# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:27:22 2021
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-methoxy-3,5-dimethyl-6-[(2~{R},4~{Z})-4-[(~{E})-2-methyl-3-(4-nitrophenyl)prop-2-enylidene]oxolan-2-yl]pyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=C(C)C(=O)C(=C(O1)[C@H]2C/C(CO2)=C/C(C)=C/c3ccc(cc3)[N+]([O-])=O)C
#
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
 HQW  HQW  2-methoxy-3,5-dimethyl-6-[(2~{R},4~{Z})-4-[(~{E})-2-methyl-3-(4-nitrophenyl)prop-2-enylidene]oxolan-2-yl]pyran-4-one  ligand  52  29  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HQW
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
 HQW  C12  C  CH3    0  -0.723  11.7658  -11.3486  303.0103
 HQW  C13  C  C      0   0.632  13.6006   -8.0413  301.1091
 HQW  C9   C  C      0   0.452  11.7693   -8.8983  302.4005
 HQW  C3   C  CH2    0  -0.522  14.3357  -12.0416  299.9983
 HQW  C7   C  C      0  -0.195  12.4491  -10.2016  302.3367
 HQW  C11  C  C      0  -0.279  12.4246   -7.7966  301.7400
 HQW  C14  C  C1     0  -0.363  17.7732  -10.1854  297.6918
 HQW  C10  C  C      0   0.102  16.4695  -10.1040  297.3644
 HQW  C6   C  C      0   0.395  13.6149  -10.3047  301.6784
 HQW  C4   C  CR5    0   0.077  15.4561  -11.3066  299.3296
 HQW  C5   C  CH2    0  -0.202  16.4769  -11.0555  300.3984
 HQW  C2   C  CR15   0  -0.095  14.4440  -11.5373  301.4424
 HQW  C15  C  CH3    0  -0.764  15.9129   -9.1977  296.3017
 HQW  C16  C  CH3    0  -0.711  11.8284   -6.4229  301.7442
 HQW  C17  C  CR6    0   0.136  18.8915   -9.4310  297.1282
 HQW  C18  C  CR16   0  -0.312  18.9981   -9.1020  295.7725
 HQW  C19  C  CR16   0  -0.303  19.9361   -9.0528  297.9814
 HQW  C20  C  CH3    0  -0.435  15.5126   -7.3580  299.8529
 HQW  C21  C  CR16   0  -0.250  20.0786   -8.3861  295.2925
 HQW  C22  C  CR16   0  -0.253  21.0189   -8.3313  297.5213
 HQW  C23  C  CR6    0   0.233  21.0762   -7.9955  296.1745
 HQW  N1   N  N      1   0.329  22.2050   -7.2327  295.6785
 HQW  O24  O  O      0  -0.494  15.8159  -11.2638  301.6388
 HQW  O25  O  O2     0  -0.451  14.1786   -9.2321  301.0735
 HQW  O27  O  O      0  -0.472  10.6966   -8.7810  302.9938
 HQW  O28  O  O      0  -0.384  22.2373   -6.9614  294.5000
 HQW  O29  O  O     -1  -0.383  23.0601   -6.9008  296.4672
 HQW  H1   H  HCH3   0   0.251  11.5110  -11.0906  304.0378
 HQW  H2   H  HCH3   0   0.252  10.8317  -11.5912  302.5015
 HQW  H3   H  HCH3   0   0.246  12.3680  -12.2529  303.0340
 HQW  H4   H  H      0   0.254  14.5611  -11.1112  297.4751
 HQW  H5   H  HCH2   0   0.278  13.3621  -11.8670  299.5424
 HQW  H6   H  HCH2   0   0.286  14.5236  -13.1198  299.9842
 HQW  H7   H  H      0   0.264  18.0632  -10.8779  298.4734
 HQW  H8   H  HCH2   0   0.251  17.3191  -11.7535  300.3320
 HQW  H9   H  HCH2   0   0.240  16.8879  -10.0415  300.3426
 HQW  H10  H  HCR5   0   0.281  14.1451  -12.3066  302.1543
 HQW  H11  H  HCH3   0   0.257  14.9218   -8.8426  296.5854
 HQW  H12  H  HCH3   0   0.258  16.5372   -8.3256  296.1195
 HQW  H13  H  HCH3   0   0.263  15.7979   -9.7296  295.3543
