# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 03:16:46 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: ~{N}-(2,3-dimethylphenyl)-7-oxidanylidene-12-sulfanylidene-5,11-dithia-1,8-diazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,9-triene-10-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(NC(=O)C2=C3NC(=O)c4sccc4N3C(=S)S2)c1C
#
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
 1FJ  1FJ  ~{N}-(2,3-dimethylphenyl)-7-oxidanylidene-12-sulfanylidene-5,11-dithia-1,8-diazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,9-triene-10-carboxamide  ligand  38  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1FJ
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
 1FJ  C10  C  C     0   0.621  -1.4281  -0.4018   0.2027
 1FJ  C13  C  CR15  0  -0.173   4.6595   0.8589   0.0419
 1FJ  C17  C  CR15  0  -0.444   5.6961   0.0373  -0.2903
 1FJ  C20  C  CR6   0   0.065  -6.1313  -0.0783  -0.3546
 1FJ  C21  C  CR16  0  -0.287  -4.1671  -1.3570   1.1719
 1FJ  C22  C  CR16  0  -0.264  -5.4564  -1.8561   1.1441
 1FJ  C24  C  CR16  0  -0.301  -6.4288  -1.2146   0.3909
 1FJ  N01  N  N     0  -0.641   2.1223   0.6372   0.2035
 1FJ  C02  C  CR56  0   0.876   1.0550  -0.2362   0.0431
 1FJ  C03  C  CR5   0  -0.572  -0.1602   0.3153   0.3120
 1FJ  C04  C  CR5   0  -0.005   1.7602   1.9071   0.6067
 1FJ  C05  C  CR56  0   0.460   3.4210   0.1730  -0.0473
 1FJ  C06  C  CR56  0  -0.455   3.5762  -1.1350  -0.4423
 1FJ  N07  N  NR16  0  -0.768   1.2730  -1.5156  -0.3505
 1FJ  S08  S  S2    0   0.292   0.0517   1.9733   0.7866
 1FJ  C09  C  CR6   0   0.580   2.4970  -2.0751  -0.6210
 1FJ  N11  N  NH1   0  -0.775  -2.5472   0.3062   0.4698
 1FJ  S12  S  S2    0   0.324   5.2109  -1.5408  -0.7064
 1FJ  C14  C  CR6   0   0.304  -3.8556  -0.2295   0.4201
 1FJ  S15  S  S1    0  -0.225   2.7054   3.2188   0.9043
 1FJ  C16  C  CR6   0   0.025  -4.8184   0.4163  -0.3612
 1FJ  O18  O  O     0  -0.426   2.6250  -3.2299  -0.9682
 1FJ  O19  O  O     0  -0.488  -1.4479  -1.5865  -0.1196
 1FJ  C23  C  CH3   0  -0.754  -4.4464   1.6263  -1.1699
 1FJ  H1   H  HCR5  0   0.309   4.7900   1.8862   0.3296
 1FJ  H2   H  HCR5  0   0.323   6.7418   0.3029  -0.3066
 1FJ  H3   H  HCR6  0   0.263  -3.4133  -1.8277   1.7878
 1FJ  H4   H  HCR6  0   0.257  -5.7075  -2.7357   1.7221
 1FJ  H5   H  HCR6  0   0.249  -7.4417  -1.5987   0.3873
 1FJ  H6   H  HNH1  0   0.413  -2.4771   1.2977   0.6418
 1FJ  H7   H  HCH3  0   0.257  -4.4618   2.5355  -0.5625
 1FJ  H8   H  HCH3  0   0.250  -3.4459   1.5365  -1.5924
