# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:39:19 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cc2ccccc2[C@H]1O
#
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
 5V4  5V4  (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol  ligand  21  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V4
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
 5V4  O01  O  OH1   0  -0.669   3.0943   0.5338   0.1895
 5V4  O    O  OH1   0  -0.664   1.5132  -2.0085  -0.2789
 5V4  C01  C  CR15  0   0.037   1.7830   0.3987  -0.2864
 5V4  C02  C  CR15  0  -0.018   1.1037  -0.8188   0.3430
 5V4  C03  C  CH2   0  -0.537   0.8347   1.5661   0.0394
 5V4  C04  C  CR56  0   0.050  -0.3559  -0.4773   0.1794
 5V4  C05  C  CR56  0   0.098  -0.5093   0.8961   0.0153
 5V4  C06  C  CR16  0  -0.319  -1.4526  -1.3218   0.1798
 5V4  C07  C  CR16  0  -0.328  -1.7706   1.4462  -0.1488
 5V4  C08  C  CR16  0  -0.261  -2.7204  -0.7707   0.0187
 5V4  C    C  CR16  0  -0.257  -2.8774   0.6021  -0.1437
 5V4  H1   H  HOH1  0   0.454   3.5291   1.2333  -0.3074
 5V4  H3   H  HCR5  0   0.216   1.7682   0.2483  -1.3767
 5V4  H4   H  HCR5  0   0.229   1.3463  -0.8359   1.4169
 5V4  H5   H  HCH2  0   0.252   1.0566   1.9532   1.0398
 5V4  H6   H  HCH2  0   0.256   0.9215   2.3977  -0.6619
 5V4  H7   H  HCR6  0   0.247  -1.3362  -2.3927   0.2958
 5V4  H8   H  HCR6  0   0.248  -1.8977   2.5131  -0.2874
 5V4  H9   H  HCR6  0   0.253  -3.5899  -1.4154   0.0136
 5V4  H10  H  HCR6  0   0.253  -3.8690   1.0161  -0.2754
 5V4  H2   H  HOH1  0   0.458   1.3592  -2.7411   0.3243

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
 5V4  C03  C05  single    1.502  0.020  1.502
 5V4  C03  C01  single    1.539  0.020  1.539
 5V4  O01  C01  single    1.401  0.020  1.401
 5V4  C07  C05  aromatic  1.386  0.020  1.386
 5V4  C07  C    aromatic  1.392  0.020  1.392
 5V4  C05  C04  aromatic  1.392  0.020  1.392
 5V4  C01  C02  single    1.530  0.020  1.530
 5V4  C    C08  aromatic  1.391  0.020  1.391
 5V4  C02  C04  single    1.508  0.020  1.508
 5V4  C02  O    single    1.404  0.020  1.404
 5V4  C04  C06  aromatic  1.384  0.020  1.384
 5V4  C08  C06  aromatic  1.392  0.020  1.392
 5V4  O01  H1   single    0.850  0.020  0.980
 5V4  O    H2   single    0.850  0.020  0.980
 5V4  C01  H3   single    0.970  0.020  1.090
 5V4  C02  H4   single    0.970  0.020  1.090
 5V4  C03  H5   single    0.970  0.020  1.090
 5V4  C03  H6   single    0.970  0.020  1.090
 5V4  C06  H7   single    0.930  0.020  1.080
 5V4  C07  H8   single    0.930  0.020  1.080
 5V4  C08  H9   single    0.930  0.020  1.080
 5V4  C    H10  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
 5V4  H1   O01  C01  108.52  3.000
 5V4  H2   O    C02  108.74  3.000
 5V4  H3   C01  C03  107.76  3.000
 5V4  H3   C01  C02  107.03  3.000
 5V4  C03  C01  C02  104.06  3.000
 5V4  H3   C01  O01  111.23  3.000
 5V4  C02  C01  O01  110.64  3.000
 5V4  C03  C01  O01  115.57  3.000
 5V4  H4   C02  C04  108.82  3.000
 5V4  H4   C02  C01  108.41  3.000
 5V4  C04  C02  C01  101.83  3.000
 5V4  H4   C02  O    110.78  3.000
 5V4  C04  C02  O    115.24  3.000
 5V4  C01  C02  O    111.27  3.000
 5V4  H6   C03  H5   107.55  3.000
 5V4  H6   C03  C05  113.63  3.000
 5V4  H5   C03  C05  110.71  3.000
 5V4  H6   C03  C01  113.14  3.000
 5V4  H5   C03  C01  109.66  3.000
 5V4  C05  C03  C01  102.10  3.000
 5V4  C06  C04  C05  120.99  3.000
 5V4  C06  C04  C02  128.95  3.000
 5V4  C05  C04  C02  110.06  3.000
 5V4  C07  C05  C04  120.40  3.000
 5V4  C04  C05  C03  109.86  3.000
 5V4  C07  C05  C03  129.74  3.000
 5V4  H7   C06  C08  120.11  3.000
 5V4  H7   C06  C04  121.20  3.000
 5V4  C08  C06  C04  118.69  3.000
 5V4  H8   C07  C    120.29  3.000
 5V4  H8   C07  C05  120.86  3.000
 5V4  C    C07  C05  118.85  3.000
 5V4  H9   C08  C    119.77  3.000
 5V4  H9   C08  C06  119.77  3.000
 5V4  C    C08  C06  120.47  3.000
 5V4  H10  C    C08  119.66  3.000
 5V4  H10  C    C07  119.74  3.000
 5V4  C08  C    C07  120.60  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
 5V4  CONST_01  C    C07  C05  C04     0.00   0.0  0
 5V4  CONST_02  C    C08  C06  C04     0.00   0.0  0
 5V4  CONST_03  C08  C    C07  C05     0.00   0.0  0
 5V4  CONST_04  C08  C06  C04  C05     0.00   0.0  0
 5V4  CONST_05  C07  C05  C04  C06     0.00   0.0  0
 5V4  CONST_06  C07  C    C08  C06     0.00   0.0  0
 5V4  CONST_07  H7   C06  C04  C02     0.00   0.0  0
 5V4  CONST_08  H8   C07  C05  C03     0.00   0.0  0
 5V4  CONST_09  H9   C08  C06  C04   180.00   0.0  0
 5V4  CONST_10  H10  C    C07  C05   180.00   0.0  0
 5V4  Var_01    C07  C05  C03  C01  -159.21  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
 5V4  chir_01  C01  C03  O01  C02  negativ
 5V4  chir_02  C02  O    C01  C04  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
 5V4  plan-1  C02  0.020
 5V4  plan-1  C03  0.020
 5V4  plan-1  C04  0.020
 5V4  plan-1  C05  0.020
 5V4  plan-1  C06  0.020
 5V4  plan-1  C07  0.020
 5V4  plan-1  C08  0.020
 5V4  plan-1  C    0.020
 5V4  plan-1  H7   0.020
 5V4  plan-1  H8   0.020
 5V4  plan-1  H9   0.020
 5V4  plan-1  H10  0.020

