# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 09:15:06 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: ~{N}-methyl-5-(5-methylthiophen-2-yl)-1~{H}-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc([nH]n1)c2sc(C)cc2
#
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
 7RN  7RN  "N-methyl-3-(5-methylthiophen-2-yl)-1H-pyrazole-5-carboxamide"
  ligand  26  15  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7RN
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
 7RN  C01  C  CH3   0  -0.714  25.1770  -19.1014  24.6695
 7RN  C02  C  CR5   0  -0.163  24.1329  -20.1506  24.8386
 7RN  C03  C  CR15  0  -0.196  22.7888  -19.9906  24.9993
 7RN  C04  C  CR15  0  -0.213  22.0861  -21.2141  25.1408
 7RN  C05  C  CR5   0  -0.251  22.9057  -22.3068  25.0847
 7RN  C06  C  CR5   0   0.468  22.5695  -23.7085  25.1889
 7RN  C07  C  CR15  0  -0.519  23.3665  -24.8356  25.2318
 7RN  C08  C  CR5   0   0.129  22.4622  -25.9031  25.3352
 7RN  C09  C  C     0   0.505  22.8056  -27.3424  25.4113
 7RN  C11  C  CH3   0  -0.512  21.9375  -29.6141  25.5644
 7RN  N10  N  NH1   0  -0.637  21.7678  -28.1835  25.4911
 7RN  N13  N  N     0  -0.270  21.2113  -25.4735  25.3555
 7RN  N14  N  NR15  0  -0.507  21.2965  -24.1608  25.2669
 7RN  O12  O  O     0  -0.484  23.9739  -27.7077  25.3972
 7RN  S15  S  S2    0   0.226  24.5480  -21.8234  24.8560
 7RN  H1   H  HCH3  0   0.257  25.9132  -19.1305  25.4737
 7RN  H2   H  HCH3  0   0.257  25.7162  -19.2132  23.7281
 7RN  H3   H  HCH3  0   0.259  24.7129  -18.1165  24.6753
 7RN  H4   H  HCR5  0   0.265  22.3132  -19.0199  25.0190
 7RN  H5   H  HCR5  0   0.266  21.0155  -21.2694  25.2835
 7RN  H6   H  HCR5  0   0.275  24.4424  -24.8827  25.1977
 7RN  H7   H  HCH3  0   0.251  20.9549  -30.0755  25.5944
 7RN  H8   H  HCH3  0   0.238  22.4715  -30.0013  24.6959
 7RN  H9   H  HCH3  0   0.238  22.4829  -29.9121  26.4609
 7RN  H10  H  HNH1  0   0.406  20.8355  -27.8031  25.4973
 7RN  H11  H  HNR5  0   0.429  20.4499  -23.6119  25.2565

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
 7RN  O12  C09  double    1.224  0.020  1.224
 7RN  C04  C03  aromatic  1.418  0.020  1.418
 7RN  C04  C05  aromatic  1.367  0.020  1.367
 7RN  C03  C02  aromatic  1.363  0.020  1.363
 7RN  C05  C06  single    1.445  0.020  1.445
 7RN  C05  S15  aromatic  1.727  0.020  1.727
 7RN  C07  C06  aromatic  1.381  0.020  1.381
 7RN  C07  C08  aromatic  1.403  0.020  1.403
 7RN  C06  N14  aromatic  1.353  0.020  1.353
 7RN  C02  C01  single    1.490  0.020  1.490
 7RN  C02  S15  aromatic  1.724  0.020  1.724
 7RN  C08  C09  single    1.482  0.020  1.482
 7RN  C08  N13  aromatic  1.323  0.020  1.323
 7RN  C09  N10  single    1.338  0.020  1.338
 7RN  N14  N13  aromatic  1.318  0.020  1.318
