# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:45:13 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: (1~{S},2~{S},3~{S},4~{S})-4-(hydroxymethyl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1C[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
 PJ5  PJ5  (1~{S},2~{S},3~{S},4~{S})-4-(hydroxymethyl)cyclopentane-1,2,3-triol  ligand  22  10  .  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_PJ5
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
 PJ5  O1'   O  OH1   0  -0.695  34.8911  -28.8361  6.0532
 PJ5  C1'   C  CH1   0  -0.020  33.9140  -28.0578  5.4026
 PJ5  C6'   C  CH2   0  -0.508  33.2339  -27.0434  6.3204
 PJ5  C2'   C  CH1   0   0.035  34.5078  -27.1279  4.3367
 PJ5  O2'   O  OH1   0  -0.671  35.4464  -27.7016  3.4690
 PJ5  C3'   C  CH1   0   0.045  35.1338  -26.0015  5.1452
 PJ5  O3'   O  OH1   0  -0.674  35.2816  -24.8542  4.3415
 PJ5  C4'   C  CH1   0  -0.316  34.1853  -25.8224  6.3579
 PJ5  C5'   C  CH2   0  -0.162  34.9253  -25.6778  7.6746
 PJ5  O5'   O  OH1   0  -0.676  35.6717  -26.8583  7.9137
 PJ5  HA    H  HOH1  0   0.446  35.2803  -28.3039  6.7650
 PJ5  H1'   H  HCH1  0   0.231  33.1950  -28.7546  4.9601
 PJ5  H6'   H  HCH2  0   0.250  32.2762  -26.7521  5.8855
 PJ5  H6'1  H  HCH2  0   0.249  33.0164  -27.4555  7.3079
 PJ5  H2'   H  HCH1  0   0.199  33.6562  -26.7045  3.7795
 PJ5  HB    H  HOH1  0   0.450  34.9901  -28.3270  2.8981
 PJ5  H3'   H  HCH1  0   0.208  36.1193  -26.3412  5.4939
 PJ5  HC    H  HOH1  0   0.448  35.7974  -24.2062  4.8303
 PJ5  H4'   H  HCH1  0   0.260  33.6119  -24.9022  6.2175
 PJ5  H5'1  H  HCH2  0   0.211  35.5864  -24.8023  7.6354
 PJ5  H5'2  H  HCH2  0   0.219  34.2006  -25.5031  8.4780
 PJ5  H5'   H  HOH1  0   0.470  36.0368  -26.8379  8.8030

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
 PJ5  O2'  C2'   single  1.401  0.020  1.401
 PJ5  C2'  C3'   single  1.521  0.020  1.521
 PJ5  C2'  C1'   single  1.534  0.020  1.534
 PJ5  O3'  C3'   single  1.409  0.020  1.409
 PJ5  C3'  C4'   single  1.550  0.020  1.550
 PJ5  C1'  O1'   single  1.408  0.020  1.408
 PJ5  C1'  C6'   single  1.528  0.020  1.528
 PJ5  C4'  C6'   single  1.548  0.020  1.548
 PJ5  C4'  C5'   single  1.517  0.020  1.517
 PJ5  C5'  O5'   single  1.417  0.020  1.417
 PJ5  O1'  HA    single  0.850  0.020  0.980
 PJ5  C1'  H1'   single  0.970  0.020  1.090
 PJ5  C6'  H6'   single  0.970  0.020  1.090
 PJ5  C6'  H6'1  single  0.970  0.020  1.090
 PJ5  C2'  H2'   single  0.970  0.020  1.090
 PJ5  O2'  HB    single  0.850  0.020  0.980
 PJ5  C3'  H3'   single  0.970  0.020  1.090
 PJ5  O3'  HC    single  0.850  0.020  0.980
 PJ5  C4'  H4'   single  0.970  0.020  1.090
 PJ5  C5'  H5'1  single  0.970  0.020  1.090
 PJ5  C5'  H5'2  single  0.970  0.020  1.090
 PJ5  O5'  H5'   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
 PJ5  HA    O1'  C1'   108.30  3.000
 PJ5  H1'   C1'  C2'   111.05  3.000
 PJ5  H1'   C1'  C6'   111.91  3.000
 PJ5  C2'   C1'  C6'   100.79  3.000
 PJ5  H1'   C1'  O1'   106.90  3.000
 PJ5  C6'   C1'  O1'   113.47  3.000
 PJ5  C2'   C1'  O1'   112.79  3.000
 PJ5  H6'1  C6'  H6'   106.64  3.000
 PJ5  H6'1  C6'  C4'   113.46  3.000
 PJ5  H6'   C6'  C4'   109.78  3.000
 PJ5  H6'1  C6'  C1'   112.42  3.000
 PJ5  H6'   C6'  C1'   109.18  3.000
 PJ5  C4'   C6'  C1'   105.34  3.000
 PJ5  H2'   C2'  C3'   107.59  3.000
 PJ5  H2'   C2'  O2'   111.21  3.000
 PJ5  C3'   C2'  O2'   110.89  3.000
 PJ5  H2'   C2'  C1'   106.56  3.000
 PJ5  C3'   C2'  C1'   103.82  3.000
 PJ5  O2'   C2'  C1'   116.19  3.000
 PJ5  HB    O2'  C2'   108.42  3.000
 PJ5  H3'   C3'  C4'   109.64  3.000
 PJ5  H3'   C3'  O3'   109.80  3.000
 PJ5  C4'   C3'  O3'   114.61  3.000
 PJ5  H3'   C3'  C2'   107.98  3.000
 PJ5  C4'   C3'  C2'   104.45  3.000
 PJ5  O3'   C3'  C2'   110.06  3.000
 PJ5  HC    O3'  C3'   108.36  3.000
 PJ5  H4'   C4'  C5'   106.68  3.000
 PJ5  H4'   C4'  C3'   108.52  3.000
 PJ5  C5'   C4'  C3'   113.05  3.000
 PJ5  H4'   C4'  C6'   109.77  3.000
 PJ5  C5'   C4'  C6'   113.32  3.000
 PJ5  C3'   C4'  C6'   105.42  3.000
 PJ5  H5'2  C5'  H5'1  107.29  3.000
 PJ5  H5'2  C5'  O5'   110.94  3.000
 PJ5  H5'1  C5'  O5'   110.69  3.000
 PJ5  H5'2  C5'  C4'   109.20  3.000
 PJ5  H5'1  C5'  C4'   109.80  3.000
 PJ5  O5'   C5'  C4'   108.90  3.000
 PJ5  H5'   O5'  C5'   109.78  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
 PJ5  chir_01  C1'  C2'  O1'  C6'  negativ
 PJ5  chir_02  C2'  O2'  C3'  C1'  positiv
 PJ5  chir_03  C3'  O3'  C4'  C2'  negativ
 PJ5  chir_04  C4'  C3'  C6'  C5'  negativ

