# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:57:59 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2R,4S)-6-chloro-4-(cyclopropylethynyl)-2-methyl-4-(trifluoromethyl)-1,4-dihydro-2H-3,1-benzoxazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1Nc2ccc(Cl)cc2[C@@](O1)(C#CC3CC3)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
 9ZJ  9ZJ  (2R,4S)-6-chloro-4-(cyclopropylethynyl)-2-methyl-4-(trifluoromethyl)-1,4-dihydro-2H-3,1-benzoxazine  ligand  34  21  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9ZJ
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
 9ZJ  CAK  C   CH2   0  -0.476   4.7981   1.8403  -1.0842
 9ZJ  CAL  C   CH2   0  -0.476   3.9524   3.0181  -0.7529
 9ZJ  CAS  C   CH1   0  -0.502   3.3441   1.8497  -1.4912
 9ZJ  CAF  C   CSP   0   0.069   2.4166   0.9933  -0.8150
 9ZJ  CAG  C   CSP   0   0.214   1.6342   0.2739  -0.2508
 9ZJ  CAU  C   CT    0  -0.133   0.6728  -0.6027   0.4202
 9ZJ  CAT  C   CT    0   1.025   0.5693  -0.1871   1.9056
 9ZJ  FAC  F   F     0  -0.294   0.2225   1.0938   2.0386
 9ZJ  FAD  F   F     0  -0.294  -0.3420  -0.9212   2.5417
 9ZJ  FAB  F   F     0  -0.298   1.7339  -0.3507   2.5325
 9ZJ  OAN  O   O2    0  -0.501   1.1510  -1.9238   0.5075
 9ZJ  CAR  C   CH1   0   0.110   0.6509  -2.8631  -0.4190
 9ZJ  CAA  C   CH3   0  -0.684   1.1608  -2.6233  -1.8334
 9ZJ  NAM  N   NH1   0  -0.685  -0.7888  -2.8826  -0.3109
 9ZJ  CAP  C   CR6   0   0.346  -1.4042  -1.6727  -0.5170
 9ZJ  CAQ  C   CR6   0  -0.019  -0.7026  -0.4988  -0.2212
 9ZJ  CAJ  C   CR16  0  -0.236  -1.2737   0.7391  -0.4883
 9ZJ  CAO  C   CR6   0  -0.061  -2.5575   0.8109  -0.9941
 9ZJ  CL   CL  CL    0  -0.138  -3.2653   2.3617  -1.3197
 9ZJ  CAH  C   CR16  0  -0.209  -3.2851  -0.3445  -1.2471
 9ZJ  CAI  C   CR16  0  -0.352  -2.7050  -1.5762  -1.0204
 9ZJ  H1   H   HCH2  0   0.269   5.5243   1.9303  -1.8806
 9ZJ  H2   H   HCH2  0   0.264   5.0847   1.1738  -0.2818
 9ZJ  H3   H   HCH2  0   0.264   3.6564   3.1638   0.2774
 9ZJ  H4   H   HCH2  0   0.269   4.0876   3.9297  -1.3196
 9ZJ  H5   H   HCH1  0   0.297   3.1377   2.0001  -2.5449
 9ZJ  H6   H   HCH1  0   0.269   1.0207  -3.8259  -0.0667
 9ZJ  H7   H   HCH3  0   0.247   2.2505  -2.6060  -1.8500
 9ZJ  H8   H   HCH3  0   0.247   0.8299  -3.4407  -2.4748
 9ZJ  H9   H   HCH3  0   0.239   0.7981  -1.6900  -2.2655
 9ZJ  H10  H   HNH1  0   0.393  -1.2346  -3.6814  -0.7368
 9ZJ  H11  H   HCR6  0   0.280  -0.7157   1.6488  -0.3117
 9ZJ  H12  H   HCR6  0   0.283  -4.2907  -0.2868  -1.6411
 9ZJ  H13  H   HCR6  0   0.275  -3.2580  -2.4799  -1.2446

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
