# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:17:04 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-undec-10-enoxy-oxane-2,3,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](OCCCCCCCCCC=C)[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
 F00  F00  (2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-undec-10-enoxy-oxane-2,3,5-triol  ligand  55  23  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F00
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
 F00  C4   C  CH1   0   0.007  -27.0064  -46.3081  -0.5507
 F00  C5   C  CH1   0  -0.015  -27.8594  -46.5475  -1.8055
 F00  C6   C  CH2   0  -0.163  -29.3258  -46.2885  -1.5361
 F00  C3   C  CH1   0   0.002  -25.5293  -46.4218  -0.9066
 F00  CAN  C  CH2   0  -0.459  -22.8989  -46.6928   1.5903
 F00  CAO  C  CH2   0  -0.436  -22.4297  -47.6974   2.6351
 F00  CAP  C  CH2   0  -0.433  -21.0089  -47.4246   3.1190
 F00  CAQ  C  CH2   0  -0.430  -20.5118  -48.4042   4.1924
 F00  CAR  C  CH2   0  -0.422  -20.5815  -47.8738   5.6224
 F00  CAS  C  CH2   0  -0.424  -21.9749  -47.4881   6.1020
 F00  CAT  C  CH2   0  -0.412  -21.9743  -47.0035   7.5478
 F00  CAU  C  CH2   0  -0.491  -23.3609  -46.6569   8.0989
 F00  CAV  C  C1    0  -0.157  -24.0326  -45.5372   7.3669
 F00  CAW  C  C2    0  -0.538  -24.3087  -44.3479   7.8911
 F00  C1   C  CH1   0   0.232  -26.1292  -45.7848  -3.2599
 F00  O1   O  OH1   0  -0.664  -25.8219  -47.0404  -3.7683
 F00  C2   C  CH1   0   0.013  -25.2103  -45.4965  -2.0788
 F00  O2   O  OH1   0  -0.669  -23.8786  -45.6157  -2.5012
 F00  O3   O  O2    0  -0.512  -24.6859  -46.0291   0.1480
 F00  O4   O  OH1   0  -0.664  -27.3033  -47.2575   0.4478
 F00  O5   O  O2    0  -0.504  -27.4654  -45.6730  -2.8500
 F00  O6   O  OH1   0  -0.670  -30.0712  -46.6208  -2.6828
 F00  H1   H  HCH1  0   0.220  -27.1939  -45.2855  -0.1913
 F00  H2   H  HCH1  0   0.222  -27.7380  -47.5963  -2.1110
 F00  H3   H  HCH2  0   0.196  -29.4569  -45.2342  -1.2541
 F00  H4   H  HCH2  0   0.203  -29.6303  -46.8921  -0.6733
 F00  H5   H  HCH1  0   0.220  -25.3156  -47.4625  -1.1952
 F00  H6   H  HCH2  0   0.202  -24.9929  -47.0879   1.9017
 F00  H7   H  HCH2  0   0.195  -24.2695  -48.0105   0.5881
 F00  H8   H  HCH2  0   0.216  -22.1922  -46.6733   0.7540
 F00  H9   H  HCH2  0   0.221  -22.9006  -45.6879   2.0251
 F00  H10  H  HCH2  0   0.220  -23.1253  -47.6951   3.4800
 F00  H11  H  HCH2  0   0.216  -22.4705  -48.7094   2.2171
 F00  H12  H  HCH2  0   0.223  -20.3434  -47.4621   2.2520
 F00  H13  H  HCH2  0   0.215  -20.9441  -46.3971   3.4949
 F00  H14  H  HCH2  0   0.212  -21.0776  -49.3398   4.1234
 F00  H15  H  HCH2  0   0.226  -19.4728  -48.6731   3.9863
 F00  H16  H  HCH2  0   0.214  -20.1689  -48.6292   6.2993
