# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:07:40 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2Z,3Z)-bis{amino[(2-aminophenyl)sulfanyl]methylidene}butanedinitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N\C(Sc1ccccc1N)=C(C#N)/C(C#N)=C(\N)Sc2ccccc2N
#
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
 5BM  5BM  (2Z,3Z)-bis{amino[(2-aminophenyl)sulfanyl]methylidene}butanedinitrile  ligand  42  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5BM
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
 5BM  C01   C  C     0  -0.177   0.7530   1.6834  -0.1429
 5BM  C02   C  CSP   0   0.019   1.1336   2.9349   0.3784
 5BM  N03   N  NS    0  -0.295   1.4099   3.9792   0.7980
 5BM  C04   C  C     0   0.234   1.6092   0.6060  -0.0521
 5BM  N05   N  NH2   0  -0.779   1.3307  -0.5844  -0.5640
 5BM  S06   S  S2    0   0.105   3.1346   0.8299   0.8114
 5BM  C07   C  CR6   0  -0.322   4.0000  -0.6742   0.4941
 5BM  C08   C  CR6   0   0.414   4.7969  -0.7983  -0.6628
 5BM  C09   C  CR16  0  -0.333   5.5089  -2.0009  -0.8257
 5BM  C10   C  CR16  0  -0.236   5.4348  -3.0072   0.1141
 5BM  C11   C  CR16  0  -0.288   4.6518  -2.8709   1.2601
 5BM  C12   C  CR16  0  -0.196   3.9428  -1.6996   1.4399
 5BM  N13   N  NH2   0  -0.852   4.9156   0.1964  -1.5776
 5BM  C21   C  C     0  -0.182  -0.5601   1.5633  -0.8110
 5BM  C22   C  CSP   0   0.021  -0.6470   1.8654  -2.1843
 5BM  N23   N  NS    0  -0.295  -0.6742   2.1190  -3.3147
 5BM  C24   C  C     0   0.238  -1.6875   1.1940  -0.1089
 5BM  N25   N  NH2   0  -0.778  -1.6667   0.8639   1.1739
 5BM  S26   S  S2    0   0.106  -3.2366   1.1933  -0.9593
 5BM  C27   C  CR6   0  -0.310  -4.2549   0.2221   0.1056
 5BM  C28   C  CR6   0   0.397  -4.1386  -1.1820   0.0986
 5BM  C29   C  CR16  0  -0.325  -5.0126  -1.9039   0.9273
 5BM  C30   C  CR16  0  -0.237  -5.9512  -1.2584   1.7072
 5BM  C31   C  CR16  0  -0.285  -6.0643   0.1303   1.7002
 5BM  C32   C  CR16  0  -0.205  -5.2100   0.8609   0.8957
 5BM  N33   N  NH2   0  -0.846  -3.1792  -1.8233  -0.6292
 5BM  HN05  H  HNH2  0   0.418   0.4601  -0.7368  -1.0479
 5BM  HN0A  H  HNH2  0   0.430   1.9398  -1.3760  -0.4370
 5BM  H09   H  HCR6  0   0.268   6.1281  -2.1277  -1.7054
 5BM  H10   H  HCR6  0   0.264   5.9986  -3.9171  -0.0480
 5BM  H11   H  HCR6  0   0.259   4.5989  -3.6627   1.9938
 5BM  H12   H  HCR6  0   0.275   3.3266  -1.5639   2.3199
 5BM  HN13  H  HNH2  0   0.393   4.2627   0.9610  -1.5714
 5BM  HN1A  H  HNH2  0   0.398   5.2982  -0.0284  -2.4799
 5BM  HN25  H  HNH2  0   0.423  -0.7973   0.8505   1.6831
 5BM  HN2A  H  HNH2  0   0.429  -2.5061   0.6279   1.6772
 5BM  H29   H  HCR6  0   0.268  -4.9447  -2.9850   0.9470
