# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:26:18 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 3-methylpentane-1,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(CCO)CCO
#
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
 40S  40S  '3-methylpentane-1,5-diol '  ligand  22  8  .  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_40S
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
 40S  C01  C  CH3   0  -0.667  -0.0256   1.7374  -0.2873
 40S  C02  C  CH1   0  -0.248  -0.0204   0.3046   0.2415
 40S  C03  C  CH2   0  -0.439  -1.2717  -0.4651  -0.1873
 40S  C04  C  CH2   0  -0.142  -2.5645   0.1043   0.3664
 40S  O05  O  OH1   0  -0.677  -3.6227  -0.7695   0.0276
 40S  C06  C  CH2   0  -0.440   1.2287  -0.4619  -0.2003
 40S  C07  C  CH2   0  -0.142   2.5228   0.0913   0.3669
 40S  O08  O  OH1   0  -0.677   3.5797  -0.7737   0.0025
 40S  H1   H  HCH3  0   0.216  -0.0490   1.7455  -1.3800
 40S  H2   H  HCH3  0   0.231  -0.8910   2.2991   0.0654
 40S  H3   H  HCH3  0   0.232   0.8587   2.2920   0.0274
 40S  H4   H  HCH1  0   0.213  -0.0153   0.3420   1.3389
 40S  H5   H  HCH2  0   0.216  -1.3229  -0.4971  -1.2815
 40S  H6   H  HCH2  0   0.224  -1.1782  -1.5016   0.1523
 40S  H7   H  HCH2  0   0.186  -2.4707   0.2144   1.4561
 40S  H8   H  HCH2  0   0.193  -2.7435   1.1077  -0.0376
 40S  H9   H  HOH1  0   0.451  -4.4413  -0.3905   0.3599
 40S  H10  H  HCH2  0   0.224   1.1308  -1.5044   0.1193
 40S  H11  H  HCH2  0   0.216   1.2814  -0.4727  -1.2948
 40S  H12  H  HCH2  0   0.192   2.7022   1.1058  -0.0087
 40S  H13  H  HCH2  0   0.186   2.4302   0.1702   1.4592
 40S  H14  H  HOH1  0   0.451   4.3986  -0.4086   0.3494

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
 40S  O08  C07  single  1.413  0.020  1.413
 40S  C07  C06  single  1.517  0.020  1.517
 40S  C06  C02  single  1.531  0.020  1.531
 40S  C01  C02  single  1.527  0.020  1.527
 40S  C02  C03  single  1.530  0.020  1.530
 40S  C03  C04  single  1.517  0.020  1.517
 40S  C04  O05  single  1.414  0.020  1.414
 40S  C01  H1   single  0.970  0.020  1.090
 40S  C01  H2   single  0.970  0.020  1.090
 40S  C01  H3   single  0.970  0.020  1.090
 40S  C02  H4   single  0.970  0.020  1.090
 40S  C03  H5   single  0.970  0.020  1.090
 40S  C03  H6   single  0.970  0.020  1.090
 40S  C04  H7   single  0.970  0.020  1.090
 40S  C04  H8   single  0.970  0.020  1.090
 40S  O05  H9   single  0.850  0.020  0.980
 40S  C06  H10  single  0.970  0.020  1.090
 40S  C06  H11  single  0.970  0.020  1.090
 40S  C07  H12  single  0.970  0.020  1.090
 40S  C07  H13  single  0.970  0.020  1.090
 40S  O08  H14  single  0.850  0.020  0.980

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
 40S  H3   C01  H2   106.76  3.000
 40S  H3   C01  H1   107.59  3.000
 40S  H2   C01  H1   107.61  3.000
 40S  H3   C01  C02  111.99  3.000
 40S  H2   C01  C02  111.96  3.000
 40S  H1   C01  C02  110.69  3.000
 40S  H4   C02  C06  107.56  3.000
 40S  H4   C02  C03  107.52  3.000
 40S  C06  C02  C03  109.54  3.000
 40S  H4   C02  C01  108.31  3.000
 40S  C03  C02  C01  111.84  3.000
 40S  C06  C02  C01  111.88  3.000
 40S  H6   C03  H5   106.63  3.000
 40S  H6   C03  C04  108.35  3.000
 40S  H5   C03  C04  109.60  3.000
 40S  H6   C03  C02  108.63  3.000
 40S  H5   C03  C02  109.43  3.000
 40S  C04  C03  C02  113.93  3.000
 40S  H8   C04  H7   106.71  3.000
 40S  H8   C04  O05  110.80  3.000
 40S  H7   C04  O05  111.31  3.000
 40S  H8   C04  C03  110.37  3.000
 40S  H7   C04  C03  109.07  3.000
 40S  O05  C04  C03  108.57  3.000
 40S  H9   O05  C04  108.12  3.000
 40S  H11  C06  H10  106.64  3.000
 40S  H11  C06  C07  109.63  3.000
 40S  H10  C06  C07  108.32  3.000
 40S  H11  C06  C02  109.42  3.000
 40S  H10  C06  C02  108.64  3.000
 40S  C07  C06  C02  113.92  3.000
 40S  H13  C07  H12  106.73  3.000
 40S  H13  C07  O08  111.29  3.000
 40S  H12  C07  O08  110.83  3.000
 40S  H13  C07  C06  109.02  3.000
 40S  H12  C07  C06  110.41  3.000
 40S  O08  C07  C06  108.56  3.000
 40S  H14  O08  C07  108.15  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
 40S  Var_01  C07  C06  C02  C01    64.83  30.0  2
 40S  Var_02  C04  C03  C02  C01   -63.43  30.0  3
 40S  Var_03  O08  C07  C06  C02   174.09  30.0  1
 40S  Var_04  O05  C04  C03  C02  -173.57  30.0  3
 40S  Var_05  H1   C01  C02  C03   -60.67  30.0  3

