# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:07:38 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (6aS,12aR)-3-methoxy-6a,10,11,12a-tetrahydro-6H,7H,9H-[1]benzopyrano[4,3-c]pyrazolo[1,2-a]pyrazol-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[C@H]3[C@@H](COc2c1)CN4N3CCC4=O
#
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
 JQD  JQD  (6aS,12aR)-3-methoxy-6a,10,11,12a-tetrahydro-6H,7H,9H-[1]benzopyrano[4,3-c]pyrazolo[1,2-a]pyrazol-9-one  ligand  35  19  .  2022-07-25  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_JQD
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
 JQD  C13   C  CH2   0  -0.259   2.4411   1.4972   0.2000
 JQD  C17   C  CH2   0  -0.609   3.3948  -2.0733   0.1786
 JQD  C01   C  CH3   0  -0.436  -5.3502  -1.5572   0.3588
 JQD  O02   O  O2    0  -0.472  -4.5620  -0.4430   0.7285
 JQD  C03   C  CR6   0   0.387  -3.3134  -0.3464   0.2364
 JQD  C04   C  CR16  0  -0.392  -2.7384  -1.2708  -0.6346
 JQD  C05   C  CR16  0  -0.289  -1.4339  -1.0691  -1.0681
 JQD  C06   C  CR6   0   0.039  -0.6849   0.0227  -0.6606
 JQD  C07   C  CH1   0  -0.135   0.7704   0.1602  -0.9962
 JQD  C08   C  CH1   0  -0.341   1.3133   1.6075  -0.8401
 JQD  C09   C  CH2   0  -0.216   0.2244   2.5850  -0.4511
 JQD  O10   O  O2    0  -0.486  -0.6187   2.0634   0.5701
 JQD  C11   C  CR6   0   0.372  -1.2924   0.9529   0.1837
 JQD  C12   C  CR16  0  -0.451  -2.5906   0.7804   0.6304
 JQD  N14   N  NR5   0  -0.316   2.7445   0.1012   0.1668
 JQD  N15   N  NR5   0  -0.296   1.5585  -0.6344  -0.0374
 JQD  C16   C  CH2   0  -0.281   2.0327  -1.9413  -0.4963
 JQD  C18   C  CR5   0   0.513   3.8447  -0.6310   0.3282
 JQD  O19   O  O     0  -0.504   4.9653  -0.2121   0.5848
 JQD  H132  H  HCH2  0   0.277   3.3167   2.0890  -0.0569
 JQD  H131  H  HCH2  0   0.257   2.0983   1.7933   1.1962
 JQD  H172  H  HCH2  0   0.280   3.3152  -2.5164   1.1750
 JQD  H171  H  HCH2  0   0.280   4.1077  -2.6636  -0.3941
 JQD  H011  H  HCH3  0   0.229  -5.5208  -1.5974  -0.7200
 JQD  H012  H  HCH3  0   0.229  -4.8996  -2.5003   0.6785
 JQD  H013  H  HCH3  0   0.260  -6.3073  -1.4381   0.8606
 JQD  H041  H  HCR6  0   0.277  -3.2789  -2.1419  -0.9778
 JQD  H051  H  HCR6  0   0.258  -0.9880  -1.7968  -1.7369
 JQD  H071  H  HCH1  0   0.264   0.9524  -0.1926  -2.0196
 JQD  H081  H  HCH1  0   0.294   1.7330   1.9326  -1.7928
 JQD  H091  H  HCH2  0   0.263   0.6506   3.5084  -0.0586
 JQD  H092  H  HCH2  0   0.244  -0.3804   2.8423  -1.3274
 JQD  H121  H  HCR6  0   0.268  -3.0465   1.5173   1.2806
 JQD  H162  H  HCH2  0   0.230   2.1513  -1.9547  -1.5875
 JQD  H161  H  HCH2  0   0.261   1.3285  -2.7239  -0.2195

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
 JQD  O19  C18   double    1.223  0.020  1.223
 JQD  C18  C17   single    1.518  0.020  1.518
 JQD  C18  N14   single    1.331  0.020  1.331
 JQD  C13  N14   single    1.429  0.020  1.429
 JQD  C13  C08   single    1.538  0.020  1.538
 JQD  C17  C16   single    1.526  0.020  1.526
 JQD  N14  N15   single    1.410  0.020  1.410
