# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 22:41:12 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)[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
 PBW  PBW  (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol  ligand  27  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PBW
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
 PBW  O4'   O  OH1   0  -0.675  11.6053  11.2453  14.7941
 PBW  O7    O  OH1   0  -0.672   9.8990   9.7495  10.5259
 PBW  C1'   C  CH1   0   0.039  10.8365  11.9141  10.6814
 PBW  C2'   C  CH1   0   0.002  11.0739  13.1148  11.5883
 PBW  O2'   O  OH1   0  -0.674  11.8446  14.0354  10.8492
 PBW  C3'   C  CH1   0   0.009  11.7671  12.7029  12.8770
 PBW  O3'   O  OH1   0  -0.676  11.9369  13.8706  13.6509
 PBW  C4'   C  CH1   0   0.051  10.9458  11.6451  13.6102
 PBW  C5'   C  CH1   0  -0.358  10.7504  10.4252  12.7099
 PBW  C6'   C  CH2   0  -0.167  10.0315   9.2857  13.4141
 PBW  C7'   C  CH1   0   0.058  10.0422  10.8393  11.4086
 PBW  H1    H  HOH1  0   0.451  11.3749  11.8581  15.4978
 PBW  HO7   H  HOH1  0   0.453   9.1183   9.2499  10.7791
 PBW  H1'1  H  HCH1  0   0.201  11.8204  11.4930  10.4125
 PBW  H2'   H  HCH1  0   0.208  10.0939  13.5506  11.8440
 PBW  HO2'  H  HOH1  0   0.451  11.9210  14.8456  11.3632
 PBW  H3'   H  HCH1  0   0.208  12.7435  12.2618  12.6224
 PBW  HO3'  H  HOH1  0   0.452  12.6289  13.7155  14.3005
 PBW  H4'   H  HCH1  0   0.212   9.9624  12.0752  13.8489
 PBW  H5'   H  HCH1  0   0.240  11.7431  10.0387  12.4393
 PBW  HO6'  H  HOH1  0   0.453   8.2864   8.9686  14.2024
 PBW  H6'2  H  HCH2  0   0.203  10.0103   8.4115  12.7513
 PBW  H6'1  H  HCH2  0   0.214  10.6107   8.9879  14.2944
 PBW  H7'   H  HCH1  0   0.213   9.0592  11.2631  11.6587
 PBW  O1'   O  OH1   0  -0.669  10.1219  12.2885   9.5296
 PBW  H2    H  HOH1  0   0.445  10.5941  13.0191   9.1165
 PBW  O6'   O  OH1   0  -0.671   8.7294   9.7007  13.7647

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
 PBW  O7   C7'   single  1.410  0.020  1.410
 PBW  C1'  C7'   single  1.521  0.020  1.521
 PBW  C1'  C2'   single  1.523  0.020  1.523
 PBW  O2'  C2'   single  1.410  0.020  1.410
 PBW  C7'  C5'   single  1.538  0.020  1.538
 PBW  C2'  C3'   single  1.520  0.020  1.520
 PBW  C5'  C6'   single  1.520  0.020  1.520
 PBW  C5'  C4'   single  1.529  0.020  1.529
 PBW  C3'  C4'   single  1.527  0.020  1.527
 PBW  C3'  O3'   single  1.411  0.020  1.411
 PBW  C6'  O6'   single  1.411  0.020  1.411
 PBW  C4'  O4'   single  1.413  0.020  1.413
 PBW  O4'  H1    single  0.850  0.020  0.980
 PBW  O7   HO7   single  0.850  0.020  0.980
 PBW  C1'  H1'1  single  0.970  0.020  1.090
