# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 23:36:12 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-[(3,5-dimethylpyrazol-1-yl)methyl]-~{N}-ethyl-1,3,4-thiadiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNc1sc(Cn2nc(C)cc2C)nn1
#
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
 9VT  9VT  5-[(3,5-dimethylpyrazol-1-yl)methyl]-~{N}-ethyl-1,3,4-thiadiazol-2-amine  ligand  31  16  .  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_9VT
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
 9VT  C10  C  CR5   0   0.335  -2.2373  -0.1606   0.1006
 9VT  N12  N  N     0  -0.241  -0.9932  -0.1671   1.9256
 9VT  C13  C  CR5   0   0.087  -0.1424   0.3415   1.1139
 9VT  C24  C  CR15  0  -0.572   3.5664   0.2870  -1.1869
 9VT  C26  C  CR5   0   0.423   2.8026   1.1484  -0.4349
 9VT  C01  C  CH3   0  -0.698  -5.5961  -0.9763  -1.2245
 9VT  N08  N  NH1   0  -0.652  -3.3163  -0.3269  -0.6730
 9VT  N11  N  N     0  -0.337  -2.1896  -0.4599   1.3693
 9VT  C14  C  CH2   0  -0.384   1.2339   0.7836   1.4871
 9VT  N17  N  NR5   0  -0.337   2.2063   0.3806   0.5066
 9VT  N18  N  N     0  -0.305   2.5246  -0.9140   0.3959
 9VT  C19  C  CR5   0   0.279   3.3559  -0.9887  -0.6247
 9VT  S31  S  S2    0   0.155  -0.7515   0.5178  -0.5077
 9VT  H21  H  HCH3  0   0.245   3.7837  -2.4655  -2.1130
 9VT  H22  H  HCH3  0   0.246   5.0297  -2.3003  -0.8891
 9VT  H23  H  HCH3  0   0.245   3.5177  -3.1161  -0.4933
 9VT  H25  H  HCR5  0   0.258   4.1907   0.5445  -2.0278
 9VT  H02  H  HCH3  0   0.238  -5.8732   0.0435  -1.4918
 9VT  H03  H  HCH3  0   0.235  -5.2836  -1.4973  -2.1306
 9VT  H04  H  HCH3  0   0.248  -6.4843  -1.4788  -0.8452
 9VT  H06  H  HCH2  0   0.242  -4.8413  -0.4827   0.7297
 9VT  H07  H  HCH2  0   0.235  -4.2723  -2.0253   0.1144
 9VT  H09  H  HNH1  0   0.409  -3.2040  -0.2605  -1.6714
 9VT  H16  H  HCH2  0   0.303   1.2697   1.8694   1.5836
 9VT  H15  H  HCH2  0   0.307   1.4856   0.3609   2.4594
 9VT  H29  H  HCH3  0   0.251   1.5565   2.8768  -0.7325
 9VT  H30  H  HCH3  0   0.263   2.9204   3.1476   0.3475
 9VT  H28  H  HCH3  0   0.272   3.1838   3.0003  -1.3856
 9VT  C27  C  CH3   0  -0.746   2.6012   2.6173  -0.5510
 9VT  C20  C  CH3   0  -0.735   3.9507  -2.2868  -1.0505
 9VT  C05  C  CH2   0  -0.267  -4.5049  -0.9953  -0.1728

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
 9VT  C20  C19  single    1.490  0.020  1.490
 9VT  N18  C19  aromatic  1.318  0.020  1.318
 9VT  N18  N17  aromatic  1.338  0.020  1.338
 9VT  N12  N11  aromatic  1.351  0.020  1.351
 9VT  N12  C13  aromatic  1.281  0.020  1.281
 9VT  C19  C24  aromatic  1.410  0.020  1.410
 9VT  N11  C10  aromatic  1.304  0.020  1.304
