# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:39:22 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3,6-diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2sc(C#N)c(N)c2c(c3ccccc3Cl)c1C#N
#
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
 UGJ  UGJ  3,6-diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile  ligand  30  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UGJ
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
 UGJ  N01   N   NH2   0  -0.849   1.2429   2.1782  -0.3056
 UGJ  C02   C   CR5   0   0.403   1.6952   0.9226  -0.1972
 UGJ  C03   C   CR5   0  -0.384   3.0290   0.5774  -0.0785
 UGJ  S04   S   S2    0   0.261   3.3100  -1.1544   0.0120
 UGJ  C05   C   CR56  0  -0.009   1.6144  -1.4453  -0.1035
 UGJ  C06   C   CR56  0   0.029   0.8645  -0.2580  -0.2134
 UGJ  C07   C   CR6   0   0.316  -0.5197  -0.4060  -0.3121
 UGJ  C08   C   CR6   0  -0.058  -1.4408   0.7442  -0.4507
 UGJ  C09   C   CR16  0  -0.250  -1.8036   1.1953  -1.7166
 UGJ  C10   C   CR16  0  -0.234  -2.6671   2.2699  -1.8590
 UGJ  C11   C   CR16  0  -0.253  -3.1764   2.9006  -0.7324
 UGJ  C12   C   CR16  0  -0.197  -2.8296   2.4609   0.5364
 UGJ  C13   C   CR6   0  -0.068  -1.9661   1.3849   0.6678
 UGJ  CL    CL  CL    0  -0.103  -1.5206   0.8352   2.2451
 UGJ  C15   C   CR6   0  -0.160  -1.0434  -1.6880  -0.2924
 UGJ  C16   C   CSP   0   0.003  -2.4460  -1.8824  -0.3717
 UGJ  N17   N   NS    0  -0.233  -3.5808  -2.0801  -0.4319
 UGJ  C18   C   CR6   0   0.521  -0.1795  -2.8233  -0.1759
 UGJ  N19   N   NH2   0  -0.824  -0.6660  -4.0628  -0.1576
 UGJ  N20   N   N     0  -0.479   1.1376  -2.6707  -0.0844
 UGJ  C21   C   CSP   0   0.031   4.0903   1.4827  -0.0298
 UGJ  N22   N   NS    0  -0.265   4.9630   2.2424   0.0103
 UGJ  H011  H   HNH2  0   0.412   1.8652   2.9603  -0.1928
 UGJ  H012  H   HNH2  0   0.423   0.2615   2.3861  -0.2923
 UGJ  H09   H   HCR6  0   0.278  -1.3973   0.7021  -2.5900
 UGJ  H10   H   HCR6  0   0.277  -2.9375   2.6149  -2.8472
 UGJ  H11   H   HCR6  0   0.279  -3.8468   3.7429  -0.8354
 UGJ  H12   H   HCR6  0   0.292  -3.2239   2.9513   1.4156
 UGJ  H191  H   HNH2  0   0.422  -1.6503  -4.2618  -0.2055
 UGJ  H192  H   HNH2  0   0.417  -0.0378  -4.8416  -0.0511

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
 UGJ  N01  C02   single    1.339  0.020  1.339
 UGJ  C02  C03   aromatic  1.383  0.020  1.383
 UGJ  C02  C06   aromatic  1.444  0.020  1.444
 UGJ  C03  S04   aromatic  1.757  0.020  1.757
 UGJ  C03  C21   single    1.396  0.020  1.396
 UGJ  S04  C05   aromatic  1.724  0.020  1.724
 UGJ  C05  C06   aromatic  1.409  0.020  1.409
 UGJ  C05  N20   aromatic  1.315  0.020  1.315
 UGJ  C06  C07   aromatic  1.396  0.020  1.396
 UGJ  C07  C08   single    1.480  0.020  1.480
 UGJ  C07  C15   aromatic  1.385  0.020  1.385
 UGJ  C08  C09   aromatic  1.392  0.020  1.392
 UGJ  C08  C13   aromatic  1.392  0.020  1.392
 UGJ  C09  C10   aromatic  1.386  0.020  1.386
 UGJ  C10  C11   aromatic  1.388  0.020  1.388
 UGJ  C11  C12   aromatic  1.387  0.020  1.387
 UGJ  C12  C13   aromatic  1.386  0.020  1.386