 7RN  N10  C11  single    1.442  0.020  1.442
 7RN  C01  H1   single    0.970  0.020  1.090
 7RN  C01  H2   single    0.970  0.020  1.090
 7RN  C01  H3   single    0.970  0.020  1.090
 7RN  C03  H4   single    0.930  0.020  1.080
 7RN  C04  H5   single    0.930  0.020  1.080
 7RN  C07  H6   single    0.930  0.020  1.080
 7RN  C11  H7   single    0.970  0.020  1.090
 7RN  C11  H8   single    0.970  0.020  1.090
 7RN  C11  H9   single    0.970  0.020  1.090
 7RN  N10  H10  single    0.860  0.020  1.020
 7RN  N14  H11  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
 7RN  H3   C01  H2   107.94  3.000
 7RN  H3   C01  H1   107.94  3.000
 7RN  H2   C01  H1   107.46  3.000
 7RN  H3   C01  C02  109.73  3.000
 7RN  H2   C01  C02  111.85  3.000
 7RN  H1   C01  C02  111.75  3.000
 7RN  S15  C02  C03  110.50  3.000
 7RN  S15  C02  C01  121.05  3.000
 7RN  C03  C02  C01  128.45  3.000
 7RN  H4   C03  C04  123.71  3.000
 7RN  H4   C03  C02  122.77  3.000
 7RN  C04  C03  C02  113.52  3.000
 7RN  H5   C04  C05  123.92  3.000
 7RN  H5   C04  C03  123.21  3.000
 7RN  C05  C04  C03  112.86  3.000
 7RN  S15  C05  C06  120.14  3.000
 7RN  S15  C05  C04  110.60  3.000
 7RN  C06  C05  C04  129.26  3.000
 7RN  N14  C06  C07  105.56  3.000
 7RN  N14  C06  C05  123.18  3.000
 7RN  C07  C06  C05  131.26  3.000
 7RN  H6   C07  C08  127.78  3.000
 7RN  H6   C07  C06  127.66  3.000
 7RN  C08  C07  C06  104.55  3.000
 7RN  N13  C08  C09  122.27  3.000
 7RN  N13  C08  C07  111.32  3.000
 7RN  C09  C08  C07  126.41  3.000
 7RN  O12  C09  N10  123.59  3.000
 7RN  N10  C09  C08  115.71  3.000
 7RN  O12  C09  C08  120.69  3.000
 7RN  H9   C11  H8   108.22  3.000
 7RN  H9   C11  H7   108.28  3.000
 7RN  H8   C11  H7   108.31  3.000
 7RN  H9   C11  N10  111.81  3.000
 7RN  H8   C11  N10  111.67  3.000
 7RN  H7   C11  N10  108.44  3.000
 7RN  H10  N10  C11  118.90  3.000
 7RN  H10  N10  C09  118.75  3.000
 7RN  C11  N10  C09  122.35  3.000
 7RN  N14  N13  C08  105.14  3.000
 7RN  H11  N14  N13  119.22  3.000
 7RN  H11  N14  C06  127.36  3.000
 7RN  N13  N14  C06  113.42  3.000
 7RN  C05  S15  C02   92.52  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
 7RN  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 7RN  CONST_02  C04  C05  S15  C02     0.00   0.0  0
 7RN  CONST_03  C06  C05  S15  C02   180.00   0.0  0
 7RN  CONST_04  C06  C05  C04  C03   180.00   0.0  0
 7RN  CONST_05  S15  C05  C04  C03     0.00   0.0  0
 7RN  CONST_06  C05  S15  C02  C03     0.00   0.0  0
 7RN  CONST_07  S15  C02  C03  C04     0.00   0.0  0
 7RN  CONST_08  C07  C06  C05  C04   180.00   0.0  0
 7RN  CONST_09  N14  C06  C05  C04     0.00   0.0  0
 7RN  CONST_10  C08  C07  C06  C05   180.00   0.0  0
 7RN  CONST_11  N13  N14  C06  C05   180.00   0.0  0