 F00  H17  H  HCH2  0   0.209  -19.9246  -47.0015   5.7085
 F00  H18  H  HCH2  0   0.217  -22.3792  -46.7053   5.4532
 F00  H19  H  HCH2  0   0.207  -22.6516  -48.3444   6.0044
 F00  H20  H  HCH2  0   0.221  -21.5342  -47.7780   8.1839
 F00  H21  H  HCH2  0   0.214  -21.3236  -46.1277   7.6372
 F00  H22  H  HCH2  0   0.228  -23.9919  -47.5508   8.0468
 F00  H23  H  HCH2  0   0.234  -23.2721  -46.3970   9.1568
 F00  H24  H  H     0   0.237  -24.3029  -45.7246   6.3313
 F00  H25  H  H     0   0.233  -24.7904  -43.5687   7.3143
 F00  H26  H  H     0   0.228  -24.0643  -44.1106   8.9205
 F00  H27  H  HCH1  0   0.239  -26.0070  -45.0074  -4.0232
 F00  H28  H  HOH1  0   0.463  -26.2547  -47.1464  -4.6223
 F00  H29  H  HCH1  0   0.220  -25.4308  -44.4657  -1.7609
 F00  H30  H  HOH1  0   0.448  -23.3187  -45.4282  -1.7403
 F00  H31  H  HOH1  0   0.459  -27.9838  -46.9012   1.0248
 F00  H32  H  HOH1  0   0.456  -31.0025  -46.5064  -2.4743
 F00  CAM  C  CH2   0  -0.124  -24.2837  -47.0245   1.0697

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
 F00  O1   C1   single  1.389  0.020  1.389
 F00  C1   C2   single  1.524  0.020  1.524
 F00  C1   O5   single  1.402  0.020  1.402
 F00  O2   C2   single  1.402  0.020  1.402
 F00  C2   C3   single  1.527  0.020  1.527
 F00  O5   C5   single  1.418  0.020  1.418
 F00  O6   C6   single  1.407  0.020  1.407
 F00  C3   O3   single  1.406  0.020  1.406
 F00  C3   C4   single  1.524  0.020  1.524
 F00  C5   C6   single  1.513  0.020  1.513
 F00  C5   C4   single  1.536  0.020  1.536
 F00  O3   CAM  single  1.415  0.020  1.415
 F00  C4   O4   single  1.409  0.020  1.409
 F00  CAM  CAN  single  1.516  0.020  1.516
 F00  CAN  CAO  single  1.523  0.020  1.523
 F00  CAO  CAP  single  1.526  0.020  1.526
 F00  CAP  CAQ  single  1.536  0.020  1.536
 F00  CAQ  CAR  single  1.527  0.020  1.527
 F00  CAR  CAS  single  1.523  0.020  1.523
 F00  CAS  CAT  single  1.525  0.020  1.525
 F00  CAT  CAU  single  1.532  0.020  1.532
 F00  CAV  CAU  single  1.497  0.020  1.497
 F00  CAV  CAW  double  1.329  0.020  1.329
 F00  C4   H1   single  0.970  0.020  1.090
 F00  C5   H2   single  0.970  0.020  1.090
 F00  C6   H3   single  0.970  0.020  1.090
 F00  C6   H4   single  0.970  0.020  1.090
 F00  C3   H5   single  0.970  0.020  1.090
 F00  CAM  H6   single  0.970  0.020  1.090
 F00  CAM  H7   single  0.970  0.020  1.090
 F00  CAN  H8   single  0.970  0.020  1.090
 F00  CAN  H9   single  0.970  0.020  1.090
 F00  CAO  H10  single  0.970  0.020  1.090
 F00  CAO  H11  single  0.970  0.020  1.090
 F00  CAP  H12  single  0.970  0.020  1.090
 F00  CAP  H13  single  0.970  0.020  1.090
 F00  CAQ  H14  single  0.970  0.020  1.090