 9VT  C14  N17  single    1.439  0.020  1.439
 9VT  C14  C13  single    1.493  0.020  1.493
 9VT  N17  C26  aromatic  1.353  0.020  1.353
 9VT  C13  S31  aromatic  1.741  0.020  1.741
 9VT  C24  C26  aromatic  1.375  0.020  1.375
 9VT  C10  N08  single    1.338  0.020  1.338
 9VT  C10  S31  aromatic  1.743  0.020  1.743
 9VT  C26  C27  single    1.487  0.020  1.487
 9VT  N08  C05  single    1.452  0.020  1.452
 9VT  C05  C01  single    1.516  0.020  1.516
 9VT  C20  H21  single    0.970  0.020  1.090
 9VT  C20  H22  single    0.970  0.020  1.090
 9VT  C20  H23  single    0.970  0.020  1.090
 9VT  C24  H25  single    0.930  0.020  1.080
 9VT  C01  H02  single    0.970  0.020  1.090
 9VT  C01  H03  single    0.970  0.020  1.090
 9VT  C01  H04  single    0.970  0.020  1.090
 9VT  C05  H06  single    0.970  0.020  1.090
 9VT  C05  H07  single    0.970  0.020  1.090
 9VT  N08  H09  single    0.860  0.020  1.020
 9VT  C14  H16  single    0.970  0.020  1.090
 9VT  C14  H15  single    0.970  0.020  1.090
 9VT  C27  H29  single    0.970  0.020  1.090
 9VT  C27  H30  single    0.970  0.020  1.090
 9VT  C27  H28  single    0.970  0.020  1.090

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
 9VT  S31  C10  N11  113.43  3.000
 9VT  S31  C10  N08  122.28  3.000
 9VT  N11  C10  N08  124.29  3.000
 9VT  N11  N12  C13  114.40  3.000
 9VT  S31  C13  C14  121.69  3.000
 9VT  S31  C13  N12  113.45  3.000
 9VT  C14  C13  N12  124.84  3.000
 9VT  H25  C24  C19  127.83  3.000
 9VT  H25  C24  C26  126.76  3.000
 9VT  C19  C24  C26  105.41  3.000
 9VT  C27  C26  N17  123.71  3.000
 9VT  C27  C26  C24  130.63  3.000
 9VT  N17  C26  C24  105.66  3.000
 9VT  H04  C01  H03  107.61  3.000
 9VT  H04  C01  H02  108.05  3.000
 9VT  H03  C01  H02  108.42  3.000
 9VT  H04  C01  C05  109.87  3.000
 9VT  H03  C01  C05  111.35  3.000
 9VT  H02  C01  C05  111.40  3.000
 9VT  H09  N08  C05  117.59  3.000
 9VT  H09  N08  C10  118.37  3.000
 9VT  C05  N08  C10  121.19  3.000
 9VT  N12  N11  C10  112.52  3.000
 9VT  H15  C14  H16  107.44  3.000
 9VT  H15  C14  N17  110.08  3.000
 9VT  H16  C14  N17  108.49  3.000
 9VT  H15  C14  C13  108.73  3.000
 9VT  H16  C14  C13  110.31  3.000
 9VT  N17  C14  C13  111.70  3.000
 9VT  N18  N17  C14  119.23  3.000
 9VT  C14  N17  C26  127.81  3.000
 9VT  N18  N17  C26  112.75  3.000
 9VT  C19  N18  N17  105.60  3.000
 9VT  N18  C19  C24  110.58  3.000
 9VT  C24  C19  C20  127.93  3.000
 9VT  N18  C19  C20  121.49  3.000
 9VT  C13  S31  C10   86.20  3.000
 9VT  H28  C27  H30  107.71  3.000
 9VT  H28  C27  H29  107.54  3.000
 9VT  H30  C27  H29  107.54  3.000
 9VT  H28  C27  C26  109.58  3.000