 JQD  C08  C09   single    1.514  0.020  1.514
 JQD  C08  C07   single    1.554  0.020  1.554
 JQD  N15  C16   single    1.464  0.020  1.464
 JQD  N15  C07   single    1.474  0.020  1.474
 JQD  C09  O10   single    1.423  0.020  1.423
 JQD  C07  C06   single    1.500  0.020  1.500
 JQD  O10  C11   single    1.355  0.020  1.355
 JQD  C06  C11   aromatic  1.395  0.020  1.395
 JQD  C06  C05   aromatic  1.385  0.020  1.385
 JQD  C11  C12   aromatic  1.384  0.020  1.384
 JQD  C12  C03   aromatic  1.396  0.020  1.396
 JQD  C05  C04   aromatic  1.389  0.020  1.389
 JQD  C04  C03   aromatic  1.394  0.020  1.394
 JQD  C03  O02   single    1.345  0.020  1.345
 JQD  O02  C01   single    1.414  0.020  1.414
 JQD  C13  H132  single    0.970  0.020  1.090
 JQD  C13  H131  single    0.970  0.020  1.090
 JQD  C17  H172  single    0.970  0.020  1.090
 JQD  C17  H171  single    0.970  0.020  1.090
 JQD  C01  H011  single    0.970  0.020  1.090
 JQD  C01  H012  single    0.970  0.020  1.090
 JQD  C01  H013  single    0.970  0.020  1.090
 JQD  C04  H041  single    0.930  0.020  1.080
 JQD  C05  H051  single    0.930  0.020  1.080
 JQD  C07  H071  single    0.970  0.020  1.090
 JQD  C08  H081  single    0.970  0.020  1.090
 JQD  C09  H091  single    0.970  0.020  1.090
 JQD  C09  H092  single    0.970  0.020  1.090
 JQD  C12  H121  single    0.930  0.020  1.080
 JQD  C16  H162  single    0.970  0.020  1.090
 JQD  C16  H161  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
 JQD  H131  C13  H132  108.66  3.000
 JQD  H131  C13  N14   110.61  3.000
 JQD  H132  C13  N14   110.81  3.000
 JQD  H131  C13  C08   111.50  3.000
 JQD  H132  C13  C08   113.05  3.000
 JQD  N14   C13  C08   102.12  3.000
 JQD  H171  C17  H172  107.90  3.000
 JQD  H171  C17  C18   111.90  3.000
 JQD  H172  C17  C18   108.46  3.000
 JQD  H171  C17  C16   113.51  3.000
 JQD  H172  C17  C16   111.91  3.000
 JQD  C18   C17  C16   103.06  3.000
 JQD  H013  C01  H012  108.81  3.000
 JQD  H013  C01  H011  108.79  3.000
 JQD  H012  C01  H011  108.75  3.000
 JQD  H013  C01  O02   106.49  3.000
 JQD  H012  C01  O02   111.94  3.000
 JQD  H011  C01  O02   111.96  3.000
 JQD  C03   O02  C01   118.57  3.000
 JQD  C12   C03  C04   119.88  3.000
 JQD  C04   C03  O02   124.31  3.000
 JQD  C12   C03  O02   115.81  3.000
 JQD  H041  C04  C05   119.17  3.000
 JQD  H041  C04  C03   121.76  3.000
 JQD  C05   C04  C03   119.07  3.000
 JQD  H051  C05  C06   119.21  3.000
 JQD  H051  C05  C04   118.76  3.000
 JQD  C06   C05  C04   122.03  3.000
 JQD  C11   C06  C07   119.78  3.000
 JQD  C11   C06  C05   117.90  3.000
 JQD  C07   C06  C05   122.08  3.000
 JQD  H071  C07  N15   110.16  3.000
 JQD  H071  C07  C08   109.58  3.000
 JQD  N15   C07  C08   104.48  3.000
 JQD  H071  C07  C06   109.88  3.000
 JQD  N15   C07  C06   108.90  3.000
 JQD  C08   C07  C06   113.71  3.000
 JQD  H081  C08  C09   107.98  3.000
 JQD  H081  C08  C07   108.93  3.000
 JQD  C09   C08  C07   112.08  3.000
 JQD  H081  C08  C13   109.26  3.000
 JQD  C07   C08  C13   104.91  3.000