 1FJ  H9   H  HCH3  0   0.261  -5.1333   1.7863  -1.9973
 1FJ  H10  H  HCH3  0   0.247  -7.3225   1.6469  -0.8753
 1FJ  H11  H  HCH3  0   0.248  -7.0200   0.5589  -2.2187
 1FJ  H12  H  HCH3  0   0.252  -8.1779   0.1122  -0.9733
 1FJ  H13  H  HNR6  0   0.450   0.4293  -2.0810  -0.4342
 1FJ  C25  C  CH3   0  -0.745  -7.2170   0.5948  -1.1453

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
 1FJ  S12  C17  aromatic  1.703  0.020  1.703
 1FJ  S12  C06  aromatic  1.705  0.020  1.705
 1FJ  C17  C13  aromatic  1.364  0.020  1.364
 1FJ  O18  C09  double    1.213  0.020  1.213
 1FJ  C06  C09  single    1.442  0.020  1.442
 1FJ  C06  C05  aromatic  1.375  0.020  1.375
 1FJ  C13  C05  aromatic  1.419  0.020  1.419
 1FJ  C09  N07  single    1.373  0.020  1.373
 1FJ  C05  N01  single    1.402  0.020  1.402
 1FJ  N07  C02  single    1.356  0.020  1.356
 1FJ  N01  C02  single    1.388  0.020  1.388
 1FJ  N01  C04  single    1.381  0.020  1.381
 1FJ  C02  C03  double    1.361  0.020  1.361
 1FJ  C23  C16  single    1.502  0.020  1.502
 1FJ  C04  S15  double    1.644  0.020  1.644
 1FJ  C04  S08  single    1.719  0.020  1.719
 1FJ  C03  S08  single    1.738  0.020  1.738
 1FJ  C03  C10  single    1.461  0.020  1.461
 1FJ  C25  C20  single    1.502  0.020  1.502
 1FJ  C16  C20  aromatic  1.403  0.020  1.403
 1FJ  C16  C14  aromatic  1.398  0.020  1.398
 1FJ  N11  C10  single    1.351  0.020  1.351
 1FJ  N11  C14  single    1.415  0.020  1.415
 1FJ  C10  O19  double    1.228  0.020  1.228
 1FJ  C20  C24  aromatic  1.391  0.020  1.391
 1FJ  C14  C21  aromatic  1.391  0.020  1.391
 1FJ  C24  C22  aromatic  1.387  0.020  1.387
 1FJ  C21  C22  aromatic  1.383  0.020  1.383
 1FJ  C13  H1   single    0.930  0.020  1.080
 1FJ  C17  H2   single    0.930  0.020  1.080
 1FJ  C21  H3   single    0.930  0.020  1.080
 1FJ  C22  H4   single    0.930  0.020  1.080
 1FJ  C24  H5   single    0.930  0.020  1.080
 1FJ  N11  H6   single    0.860  0.020  1.020
 1FJ  C23  H7   single    0.970  0.020  1.090
 1FJ  C23  H8   single    0.970  0.020  1.090
 1FJ  C23  H9   single    0.970  0.020  1.090
 1FJ  C25  H10  single    0.970  0.020  1.090
 1FJ  C25  H11  single    0.970  0.020  1.090
 1FJ  C25  H12  single    0.970  0.020  1.090
 1FJ  N07  H13  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
 1FJ  O19  C10  N11  122.97  3.000
 1FJ  O19  C10  C03  120.48  3.000
 1FJ  N11  C10  C03  116.55  3.000
 1FJ  H1   C13  C05  125.80  3.000
 1FJ  H1   C13  C17  123.28  3.000
 1FJ  C05  C13  C17  110.92  3.000