 HQW  H14  H  HCH3   0   0.248  10.9135   -6.4177  302.3316
 HQW  H15  H  HCH3   0   0.243  12.5050   -5.6857  302.1790
 HQW  H16  H  HCH3   0   0.243  11.5777   -6.0814  300.7386
 HQW  H17  H  HCR6   0   0.283  18.2464   -9.4319  295.0701
 HQW  H18  H  HCR6   0   0.270  19.8892   -9.3176  299.0300
 HQW  H19  H  HCH3   0   0.268  15.8039   -6.4243  299.3820
 HQW  H20  H  HCH3   0   0.247  16.2686   -7.6398  300.5863
 HQW  H21  H  HCH3   0   0.244  15.4332   -8.1337  299.0916
 HQW  H22  H  HCR6   0   0.297  20.1365   -8.1490  294.2403
 HQW  H23  H  HCR6   0   0.296  21.8007   -8.0390  298.2069
 HQW  O26  O  O2     0  -0.449  14.2535   -7.0925  300.4745
 HQW  C8   C  C1     0  -0.336  15.4526  -10.8968  298.0582

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
 HQW  O28  N1   double    1.210  0.020  1.210
 HQW  N1   O29  single    1.210  0.020  1.210
 HQW  N1   C23  single    1.450  0.020  1.450
 HQW  C15  C10  single    1.503  0.020  1.503
 HQW  C21  C23  aromatic  1.388  0.020  1.388
 HQW  C21  C18  aromatic  1.382  0.020  1.382
 HQW  C23  C22  aromatic  1.389  0.020  1.389
 HQW  C18  C17  aromatic  1.399  0.020  1.399
 HQW  C22  C19  aromatic  1.380  0.020  1.380
 HQW  C10  C14  double    1.347  0.020  1.347
 HQW  C10  C8   single    1.464  0.020  1.464
 HQW  C17  C19  aromatic  1.401  0.020  1.401
 HQW  C17  C14  single    1.462  0.020  1.462
 HQW  C8   C4   double    1.336  0.020  1.336
 HQW  C4   C3   single    1.498  0.020  1.498
 HQW  C4   C5   single    1.499  0.020  1.499
 HQW  C3   C2   single    1.533  0.020  1.533
 HQW  C20  O26  single    1.429  0.020  1.429
 HQW  C5   O24  single    1.421  0.020  1.421
 HQW  C2   O24  single    1.413  0.020  1.413
 HQW  C2   C6   single    1.504  0.020  1.504
 HQW  O26  C13  single    1.315  0.020  1.315
 HQW  O25  C6   single    1.354  0.020  1.354
 HQW  O25  C13  single    1.324  0.020  1.324
 HQW  C6   C7   double    1.343  0.020  1.343
 HQW  C13  C11  double    1.357  0.020  1.357
 HQW  C7   C9   single    1.471  0.020  1.471
 HQW  C7   C12  single    1.495  0.020  1.495
 HQW  C11  C16  single    1.497  0.020  1.497
 HQW  C11  C9   single    1.442  0.020  1.442
 HQW  C9   O27  double    1.231  0.020  1.231
 HQW  C12  H1   single    0.970  0.020  1.090
 HQW  C12  H2   single    0.970  0.020  1.090
 HQW  C12  H3   single    0.970  0.020  1.090
 HQW  C8   H4   single    0.930  0.020  1.080
 HQW  C3   H5   single    0.970  0.020  1.090
 HQW  C3   H6   single    0.970  0.020  1.090
 HQW  C14  H7   single    0.930  0.020  1.080
 HQW  C5   H8   single    0.970  0.020  1.090
 HQW  C5   H9   single    0.970  0.020  1.090
 HQW  C2   H10  single    0.970  0.020  1.090
 HQW  C15  H11  single    0.970  0.020  1.090
 HQW  C15  H12  single    0.970  0.020  1.090
 HQW  C15  H13  single    0.970  0.020  1.090
 HQW  C16  H14  single    0.970  0.020  1.090
 HQW  C16  H15  single    0.970  0.020  1.090
 HQW  C16  H16  single    0.970  0.020  1.090
 HQW  C18  H17  single    0.930  0.020  1.080
 HQW  C19  H18  single    0.930  0.020  1.080
 HQW  C20  H19  single    0.970  0.020  1.090