 5BM  H30   H  HCR6  0   0.265  -6.6101  -1.8497   2.3299
 5BM  H31   H  HCR6  0   0.259  -6.8039   0.6308   2.3094
 5BM  H32   H  HCR6  0   0.276  -5.2724   1.9414   0.8708
 5BM  HN33  H  HNH2  0   0.388  -2.8153  -1.3413  -1.4363
 5BM  HN3A  H  HNH2  0   0.393  -3.3236  -2.8069  -0.7904

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
 5BM  C01  C02   single    1.408  0.020  1.408
 5BM  C01  C04   double    1.379  0.020  1.379
 5BM  C01  C21   single    1.478  0.020  1.478
 5BM  C02  N03   triple    1.159  0.020  1.159
 5BM  C04  N05   single    1.325  0.020  1.325
 5BM  C04  S06   single    1.767  0.020  1.767
 5BM  S06  C07   single    1.764  0.020  1.764
 5BM  C07  C08   aromatic  1.410  0.020  1.410
 5BM  C07  C12   aromatic  1.396  0.020  1.396
 5BM  C08  C09   aromatic  1.407  0.020  1.407
 5BM  C08  N13   single    1.357  0.020  1.357
 5BM  C09  C10   aromatic  1.379  0.020  1.379
 5BM  C10  C11   aromatic  1.395  0.020  1.395
 5BM  C11  C12   aromatic  1.381  0.020  1.381
 5BM  C21  C22   single    1.409  0.020  1.409
 5BM  C21  C24   double    1.379  0.020  1.379
 5BM  C22  N23   triple    1.159  0.020  1.159
 5BM  C24  N25   single    1.325  0.020  1.325
 5BM  C24  S26   single    1.767  0.020  1.767
 5BM  S26  C27   single    1.765  0.020  1.765
 5BM  C27  C28   aromatic  1.409  0.020  1.409
 5BM  C27  C32   aromatic  1.394  0.020  1.394
 5BM  C28  C29   aromatic  1.404  0.020  1.404
 5BM  C28  N33   single    1.364  0.020  1.364
 5BM  C29  C30   aromatic  1.381  0.020  1.381
 5BM  C30  C31   aromatic  1.393  0.020  1.393
 5BM  C31  C32   aromatic  1.382  0.020  1.382
 5BM  N05  HN05  single    0.860  0.020  1.020
 5BM  N05  HN0A  single    0.860  0.020  1.020
 5BM  C09  H09   single    0.930  0.020  1.080
 5BM  C10  H10   single    0.930  0.020  1.080
 5BM  C11  H11   single    0.930  0.020  1.080
 5BM  C12  H12   single    0.930  0.020  1.080
 5BM  N13  HN13  single    0.890  0.020  1.040
 5BM  N13  HN1A  single    0.890  0.020  1.040
 5BM  N25  HN25  single    0.860  0.020  1.020
 5BM  N25  HN2A  single    0.860  0.020  1.020
 5BM  C29  H29   single    0.930  0.020  1.080
 5BM  C30  H30   single    0.930  0.020  1.080
 5BM  C31  H31   single    0.930  0.020  1.080
 5BM  C32  H32   single    0.930  0.020  1.080
 5BM  N33  HN33  single    0.890  0.020  1.040
 5BM  N33  HN3A  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
 5BM  C21   C01  C04   121.18  3.000
 5BM  C21   C01  C02   118.66  3.000
 5BM  C04   C01  C02   120.14  3.000
 5BM  N03   C02  C01   180.00  3.000
 5BM  S06   C04  N05   118.94  3.000
 5BM  S06   C04  C01   117.97  3.000