 9ZJ  CL   CAO  single    1.735  0.020  1.735
 9ZJ  CAO  CAH  aromatic  1.389  0.020  1.389
 9ZJ  CAO  CAJ  aromatic  1.382  0.020  1.382
 9ZJ  CAH  CAI  aromatic  1.380  0.020  1.380
 9ZJ  CAJ  CAQ  aromatic  1.389  0.020  1.389
 9ZJ  FAC  CAT  single    1.334  0.020  1.334
 9ZJ  CAI  CAP  aromatic  1.398  0.020  1.398
 9ZJ  CAQ  CAP  aromatic  1.399  0.020  1.399
 9ZJ  CAQ  CAU  single    1.521  0.020  1.521
 9ZJ  CAP  NAM  single    1.373  0.020  1.373
 9ZJ  CAT  FAB  single    1.333  0.020  1.333
 9ZJ  CAT  FAD  single    1.332  0.020  1.332
 9ZJ  CAT  CAU  single    1.546  0.020  1.546
 9ZJ  CAU  OAN  single    1.408  0.020  1.408
 9ZJ  CAU  CAG  single    1.464  0.020  1.464
 9ZJ  NAM  CAR  single    1.444  0.020  1.444
 9ZJ  CAR  OAN  single    1.411  0.020  1.411
 9ZJ  CAR  CAA  single    1.522  0.020  1.522
 9ZJ  CAG  CAF  triple    1.203  0.020  1.203
 9ZJ  CAF  CAS  single    1.432  0.020  1.432
 9ZJ  CAK  CAS  single    1.510  0.020  1.510
 9ZJ  CAK  CAL  single    1.487  0.020  1.487
 9ZJ  CAS  CAL  single    1.510  0.020  1.510
 9ZJ  CAK  H1   single    0.970  0.020  1.090
 9ZJ  CAK  H2   single    0.970  0.020  1.090
 9ZJ  CAL  H3   single    0.970  0.020  1.090
 9ZJ  CAL  H4   single    0.970  0.020  1.090
 9ZJ  CAS  H5   single    0.970  0.020  1.090
 9ZJ  CAR  H6   single    0.970  0.020  1.090
 9ZJ  CAA  H7   single    0.970  0.020  1.090
 9ZJ  CAA  H8   single    0.970  0.020  1.090
 9ZJ  CAA  H9   single    0.970  0.020  1.090
 9ZJ  NAM  H10  single    0.890  0.020  1.040
 9ZJ  CAJ  H11  single    0.930  0.020  1.080
 9ZJ  CAH  H12  single    0.930  0.020  1.080
 9ZJ  CAI  H13  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
 9ZJ  H2   CAK  H1   114.80  3.000
 9ZJ  H2   CAK  CAS  117.32  3.000
 9ZJ  H1   CAK  CAS  116.59  3.000
 9ZJ  H2   CAK  CAL  118.25  3.000
 9ZJ  H1   CAK  CAL  118.69  3.000
 9ZJ  CAS  CAK  CAL   60.50  3.000
 9ZJ  H4   CAL  H3   114.81  3.000
 9ZJ  H4   CAL  CAS  116.50  3.000
 9ZJ  H3   CAL  CAS  117.36  3.000
 9ZJ  H4   CAL  CAK  118.65  3.000
 9ZJ  H3   CAL  CAK  118.32  3.000
 9ZJ  CAS  CAL  CAK   60.49  3.000
 9ZJ  H5   CAS  CAF  114.74  3.000
 9ZJ  H5   CAS  CAL  116.40  3.000
 9ZJ  CAF  CAS  CAL  119.52  3.000
 9ZJ  H5   CAS  CAK  116.50  3.000
 9ZJ  CAL  CAS  CAK   59.01  3.000
 9ZJ  CAF  CAS  CAK  119.51  3.000
 9ZJ  CAG  CAF  CAS  180.00  3.000
 9ZJ  CAU  CAG  CAF  180.00  3.000
 9ZJ  CAQ  CAU  OAN  113.41  3.000
 9ZJ  OAN  CAU  CAT  102.44  3.000
 9ZJ  CAQ  CAU  CAT  109.04  3.000
 9ZJ  OAN  CAU  CAG  111.55  3.000
 9ZJ  CAT  CAU  CAG  108.87  3.000
 9ZJ  CAQ  CAU  CAG  111.08  3.000
 9ZJ  FAB  CAT  FAD  107.79  3.000
