# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:02:48 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 5-amino-3-(methylsulfanyl)-1-phenyl-1H-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nn(c(N)c1C#N)c2ccccc2
#
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
 TR4  TR4  5-amino-3-(methylsulfanyl)-1-phenyl-1H-pyrazole-4-carbonitrile  ligand  26  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TR4
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
 TR4  C01   C  CH3   0  -0.767   2.4248   3.0040  -0.3397
 TR4  S02   S  S2    0   0.058   3.0834   1.3302  -0.1904
 TR4  C03   C  CR5   0   0.162   1.6158   0.4043  -0.0787
 TR4  N04   N  N     0  -0.302   0.4215   0.9160  -0.1491
 TR4  N05   N  NR5   0  -0.454  -0.4347  -0.1416  -0.0402
 TR4  C06   C  CR5   0   0.647   0.2083  -1.3140   0.1180
 TR4  N07   N  NH2   0  -0.838  -0.3983  -2.5099   0.2368
 TR4  C08   C  CR5   0  -0.256   1.5706  -1.0070   0.0886
 TR4  C09   C  CSP   0  -0.019   2.6375  -1.9033   0.2196
 TR4  N10   N  NS    0  -0.261   3.5211  -2.6409   0.3277
 TR4  C11   C  CR6   0   0.316  -1.8275   0.0896  -0.0484
 TR4  C12   C  CR16  0  -0.272  -2.3495   1.1051   0.7446
 TR4  C13   C  CR16  0  -0.253  -3.7142   1.3452   0.7301
 TR4  C14   C  CR16  0  -0.250  -4.5559   0.5694  -0.0583
 TR4  C15   C  CR16  0  -0.249  -4.0254  -0.4411  -0.8472
 TR4  C16   C  CR16  0  -0.301  -2.6576  -0.6783  -0.8563
 TR4  H01   H  HCH3  0   0.287   3.2881   3.6563  -0.4494
 TR4  H01A  H  HCH3  0   0.279   1.7908   3.0973  -1.2177
 TR4  H01B  H  HCH3  0   0.279   1.8709   3.2881   0.5516
 TR4  HN07  H  HNH2  0   0.415  -1.3528  -2.5306   0.5614
 TR4  HN0A  H  HNH2  0   0.413   0.1626  -3.2650   0.5971
 TR4  H12   H  HCR6  0   0.275  -1.6917   1.6992   1.3645
 TR4  H13   H  HCR6  0   0.268  -4.1233   2.1373   1.3431
 TR4  H14   H  HCR6  0   0.266  -5.6213   0.7573  -0.0607
 TR4  H15   H  HCR6  0   0.269  -4.6719  -1.0393  -1.4749
 TR4  H16   H  HCR6  0   0.288  -2.2447  -1.4433  -1.5011

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
 TR4  C01  S02   single    1.805  0.020  1.805
 TR4  S02  C03   single    1.739  0.020  1.739
 TR4  C03  N04   aromatic  1.301  0.020  1.301
 TR4  C03  C08   aromatic  1.422  0.020  1.422
 TR4  N04  N05   aromatic  1.365  0.020  1.365
 TR4  N05  C06   aromatic  1.346  0.020  1.346
 TR4  N05  C11   single    1.412  0.020  1.412
 TR4  C06  N07   single    1.346  0.020  1.346
 TR4  C06  C08   aromatic  1.397  0.020  1.397
 TR4  C08  C09   single    1.400  0.020  1.400
 TR4  C09  N10   triple    1.156  0.020  1.156
 TR4  C11  C12   aromatic  1.390  0.020  1.390
 TR4  C11  C16   aromatic  1.390  0.020  1.390
 TR4  C12  C13   aromatic  1.386  0.020  1.386
 TR4  C13  C14   aromatic  1.390  0.020  1.390
 TR4  C14  C15   aromatic  1.387  0.020  1.387
 TR4  C15  C16   aromatic  1.388  0.020  1.388
 TR4  C01  H01   single    0.970  0.020  1.090
 TR4  C01  H01A  single    0.970  0.020  1.090
 TR4  C01  H01B  single    0.970  0.020  1.090
 TR4  N07  HN07  single    0.890  0.020  1.040
 TR4  N07  HN0A  single    0.890  0.020  1.040
 TR4  C12  H12   single    0.930  0.020  1.080
 TR4  C13  H13   single    0.930  0.020  1.080
 TR4  C14  H14   single    0.930  0.020  1.080
 TR4  C15  H15   single    0.930  0.020  1.080
 TR4  C16  H16   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
 TR4  H01B  C01  H01A  110.03  3.000
 TR4  H01B  C01  H01   109.30  3.000
 TR4  H01A  C01  H01   109.27  3.000
 TR4  H01B  C01  S02   111.12  3.000
 TR4  H01A  C01  S02   111.05  3.000
 TR4  H01   C01  S02   105.96  3.000
 TR4  C03   S02  C01   101.02  3.000
