# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:44:43 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-methyl-N-[(1Z)-3-nitrocyclohexa-2,4-dien-1-ylidene]-4,5-dihydro[1,3]thiazolo[4,5-h]quinazolin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc2c(CCc3cnc(N=C4CC=CC(=C4)[N+]([O-])=O)nc23)n1
#
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
 X1N  X1N  2-methyl-N-[(1Z)-3-nitrocyclohexa-2,4-dien-1-ylidene]-4,5-dihydro[1,3]thiazolo[4,5-h]quinazolin-8-amine  ligand  37  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X1N
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
 X1N  O9B   O  O     -1  -0.368   3.8834   0.7581   2.6649
 X1N  N7B   N  N      1   0.335   4.6518   1.0002   1.7670
 X1N  O8B   O  O      0  -0.360   5.6818   1.6151   1.9002
 X1N  C3B   C  CR6    0   0.301   4.3270   0.5212   0.4184
 X1N  C2B   C  CR16   0  -0.314   3.1259  -0.0449   0.2270
 X1N  C4B   C  CR16   0  -0.275   5.3148   0.7201  -0.6196
 X1N  C5B   C  CR16   0  -0.213   5.0483   0.2676  -1.8464
 X1N  C6B   C  C      0  -0.551   3.7958  -0.4554  -2.1841
 X1N  C1B   C  CR6    0   0.244   2.7409  -0.4766  -1.1134
 X1N  N7    N  N      0  -0.427   1.5677  -0.8525  -1.4443
 X1N  C2    C  CR6    0   0.453   0.5445  -1.0699  -0.5398
 X1N  N3    N  N      0  -0.449  -0.6028  -0.4624  -0.8258
 X1N  C4    C  CR66   0   0.307  -1.6227  -0.7084  -0.0154
 X1N  C5A   C  CR56   0  -0.357  -2.8842  -0.0410  -0.2157
 X1N  S4A   S  S2     0   0.264  -3.3413   0.9262  -1.5556
 X1N  C3A   C  CR5    0   0.059  -4.8410   1.2584  -0.7663
 X1N  C20   C  CH3    0  -0.717  -5.8799   2.1089  -1.4059
 X1N  N2A   N  N      0  -0.397  -4.9711   0.7008   0.4023
 X1N  C1A   C  CR56   0   0.333  -3.8772  -0.0342   0.7246
 X1N  C6A   C  C      0  -0.523  -3.6989  -0.7349   2.0323
 X1N  C60   C  C      0  -0.519  -2.7612  -1.9314   1.8694
 X1N  C5    C  CR66   0  -0.010  -1.5385  -1.6007   1.0629
 X1N  C6    C  CR16   0  -0.060  -0.2953  -2.1675   1.2512
 X1N  N1    N  N      0  -0.433   0.7505  -1.9042   0.4715
 X1N  H2B   H  HCR6   0   0.317   2.4190  -0.1337   1.0375
 X1N  H4B   H  HCR6   0   0.296   6.2425   1.2248  -0.3983
 X1N  H5B   H  HCR6   0   0.288   5.7723   0.3982  -2.6397
 X1N  H6B1  H  H      0   0.306   3.3706  -0.0738  -3.1154
 X1N  H6B2  H  H      0   0.314   4.0595  -1.4978  -2.4080
 X1N  H201  H  HCH3   0   0.258  -5.5698   2.4666  -2.3849
 X1N  H202  H  HCH3   0   0.273  -6.8055   1.5455  -1.5250
 X1N  H203  H  HCH3   0   0.273  -6.0966   2.9743  -0.7794
 X1N  H6A1  H  H      0   0.268  -3.2892  -0.0252   2.7587
 X1N  H6A2  H  H      0   0.273  -4.6622  -1.0632   2.4229
 X1N  H601  H  H      0   0.270  -2.4748  -2.3220   2.8462
 X1N  H602  H  H      0   0.266  -3.3017  -2.7348   1.3576
 X1N  H6    H  HCR6   0   0.274  -0.1278  -2.8663   2.0649

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
 X1N  O9B  N7B   single    1.206  0.020  1.206
 X1N  N7B  O8B   double    1.207  0.020  1.207
 X1N  N7B  C3B   single    1.468  0.020  1.468
 X1N  C3B  C2B   double    1.342  0.020  1.342
 X1N  C3B  C4B   single    1.447  0.020  1.447
 X1N  C2B  C1B   single    1.460  0.020  1.460
 X1N  C4B  C5B   double    1.334  0.020  1.334
 X1N  C5B  C6B   single    1.485  0.020  1.485
 X1N  C6B  C1B   single    1.503  0.020  1.503
 X1N  C1B  N7    double    1.276  0.020  1.276