 F00  CAQ  H15  single  0.970  0.020  1.090
 F00  CAR  H16  single  0.970  0.020  1.090
 F00  CAR  H17  single  0.970  0.020  1.090
 F00  CAS  H18  single  0.970  0.020  1.090
 F00  CAS  H19  single  0.970  0.020  1.090
 F00  CAT  H20  single  0.970  0.020  1.090
 F00  CAT  H21  single  0.970  0.020  1.090
 F00  CAU  H22  single  0.970  0.020  1.090
 F00  CAU  H23  single  0.970  0.020  1.090
 F00  CAV  H24  single  0.930  0.020  1.080
 F00  CAW  H25  single  0.930  0.020  1.080
 F00  CAW  H26  single  0.930  0.020  1.080
 F00  C1   H27  single  0.970  0.020  1.090
 F00  O1   H28  single  0.850  0.020  0.980
 F00  C2   H29  single  0.970  0.020  1.090
 F00  O2   H30  single  0.850  0.020  0.980
 F00  O4   H31  single  0.850  0.020  0.980
 F00  O6   H32  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
 F00  H1   C4   O4   111.03  3.000
 F00  H1   C4   C3   108.11  3.000
 F00  O4   C4   C3   108.63  3.000
 F00  H1   C4   C5   108.48  3.000
 F00  O4   C4   C5   110.90  3.000
 F00  C3   C4   C5   109.63  3.000
 F00  H2   C5   O5   110.67  3.000
 F00  H2   C5   C6   108.65  3.000
 F00  O5   C5   C6   107.15  3.000
 F00  H2   C5   C4   108.33  3.000
 F00  C6   C5   C4   111.47  3.000
 F00  O5   C5   C4   110.57  3.000
 F00  H4   C6   H3   107.05  3.000
 F00  H4   C6   O6   111.36  3.000
 F00  H3   C6   O6   111.86  3.000
 F00  H4   C6   C5   108.37  3.000
 F00  H3   C6   C5   108.99  3.000
 F00  O6   C6   C5   109.13  3.000
 F00  H5   C3   O3   110.13  3.000
 F00  H5   C3   C2   109.33  3.000
 F00  O3   C3   C2   106.33  3.000
 F00  H5   C3   C4   108.66  3.000
 F00  O3   C3   C4   112.67  3.000
 F00  C2   C3   C4   109.67  3.000
 F00  H9   CAN  H8   106.73  3.000
 F00  H9   CAN  CAO  109.48  3.000
 F00  H8   CAN  CAO  109.68  3.000
 F00  H9   CAN  CAM  109.62  3.000
 F00  H8   CAN  CAM  109.33  3.000
 F00  CAO  CAN  CAM  111.87  3.000
 F00  H11  CAO  H10  105.83  3.000
 F00  H11  CAO  CAP  108.71  3.000
 F00  H10  CAO  CAP  110.29  3.000
 F00  H11  CAO  CAN  109.63  3.000
 F00  H10  CAO  CAN  109.41  3.000
 F00  CAP  CAO  CAN  112.73  3.000
 F00  H13  CAP  H12  105.54  3.000
 F00  H13  CAP  CAQ  109.82  3.000
 F00  H12  CAP  CAQ  109.58  3.000
 F00  H13  CAP  CAO  109.36  3.000
 F00  H12  CAP  CAO  108.01  3.000
 F00  CAQ  CAP  CAO  114.15  3.000
 F00  H15  CAQ  H14  105.61  3.000
 F00  H15  CAQ  CAR  107.79  3.000
 F00  H14  CAQ  CAR  109.39  3.000
 F00  H15  CAQ  CAP  109.44  3.000
 F00  H14  CAQ  CAP  109.48  3.000
 F00  CAR  CAQ  CAP  114.72  3.000
 F00  H17  CAR  H16  105.95  3.000
 F00  H17  CAR  CAS  108.80  3.000
 F00  H16  CAR  CAS  108.95  3.000
 F00  H17  CAR  CAQ  108.84  3.000
 F00  H16  CAR  CAQ  108.79  3.000
 F00  CAS  CAR  CAQ  115.13  3.000
 F00  H19  CAS  H18  106.14  3.000