 1FJ  H2   C17  S12  120.04  3.000
 1FJ  H2   C17  C13  126.30  3.000
 1FJ  S12  C17  C13  113.66  3.000
 1FJ  C25  C20  C16  121.05  3.000
 1FJ  C16  C20  C24  119.38  3.000
 1FJ  C25  C20  C24  119.57  3.000
 1FJ  H3   C21  C14  120.32  3.000
 1FJ  H3   C21  C22  120.29  3.000
 1FJ  C14  C21  C22  119.39  3.000
 1FJ  H4   C22  C24  120.21  3.000
 1FJ  H4   C22  C21  119.94  3.000
 1FJ  C24  C22  C21  119.84  3.000
 1FJ  H5   C24  C22  119.56  3.000
 1FJ  H5   C24  C20  119.20  3.000
 1FJ  C22  C24  C20  121.25  3.000
 1FJ  C05  N01  C04  126.86  3.000
 1FJ  C04  N01  C02  114.25  3.000
 1FJ  C05  N01  C02  118.89  3.000
 1FJ  N07  C02  C03  125.66  3.000
 1FJ  C03  C02  N01  114.11  3.000
 1FJ  N07  C02  N01  120.23  3.000
 1FJ  S08  C03  C02  109.37  3.000
 1FJ  S08  C03  C10  126.49  3.000
 1FJ  C02  C03  C10  124.14  3.000
 1FJ  S15  C04  S08  121.45  3.000
 1FJ  S08  C04  N01  109.06  3.000
 1FJ  S15  C04  N01  129.49  3.000
 1FJ  C06  C05  N01  118.09  3.000
 1FJ  N01  C05  C13  129.60  3.000
 1FJ  C06  C05  C13  112.30  3.000
 1FJ  S12  C06  C09  122.90  3.000
 1FJ  C09  C06  C05  124.83  3.000
 1FJ  S12  C06  C05  112.28  3.000
 1FJ  H13  N07  C09  119.72  3.000
 1FJ  H13  N07  C02  114.47  3.000
 1FJ  C09  N07  C02  125.80  3.000
 1FJ  C04  S08  C03   93.20  3.000
 1FJ  O18  C09  N07  122.60  3.000
 1FJ  N07  C09  C06  112.15  3.000
 1FJ  O18  C09  C06  125.25  3.000
 1FJ  H6   N11  C14  116.26  3.000
 1FJ  H6   N11  C10  119.43  3.000
 1FJ  C14  N11  C10  124.11  3.000
 1FJ  C06  S12  C17   90.85  3.000
 1FJ  C16  C14  N11  118.79  3.000
 1FJ  N11  C14  C21  119.68  3.000
 1FJ  C16  C14  C21  121.50  3.000
 1FJ  C23  C16  C14  120.16  3.000
 1FJ  C14  C16  C20  118.62  3.000
 1FJ  C23  C16  C20  121.21  3.000
 1FJ  H9   C23  H8   107.29  3.000
 1FJ  H9   C23  H7   106.95  3.000
 1FJ  H8   C23  H7   107.26  3.000
 1FJ  H9   C23  C16  111.83  3.000
 1FJ  H8   C23  C16  111.69  3.000
 1FJ  H7   C23  C16  111.54  3.000
 1FJ  H12  C25  H11  107.45  3.000
 1FJ  H12  C25  H10  107.63  3.000
 1FJ  H11  C25  H10  107.00  3.000
 1FJ  H12  C25  C20  110.86  3.000
 1FJ  H11  C25  C20  111.86  3.000
 1FJ  H10  C25  C20  111.81  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
 1FJ  CONST_01  C06  S12  C17  C13     0.00   0.0  0
 1FJ  CONST_02  S12  C06  C05  C13     0.00   0.0  0
 1FJ  CONST_03  C05  C06  S12  C17     0.00   0.0  0
 1FJ  CONST_04  C06  C05  C13  C17     0.00   0.0  0
 1FJ  CONST_05  C21  C14  C16  C20     0.00   0.0  0
 1FJ  CONST_06  C21  C22  C24  C20     0.00   0.0  0