 UGJ  C13  CL    single    1.729  0.020  1.729
 UGJ  C15  C16   single    1.418  0.020  1.418
 UGJ  C15  C18   aromatic  1.431  0.020  1.431
 UGJ  C16  N17   triple    1.153  0.020  1.153
 UGJ  C18  N19   single    1.332  0.020  1.332
 UGJ  C18  N20   aromatic  1.329  0.020  1.329
 UGJ  C21  N22   triple    1.158  0.020  1.158
 UGJ  N01  H011  single    0.860  0.020  1.020
 UGJ  N01  H012  single    0.860  0.020  1.020
 UGJ  C09  H09   single    0.930  0.020  1.080
 UGJ  C10  H10   single    0.930  0.020  1.080
 UGJ  C11  H11   single    0.930  0.020  1.080
 UGJ  C12  H12   single    0.930  0.020  1.080
 UGJ  N19  H191  single    0.860  0.020  1.020
 UGJ  N19  H192  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
 UGJ  H012  N01  H011  116.26  3.000
 UGJ  H012  N01  C02   121.58  3.000
 UGJ  H011  N01  C02   120.74  3.000
 UGJ  C06   C02  C03   110.60  3.000
 UGJ  C06   C02  N01   124.86  3.000
 UGJ  C03   C02  N01   124.53  3.000
 UGJ  C21   C03  S04   121.06  3.000
 UGJ  C21   C03  C02   125.06  3.000
 UGJ  S04   C03  C02   113.88  3.000
 UGJ  C05   S04  C03    90.32  3.000
 UGJ  N20   C05  C06   126.41  3.000
 UGJ  N20   C05  S04   120.85  3.000
 UGJ  C06   C05  S04   112.74  3.000
 UGJ  C07   C06  C05   116.37  3.000
 UGJ  C07   C06  C02   131.16  3.000
 UGJ  C05   C06  C02   112.46  3.000
 UGJ  C15   C07  C08   119.04  3.000
 UGJ  C15   C07  C06   118.17  3.000
 UGJ  C08   C07  C06   122.78  3.000
 UGJ  C13   C08  C09   118.90  3.000
 UGJ  C13   C08  C07   121.15  3.000
 UGJ  C09   C08  C07   119.95  3.000
 UGJ  H09   C09  C10   120.29  3.000
 UGJ  H09   C09  C08   119.24  3.000
 UGJ  C10   C09  C08   120.47  3.000
 UGJ  H10   C10  C11   120.34  3.000
 UGJ  H10   C10  C09   119.81  3.000
 UGJ  C11   C10  C09   119.84  3.000
 UGJ  H11   C11  C12   119.28  3.000
 UGJ  H11   C11  C10   120.27  3.000
 UGJ  C12   C11  C10   120.44  3.000
 UGJ  H12   C12  C13   120.15  3.000
 UGJ  H12   C12  C11   120.59  3.000
 UGJ  C13   C12  C11   119.26  3.000
 UGJ  CL    C13  C12   119.60  3.000
 UGJ  CL    C13  C08   119.31  3.000
 UGJ  C12   C13  C08   121.08  3.000
 UGJ  C18   C15  C16   119.52  3.000
 UGJ  C18   C15  C07   120.48  3.000
 UGJ  C16   C15  C07   120.00  3.000
 UGJ  N17   C16  C15   180.00  3.000
 UGJ  N20   C18  N19   117.90  3.000
 UGJ  N20   C18  C15   120.84  3.000
 UGJ  N19   C18  C15   121.26  3.000
 UGJ  H192  N19  H191  117.58  3.000
 UGJ  H192  N19  C18   119.59  3.000
 UGJ  H191  N19  C18   122.77  3.000
 UGJ  C18   N20  C05   117.73  3.000
 UGJ  N22   C21  C03   180.00  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
 UGJ  CONST_01  C05   S04  C03  C02    0.00  0.0  0
 UGJ  CONST_02  S04   C05  C06  C02    0.00  0.0  0
 UGJ  CONST_03  N20   C05  C06  C02  180.00  0.0  0
 UGJ  CONST_04  C08   C07  C06  C02    0.00  0.0  0
 UGJ  CONST_05  C15   C07  C06  C02  180.00  0.0  0
 UGJ  CONST_06  C05   C06  C02  C03    0.00  0.0  0
 UGJ  CONST_07  C07   C06  C02  C03  180.00  0.0  0
 UGJ  CONST_08  C06   C05  S04  C03    0.00  0.0  0
 UGJ  CONST_09  N20   C05  S04  C03  180.00  0.0  0