 F00  H19  CAS  CAT  109.46  3.000
 F00  H18  CAS  CAT  109.58  3.000
 F00  H19  CAS  CAR  109.81  3.000
 F00  H18  CAS  CAR  109.42  3.000
 F00  CAT  CAS  CAR  112.25  3.000
 F00  H21  CAT  H20  106.24  3.000
 F00  H21  CAT  CAU  109.13  3.000
 F00  H20  CAT  CAU  108.36  3.000
 F00  H21  CAT  CAS  109.38  3.000
 F00  H20  CAT  CAS  109.04  3.000
 F00  CAU  CAT  CAS  114.37  3.000
 F00  H23  CAU  H22  106.67  3.000
 F00  H23  CAU  CAV  109.38  3.000
 F00  H22  CAU  CAV  109.19  3.000
 F00  H23  CAU  CAT  109.17  3.000
 F00  H22  CAU  CAT  108.65  3.000
 F00  CAV  CAU  CAT  113.55  3.000
 F00  H24  CAV  CAW  118.60  3.000
 F00  H24  CAV  CAU  116.66  3.000
 F00  CAW  CAV  CAU  124.74  3.000
 F00  H26  CAW  H25  116.66  3.000
 F00  H26  CAW  CAV  121.57  3.000
 F00  H25  CAW  CAV  121.77  3.000
 F00  H27  C1   O5   104.67  3.000
 F00  H27  C1   C2   109.77  3.000
 F00  O5   C1   C2   109.45  3.000
 F00  H27  C1   O1   111.19  3.000
 F00  O5   C1   O1   112.95  3.000
 F00  C2   C1   O1   108.74  3.000
 F00  H28  O1   C1   108.94  3.000
 F00  H29  C2   O2   110.90  3.000
 F00  H29  C2   C1   106.27  3.000
 F00  O2   C2   C1   108.85  3.000
 F00  H29  C2   C3   107.68  3.000
 F00  O2   C2   C3   112.22  3.000
 F00  C1   C2   C3   110.76  3.000
 F00  H30  O2   C2   107.32  3.000
 F00  CAM  O3   C3   117.55  3.000
 F00  H31  O4   C4   108.96  3.000
 F00  C1   O5   C5   115.52  3.000
 F00  H32  O6   C6   107.96  3.000
 F00  H7   CAM  H6   106.84  3.000
 F00  H7   CAM  O3   110.48  3.000
 F00  H6   CAM  O3   110.58  3.000
 F00  H7   CAM  CAN  109.60  3.000
 F00  H6   CAM  CAN  110.08  3.000
 F00  O3   CAM  CAN  109.23  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
 F00  Var_01  CAN  CAM  O3   C3    148.54  30.0  3
 F00  Var_02  CAP  CAO  CAN  CAM   176.98  30.0  3
 F00  Var_03  CAQ  CAP  CAO  CAN   178.96  30.0  3
 F00  Var_04  O3   CAM  CAN  CAO   177.58  30.0  2
 F00  Var_05  CAR  CAQ  CAP  CAO  -100.12  30.0  3
 F00  Var_06  CAS  CAR  CAQ  CAP    59.68  30.0  3
 F00  Var_07  CAT  CAS  CAR  CAQ   178.45  30.0  3
 F00  Var_08  CAU  CAT  CAS  CAR  -177.61  30.0  3
 F00  Var_09  CAV  CAU  CAT  CAS   -62.09  30.0  3
 F00  Var_10  CAW  CAV  CAU  CAT  -113.87  30.0  2
 F00  Var_11  H25  CAW  CAV  CAU   179.53   0.0  2

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
 F00  chir_01  C4  C3  C5  O4  negativ
 F00  chir_02  C5  O5  C4  C6  negativ
 F00  chir_03  C3  O3  C4  C2  negativ
 F00  chir_04  C1  O1  O5  C2  negativ
 F00  chir_05  C2  O2  C1  C3  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
 F00  plan-1  CAU  0.020
 F00  plan-1  CAV  0.020
 F00  plan-1  CAW  0.020
 F00  plan-1  H24  0.020
 F00  plan-1  H25  0.020
 F00  plan-1  H26  0.020

