# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 13:06:44 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 3,4-dichlorobenzyl carbamimidothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)SCc1ccc(Cl)c(Cl)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
 QH3  QH3  '3,4-dichlorobenzyl carbamimidothioate'  ligand  21  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QH3
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
 QH3  CL1   CL  CL    0  -0.095  -3.9934   0.8427   0.5419
 QH3  C02   C   CR6   0  -0.015  -2.3413   0.6474   0.0992
 QH3  C03   C   CR16  0  -0.199  -1.5427   1.7667  -0.0806
 QH3  C04   C   CR16  0  -0.286  -0.2131   1.6191  -0.4371
 QH3  C05   C   CR6   0   0.097   0.3352   0.3550  -0.6258
 QH3  C06   C   CH2   0  -0.612   1.7809   0.1904  -0.9863
 QH3  S07   S   S2    0   0.014   2.6907  -0.0552   0.5680
 QH3  C08   C   C     0   0.283   4.3636  -0.1790  -0.0172
 QH3  N09   N   N     0  -0.644   4.6069  -0.1165  -1.2619
 QH3  N10   N   NH2   0  -0.806   5.2367  -0.3950   1.0060
 QH3  C11   C   CR16  0  -0.245  -0.4695  -0.7630  -0.4421
 QH3  C12   C   CR6   0   0.022  -1.8005  -0.6207  -0.0840
 QH3  CL2   CL  CL    0  -0.095  -2.7716  -2.0270   0.1303
 QH3  H03   H   HCR6  0   0.291  -1.9634   2.7530   0.0592
 QH3  H04   H   HCR6  0   0.274   0.3985   2.5015  -0.5747
 QH3  H061  H   HCH2  0   0.299   1.9391  -0.6710  -1.6329
 QH3  H062  H   HCH2  0   0.299   2.1680   1.0746  -1.4893
 QH3  H11   H   HCR6  0   0.287  -0.0615  -1.7556  -0.5843
 QH3  H09   H   H     0   0.334   5.6030  -0.2016  -1.4471
 QH3  H101  H   HNH2  0   0.399   4.9716  -0.1328   1.9419
 QH3  H102  H   HNH2  0   0.398   6.2157  -0.2563   0.8096

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
 QH3  CL1  C02   single    1.721  0.020  1.721
 QH3  C02  C03   aromatic  1.387  0.020  1.387
 QH3  C02  C12   aromatic  1.391  0.020  1.391
 QH3  C03  C04   aromatic  1.385  0.020  1.385
 QH3  C04  C05   aromatic  1.391  0.020  1.391
 QH3  C05  C06   single    1.499  0.020  1.499
 QH3  C05  C11   aromatic  1.390  0.020  1.390
 QH3  C06  S07   single    1.818  0.020  1.818
 QH3  S07  C08   single    1.777  0.020  1.777
 QH3  C08  N09   double    1.270  0.020  1.270
 QH3  C08  N10   single    1.362  0.020  1.362
 QH3  C11  C12   aromatic  1.386  0.020  1.386
 QH3  C12  CL2   single    1.722  0.020  1.722
 QH3  C03  H03   single    0.930  0.020  1.080
 QH3  C04  H04   single    0.930  0.020  1.080
 QH3  C06  H061  single    0.970  0.020  1.090
 QH3  C06  H062  single    0.970  0.020  1.090
 QH3  C11  H11   single    0.930  0.020  1.080
 QH3  N09  H09   single    0.890  0.020  1.040
 QH3  N10  H101  single    0.890  0.020  1.040
 QH3  N10  H102  single    0.890  0.020  1.040

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