 X1N  N7   C2    single    1.383  0.020  1.383
 X1N  C2   N3    aromatic  1.329  0.020  1.329
 X1N  C2   N1    aromatic  1.327  0.020  1.327
 X1N  N3   C4    aromatic  1.326  0.020  1.326
 X1N  C4   C5A   aromatic  1.441  0.020  1.441
 X1N  C4   C5    aromatic  1.402  0.020  1.402
 X1N  C5A  S4A   aromatic  1.715  0.020  1.715
 X1N  C5A  C1A   aromatic  1.368  0.020  1.368
 X1N  S4A  C3A   aromatic  1.727  0.020  1.727
 X1N  C3A  C20   single    1.487  0.020  1.487
 X1N  C3A  N2A   aromatic  1.301  0.020  1.301
 X1N  N2A  C1A   aromatic  1.357  0.020  1.357
 X1N  C1A  C6A   single    1.494  0.020  1.494
 X1N  C6A  C60   single    1.529  0.020  1.529
 X1N  C60  C5    single    1.502  0.020  1.502
 X1N  C5   C6    aromatic  1.379  0.020  1.379
 X1N  C6   N1    aromatic  1.331  0.020  1.331
 X1N  C2B  H2B   single    0.930  0.020  1.080
 X1N  C4B  H4B   single    0.930  0.020  1.080
 X1N  C5B  H5B   single    0.930  0.020  1.080
 X1N  C6B  H6B1  single    0.970  0.020  1.090
 X1N  C6B  H6B2  single    0.970  0.020  1.090
 X1N  C20  H201  single    0.970  0.020  1.090
 X1N  C20  H202  single    0.970  0.020  1.090
 X1N  C20  H203  single    0.970  0.020  1.090
 X1N  C6A  H6A1  single    0.970  0.020  1.090
 X1N  C6A  H6A2  single    0.970  0.020  1.090
 X1N  C60  H601  single    0.970  0.020  1.090
 X1N  C60  H602  single    0.970  0.020  1.090
 X1N  C6   H6    single    0.930  0.020  1.080

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
 X1N  C3B   N7B  O8B   117.16  3.000
 X1N  C3B   N7B  O9B   118.52  3.000
 X1N  O8B   N7B  O9B   124.32  3.000
 X1N  C4B   C3B  C2B   124.54  3.000
 X1N  C4B   C3B  N7B   117.61  3.000
 X1N  C2B   C3B  N7B   117.84  3.000
 X1N  H2B   C2B  C1B   119.51  3.000
 X1N  H2B   C2B  C3B   120.94  3.000
 X1N  C1B   C2B  C3B   119.46  3.000
 X1N  H4B   C4B  C5B   121.26  3.000
 X1N  H4B   C4B  C3B   120.28  3.000
 X1N  C5B   C4B  C3B   118.47  3.000
 X1N  H5B   C5B  C6B   117.16  3.000
 X1N  H5B   C5B  C4B   119.96  3.000
 X1N  C6B   C5B  C4B   122.86  3.000
 X1N  H6B2  C6B  H6B1  104.55  3.000
 X1N  H6B2  C6B  C1B   107.47  3.000
 X1N  H6B1  C6B  C1B   109.81  3.000
 X1N  H6B2  C6B  C5B   107.81  3.000
 X1N  H6B1  C6B  C5B   110.61  3.000
 X1N  C1B   C6B  C5B   115.90  3.000
 X1N  N7    C1B  C6B   117.70  3.000
 X1N  N7    C1B  C2B   124.60  3.000
 X1N  C6B   C1B  C2B   117.69  3.000
 X1N  C2    N7   C1B   123.86  3.000
 X1N  N1    C2   N3    125.82  3.000
 X1N  N1    C2   N7    118.84  3.000
 X1N  N3    C2   N7    115.22  3.000
 X1N  C4    N3   C2    116.60  3.000
 X1N  C5    C4   C5A   117.01  3.000
 X1N  C5    C4   N3    122.82  3.000
 X1N  C5A   C4   N3    120.17  3.000
 X1N  C1A   C5A  S4A   109.93  3.000
 X1N  C1A   C5A  C4    122.84  3.000
 X1N  S4A   C5A  C4    127.10  3.000
 X1N  C3A   S4A  C5A    89.02  3.000
 X1N  N2A   C3A  C20   124.15  3.000
 X1N  N2A   C3A  S4A   114.51  3.000
 X1N  C20   C3A  S4A   121.34  3.000
 X1N  H203  C20  H202  107.72  3.000
 X1N  H203  C20  H201  108.24  3.000
 X1N  H202  C20  H201  108.29  3.000
 X1N  H203  C20  C3A   110.22  3.000
 X1N  H202  C20  C3A   110.16  3.000
 X1N  H201  C20  C3A   112.09  3.000
 X1N  C1A   N2A  C3A   111.39  3.000
 X1N  C6A   C1A  N2A   123.93  3.000
 X1N  C6A   C1A  C5A   120.84  3.000
 X1N  N2A   C1A  C5A   115.14  3.000