 5BM  N05   C04  C01   123.08  3.000
 5BM  HN0A  N05  HN05  117.67  3.000
 5BM  HN0A  N05  C04   122.03  3.000
 5BM  HN05  N05  C04   120.19  3.000
 5BM  C07   S06  C04   103.15  3.000
 5BM  C12   C07  C08   120.94  3.000
 5BM  C12   C07  S06   118.96  3.000
 5BM  C08   C07  S06   119.99  3.000
 5BM  N13   C08  C09   120.29  3.000
 5BM  N13   C08  C07   122.55  3.000
 5BM  C09   C08  C07   117.14  3.000
 5BM  H09   C09  C10   119.92  3.000
 5BM  H09   C09  C08   118.90  3.000
 5BM  C10   C09  C08   121.18  3.000
 5BM  H10   C10  C11   119.84  3.000
 5BM  H10   C10  C09   118.90  3.000
 5BM  C11   C10  C09   121.26  3.000
 5BM  H11   C11  C12   120.52  3.000
 5BM  H11   C11  C10   120.91  3.000
 5BM  C12   C11  C10   118.57  3.000
 5BM  H12   C12  C11   120.29  3.000
 5BM  H12   C12  C07   118.80  3.000
 5BM  C11   C12  C07   120.91  3.000
 5BM  HN1A  N13  HN13  115.00  3.000
 5BM  HN1A  N13  C08   118.33  3.000
 5BM  HN13  N13  C08   119.78  3.000
 5BM  C24   C21  C22   120.23  3.000
 5BM  C24   C21  C01   121.20  3.000
 5BM  C22   C21  C01   118.55  3.000
 5BM  N23   C22  C21   180.00  3.000
 5BM  S26   C24  N25   118.66  3.000
 5BM  S26   C24  C21   118.16  3.000
 5BM  N25   C24  C21   123.17  3.000
 5BM  HN2A  N25  HN25  117.62  3.000
 5BM  HN2A  N25  C24   121.97  3.000
 5BM  HN25  N25  C24   120.41  3.000
 5BM  C27   S26  C24   102.46  3.000
 5BM  C32   C27  C28   121.06  3.000
 5BM  C32   C27  S26   119.01  3.000
 5BM  C28   C27  S26   119.85  3.000
 5BM  N33   C28  C29   120.72  3.000
 5BM  N33   C28  C27   121.95  3.000
 5BM  C29   C28  C27   117.26  3.000
 5BM  H29   C29  C30   119.93  3.000
 5BM  H29   C29  C28   118.99  3.000
 5BM  C30   C29  C28   121.08  3.000
 5BM  H30   C30  C31   119.87  3.000
 5BM  H30   C30  C29   118.91  3.000
 5BM  C31   C30  C29   121.22  3.000
 5BM  H31   C31  C32   120.41  3.000
 5BM  H31   C31  C30   120.93  3.000
 5BM  C32   C31  C30   118.66  3.000
 5BM  H32   C32  C31   120.35  3.000
 5BM  H32   C32  C27   118.93  3.000
 5BM  C31   C32  C27   120.72  3.000
 5BM  HN3A  N33  HN33  112.99  3.000
 5BM  HN3A  N33  C28   116.34  3.000
 5BM  HN33  N33  C28   117.14  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
 5BM  CONST_01  C10   C09  C08  C07     0.00   0.0  0
 5BM  CONST_02  C10   C11  C12  C07     0.00   0.0  0
 5BM  CONST_03  C11   C12  C07  C08     0.00   0.0  0
 5BM  CONST_04  C11   C10  C09  C08     0.00   0.0  0
 5BM  CONST_05  C12   C07  C08  C09     0.00   0.0  0
 5BM  CONST_06  C12   C11  C10  C09     0.00   0.0  0
 5BM  CONST_07  C30   C29  C28  C27     0.00   0.0  0
 5BM  CONST_08  C30   C31  C32  C27     0.00   0.0  0
 5BM  CONST_09  C31   C32  C27  C28     0.00   0.0  0