 9VT  H30  C27  C26  112.10  3.000
 9VT  H29  C27  C26  112.17  3.000
 9VT  H23  C20  H22  107.95  3.000
 9VT  H23  C20  H21  108.24  3.000
 9VT  H22  C20  H21  107.07  3.000
 9VT  H23  C20  C19  111.01  3.000
 9VT  H22  C20  C19  111.30  3.000
 9VT  H21  C20  C19  111.11  3.000
 9VT  H07  C05  H06  106.90  3.000
 9VT  H07  C05  N08  110.47  3.000
 9VT  H06  C05  N08  108.72  3.000
 9VT  H07  C05  C01  110.30  3.000
 9VT  H06  C05  C01  110.25  3.000
 9VT  N08  C05  C01  110.15  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
 9VT  CONST_01  C13  N12  N11  C10    0.00   0.0  0
 9VT  CONST_02  N12  C13  S31  C10    0.00   0.0  0
 9VT  CONST_03  S31  C10  N11  N12    0.00   0.0  0
 9VT  CONST_04  N11  C10  S31  C13    0.00   0.0  0
 9VT  CONST_05  N17  N18  C19  C24    0.00   0.0  0
 9VT  CONST_06  N18  N17  C26  C24    0.00   0.0  0
 9VT  CONST_07  C19  N18  N17  C26    0.00   0.0  0
 9VT  CONST_08  N18  C19  C24  C26    0.00   0.0  0
 9VT  CONST_09  S31  C13  N12  N11    0.00   0.0  0
 9VT  CONST_10  C19  C24  C26  N17    0.00   0.0  0
 9VT  CONST_11  C14  C13  S31  C10  180.00   0.0  0
 9VT  CONST_12  N08  C10  N11  N12  180.00   0.0  0
 9VT  CONST_13  N08  C10  S31  C13  180.00   0.0  0
 9VT  CONST_14  N17  N18  C19  C20  180.00   0.0  0
 9VT  CONST_15  C26  C24  C19  C20  180.00   0.0  0
 9VT  CONST_16  C14  N17  C26  C24  180.00   0.0  0
 9VT  CONST_17  C14  C13  N12  N11  180.00   0.0  0
 9VT  CONST_18  C19  N18  N17  C14  180.00   0.0  0
 9VT  CONST_19  C27  C26  N17  N18  180.00   0.0  0
 9VT  CONST_20  C27  C26  C24  C19  180.00   0.0  0
 9VT  CONST_21  H25  C24  C26  N17  180.00   0.0  0
 9VT  CONST_22  N11  C10  N08  C05    0.00   0.0  0
 9VT  CONST_23  S31  C10  N08  C05  180.00   0.0  0
 9VT  CONST_24  H09  N08  C10  N11  180.00   0.0  0
 9VT  Var_01    N17  C14  C13  N12  137.07  30.0  3
 9VT  Var_02    N18  N17  C14  C13  -70.65  30.0  2
 9VT  Var_03    H21  C20  C19  C24  -53.39  30.0  2
 9VT  Var_04    H29  C27  C26  C24  119.29  30.0  2
 9VT  Var_05    C01  C05  N08  C10  176.80  30.0  3
 9VT  Var_06    H02  C01  C05  N08  -60.33  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
 9VT  plan-1  C10  0.020
 9VT  plan-1  N12  0.020
 9VT  plan-1  C13  0.020
 9VT  plan-1  N08  0.020
 9VT  plan-1  N11  0.020
 9VT  plan-1  C14  0.020
 9VT  plan-1  S31  0.020
 9VT  plan-2  C24  0.020
 9VT  plan-2  C26  0.020
 9VT  plan-2  C14  0.020
 9VT  plan-2  N17  0.020
 9VT  plan-2  N18  0.020
 9VT  plan-2  C19  0.020
 9VT  plan-2  H25  0.020
 9VT  plan-2  C27  0.020
 9VT  plan-2  C20  0.020
 9VT  plan-3  C10  0.020
 9VT  plan-3  N08  0.020
 9VT  plan-3  H09  0.020
 9VT  plan-3  C05  0.020