 X1N  H6A2  C6A  H6A1  106.75  3.000
 X1N  H6A2  C6A  C60   110.15  3.000
 X1N  H6A1  C6A  C60   110.39  3.000
 X1N  H6A2  C6A  C1A   110.44  3.000
 X1N  H6A1  C6A  C1A   108.74  3.000
 X1N  C60   C6A  C1A   110.30  3.000
 X1N  H602  C60  H601  106.59  3.000
 X1N  H602  C60  C5    108.20  3.000
 X1N  H601  C60  C5    110.26  3.000
 X1N  H602  C60  C6A   108.73  3.000
 X1N  H601  C60  C6A   110.24  3.000
 X1N  C5    C60  C6A   112.60  3.000
 X1N  C6    C5   C60   124.76  3.000
 X1N  C6    C5   C4    114.88  3.000
 X1N  C60   C5   C4    120.28  3.000
 X1N  H6    C6   N1    116.44  3.000
 X1N  H6    C6   C5    120.39  3.000
 X1N  N1    C6   C5    123.17  3.000
 X1N  C6    N1   C2    116.67  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
 X1N  CONST_01  C5A   C4   N3   C2   180.00   0.0  0
 X1N  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 X1N  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 X1N  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 X1N  CONST_05  S4A   C5A  C4   N3     0.00   0.0  0
 X1N  CONST_06  C1A   C5A  C4   N3   180.00   0.0  0
 X1N  CONST_07  C6    C5   C4   N3     0.00   0.0  0
 X1N  CONST_08  N1    C2   N3   C4     0.00   0.0  0
 X1N  CONST_09  C3A   S4A  C5A  C4   180.00   0.0  0
 X1N  CONST_10  N2A   C1A  C5A  C4   180.00   0.0  0
 X1N  CONST_11  N1    C6   C5   C4     0.00   0.0  0
 X1N  CONST_12  C6    C5   C4   C5A  180.00   0.0  0
 X1N  CONST_13  N2A   C3A  S4A  C5A    0.00   0.0  0
 X1N  CONST_14  C3A   N2A  C1A  C5A    0.00   0.0  0
 X1N  CONST_15  C5    C4   C5A  S4A  180.00   0.0  0
 X1N  CONST_16  N2A   C1A  C5A  S4A    0.00   0.0  0
 X1N  CONST_17  C1A   N2A  C3A  S4A    0.00   0.0  0
 X1N  CONST_18  C1A   C5A  S4A  C3A    0.00   0.0  0
 X1N  CONST_19  C5    C4   C5A  C1A    0.00   0.0  0
 X1N  CONST_20  C4    N3   C2   N7   180.00   0.0  0
 X1N  CONST_21  C6    N1   C2   N7   180.00   0.0  0
 X1N  CONST_22  C20   C3A  S4A  C5A  180.00   0.0  0
 X1N  CONST_23  C1A   N2A  C3A  C20  180.00   0.0  0
 X1N  CONST_24  H6    C6   N1   C2   180.00   0.0  0
 X1N  Var_01    C6B   C1B  C2B  C3B    9.10  30.0  1
 X1N  Var_02    C6B   C5B  C4B  C3B   -1.32  30.0  1
 X1N  Var_03    C5B   C4B  C3B  C2B   -2.76  30.0  1
 X1N  Var_04    C5B   C6B  C1B  C2B  -12.34  30.0  1
 X1N  Var_05    C1B   C2B  C3B  C4B   -1.42  30.0  1
 X1N  Var_06    C1B   C6B  C5B  C4B    8.76  30.0  1
 X1N  Var_07    C6A   C60  C5   C4   -35.78  30.0  1
 X1N  Var_08    C60   C6A  C1A  C5A  -29.57  30.0  1
 X1N  Var_09    C5    C60  C6A  C1A   45.26  30.0  1
 X1N  Var_10    N3    C2   N7   C1B  129.47  30.0  2
 X1N  Var_11    C2B   C3B  N7B  O9B    6.62  30.0  2
 X1N  Var_12    H201  C20  C3A  S4A    0.01  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
 X1N  plan-1  O9B  0.020
 X1N  plan-1  N7B  0.020
 X1N  plan-1  O8B  0.020
 X1N  plan-1  C3B  0.020
 X1N  plan-2  C4   0.020
 X1N  plan-2  C5A  0.020
 X1N  plan-2  S4A  0.020
 X1N  plan-2  C3A  0.020
 X1N  plan-2  C20  0.020
 X1N  plan-2  N2A  0.020
 X1N  plan-2  C1A  0.020
 X1N  plan-2  C6A  0.020
 X1N  plan-3  N7   0.020
 X1N  plan-3  C2   0.020
 X1N  plan-3  N3   0.020
 X1N  plan-3  C4   0.020
 X1N  plan-3  C5A  0.020
 X1N  plan-3  C60  0.020
 X1N  plan-3  C5   0.020
 X1N  plan-3  C6   0.020
 X1N  plan-3  N1   0.020
 X1N  plan-3  H6   0.020