 5BM  CONST_10  C31   C30  C29  C28     0.00   0.0  0
 5BM  CONST_11  C32   C27  C28  C29     0.00   0.0  0
 5BM  CONST_12  C32   C31  C30  C29     0.00   0.0  0
 5BM  CONST_13  C09   C08  C07  S06   180.00   0.0  0
 5BM  CONST_14  C11   C12  C07  S06   180.00   0.0  0
 5BM  CONST_15  N13   C08  C09  C10   180.00   0.0  0
 5BM  CONST_16  N13   C08  C07  C12   180.00   0.0  0
 5BM  CONST_17  C29   C28  C27  S26   180.00   0.0  0
 5BM  CONST_18  C31   C32  C27  S26   180.00   0.0  0
 5BM  CONST_19  N33   C28  C29  C30   180.00   0.0  0
 5BM  CONST_20  N33   C28  C27  C32   180.00   0.0  0
 5BM  CONST_21  H09   C09  C08  C07   180.00   0.0  0
 5BM  CONST_22  H11   C11  C12  C07   180.00   0.0  0
 5BM  CONST_23  H12   C12  C07  C08   180.00   0.0  0
 5BM  CONST_24  H10   C10  C09  C08   180.00   0.0  0
 5BM  CONST_25  H29   C29  C28  C27   180.00   0.0  0
 5BM  CONST_26  H31   C31  C32  C27   180.00   0.0  0
 5BM  CONST_27  H32   C32  C27  C28   180.00   0.0  0
 5BM  CONST_28  H30   C30  C29  C28   180.00   0.0  0
 5BM  Var_01    C08   C07  S06  C04    87.42  30.0  2
 5BM  Var_02    C28   C27  S26  C24   -77.95  30.0  2
 5BM  Var_03    N25   C24  C21  C01    -3.31   0.0  2
 5BM  Var_04    N05   C04  C01  C02  -177.53   0.0  2
 5BM  Var_05    C22   C21  C01  C02    86.85  30.0  2
 5BM  Var_06    C04   C01  C02  N03  -175.74  30.0  1
 5BM  Var_07    HN05  N05  C04  C01     0.05  30.0  2
 5BM  Var_08    HN25  N25  C24  C21    -1.57  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
 5BM  plan-1  S06   0.020
 5BM  plan-1  C07   0.020
 5BM  plan-1  C08   0.020
 5BM  plan-1  C09   0.020
 5BM  plan-1  C10   0.020
 5BM  plan-1  C11   0.020
 5BM  plan-1  C12   0.020
 5BM  plan-1  N13   0.020
 5BM  plan-1  H09   0.020
 5BM  plan-1  H10   0.020
 5BM  plan-1  H11   0.020
 5BM  plan-1  H12   0.020
 5BM  plan-2  S26   0.020
 5BM  plan-2  C27   0.020
 5BM  plan-2  C28   0.020
 5BM  plan-2  C29   0.020
 5BM  plan-2  C30   0.020
 5BM  plan-2  C31   0.020
 5BM  plan-2  C32   0.020
 5BM  plan-2  N33   0.020
 5BM  plan-2  H29   0.020
 5BM  plan-2  H30   0.020
 5BM  plan-2  H31   0.020
 5BM  plan-2  H32   0.020
 5BM  plan-3  C08   0.020
 5BM  plan-3  N13   0.020
 5BM  plan-3  HN13  0.020
 5BM  plan-3  HN1A  0.020
 5BM  plan-4  C28   0.020
 5BM  plan-4  N33   0.020
 5BM  plan-4  HN33  0.020
 5BM  plan-4  HN3A  0.020
 5BM  plan-5  C01   0.020
 5BM  plan-5  C02   0.020
 5BM  plan-5  C04   0.020
 5BM  plan-5  N05   0.020
 5BM  plan-5  S06   0.020
 5BM  plan-5  C21   0.020
 5BM  plan-6  C01   0.020
 5BM  plan-6  C21   0.020
 5BM  plan-6  C22   0.020
 5BM  plan-6  C24   0.020
 5BM  plan-6  N25   0.020
 5BM  plan-6  S26   0.020