 1FJ  CONST_07  C16  C20  C24  C22     0.00   0.0  0
 1FJ  CONST_08  C16  C14  C21  C22     0.00   0.0  0
 1FJ  CONST_09  C14  C16  C20  C24     0.00   0.0  0
 1FJ  CONST_10  C14  C21  C22  C24     0.00   0.0  0
 1FJ  CONST_11  S12  C17  C13  C05     0.00   0.0  0
 1FJ  CONST_12  C09  N07  C02  N01     0.00   0.0  0
 1FJ  CONST_13  C06  C09  N07  C02     0.00   0.0  0
 1FJ  CONST_14  C09  N07  C02  C03   180.00   0.0  0
 1FJ  CONST_15  C05  N01  C02  C03   180.00   0.0  0
 1FJ  CONST_16  C04  N01  C02  C03     0.00   0.0  0
 1FJ  CONST_17  N07  C02  N01  C04   180.00   0.0  0
 1FJ  CONST_18  N07  C02  N01  C05     0.00   0.0  0
 1FJ  CONST_19  N11  C14  C16  C20   180.00   0.0  0
 1FJ  CONST_20  C23  C16  C14  C21   180.00   0.0  0
 1FJ  CONST_21  C25  C20  C24  C22   180.00   0.0  0
 1FJ  CONST_22  N11  C14  C21  C22   180.00   0.0  0
 1FJ  CONST_23  C23  C16  C20  C24   180.00   0.0  0
 1FJ  CONST_24  C25  C20  C16  C14   180.00   0.0  0
 1FJ  CONST_25  O18  C09  N07  C02   180.00   0.0  0
 1FJ  CONST_26  H4   C22  C24  C20   180.00   0.0  0
 1FJ  CONST_27  H5   C24  C22  C21   180.00   0.0  0
 1FJ  CONST_28  H3   C21  C22  C24   180.00   0.0  0
 1FJ  CONST_29  H1   C13  C05  N01     0.00   0.0  0
 1FJ  CONST_30  H2   C17  C13  C05   180.00   0.0  0
 1FJ  CONST_31  H13  N07  C02  N01   180.00   0.0  0
 1FJ  CONST_32  C14  N11  C10  C03   180.00   0.0  0
 1FJ  CONST_36  O19  C10  N11  C14     0.00   0.0  0
 1FJ  Var_01    N11  C10  C03  C02  -178.15  30.0  2
 1FJ  Var_02    H7   C23  C16  C20    96.28  30.0  2
 1FJ  Var_03    H10  C25  C20  C24   123.94  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
 1FJ  plan-1  C20  0.020
 1FJ  plan-1  C21  0.020
 1FJ  plan-1  C22  0.020
 1FJ  plan-1  C24  0.020
 1FJ  plan-1  N11  0.020
 1FJ  plan-1  C14  0.020
 1FJ  plan-1  C16  0.020
 1FJ  plan-1  C23  0.020
 1FJ  plan-1  H3   0.020
 1FJ  plan-1  H4   0.020
 1FJ  plan-1  H5   0.020
 1FJ  plan-1  C25  0.020
 1FJ  plan-2  C10  0.020
 1FJ  plan-2  C13  0.020
 1FJ  plan-2  C17  0.020
 1FJ  plan-2  N01  0.020
 1FJ  plan-2  C02  0.020
 1FJ  plan-2  C03  0.020
 1FJ  plan-2  C04  0.020
 1FJ  plan-2  C05  0.020
 1FJ  plan-2  C06  0.020
 1FJ  plan-2  N07  0.020
 1FJ  plan-2  S08  0.020
 1FJ  plan-2  C09  0.020
 1FJ  plan-2  S12  0.020
 1FJ  plan-2  S15  0.020
 1FJ  plan-2  O18  0.020
 1FJ  plan-2  H1   0.020
 1FJ  plan-2  H2   0.020
 1FJ  plan-2  H13  0.020
 1FJ  plan-3  C10  0.020
 1FJ  plan-3  C03  0.020
 1FJ  plan-3  N11  0.020
 1FJ  plan-3  C14  0.020
 1FJ  plan-3  O19  0.020
 1FJ  plan-3  H6   0.020