 UGJ  CONST_10  C06   C02  C03  S04    0.00  0.0  0
 UGJ  CONST_11  C07   C06  C05  S04  180.00  0.0  0
 UGJ  CONST_12  C18   N20  C05  S04  180.00  0.0  0
 UGJ  CONST_13  C08   C07  C06  C05  180.00  0.0  0
 UGJ  CONST_14  C15   C07  C06  C05    0.00  0.0  0
 UGJ  CONST_15  C15   C18  N20  C05    0.00  0.0  0
 UGJ  CONST_16  C18   N20  C05  C06    0.00  0.0  0
 UGJ  CONST_19  C18   C15  C07  C06    0.00  0.0  0
 UGJ  CONST_20  N20   C05  C06  C07    0.00  0.0  0
 UGJ  CONST_21  C10   C09  C08  C07  180.00  0.0  0
 UGJ  CONST_22  C12   C13  C08  C07  180.00  0.0  0
 UGJ  CONST_23  N20   C18  C15  C07    0.00  0.0  0
 UGJ  CONST_24  C18   C15  C07  C08  180.00  0.0  0
 UGJ  CONST_25  C11   C10  C09  C08    0.00  0.0  0
 UGJ  CONST_26  C11   C12  C13  C08    0.00  0.0  0
 UGJ  CONST_28  C12   C13  C08  C09    0.00  0.0  0
 UGJ  CONST_29  C12   C11  C10  C09    0.00  0.0  0
 UGJ  CONST_30  C13   C08  C09  C10    0.00  0.0  0
 UGJ  CONST_31  C13   C12  C11  C10    0.00  0.0  0
 UGJ  CONST_33  S04   C03  C02  N01  180.00  0.0  0
 UGJ  CONST_34  C05   C06  C02  N01  180.00  0.0  0
 UGJ  CONST_35  C07   C06  C02  N01    0.00  0.0  0
 UGJ  CONST_36  C21   C03  S04  C05  180.00  0.0  0
 UGJ  CONST_37  N19   C18  N20  C05  180.00  0.0  0
 UGJ  CONST_38  C21   C03  C02  C06  180.00  0.0  0
 UGJ  CONST_39  C16   C15  C07  C06  180.00  0.0  0
 UGJ  CONST_40  CL    C13  C08  C07    0.00  0.0  0
 UGJ  CONST_41  N19   C18  C15  C07  180.00  0.0  0
 UGJ  CONST_42  C16   C15  C07  C08    0.00  0.0  0
 UGJ  CONST_43  CL    C13  C08  C09  180.00  0.0  0
 UGJ  CONST_44  CL    C13  C12  C11  180.00  0.0  0
 UGJ  CONST_45  N20   C18  C15  C16  180.00  0.0  0
 UGJ  CONST_46  H09   C09  C08  C07    0.00  0.0  0
 UGJ  CONST_47  H10   C10  C09  C08  180.00  0.0  0
 UGJ  CONST_48  H12   C12  C13  C08  180.00  0.0  0
 UGJ  CONST_49  H11   C11  C10  C09  180.00  0.0  0
 UGJ  CONST_50  H011  N01  C02  C03    0.00  0.0  0
 UGJ  CONST_51  H012  N01  C02  C03  180.00  0.0  0
 UGJ  CONST_52  H191  N19  C18  C15    0.00  0.0  0
 UGJ  CONST_53  H192  N19  C18  C15  180.00  0.0  0

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
 UGJ  plan-1  C07   0.020
 UGJ  plan-1  C08   0.020
 UGJ  plan-1  C09   0.020
 UGJ  plan-1  C10   0.020
 UGJ  plan-1  C11   0.020
 UGJ  plan-1  C12   0.020
 UGJ  plan-1  C13   0.020
 UGJ  plan-1  CL    0.020
 UGJ  plan-1  H09   0.020
 UGJ  plan-1  H10   0.020
 UGJ  plan-1  H11   0.020
 UGJ  plan-1  H12   0.020
 UGJ  plan-2  N01   0.020
 UGJ  plan-2  C02   0.020
 UGJ  plan-2  C03   0.020
 UGJ  plan-2  S04   0.020
 UGJ  plan-2  C05   0.020
 UGJ  plan-2  C06   0.020
 UGJ  plan-2  C07   0.020
 UGJ  plan-2  C08   0.020
 UGJ  plan-2  C15   0.020
 UGJ  plan-2  C16   0.020
 UGJ  plan-2  N17   0.020
 UGJ  plan-2  C18   0.020
 UGJ  plan-2  N19   0.020
 UGJ  plan-2  N20   0.020
 UGJ  plan-2  C21   0.020
 UGJ  plan-2  N22   0.020
 UGJ  plan-3  N01   0.020
 UGJ  plan-3  C02   0.020
 UGJ  plan-3  H011  0.020
 UGJ  plan-3  H012  0.020
 UGJ  plan-4  C18   0.020
 UGJ  plan-4  N19   0.020
 UGJ  plan-4  H191  0.020
 UGJ  plan-4  H192  0.020