 7RN  CONST_12  N13  C08  C07  C06     0.00   0.0  0
 7RN  CONST_13  C08  N13  N14  C06     0.00   0.0  0
 7RN  CONST_14  S15  C05  C06  C07     0.00   0.0  0
 7RN  CONST_15  N13  N14  C06  C07     0.00   0.0  0
 7RN  CONST_16  N14  N13  C08  C07     0.00   0.0  0
 7RN  CONST_17  N14  C06  C07  C08     0.00   0.0  0
 7RN  CONST_18  S15  C05  C06  N14   180.00   0.0  0
 7RN  CONST_19  C04  C03  C02  C01   180.00   0.0  0
 7RN  CONST_20  C05  S15  C02  C01   180.00   0.0  0
 7RN  CONST_21  C09  C08  C07  C06   180.00   0.0  0
 7RN  CONST_22  N14  N13  C08  C09   180.00   0.0  0
 7RN  CONST_23  H5   C04  C03  C02   180.00   0.0  0
 7RN  CONST_24  H4   C03  C04  C05   180.00   0.0  0
 7RN  CONST_25  H6   C07  C06  C05     0.00   0.0  0
 7RN  CONST_26  H11  N14  C06  C05     0.00   0.0  0
 7RN  CONST_27  H5   C04  C05  C06     0.00   0.0  0
 7RN  CONST_28  H11  N14  C06  C07   180.00   0.0  0
 7RN  CONST_29  H11  N14  N13  C08   180.00   0.0  0
 7RN  CONST_30  H6   C07  C08  N13   180.00   0.0  0
 7RN  CONST_31  H6   C07  C06  N14   180.00   0.0  0
 7RN  CONST_32  H5   C04  C05  S15   180.00   0.0  0
 7RN  CONST_33  H4   C03  C02  S15   180.00   0.0  0
 7RN  CONST_34  C11  N10  C09  C08   180.00   0.0  0
 7RN  CONST_35  H10  N10  C09  C08     0.00   0.0  0
 7RN  CONST_36  O12  C09  N10  C11     0.00   0.0  0
 7RN  CONST_37  H10  N10  C09  O12   180.00   0.0  0
 7RN  Var_01    O12  C09  C08  C07     0.56  30.0  2
 7RN  Var_02    N10  C09  C08  C07  -179.29  30.0  2
 7RN  Var_03    N13  C08  C09  N10     0.53  30.0  2
 7RN  Var_04    O12  C09  C08  N13  -179.62  30.0  2
 7RN  Var_05    H1   C01  C02  C03   118.88  30.0  2
 7RN  Var_06    H2   C01  C02  C03  -120.59  30.0  2
 7RN  Var_07    H3   C01  C02  C03    -0.82  30.0  2
 7RN  Var_08    H1   C01  C02  S15   -60.89  30.0  2
 7RN  Var_09    H2   C01  C02  S15    59.64  30.0  2
 7RN  Var_10    H3   C01  C02  S15   179.41  30.0  2
 7RN  Var_11    H7   C11  N10  C09  -178.50  30.0  3
 7RN  Var_12    H8   C11  N10  C09   -59.23  30.0  3
 7RN  Var_13    H9   C11  N10  C09    62.20  30.0  3

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
 7RN  plan-1  C01  0.020
 7RN  plan-1  C02  0.020
 7RN  plan-1  C03  0.020
 7RN  plan-1  C04  0.020
 7RN  plan-1  C05  0.020
 7RN  plan-1  C06  0.020
 7RN  plan-1  S15  0.020
 7RN  plan-1  H4   0.020
 7RN  plan-1  H5   0.020
 7RN  plan-2  C05  0.020
 7RN  plan-2  C06  0.020
 7RN  plan-2  C07  0.020
 7RN  plan-2  C08  0.020
 7RN  plan-2  C09  0.020
 7RN  plan-2  N13  0.020
 7RN  plan-2  N14  0.020
 7RN  plan-2  H6   0.020
 7RN  plan-2  H11  0.020
 7RN  plan-3  C08  0.020
 7RN  plan-3  C09  0.020
 7RN  plan-3  C11  0.020
 7RN  plan-3  N10  0.020
 7RN  plan-3  O12  0.020
 7RN  plan-3  H10  0.020