 9ZJ  FAD  CAT  FAC  107.68  3.000
 9ZJ  FAB  CAT  FAC  107.35  3.000
 9ZJ  FAD  CAT  CAU  110.89  3.000
 9ZJ  FAB  CAT  CAU  111.13  3.000
 9ZJ  FAC  CAT  CAU  111.81  3.000
 9ZJ  CAR  OAN  CAU  117.63  3.000
 9ZJ  H6   CAR  NAM  107.59  3.000
 9ZJ  H6   CAR  CAA  109.01  3.000
 9ZJ  NAM  CAR  CAA  113.93  3.000
 9ZJ  H6   CAR  OAN  104.81  3.000
 9ZJ  CAA  CAR  OAN  112.73  3.000
 9ZJ  NAM  CAR  OAN  108.25  3.000
 9ZJ  H9   CAA  H8   107.91  3.000
 9ZJ  H9   CAA  H7   108.24  3.000
 9ZJ  H8   CAA  H7   107.84  3.000
 9ZJ  H9   CAA  CAR  113.05  3.000
 9ZJ  H8   CAA  CAR  109.07  3.000
 9ZJ  H7   CAA  CAR  110.58  3.000
 9ZJ  H10  NAM  CAP  115.87  3.000
 9ZJ  H10  NAM  CAR  114.80  3.000
 9ZJ  CAP  NAM  CAR  115.08  3.000
 9ZJ  CAI  CAP  CAQ  118.99  3.000
 9ZJ  CAQ  CAP  NAM  118.87  3.000
 9ZJ  CAI  CAP  NAM  122.13  3.000
 9ZJ  CAJ  CAQ  CAP  120.06  3.000
 9ZJ  CAP  CAQ  CAU  119.03  3.000
 9ZJ  CAJ  CAQ  CAU  120.90  3.000
 9ZJ  H11  CAJ  CAO  119.70  3.000
 9ZJ  H11  CAJ  CAQ  120.40  3.000
 9ZJ  CAO  CAJ  CAQ  119.90  3.000
 9ZJ  CAH  CAO  CL   119.71  3.000
 9ZJ  CAH  CAO  CAJ  120.69  3.000
 9ZJ  CL   CAO  CAJ  119.60  3.000
 9ZJ  H12  CAH  CAI  119.88  3.000
 9ZJ  H12  CAH  CAO  120.60  3.000
 9ZJ  CAI  CAH  CAO  119.50  3.000
 9ZJ  H13  CAI  CAH  119.74  3.000
 9ZJ  H13  CAI  CAP  119.48  3.000
 9ZJ  CAH  CAI  CAP  120.78  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
 9ZJ  CONST_01  CAO  CAH  CAI  CAP    0.00   0.0  0
 9ZJ  CONST_02  CAO  CAJ  CAQ  CAP    0.00   0.0  0
 9ZJ  CONST_03  CAH  CAO  CAJ  CAQ    0.00   0.0  0
 9ZJ  CONST_04  CAH  CAI  CAP  CAQ    0.00   0.0  0
 9ZJ  CONST_05  CAI  CAH  CAO  CAJ    0.00   0.0  0
 9ZJ  CONST_06  CAI  CAP  CAQ  CAJ    0.00   0.0  0
 9ZJ  CONST_07  CL   CAO  CAJ  CAQ  180.00   0.0  0
 9ZJ  CONST_08  CAI  CAH  CAO  CL   180.00   0.0  0
 9ZJ  CONST_09  H11  CAJ  CAQ  CAU    0.00   0.0  0
 9ZJ  CONST_10  H13  CAI  CAP  NAM    0.00   0.0  0
 9ZJ  CONST_11  H12  CAH  CAI  CAP  180.00   0.0  0
 9ZJ  Var_01    CAI  CAP  NAM  CAR  151.55  30.0  1
 9ZJ  Var_02    CAF  CAS  CAL  CAK  108.68  30.0  1

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
 9ZJ  chir_02  CAU  CAQ  OAN  CAG  negativ
 9ZJ  chir_03  CAR  OAN  NAM  CAA  negativ
 9ZJ  chir_04  CAS  CAF  CAK  CAL  both

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
 9ZJ  plan-1  CAU  0.020
 9ZJ  plan-1  NAM  0.020
 9ZJ  plan-1  CAP  0.020
 9ZJ  plan-1  CAQ  0.020
 9ZJ  plan-1  CAJ  0.020
 9ZJ  plan-1  CAO  0.020
 9ZJ  plan-1  CL   0.020
 9ZJ  plan-1  CAH  0.020
 9ZJ  plan-1  CAI  0.020
 9ZJ  plan-1  H11  0.020
 9ZJ  plan-1  H12  0.020
 9ZJ  plan-1  H13  0.020

