5   H1   single    0.930  0.020  1.080
 8SM  C6   H2   single    0.930  0.020  1.080
 8SM  C7   H3   single    0.930  0.020  1.080
 8SM  C8   H4   single    0.930  0.020  1.080
 8SM  C10  H5   single    0.930  0.020  1.080
 8SM  C13  H6   single    0.930  0.020  1.080
 8SM  C1   H7   single    0.970  0.020  1.090
 8SM  C1   H8   single    0.970  0.020  1.090
 8SM  C1   H9   single    0.970  0.020  1.090
 8SM  C2   H10  single    0.930  0.020  1.080
 8SM  C11  H11  single    0.930  0.020  1.080
 8SM  C12  H12  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
 8SM  C2   N1   C1   127.53  3.000
 8SM  C2   N1   N3   112.42  3.000
 8SM  C1   N1   N3   120.05  3.000
 8SM  C9   N3   N1   105.30  3.000
 8SM  N2   C4   C3   117.34  3.000
 8SM  N2   C4   C5   122.01  3.000
 8SM  C3   C4   C5   120.64  3.000
 8SM  H1   C5   C6   120.55  3.000
 8SM  H1   C5   C4   120.49  3.000
 8SM  C6   C5   C4   118.96  3.000
 8SM  H2   C6   C7   120.81  3.000
 8SM  H2   C6   C5   120.25  3.000
 8SM  C7   C6   C5   118.94  3.000
 8SM  H3   C7   C8   120.49  3.000
 8SM  H3   C7   C6   121.64  3.000
 8SM  C8   C7   C6   117.87  3.000
 8SM  H4   C8   N2   116.20  3.000
 8SM  H4   C8   C7   120.11  3.000
 8SM  N2   C8   C7   123.69  3.000
 8SM  H5   C10  C11  131.05  3.000
 8SM  H5   C10  N4   120.94  3.000
 8SM  C11  C10  N4   108.01  3.000
 8SM  H6   C13  C12  130.64  3.000
 8SM  H6   C13  N4   121.26  3.000
 8SM  C12  C13  N4   108.09  3.000
 8SM  H9   C1   H8   109.03  3.000
 8SM  H9   C1   H7   109.06  3.000
 8SM  H8   C1   H7   109.36  3.000
 8SM  H9   C1   N1   108.74  3.000
 8SM  H8   C1   N1   110.29  3.000
 8SM  H7   C1   N1   110.33  3.000
 8SM  H10  C2   C3   130.62  3.000
 8SM  H10  C2   N1   121.86  3.000
 8SM  C3   C2   N1   107.48  3.000
 8SM  C9   C3   C2   102.96  3.000
 8SM  C9   C3   C4   130.53  3.000
 8SM  C2   C3   C4   126.46  3.000
 8SM  C8   N2   C4   118.53  3.000
 8SM  N4   C9   C3   128.88  3.000
 8SM  N4   C9   N3   119.27  3.000
 8SM  C3   C9   N3   111.84  3.000
 8SM  C9   N4   C13  125.80  3.000
 8SM  C13  N4   C10  109.33  3.000
 8SM  C9   N4   C10  124.82  3.000
 8SM  H11  C11  C12  126.95  3.000
 8SM  H11  C11  C10  125.77  3.000
 8SM  C12  C11  C10  107.28  3.000
 8SM  H12  C12  C11  127.03  3.000
 8SM  H12  C12  C13  125.68  3.000
 8SM  C11  C12  C13  107.29  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
 8SM  CONST_01  C4   C3   C2   N1   180.00   0.0  0
 8SM  CONST_02  C9   C3   C2   N1     0.00   0.0  0
 8SM  CONST_03  C3   C9   N3   N1     0.00   0.0  0