 JQD  C09   C08  C13   113.57  3.000
 JQD  H092  C09  H091  107.75  3.000
 JQD  H092  C09  O10   109.45  3.000
 JQD  H091  C09  O10   106.48  3.000
 JQD  H092  C09  C08   110.07  3.000
 JQD  H091  C09  C08   110.99  3.000
 JQD  O10   C09  C08   111.95  3.000
 JQD  C11   O10  C09   112.97  3.000
 JQD  C12   C11  O10   118.46  3.000
 JQD  C12   C11  C06   121.38  3.000
 JQD  O10   C11  C06   120.15  3.000
 JQD  H121  C12  C11   120.25  3.000
 JQD  H121  C12  C03   120.05  3.000
 JQD  C11   C12  C03   119.70  3.000
 JQD  C18   N14  N15   115.19  3.000
 JQD  N15   N14  C13   109.54  3.000
 JQD  C18   N14  C13   135.22  3.000
 JQD  C16   N15  N14   103.81  3.000
 JQD  C16   N15  C07   116.78  3.000
 JQD  N14   N15  C07   105.22  3.000
 JQD  H161  C16  H162  108.30  3.000
 JQD  H161  C16  N15   110.64  3.000
 JQD  H162  C16  N15   110.94  3.000
 JQD  H161  C16  C17   113.76  3.000
 JQD  H162  C16  C17   110.01  3.000
 JQD  N15   C16  C17   103.16  3.000
 JQD  O19   C18  N14   126.44  3.000
 JQD  N14   C18  C17   105.40  3.000
 JQD  O19   C18  C17   128.12  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
 JQD  CONST_01  C06   C11  C12  C03     0.00   0.0  0
 JQD  CONST_02  C06   C05  C04  C03     0.00   0.0  0
 JQD  CONST_03  C11   C06  C05  C04     0.00   0.0  0
 JQD  CONST_04  C11   C12  C03  C04     0.00   0.0  0
 JQD  CONST_05  C12   C11  C06  C05     0.00   0.0  0
 JQD  CONST_06  C12   C03  C04  C05     0.00   0.0  0
 JQD  CONST_07  C17   C18  N14  C13   180.00   0.0  0
 JQD  CONST_08  N15   N14  C18  C17     0.00   0.0  0
 JQD  CONST_09  C11   C12  C03  O02   180.00   0.0  0
 JQD  CONST_10  C05   C04  C03  O02   180.00   0.0  0
 JQD  CONST_11  O19   C18  N14  C13     0.00   0.0  0
 JQD  CONST_12  O19   C18  N14  N15   180.00   0.0  0
 JQD  CONST_13  H051  C05  C04  C03   180.00   0.0  0
 JQD  CONST_14  H121  C12  C03  C04   180.00   0.0  0
 JQD  CONST_15  H041  C04  C05  C06   180.00   0.0  0
 JQD  Var_01    C16   N15  N14  C13   161.58  30.0  1
 JQD  Var_02    N14   N15  C16  C17    29.40  30.0  1
 JQD  Var_03    C12   C11  O10  C09  -143.08  30.0  1
 JQD  Var_04    C16   C17  C18  N14    16.83  30.0  1
 JQD  Var_05    C18   C17  C16  N15   -28.40  30.0  1
 JQD  Var_06    H091  C09  O10  C11   175.75  30.0  1
 JQD  Var_07    C12   C03  O02  C01   179.54  30.0  3
 JQD  Var_08    H011  C01  O02  C03   -61.20  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
 JQD  chir_01  C07  C08  N15  C06  negativ
 JQD  chir_02  C08  C07  C09  C13  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
 JQD  plan-1  C13   0.020
 JQD  plan-1  C17   0.020
 JQD  plan-1  N14   0.020
 JQD  plan-1  N15   0.020
 JQD  plan-1  C18   0.020
 JQD  plan-1  O19   0.020
 JQD  plan-2  O02   0.020
 JQD  plan-2  C03   0.020
 JQD  plan-2  C04   0.020
 JQD  plan-2  C05   0.020
 JQD  plan-2  C06   0.020
 JQD  plan-2  C07   0.020
 JQD  plan-2  O10   0.020
 JQD  plan-2  C11   0.020
 JQD  plan-2  C12   0.020
 JQD  plan-2  H041  0.020
 JQD  plan-2  H051  0.020
 JQD  plan-2  H121  0.020