 TR4  C08   C03  N04   111.56  3.000
 TR4  C08   C03  S02   124.26  3.000
 TR4  N04   C03  S02   124.18  3.000
 TR4  N05   N04  C03   105.46  3.000
 TR4  C11   N05  C06   127.90  3.000
 TR4  C11   N05  N04   119.43  3.000
 TR4  C06   N05  N04   112.61  3.000
 TR4  C08   C06  N07   129.54  3.000
 TR4  C08   C06  N05   105.77  3.000
 TR4  N07   C06  N05   124.66  3.000
 TR4  HN0A  N07  HN07  113.36  3.000
 TR4  HN0A  N07  C06   116.53  3.000
 TR4  HN07  N07  C06   118.24  3.000
 TR4  C09   C08  C06   126.92  3.000
 TR4  C09   C08  C03   128.49  3.000
 TR4  C06   C08  C03   104.58  3.000
 TR4  N10   C09  C08   180.00  3.000
 TR4  C16   C11  C12   120.73  3.000
 TR4  C16   C11  N05   120.14  3.000
 TR4  C12   C11  N05   119.12  3.000
 TR4  H12   C12  C13   120.65  3.000
 TR4  H12   C12  C11   119.99  3.000
 TR4  C13   C12  C11   119.36  3.000
 TR4  H13   C13  C14   120.07  3.000
 TR4  H13   C13  C12   119.55  3.000
 TR4  C14   C13  C12   120.37  3.000
 TR4  H14   C14  C15   120.12  3.000
 TR4  H14   C14  C13   120.04  3.000
 TR4  C15   C14  C13   119.83  3.000
 TR4  H15   C15  C16   119.38  3.000
 TR4  H15   C15  C14   120.28  3.000
 TR4  C16   C15  C14   120.33  3.000
 TR4  H16   C16  C15   120.03  3.000
 TR4  H16   C16  C11   120.60  3.000
 TR4  C15   C16  C11   119.36  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
 TR4  CONST_01  C06  N05  N04  C03     0.00   0.0  0
 TR4  CONST_02  C11  N05  N04  C03   180.00   0.0  0
 TR4  CONST_03  N05  C06  C08  C03     0.00   0.0  0
 TR4  CONST_04  C06  C08  C03  N04     0.00   0.0  0
 TR4  CONST_05  C08  C06  N05  N04     0.00   0.0  0
 TR4  CONST_08  C08  C03  N04  N05     0.00   0.0  0
 TR4  CONST_09  C13  C12  C11  N05   180.00   0.0  0
 TR4  CONST_10  C15  C16  C11  N05   180.00   0.0  0
 TR4  CONST_13  C11  N05  C06  C08   180.00   0.0  0
 TR4  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 TR4  CONST_15  C14  C15  C16  C11     0.00   0.0  0
 TR4  CONST_16  C15  C16  C11  C12     0.00   0.0  0
 TR4  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 TR4  CONST_18  C16  C11  C12  C13     0.00   0.0  0
 TR4  CONST_19  C16  C15  C14  C13     0.00   0.0  0
 TR4  CONST_20  N05  N04  C03  S02   180.00   0.0  0
 TR4  CONST_21  C06  C08  C03  S02   180.00   0.0  0
 TR4  CONST_22  N07  C06  C08  C03   180.00   0.0  0
 TR4  CONST_23  C09  C08  C03  N04   180.00   0.0  0
 TR4  CONST_24  N07  C06  N05  N04   180.00   0.0  0
 TR4  CONST_25  C09  C08  C06  N05   180.00   0.0  0
 TR4  CONST_26  C11  N05  C06  N07     0.00   0.0  0
 TR4  CONST_27  H12  C12  C11  N05     0.00   0.0  0
 TR4  CONST_28  H16  C16  C11  N05     0.00   0.0  0
 TR4  CONST_29  H13  C13  C12  C11   180.00   0.0  0
 TR4  CONST_30  H15  C15  C16  C11   180.00   0.0  0
 TR4  CONST_31  H14  C14  C13  C12   180.00   0.0  0
 TR4  Var_01    N04  C03  S02  C01     2.15  30.0  2
 TR4  Var_02    H01  C01  S02  C03  -178.16  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
 TR4  plan-1  S02   0.020
 TR4  plan-1  C03   0.020
 TR4  plan-1  N04   0.020
 TR4  plan-1  N05   0.020
 TR4  plan-1  C06   0.020
 TR4  plan-1  N07   0.020
 TR4  plan-1  C08   0.020
 TR4  plan-1  C09   0.020
 TR4  plan-1  N10   0.020
 TR4  plan-1  C11   0.020
 TR4  plan-2  N05   0.020
 TR4  plan-2  C11   0.020
 TR4  plan-2  C12   0.020
 TR4  plan-2  C13   0.020
 TR4  plan-2  C14   0.020
 TR4  plan-2  C15   0.020
 TR4  plan-2  C16   0.020
 TR4  plan-2  H12   0.020
 TR4  plan-2  H13   0.020
 TR4  plan-2  H14   0.020
 TR4  plan-2  H15   0.020
 TR4  plan-2  H16   0.020
 TR4  plan-3  C06   0.020
 TR4  plan-3  N07   0.020
 TR4  plan-3  HN07  0.020
 TR4  plan-3  HN0A  0.020

