# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:26:16 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 7-hydroxy-2,2-dimethyl-2,3-dihydro-4H-1-benzopyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CC(=O)c2ccc(O)cc2O1
#
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
 JNP  JNP  7-hydroxy-2,2-dimethyl-2,3-dihydro-4H-1-benzopyran-4-one  ligand  26  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JNP
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
 JNP  C10   C  CR6   0   0.391  -2.7213   0.3606  -0.0830
 JNP  C13   C  CR6   0   0.424  -0.3238   0.4895  -0.2125
 JNP  C01   C  CH3   0  -0.661   2.0928   0.6696   1.6061
 JNP  C02   C  CT    0   0.146   2.0314   0.7385   0.0839
 JNP  C03   C  CH3   0  -0.661   3.0653   1.7138  -0.4483
 JNP  C04   C  CH2   0  -0.578   2.2147  -0.6378  -0.5472
 JNP  C05   C  C     0   0.389   1.0659  -1.5656  -0.2507
 JNP  O06   O  O     0  -0.412   1.2103  -2.7702  -0.1584
 JNP  C07   C  CR6   0  -0.169  -0.2359  -0.9084  -0.1496
 JNP  C08   C  CR16  0  -0.262  -1.4211  -1.6466  -0.0369
 JNP  C09   C  CR16  0  -0.349  -2.6514  -1.0386  -0.0034
 JNP  O11   O  OH1   0  -0.616  -3.9381   0.9146  -0.0455
 JNP  C12   C  CR16  0  -0.499  -1.5638   1.1204  -0.1816
 JNP  O14   O  O2    0  -0.478   0.7520   1.2781  -0.3113
 JNP  H013  H  HCH3  0   0.248   1.9251   1.6551   2.0413
 JNP  H011  H  HCH3  0   0.242   1.3555  -0.0150   2.0289
 JNP  H012  H  HCH3  0   0.246   3.0778   0.3247   1.9207
 JNP  H032  H  HCH3  0   0.239   4.0642   1.3846  -0.1631
 JNP  H033  H  HCH3  0   0.243   3.0278   1.7777  -1.5364
 JNP  H031  H  HCH3  0   0.246   2.9121   2.7118  -0.0358
 JNP  H041  H  HCH2  0   0.290   2.2739  -0.5371  -1.6379
 JNP  H042  H  HCH2  0   0.278   3.1555  -1.0815  -0.2175
 JNP  H081  H  HCR6  0   0.268  -1.3595  -2.7258   0.0156
 JNP  H091  H  HCR6  0   0.270  -3.5591  -1.6213   0.0799
 JNP  H111  H  HOH1  0   0.482  -3.8810   1.8763  -0.0927
 JNP  H121  H  HCR6  0   0.284  -1.6124   2.2027  -0.2249

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
 JNP  O06  C05   double    1.217  0.020  1.217
 JNP  C08  C09   aromatic  1.373  0.020  1.373
 JNP  C08  C07   aromatic  1.401  0.020  1.401
 JNP  C09  C10   aromatic  1.403  0.020  1.403
 JNP  C05  C07   single    1.462  0.020  1.462
 JNP  C05  C04   single    1.506  0.020  1.506
 JNP  C07  C13   aromatic  1.402  0.020  1.402
 JNP  C10  O11   single    1.337  0.020  1.337
 JNP  C10  C12   aromatic  1.388  0.020  1.388
 JNP  C04  C02   single    1.525  0.020  1.525
 JNP  C13  C12   aromatic  1.392  0.020  1.392
 JNP  C13  O14   single    1.338  0.020  1.338
 JNP  O14  C02   single    1.444  0.020  1.444
 JNP  C02  C03   single    1.518  0.020  1.518
 JNP  C02  C01   single    1.525  0.020  1.525
 JNP  C01  H013  single    0.970  0.020  1.090
 JNP  C01  H011  single    0.970  0.020  1.090
 JNP  C01  H012  single    0.970  0.020  1.090
 JNP  C03  H032  single    0.970  0.020  1.090
 JNP  C03  H033  single    0.970  0.020  1.090
 JNP  C03  H031  single    0.970  0.020  1.090
 JNP  C04  H041  single    0.970  0.020  1.090
 JNP  C04  H042  single    0.970  0.020  1.090
 JNP  C08  H081  single    0.930  0.020  1.080
 JNP  C09  H091  single    0.930  0.020  1.080
 JNP  O11  H111  single    0.850  0.020  0.980
