# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:46:33 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2O[C@@H](CC(=O)c2c1[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
 DY5  DY5  (2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one  ligand  27  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DY5
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
 DY5  C10  C  CH2    0  -0.634  -1.3605   1.3319  -0.3755
 DY5  C13  C  CT     0   1.020  -3.4330  -0.0377   0.1044
 DY5  C01  C  CH3    0  -0.726   4.2894  -1.4980   0.1185
 DY5  C02  C  CR6    0   0.087   2.7977  -1.3466   0.0606
 DY5  C03  C  CR6    0   0.199   2.1656  -0.1213   0.0214
 DY5  C04  C  CR6    0  -0.141   0.7785   0.0439  -0.0439
 DY5  C05  C  CR6    0   0.382  -0.0052  -1.1130  -0.0458
 DY5  C06  C  CR16   0  -0.317   0.5905  -2.3698  -0.0181
 DY5  C07  C  CR16   0  -0.294   1.9629  -2.4706   0.0297
 DY5  C09  C  CH1    0  -0.182  -1.9442   0.1367   0.3503
 DY5  C11  C  C      0   0.431   0.1361   1.3619  -0.2084
 DY5  F14  F  F      0  -0.299  -3.9174  -1.0907   0.7636
 DY5  F15  F  F      0  -0.303  -4.0991   1.0437   0.5165
 DY5  F16  F  F      0  -0.302  -3.7094  -0.2162  -1.1893
 DY5  N17  N  N      1   0.325   3.0268   1.0623   0.0627
 DY5  O08  O  O2     0  -0.478  -1.3468  -1.0685  -0.0855
 DY5  O12  O  O      0  -0.376   0.7692   2.3902  -0.2705
 DY5  O18  O  O      0  -0.354   3.5308   1.4120  -0.9731
 DY5  O19  O  O     -1  -0.356   3.2189   1.5620   1.1410
 DY5  H1   H  HCH2   0   0.319  -1.5644   1.2784  -1.4508
 DY5  H2   H  HCH2   0   0.316  -1.7820   2.2646  -0.0021
 DY5  H3   H  HCH3   0   0.269   4.7527  -1.2434  -0.8355
 DY5  H4   H  HCH3   0   0.256   4.7392  -0.8682   0.8862
 DY5  H5   H  HCH3   0   0.269   4.5532  -2.5275   0.3489
 DY5  H6   H  HCR6   0   0.294  -0.0288  -3.2566  -0.0256
 DY5  H7   H  HCR6   0   0.284   2.4143  -3.4540   0.0603
 DY5  H8   H  HCH1   0   0.312  -1.7937   0.2497   1.4323

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
 DY5  O18  N17  double    1.204  0.020  1.204
 DY5  O19  N17  single    1.204  0.020  1.204
 DY5  N17  C03  single    1.464  0.020  1.464
 DY5  O12  C11  double    1.209  0.020  1.209
 DY5  C01  C02  single    1.500  0.020  1.500
 DY5  C03  C02  aromatic  1.379  0.020  1.379
 DY5  C03  C04  aromatic  1.398  0.020  1.398
 DY5  C11  C04  single    1.475  0.020  1.475
 DY5  C11  C10  single    1.506  0.020  1.506
 DY5  C02  C07  aromatic  1.400  0.020  1.400
 DY5  C04  C05  aromatic  1.397  0.020  1.397
 DY5  C10  C09  single    1.515  0.020  1.515
 DY5  C07  C06  aromatic  1.377  0.020  1.377
 DY5  F15  C13  single    1.335  0.020  1.335
 DY5  C05  C06  aromatic  1.391  0.020  1.391
 DY5  C05  O08  single    1.343  0.020  1.343
 DY5  C09  C13  single    1.519  0.020  1.519
 DY5  C09  O08  single    1.414  0.020  1.414
 DY5  C13  F16  single    1.335  0.020  1.335
 DY5  C13  F14  single    1.333  0.020  1.333
 DY5  C10  H1   single    0.970  0.020  1.090
 DY5  C10  H2   single    0.970  0.020  1.090
 DY5  C01  H3   single    0.970  0.020  1.090
 DY5  C01  H4   single    0.970  0.020  1.090
 DY5  C01  H5   single    0.970  0.020  1.090
 DY5  C06  H6   single    0.930  0.020  1.080
 DY5  C07  H7   single    0.930  0.020  1.080
 DY5  C09  H8   single    0.970  0.020  1.090