 QH3  C12   C02  C03   119.67  3.000
 QH3  C12   C02  CL1   120.70  3.000
 QH3  C03   C02  CL1   119.63  3.000
 QH3  H03   C03  C04   120.28  3.000
 QH3  H03   C03  C02   119.70  3.000
 QH3  C04   C03  C02   120.02  3.000
 QH3  H04   C04  C05   120.07  3.000
 QH3  H04   C04  C03   119.23  3.000
 QH3  C05   C04  C03   120.70  3.000
 QH3  C11   C05  C06   120.13  3.000
 QH3  C11   C05  C04   119.01  3.000
 QH3  C06   C05  C04   120.84  3.000
 QH3  H062  C06  H061  108.46  3.000
 QH3  H062  C06  S07   109.09  3.000
 QH3  H061  C06  S07   109.16  3.000
 QH3  H062  C06  C05   111.41  3.000
 QH3  H061  C06  C05   111.70  3.000
 QH3  S07   C06  C05   106.97  3.000
 QH3  C08   S07  C06   101.48  3.000
 QH3  N10   C08  N09   128.40  3.000
 QH3  N10   C08  S07   111.54  3.000
 QH3  N09   C08  S07   120.00  3.000
 QH3  H09   N09  C08   111.24  3.000
 QH3  H102  N10  H101  113.63  3.000
 QH3  H102  N10  C08   117.02  3.000
 QH3  H101  N10  C08   119.20  3.000
 QH3  H11   C11  C12   119.35  3.000
 QH3  H11   C11  C05   120.14  3.000
 QH3  C12   C11  C05   120.51  3.000
 QH3  CL2   C12  C11   119.33  3.000
 QH3  CL2   C12  C02   120.59  3.000
 QH3  C11   C12  C02   120.08  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
 QH3  CONST_01  C05   C04  C03  C02    0.00   0.0  0
 QH3  CONST_02  C05   C11  C12  C02    0.00   0.0  0
 QH3  CONST_03  C11   C12  C02  C03    0.00   0.0  0
 QH3  CONST_04  C11   C05  C04  C03    0.00   0.0  0
 QH3  CONST_05  C12   C02  C03  C04    0.00   0.0  0
 QH3  CONST_06  C12   C11  C05  C04    0.00   0.0  0
 QH3  CONST_07  C04   C03  C02  CL1  180.00   0.0  0
 QH3  CONST_08  C11   C12  C02  CL1  180.00   0.0  0
 QH3  CONST_09  CL2   C12  C02  C03  180.00   0.0  0
 QH3  CONST_10  C06   C05  C04  C03  180.00   0.0  0
 QH3  CONST_11  CL2   C12  C11  C05  180.00   0.0  0
 QH3  CONST_12  C12   C11  C05  C06  180.00   0.0  0
 QH3  CONST_13  H04   C04  C03  C02  180.00   0.0  0
 QH3  CONST_14  H11   C11  C12  C02  180.00   0.0  0
 QH3  CONST_15  H03   C03  C04  C05  180.00   0.0  0
 QH3  CONST_16  H09   N09  C08  S07  180.00   0.0  0
 QH3  CONST_18  H102  N10  C08  S07  180.00   0.0  0
 QH3  Var_01    S07   C06  C05  C04   93.80  30.0  2
 QH3  Var_02    N09   C08  S07  C06   -1.54  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
 QH3  plan-1  CL1   0.020
 QH3  plan-1  C02   0.020
 QH3  plan-1  C03   0.020
 QH3  plan-1  C04   0.020
 QH3  plan-1  C05   0.020
 QH3  plan-1  C06   0.020
 QH3  plan-1  C11   0.020
 QH3  plan-1  C12   0.020
 QH3  plan-1  CL2   0.020
 QH3  plan-1  H03   0.020
 QH3  plan-1  H04   0.020
 QH3  plan-1  H11   0.020
 QH3  plan-2  S07   0.020
 QH3  plan-2  C08   0.020
 QH3  plan-2  N09   0.020
 QH3  plan-2  N10   0.020
 QH3  plan-2  H09   0.020
 QH3  plan-2  H101  0.020
 QH3  plan-2  H102  0.020

