# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:36:32 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-[(2~{S},6~{R})-2,6-dimethylpiperidin-1-yl]-8-nitro-6-(trifluoromethyl)-1,3-benzoxazin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC[C@@H](C)N1C2=NC(=O)c3cc(cc(c3O2)[N+]([O-])=O)C(F)(F)F
#
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
 G1H  G1H  2-[(2~{S},6~{R})-2,6-dimethylpiperidin-1-yl]-8-nitro-6-(trifluoromethyl)-1,3-benzoxazin-4-one  ligand  42  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G1H
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
 G1H  C1   C  CR16   0  -0.292   2.6218  -0.9595   0.2683
 G1H  C2   C  CR6    0   0.168   1.3092  -1.2734  -0.0178
 G1H  C3   C  CR66   0   0.499   0.3558  -0.2675  -0.1737
 G1H  C5   C  CR16   0  -0.310   2.0741   1.3756   0.1804
 G1H  C4   C  CR66   0  -0.172   0.7483   1.0576  -0.0760
 G1H  C6   C  CR6    0  -0.195   3.0090   0.3719   0.3562
 G1H  N8   N  N      1   0.336   0.9646  -2.6742  -0.1838
 G1H  O9   O  O      0  -0.357   1.4436  -3.4588   0.5969
 G1H  C7   C  CT     0   1.072   4.4292   0.7169   0.6893
 G1H  F28  F  F      0  -0.301   4.7982   1.8758   0.1389
 G1H  F27  F  F      0  -0.307   4.6012   0.8391   2.0114
 G1H  F29  F  F      0  -0.300   5.2832  -0.2184   0.2679
 G1H  O11  O  O      0  -0.453  -0.9270  -0.5879  -0.3889
 G1H  C12  C  CR6    0   0.748  -1.8582   0.3976  -0.4406
 G1H  N13  N  N      0  -0.506  -1.5713   1.6552  -0.3737
 G1H  C14  C  CR6    0   0.503  -0.2898   2.0943  -0.2539
 G1H  O15  O  O      0  -0.432  -0.0085   3.2771  -0.2558
 G1H  N16  N  NT     0  -0.488  -3.0977  -0.0618  -0.6208
 G1H  C21  C  CH1    0  -0.121  -3.6664  -1.2364   0.0962
 G1H  C22  C  CH3    0  -0.672  -2.8074  -2.4779   0.2570
 G1H  C20  C  CH2    0  -0.418  -4.1971  -0.7323   1.4407
 G1H  C19  C  CH2    0  -0.444  -5.2283   0.3809   1.2731
 G1H  C18  C  CH2    0  -0.419  -4.7384   1.4890   0.3439
 G1H  C17  C  CH1    0  -0.102  -4.1834   0.8936  -0.9452
 G1H  C23  C  CH3    0  -0.674  -3.8712   1.9133  -2.0286
 G1H  H1   H  HCR6   0   0.323   3.3395  -1.7587   0.3941
 G1H  H2   H  HCR6   0   0.300   2.3483   2.4203   0.2453
 G1H  H5   H  HCH1   0   0.258  -4.5170  -1.5327  -0.5227
 G1H  H6   H  HCH3   0   0.225  -2.0218  -2.3641   1.0015
 G1H  H7   H  HCH3   0   0.246  -3.4684  -3.2718   0.6054
 G1H  H8   H  HCH3   0   0.249  -2.3703  -2.8046  -0.6832
 G1H  H9   H  HCH2   0   0.246  -4.6407  -1.5719   1.9803
 G1H  H10  H  HCH2   0   0.228  -3.3497  -0.3861   2.0431
 G1H  H11  H  HCH2   0   0.223  -6.1457  -0.0488   0.8584
 G1H  H12  H  HCH2   0   0.241  -5.4940   0.7925   2.2487
 G1H  H13  H  HCH2   0   0.239  -5.5614   2.1657   0.1024
 G1H  H14  H  HCH2   0   0.234  -3.9639   2.0905   0.8270
 G1H  H15  H  HCH1   0   0.258  -4.9550   0.2446  -1.3697
 G1H  H16  H  HCH3   0   0.236  -3.3239   1.4604  -2.8561
 G1H  H17  H  HCH3   0   0.238  -4.8214   2.2731  -2.4251
 G1H  H18  H  HCH3   0   0.246  -3.3085   2.7679  -1.6661
 G1H  OXT  O  O     -1  -0.353   0.2487  -2.9626  -1.1097

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
 G1H  F29  C7   single    1.335  0.020  1.335
 G1H  F28  C7   single    1.335  0.020  1.335
 G1H  O15  C14  double    1.216  0.020  1.216
 G1H  C7   F27  single    1.339  0.020  1.339
 G1H  C7   C6   single    1.499  0.020  1.499
 G1H  C5   C6   aromatic  1.383  0.020  1.383