 HQW  C20  H20  single    0.970  0.020  1.090
 HQW  C20  H21  single    0.970  0.020  1.090
 HQW  C21  H22  single    0.930  0.020  1.080
 HQW  C22  H23  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
 HQW  H3   C12  H2   107.43  3.000
 HQW  H3   C12  H1   107.83  3.000
 HQW  H2   C12  H1   106.99  3.000
 HQW  H3   C12  C7   113.26  3.000
 HQW  H2   C12  C7   110.59  3.000
 HQW  H1   C12  C7   110.49  3.000
 HQW  O26  C13  O25  114.78  3.000
 HQW  O25  C13  C11  123.57  3.000
 HQW  O26  C13  C11  121.64  3.000
 HQW  O27  C9   C11  122.94  3.000
 HQW  O27  C9   C7   120.51  3.000
 HQW  C11  C9   C7   116.55  3.000
 HQW  H6   C3   H5   107.82  3.000
 HQW  H6   C3   C2   108.90  3.000
 HQW  H5   C3   C2   113.86  3.000
 HQW  H6   C3   C4   110.45  3.000
 HQW  H5   C3   C4   113.78  3.000
 HQW  C2   C3   C4   101.90  3.000
 HQW  C6   C7   C9   119.37  3.000
 HQW  C9   C7   C12  116.66  3.000
 HQW  C6   C7   C12  123.96  3.000
 HQW  C16  C11  C9   121.24  3.000
 HQW  C9   C11  C13  117.97  3.000
 HQW  C16  C11  C13  120.78  3.000
 HQW  H7   C14  C17  113.77  3.000
 HQW  H7   C14  C10  118.23  3.000
 HQW  C17  C14  C10  128.00  3.000
 HQW  C15  C10  C14  124.52  3.000
 HQW  C14  C10  C8   121.63  3.000
 HQW  C15  C10  C8   113.84  3.000
 HQW  O25  C6   C2   110.46  3.000
 HQW  O25  C6   C7   121.30  3.000
 HQW  C2   C6   C7   128.20  3.000
 HQW  C5   C4   C3   105.86  3.000
 HQW  C5   C4   C8   128.97  3.000
 HQW  C3   C4   C8   125.00  3.000
 HQW  H9   C5   H8   107.35  3.000
 HQW  H9   C5   O24  110.78  3.000
 HQW  H8   C5   O24  108.48  3.000
 HQW  H9   C5   C4   111.97  3.000
 HQW  H8   C5   C4   111.93  3.000
 HQW  O24  C5   C4   106.32  3.000
 HQW  H10  C2   O24  108.18  3.000
 HQW  H10  C2   C6   108.95  3.000
 HQW  O24  C2   C6   110.79  3.000
 HQW  H10  C2   C3   111.32  3.000
 HQW  C6   C2   C3   112.23  3.000
 HQW  O24  C2   C3   105.26  3.000
 HQW  H13  C15  H12  107.78  3.000
 HQW  H13  C15  H11  106.77  3.000
 HQW  H12  C15  H11  107.71  3.000
 HQW  H13  C15  C10  111.00  3.000
 HQW  H12  C15  C10  112.90  3.000
 HQW  H11  C15  C10  110.42  3.000
 HQW  H16  C16  H15  107.35  3.000
 HQW  H16  C16  H14  107.64  3.000
 HQW  H15  C16  H14  107.65  3.000
 HQW  H16  C16  C11  112.09  3.000
 HQW  H15  C16  C11  111.97  3.000
 HQW  H14  C16  C11  109.93  3.000
 HQW  C19  C17  C18  118.03  3.000
 HQW  C19  C17  C14  118.35  3.000
 HQW  C18  C17  C14  123.58  3.000
 HQW  H17  C18  C21  118.44  3.000
 HQW  H17  C18  C17  120.35  3.000
 HQW  C21  C18  C17  121.19  3.000
 HQW  H18  C19  C22  119.00  3.000
 HQW  H18  C19  C17  119.45  3.000
 HQW  C22  C19  C17  121.54  3.000
 HQW  H21  C20  H20  109.66  3.000
 HQW  H21  C20  H19  109.19  3.000
 HQW  H20  C20  H19  109.14  3.000
 HQW  H21  C20  O26  111.84  3.000
 HQW  H20  C20  O26  111.49  3.000
 HQW  H19  C20  O26  105.39  3.000
 HQW  H22  C21  C23  121.25  3.000
 HQW  H22  C21  C18  119.60  3.000
 HQW  C23  C21  C18  119.15  3.000
 HQW  H23  C22  C23  121.34  3.000
 HQW  H23  C22  C19  119.85  3.000
 HQW  C23  C22  C19  118.82  3.000
 HQW  N1   C23  C22  119.40  3.000