 8SM  CONST_04  N4   C9   N3   N1   180.00   0.0  0
 8SM  CONST_05  C3   C2   N1   N3     0.00   0.0  0
 8SM  CONST_06  C2   C3   C9   N3     0.00   0.0  0
 8SM  CONST_07  C4   C3   C9   N3   180.00   0.0  0
 8SM  CONST_10  N4   C9   C3   C4     0.00   0.0  0
 8SM  CONST_11  C7   C8   N2   C4     0.00   0.0  0
 8SM  CONST_12  C7   C6   C5   C4     0.00   0.0  0
 8SM  CONST_15  C8   N2   C4   C5     0.00   0.0  0
 8SM  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 8SM  CONST_17  C3   C4   C5   C6   180.00   0.0  0
 8SM  CONST_18  N2   C4   C5   C6     0.00   0.0  0
 8SM  CONST_19  N2   C8   C7   C6     0.00   0.0  0
 8SM  CONST_20  C3   C4   N2   C8   180.00   0.0  0
 8SM  CONST_22  C12  C13  N4   C10    0.00   0.0  0
 8SM  CONST_23  C13  C12  C11  C10    0.00   0.0  0
 8SM  CONST_25  C11  C10  N4   C13    0.00   0.0  0
 8SM  CONST_26  C9   N3   N1   C2     0.00   0.0  0
 8SM  CONST_28  N4   C9   C3   C2   180.00   0.0  0
 8SM  CONST_30  C12  C13  N4   C9   180.00   0.0  0
 8SM  CONST_31  C11  C10  N4   C9   180.00   0.0  0
 8SM  CONST_32  C11  C12  C13  N4     0.00   0.0  0
 8SM  CONST_33  C12  C11  C10  N4     0.00   0.0  0
 8SM  CONST_34  C3   C2   N1   C1   180.00   0.0  0
 8SM  CONST_35  C9   N3   N1   C1   180.00   0.0  0
 8SM  CONST_36  H10  C2   N1   N3   180.00   0.0  0
 8SM  CONST_37  H4   C8   N2   C4   180.00   0.0  0
 8SM  CONST_38  H2   C6   C5   C4   180.00   0.0  0
 8SM  CONST_39  H3   C7   C6   C5   180.00   0.0  0
 8SM  CONST_40  H1   C5   C6   C7   180.00   0.0  0
 8SM  CONST_41  H6   C13  N4   C10  180.00   0.0  0
 8SM  CONST_42  H12  C12  C11  C10  180.00   0.0  0
 8SM  CONST_43  H5   C10  N4   C13  180.00   0.0  0
 8SM  CONST_44  H11  C11  C12  C13  180.00   0.0  0
 8SM  Var_01    H7   C1   N1   N3   -62.01  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
 8SM  plan-1  N1   0.020
 8SM  plan-1  N3   0.020
 8SM  plan-1  C4   0.020
 8SM  plan-1  C1   0.020
 8SM  plan-1  C2   0.020
 8SM  plan-1  C3   0.020
 8SM  plan-1  C9   0.020
 8SM  plan-1  N4   0.020
 8SM  plan-1  H10  0.020
 8SM  plan-2  C10  0.020
 8SM  plan-2  C13  0.020
 8SM  plan-2  C9   0.020
 8SM  plan-2  N4   0.020
 8SM  plan-2  C11  0.020
 8SM  plan-2  C12  0.020
 8SM  plan-2  H6   0.020
 8SM  plan-2  H11  0.020
 8SM  plan-2  H12  0.020
 8SM  plan-2  H5   0.020
 8SM  plan-3  C4   0.020
 8SM  plan-3  C5   0.020
 8SM  plan-3  C6   0.020
 8SM  plan-3  C7   0.020
 8SM  plan-3  C8   0.020
 8SM  plan-3  C3   0.020
 8SM  plan-3  N2   0.020
 8SM  plan-3  H1   0.020
 8SM  plan-3  H2   0.020
 8SM  plan-3  H3   0.020
 8SM  plan-3  H4   0.020