 PBW  C2'  H2'   single  0.970  0.020  1.090
 PBW  O2'  HO2'  single  0.850  0.020  0.980
 PBW  C3'  H3'   single  0.970  0.020  1.090
 PBW  O3'  HO3'  single  0.850  0.020  0.980
 PBW  C4'  H4'   single  0.970  0.020  1.090
 PBW  C5'  H5'   single  0.970  0.020  1.090
 PBW  O6'  HO6'  single  0.850  0.020  0.980
 PBW  C6'  H6'2  single  0.970  0.020  1.090
 PBW  C6'  H6'1  single  0.970  0.020  1.090
 PBW  C7'  H7'   single  0.970  0.020  1.090
 PBW  C1'  O1'   single  1.406  0.020  1.406
 PBW  O1'  H2    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
 PBW  H1    O4'  C4'   108.73  3.000
 PBW  HO7   O7   C7'   108.63  3.000
 PBW  O1'   C1'  H1'1  110.80  3.000
 PBW  O1'   C1'  C7'   108.32  3.000
 PBW  H1'1  C1'  C7'   108.20  3.000
 PBW  O1'   C1'  C2'   110.91  3.000
 PBW  H1'1  C1'  C2'   107.88  3.000
 PBW  C7'   C1'  C2'   110.71  3.000
 PBW  H2'   C2'  C3'   108.41  3.000
 PBW  H2'   C2'  O2'   110.45  3.000
 PBW  C3'   C2'  O2'   111.85  3.000
 PBW  H2'   C2'  C1'   108.12  3.000
 PBW  C3'   C2'  C1'   111.23  3.000
 PBW  O2'   C2'  C1'   106.72  3.000
 PBW  HO2'  O2'  C2'   108.24  3.000
 PBW  H3'   C3'  C4'   108.09  3.000
 PBW  H3'   C3'  O3'   110.58  3.000
 PBW  C4'   C3'  O3'   112.00  3.000
 PBW  H3'   C3'  C2'   108.47  3.000
 PBW  O3'   C3'  C2'   107.19  3.000
 PBW  C4'   C3'  C2'   110.46  3.000
 PBW  HO3'  O3'  C3'   108.88  3.000
 PBW  H4'   C4'  C5'   109.00  3.000
 PBW  H4'   C4'  C3'   108.32  3.000
 PBW  C5'   C4'  C3'   109.80  3.000
 PBW  H4'   C4'  O4'   110.26  3.000
 PBW  C3'   C4'  O4'   110.33  3.000
 PBW  C5'   C4'  O4'   109.11  3.000
 PBW  H5'   C5'  C7'   107.59  3.000
 PBW  H5'   C5'  C6'   106.11  3.000
 PBW  C7'   C5'  C6'   112.08  3.000
 PBW  H5'   C5'  C4'   108.07  3.000
 PBW  C6'   C5'  C4'   112.69  3.000
 PBW  C7'   C5'  C4'   110.01  3.000
 PBW  H6'1  C6'  H6'2  106.21  3.000
 PBW  H6'1  C6'  O6'   111.61  3.000
 PBW  H6'2  C6'  O6'   111.51  3.000
 PBW  H6'1  C6'  C5'   109.03  3.000
 PBW  H6'2  C6'  C5'   109.06  3.000
 PBW  O6'   C6'  C5'   109.33  3.000
 PBW  H7'   C7'  C5'   108.84  3.000
 PBW  H7'   C7'  C1'   107.65  3.000
 PBW  C5'   C7'  C1'   110.74  3.000
 PBW  H7'   C7'  O7    110.47  3.000
 PBW  C5'   C7'  O7    111.61  3.000
 PBW  C1'   C7'  O7    107.45  3.000
 PBW  H2    O1'  C1'   107.70  3.000
 PBW  HO6'  O6'  C6'   108.33  3.000

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
 PBW  chir_01  C1'  C7'  C2'  O1'  positiv
 PBW  chir_02  C2'  O2'  C1'  C3'  negativ
 PBW  chir_03  C3'  O3'  C4'  C2'  negativ
 PBW  chir_04  C4'  O4'  C3'  C5'  negativ
 PBW  chir_05  C5'  C4'  C6'  C7'  negativ
 PBW  chir_06  C7'  O7   C5'  C1'  negativ