 HQW  C22  C23  C21  121.23  3.000
 HQW  N1   C23  C21  119.37  3.000
 HQW  O29  N1   O28  123.69  3.000
 HQW  O29  N1   C23  118.14  3.000
 HQW  O28  N1   C23  118.17  3.000
 HQW  C2   O24  C5   111.02  3.000
 HQW  C6   O25  C13  121.23  3.000
 HQW  C20  O26  C13  120.88  3.000
 HQW  H4   C8   C4   116.90  3.000
 HQW  H4   C8   C10  114.98  3.000
 HQW  C4   C8   C10  127.97  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
 HQW  CONST_01  C23  C21  C18  C17     0.00   0.0  0
 HQW  CONST_02  C23  C22  C19  C17     0.00   0.0  0
 HQW  CONST_03  C22  C23  C21  C18     0.00   0.0  0
 HQW  CONST_04  C22  C19  C17  C18     0.00   0.0  0
 HQW  CONST_05  C21  C23  C22  C19     0.00   0.0  0
 HQW  CONST_06  C21  C18  C17  C19     0.00   0.0  0
 HQW  CONST_07  C21  C18  C17  C14   180.00   0.0  0
 HQW  CONST_08  C22  C19  C17  C14   180.00   0.0  0
 HQW  CONST_09  N1   C23  C21  C18   180.00   0.0  0
 HQW  CONST_10  N1   C23  C22  C19   180.00   0.0  0
 HQW  CONST_11  H22  C21  C18  C17   180.00   0.0  0
 HQW  CONST_12  H23  C22  C19  C17   180.00   0.0  0
 HQW  CONST_13  H18  C19  C17  C18   180.00   0.0  0
 HQW  CONST_14  H17  C18  C17  C19   180.00   0.0  0
 HQW  CONST_15  O28  N1   C23  C21     0.00   0.0  0
 HQW  CONST_16  O29  N1   C23  C21   180.00   0.0  0
 HQW  CONST_17  O28  N1   C23  C22   180.00   0.0  0
 HQW  CONST_18  O29  N1   C23  C22     0.00   0.0  0
 HQW  Var_01    C2   C6   O25  C13   177.82  30.0  1
 HQW  Var_02    C7   C9   C11  C13     0.41  30.0  1
 HQW  Var_03    O25  C13  C11  C9     -0.33  30.0  1
 HQW  Var_04    O24  C5   C4   C3    -16.17  30.0  1
 HQW  Var_05    C6   C7   C9   C11    -0.31  30.0  1
 HQW  Var_06    C2   C3   C4   C5     28.02  30.0  1
 HQW  Var_07    C10  C8   C4   C3    175.78   0.0  2
 HQW  Var_08    C18  C17  C14  C10   -38.10  30.0  2
 HQW  Var_09    H14  C16  C11  C13  -177.65  30.0  3
 HQW  Var_10    H1   C12  C7   C9    -51.96  30.0  3
 HQW  Var_11    C17  C14  C10  C8   -177.71   0.0  2
 HQW  Var_12    C4   C8   C10  C14    31.03  30.0  2
 HQW  Var_13    H19  C20  O26  C13   178.09  30.0  3
 HQW  Var_14    H11  C15  C10  C8     32.95  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
 HQW  chir_01  C2  C3  O24  C6  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
 HQW  plan-1  C14  0.020
 HQW  plan-1  C17  0.020
 HQW  plan-1  C18  0.020
 HQW  plan-1  C19  0.020
 HQW  plan-1  C21  0.020
 HQW  plan-1  C22  0.020
 HQW  plan-1  C23  0.020
 HQW  plan-1  N1   0.020
 HQW  plan-1  H17  0.020
 HQW  plan-1  H18  0.020
 HQW  plan-1  H22  0.020
 HQW  plan-1  H23  0.020
 HQW  plan-2  C23  0.020
 HQW  plan-2  N1   0.020
 HQW  plan-2  O28  0.020
 HQW  plan-2  O29  0.020
 HQW  plan-3  C9   0.020
 HQW  plan-3  C7   0.020
 HQW  plan-3  C11  0.020
 HQW  plan-3  O27  0.020
 HQW  plan-4  C14  0.020
 HQW  plan-4  C10  0.020
 HQW  plan-4  C15  0.020
 HQW  plan-4  C17  0.020
 HQW  plan-4  H7   0.020
 HQW  plan-4  C8   0.020
 HQW  plan-5  C3   0.020
 HQW  plan-5  C10  0.020
 HQW  plan-5  C4   0.020
 HQW  plan-5  C5   0.020
 HQW  plan-5  H4   0.020
 HQW  plan-5  C8   0.020