 JNP  C12  H121  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
 JNP  C12   C10  O11   122.27  3.000
 JNP  C12   C10  C09   120.55  3.000
 JNP  O11   C10  C09   117.18  3.000
 JNP  O14   C13  C12   116.81  3.000
 JNP  O14   C13  C07   122.73  3.000
 JNP  C12   C13  C07   120.46  3.000
 JNP  H012  C01  H011  107.48  3.000
 JNP  H012  C01  H013  108.05  3.000
 JNP  H011  C01  H013  107.97  3.000
 JNP  H012  C01  C02   109.80  3.000
 JNP  H011  C01  C02   112.82  3.000
 JNP  H013  C01  C02   110.57  3.000
 JNP  O14   C02  C04   109.30  3.000
 JNP  O14   C02  C03   105.52  3.000
 JNP  C04   C02  C03   110.66  3.000
 JNP  C03   C02  C01   110.59  3.000
 JNP  O14   C02  C01   109.01  3.000
 JNP  C04   C02  C01   111.56  3.000
 JNP  H031  C03  H033  108.59  3.000
 JNP  H031  C03  H032  107.83  3.000
 JNP  H033  C03  H032  108.08  3.000
 JNP  H031  C03  C02   111.08  3.000
 JNP  H033  C03  C02   111.35  3.000
 JNP  H032  C03  C02   109.79  3.000
 JNP  H042  C04  H041  106.93  3.000
 JNP  H042  C04  C05   110.34  3.000
 JNP  H041  C04  C05   107.06  3.000
 JNP  H042  C04  C02   110.22  3.000
 JNP  H041  C04  C02   109.58  3.000
 JNP  C05   C04  C02   112.50  3.000
 JNP  C07   C05  O06   123.06  3.000
 JNP  C07   C05  C04   114.58  3.000
 JNP  O06   C05  C04   122.30  3.000
 JNP  C08   C07  C05   121.48  3.000
 JNP  C05   C07  C13   120.06  3.000
 JNP  C08   C07  C13   118.42  3.000
 JNP  H081  C08  C09   119.44  3.000
 JNP  H081  C08  C07   118.76  3.000
 JNP  C09   C08  C07   121.79  3.000
 JNP  H091  C09  C08   121.02  3.000
 JNP  H091  C09  C10   119.97  3.000
 JNP  C08   C09  C10   119.01  3.000
 JNP  H111  O11  C10   110.96  3.000
 JNP  H121  C12  C13   119.44  3.000
 JNP  H121  C12  C10   120.79  3.000
 JNP  C13   C12  C10   119.77  3.000
 JNP  C02   O14  C13   118.18  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
 JNP  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 JNP  CONST_02  C07   C13  C12  C10     0.00   0.0  0
 JNP  CONST_03  C09   C08  C07  C13     0.00   0.0  0
 JNP  CONST_04  C09   C10  C12  C13     0.00   0.0  0
 JNP  CONST_05  C12   C10  C09  C08     0.00   0.0  0
 JNP  CONST_06  C12   C13  C07  C08     0.00   0.0  0
 JNP  CONST_07  O11   C10  C12  C13   180.00   0.0  0
 JNP  CONST_08  O11   C10  C09  C08   180.00   0.0  0
 JNP  CONST_09  H081  C08  C09  C10   180.00   0.0  0
 JNP  CONST_10  H091  C09  C08  C07   180.00   0.0  0
 JNP  CONST_11  H121  C12  C13  C07   180.00   0.0  0
 JNP  Var_01    C04   C05  C07  C13    -5.39  30.0  1
 JNP  Var_02    C04   C02  O14  C13    47.61  30.0  1
 JNP  Var_03    C07   C05  C04  C02    33.50  30.0  1
 JNP  Var_04    C07   C13  O14  C02   -20.22  30.0  1
 JNP  Var_05    O14   C02  C04  C05   -53.52  30.0  1
 JNP  Var_06    H032  C03  C02  C04   -63.42  30.0  3
 JNP  Var_07    H013  C01  C02  C04  -178.01  30.0  3

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
 JNP  plan-1  C04   0.020
 JNP  plan-1  C05   0.020
 JNP  plan-1  O06   0.020
 JNP  plan-1  C07   0.020
 JNP  plan-2  C10   0.020
 JNP  plan-2  C13   0.020
 JNP  plan-2  C05   0.020
 JNP  plan-2  C07   0.020
 JNP  plan-2  C08   0.020
 JNP  plan-2  C09   0.020
 JNP  plan-2  O11   0.020
 JNP  plan-2  C12   0.020
 JNP  plan-2  O14   0.020
 JNP  plan-2  H081  0.020
 JNP  plan-2  H091  0.020
 JNP  plan-2  H121  0.020