 G1H  C5   C4   aromatic  1.387  0.020  1.387
 G1H  C14  C4   single    1.478  0.020  1.478
 G1H  C14  N13  single    1.360  0.020  1.360
 G1H  C6   C1   aromatic  1.389  0.020  1.389
 G1H  C4   C3   aromatic  1.385  0.020  1.385
 G1H  N13  C12  double    1.292  0.020  1.292
 G1H  C1   C2   aromatic  1.380  0.020  1.380
 G1H  C3   C2   aromatic  1.395  0.020  1.395
 G1H  C3   O11  single    1.340  0.020  1.340
 G1H  C22  C21  single    1.518  0.020  1.518
 G1H  C12  O11  single    1.357  0.020  1.357
 G1H  C12  N16  single    1.334  0.020  1.334
 G1H  C2   N8   single    1.452  0.020  1.452
 G1H  C21  N16  single    1.489  0.020  1.489
 G1H  C21  C20  single    1.531  0.020  1.531
 G1H  N16  C17  single    1.482  0.020  1.482
 G1H  N8   O9   double    1.206  0.020  1.206
 G1H  C20  C19  single    1.527  0.020  1.527
 G1H  C23  C17  single    1.520  0.020  1.520
 G1H  C17  C18  single    1.525  0.020  1.525
 G1H  C19  C18  single    1.527  0.020  1.527
 G1H  C1   H1   single    0.930  0.020  1.080
 G1H  C5   H2   single    0.930  0.020  1.080
 G1H  C21  H5   single    0.970  0.020  1.090
 G1H  C22  H6   single    0.970  0.020  1.090
 G1H  C22  H7   single    0.970  0.020  1.090
 G1H  C22  H8   single    0.970  0.020  1.090
 G1H  C20  H9   single    0.970  0.020  1.090
 G1H  C20  H10  single    0.970  0.020  1.090
 G1H  C19  H11  single    0.970  0.020  1.090
 G1H  C19  H12  single    0.970  0.020  1.090
 G1H  C18  H13  single    0.970  0.020  1.090
 G1H  C18  H14  single    0.970  0.020  1.090
 G1H  C17  H15  single    0.970  0.020  1.090
 G1H  C23  H16  single    0.970  0.020  1.090
 G1H  C23  H17  single    0.970  0.020  1.090
 G1H  C23  H18  single    0.970  0.020  1.090
 G1H  N8   OXT  single    1.205  0.020  1.205

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
 G1H  H1   C1   C6   121.06  3.000
 G1H  H1   C1   C2   119.16  3.000
 G1H  C6   C1   C2   119.76  3.000
 G1H  N8   C2   C3   121.38  3.000
 G1H  N8   C2   C1   117.97  3.000
 G1H  C3   C2   C1   120.63  3.000
 G1H  O11  C3   C4   120.76  3.000
 G1H  O11  C3   C2   120.01  3.000
 G1H  C4   C3   C2   119.22  3.000
 G1H  H2   C5   C6   121.46  3.000
 G1H  H2   C5   C4   118.33  3.000
 G1H  C6   C5   C4   120.21  3.000
 G1H  C14  C4   C5   122.19  3.000
 G1H  C14  C4   C3   117.61  3.000
 G1H  C5   C4   C3   120.20  3.000
 G1H  C7   C6   C5   120.11  3.000
 G1H  C5   C6   C1   119.94  3.000
 G1H  C7   C6   C1   119.91  3.000
 G1H  OXT  N8   O9   125.28  3.000
 G1H  OXT  N8   C2   117.36  3.000
 G1H  O9   N8   C2   117.34  3.000
 G1H  F29  C7   F27  107.08  3.000
 G1H  F27  C7   F28  107.00  3.000
 G1H  F29  C7   F28  107.53  3.000
 G1H  F27  C7   C6   111.23  3.000
 G1H  F28  C7   C6   111.71  3.000
 G1H  F29  C7   C6   112.01  3.000
 G1H  C12  O11  C3   119.32  3.000
 G1H  N16  C12  N13  123.28  3.000
 G1H  N16  C12  O11  113.12  3.000
 G1H  N13  C12  O11  123.55  3.000
 G1H  C14  N13  C12  121.89  3.000
 G1H  O15  C14  N13  122.14  3.000
 G1H  N13  C14  C4   116.49  3.000
 G1H  O15  C14  C4   121.34  3.000
 G1H  C17  N16  C21  109.52  3.000
 G1H  C17  N16  C12  119.22  3.000
 G1H  C21  N16  C12  124.15  3.000
 G1H  H5   C21  C20  108.47  3.000
 G1H  H5   C21  C22  106.18  3.000
 G1H  C20  C21  C22  111.87  3.000
 G1H  H5   C21  N16  103.79  3.000
 G1H  C20  C21  N16  107.19  3.000
 G1H  C22  C21  N16  118.68  3.000