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
 DY5  H2   C10  H1   107.83  3.000
 DY5  H2   C10  C11  109.23  3.000
 DY5  H1   C10  C11  107.14  3.000
 DY5  H2   C10  C09  111.23  3.000
 DY5  H1   C10  C09  111.09  3.000
 DY5  C11  C10  C09  110.20  3.000
 DY5  F16  C13  F15  107.71  3.000
 DY5  F16  C13  F14  107.36  3.000
 DY5  F15  C13  F14  107.81  3.000
 DY5  F14  C13  C09  111.51  3.000
 DY5  F16  C13  C09  112.04  3.000
 DY5  F15  C13  C09  110.24  3.000
 DY5  H5   C01  H4   107.31  3.000
 DY5  H5   C01  H3   107.66  3.000
 DY5  H4   C01  H3   107.81  3.000
 DY5  H5   C01  C02  110.18  3.000
 DY5  H4   C01  C02  112.28  3.000
 DY5  H3   C01  C02  111.41  3.000
 DY5  C07  C02  C03  116.05  3.000
 DY5  C07  C02  C01  120.83  3.000
 DY5  C03  C02  C01  123.12  3.000
 DY5  N17  C03  C04  119.29  3.000
 DY5  C04  C03  C02  124.12  3.000
 DY5  N17  C03  C02  116.60  3.000
 DY5  C11  C04  C05  119.68  3.000
 DY5  C05  C04  C03  117.29  3.000
 DY5  C11  C04  C03  122.87  3.000
 DY5  O08  C05  C06  117.28  3.000
 DY5  O08  C05  C04  122.20  3.000
 DY5  C06  C05  C04  120.52  3.000
 DY5  H6   C06  C07  120.72  3.000
 DY5  H6   C06  C05  119.69  3.000
 DY5  C07  C06  C05  119.58  3.000
 DY5  H7   C07  C06  118.89  3.000
 DY5  H7   C07  C02  118.68  3.000
 DY5  C06  C07  C02  122.42  3.000
 DY5  H8   C09  O08  109.48  3.000
 DY5  H8   C09  C13  107.80  3.000
 DY5  O08  C09  C13  105.44  3.000
 DY5  H8   C09  C10  109.76  3.000
 DY5  O08  C09  C10  111.22  3.000
 DY5  C13  C09  C10  112.99  3.000
 DY5  O12  C11  C04  122.50  3.000
 DY5  C04  C11  C10  115.29  3.000
 DY5  O12  C11  C10  122.11  3.000
 DY5  O19  N17  O18  125.68  3.000
 DY5  O19  N17  C03  117.04  3.000
 DY5  O18  N17  C03  117.18  3.000
 DY5  C09  O08  C05  116.18  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
 DY5  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 DY5  CONST_02  C05  C06  C07  C02    0.00   0.0  0
 DY5  CONST_03  C06  C07  C02  C03    0.00   0.0  0
 DY5  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 DY5  CONST_05  C07  C02  C03  C04    0.00   0.0  0
 DY5  CONST_06  C07  C06  C05  C04    0.00   0.0  0
 DY5  CONST_07  C04  C03  C02  C01  180.00   0.0  0
 DY5  CONST_08  C06  C07  C02  C01  180.00   0.0  0
 DY5  CONST_09  N17  C03  C04  C05  180.00   0.0  0
 DY5  CONST_10  N17  C03  C02  C07  180.00   0.0  0
 DY5  CONST_11  N17  C03  C04  C11    0.00   0.0  0
 DY5  CONST_12  H6   C06  C07  C02  180.00   0.0  0
 DY5  CONST_13  H7   C07  C02  C03  180.00   0.0  0
 DY5  Var_01    C03  C04  C11  C10  175.01  30.0  1
 DY5  Var_02    C09  C10  C11  C04   29.60  30.0  1
 DY5  Var_03    H3   C01  C02  C03  -72.30  30.0  2

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
 DY5  chir_01  C09  C10  C13  O08  negativ

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
 DY5  plan-1  C01  0.020
 DY5  plan-1  C02  0.020
 DY5  plan-1  C03  0.020
 DY5  plan-1  C04  0.020
 DY5  plan-1  C05  0.020
 DY5  plan-1  C06  0.020
 DY5  plan-1  C07  0.020
 DY5  plan-1  C11  0.020
 DY5  plan-1  N17  0.020
 DY5  plan-1  O08  0.020
 DY5  plan-1  H6   0.020
 DY5  plan-1  H7   0.020
 DY5  plan-2  C03  0.020
 DY5  plan-2  N17  0.020
 DY5  plan-2  O18  0.020
 DY5  plan-2  O19  0.020
 DY5  plan-3  C10  0.020
 DY5  plan-3  C04  0.020
 DY5  plan-3  C11  0.020
 DY5  plan-3  O12  0.020