 G1H  H8   C22  H7   107.54  3.000
 G1H  H8   C22  H6   109.44  3.000
 G1H  H7   C22  H6   107.17  3.000
 G1H  H8   C22  C21  112.44  3.000
 G1H  H7   C22  C21  106.63  3.000
 G1H  H6   C22  C21  113.29  3.000
 G1H  H10  C20  H9   106.58  3.000
 G1H  H10  C20  C19  110.63  3.000
 G1H  H9   C20  C19  109.90  3.000
 G1H  H10  C20  C21  108.59  3.000
 G1H  H9   C20  C21  108.76  3.000
 G1H  C19  C20  C21  112.21  3.000
 G1H  H12  C19  H11  106.41  3.000
 G1H  H12  C19  C18  110.38  3.000
 G1H  H11  C19  C18  108.86  3.000
 G1H  H12  C19  C20  109.95  3.000
 G1H  H11  C19  C20  108.75  3.000
 G1H  C18  C19  C20  112.29  3.000
 G1H  H14  C18  H13  106.90  3.000
 G1H  H14  C18  C17  109.31  3.000
 G1H  H13  C18  C17  109.23  3.000
 G1H  H14  C18  C19  110.95  3.000
 G1H  H13  C18  C19  110.02  3.000
 G1H  C17  C18  C19  110.36  3.000
 G1H  H15  C17  C23  105.44  3.000
 G1H  H15  C17  C18  107.64  3.000
 G1H  C23  C17  C18  114.54  3.000
 G1H  H15  C17  N16  102.66  3.000
 G1H  C18  C17  N16  109.48  3.000
 G1H  C23  C17  N16  115.97  3.000
 G1H  H18  C23  H17  108.25  3.000
 G1H  H18  C23  H16  108.67  3.000
 G1H  H17  C23  H16  107.36  3.000
 G1H  H18  C23  C17  113.37  3.000
 G1H  H17  C23  C17  107.54  3.000
 G1H  H16  C23  C17  111.42  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
 G1H  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 G1H  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 G1H  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 G1H  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 G1H  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 G1H  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 G1H  CONST_07  C14  N13  C12  O11    0.00   0.0  0
 G1H  CONST_09  C17  N16  C12  O11  180.00   0.0  0
 G1H  CONST_11  C17  N16  C12  N13    0.00   0.0  0
 G1H  CONST_12  N16  C12  N13  C14  180.00   0.0  0
 G1H  CONST_13  C7   C6   C1   C2   180.00   0.0  0
 G1H  CONST_14  C7   C6   C5   C4   180.00   0.0  0
 G1H  CONST_15  N8   C2   C3   C4   180.00   0.0  0
 G1H  CONST_16  N8   C2   C1   C6   180.00   0.0  0
 G1H  CONST_17  O11  C3   C2   N8     0.00   0.0  0
 G1H  CONST_18  H2   C5   C6   C1   180.00   0.0  0
 G1H  CONST_19  H1   C1   C2   C3   180.00   0.0  0
 G1H  Var_01    N13  C14  C4   C3     6.03  30.0  1
 G1H  Var_02    N13  C12  O11  C3     4.36  30.0  1
 G1H  Var_03    C18  C19  C20  C21  -50.05  30.0  1
 G1H  Var_04    C17  C18  C19  C20   48.93  30.0  1
 G1H  Var_05    F29  C7   C6   C1    29.42  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 G1H  chir_01  C21  C22  N16  C20  positiv
 G1H  chir_02  C17  N16  C23  C18  positiv

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
 G1H  plan-1  C1   0.020
 G1H  plan-1  C2   0.020
 G1H  plan-1  C3   0.020
 G1H  plan-1  C5   0.020
 G1H  plan-1  C4   0.020
 G1H  plan-1  C6   0.020
 G1H  plan-1  N8   0.020
 G1H  plan-1  C7   0.020
 G1H  plan-1  O11  0.020
 G1H  plan-1  C14  0.020
 G1H  plan-1  H1   0.020
 G1H  plan-1  H2   0.020
 G1H  plan-2  C2   0.020
 G1H  plan-2  N8   0.020
 G1H  plan-2  O9   0.020
 G1H  plan-2  OXT  0.020
 G1H  plan-3  C4   0.020
 G1H  plan-3  N13  0.020
 G1H  plan-3  C14  0.020
 G1H  plan-3  O15  0.020
 G1H  plan-4  O11  0.020
 G1H  plan-4  C12  0.020
 G1H  plan-4  N13  0.020
 G1H  plan-4  C14  0.020
 G1H  plan-4  N16  0.020
 G1H  plan-4  C21  0.020
 G1H  plan-4  C17  0.020

