# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:43:39 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: [(1R,2R,3S,5R)-3-hydroxybicyclo[3.1.0]hex-2-yl]methyl hydrogen (S)-phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H]2C[C@H]2[C@@H]1CO[P@H](O)=O
#
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
 HCX  HCX  '[(1R,2R,3S,5R)-3-hydroxybicyclo[3.1.0]hex-2-yl]methyl hydrogen (S)-phosphonate'  ligand  25  12  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HCX
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
 HCX  P     P  P     0   1.156   1.3238  -4.5570   4.5595
 HCX  O1P   O  O     0  -0.706   0.9967  -3.8308   5.8062
 HCX  O2P   O  OH1   0  -0.746   0.5187  -5.9150   4.2778
 HCX  O5'   O  O2    0  -0.581   1.1173  -3.6113   3.2848
 HCX  C4    C  CR15  0  -0.258   0.6840  -1.8578   1.0387
 HCX  C7    C  CH2   0  -0.483   0.9593  -0.5528   0.3510
 HCX  C2'   C  CH2   0  -0.423   2.4595  -0.9134   2.4179
 HCX  C5'   C  CH2   0  -0.202   1.4501  -4.0645   1.9665
 HCX  C4'   C  CR15  0  -0.276   1.8070  -2.8744   1.0981
 HCX  C1'   C  CR15  0  -0.259   1.0850  -0.6557   1.8409
 HCX  C3'   C  CR15  0   0.014   3.0358  -2.1003   1.6366
 HCX  O3'   O  OH1   0  -0.672   3.8602  -1.6015   0.5998
 HCX  H2P   H  HOH1  0   0.496  -0.4402  -5.8478   4.3871
 HCX  H71   H  HCH2  0   0.248   0.0983  -0.0192  -0.0323
 HCX  H72   H  HCH2  0   0.243   1.8506  -0.4479  -0.2541
 HCX  H2'1  H  HCH2  0   0.233   3.1274  -0.0500   2.3693
 HCX  H2'2  H  HCH2  0   0.237   2.3620  -1.1840   3.4703
 HCX  H5'1  H  HCH2  0   0.241   2.2977  -4.7588   1.9995
 HCX  H5'2  H  HCH2  0   0.250   0.5963  -4.6016   1.5469
 HCX  H4'   H  HCR5  0   0.259   2.0321  -3.2939   0.1098
 HCX  H1'   H  HCR5  0   0.246   0.3621  -0.1317   2.4549
 HCX  H1    H  HCR5  0   0.217   3.6322  -2.7444   2.2973
 HCX  H3'   H  HOH1  0   0.446   4.1424  -2.3452   0.0578
 HCX  HP1   H  H     0   0.071   2.6293  -5.0499   4.4394
 HCX  H4    H  HCR5  0   0.248  -0.3375  -2.2223   1.0471

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
 HCX  P    O1P   double  1.479  0.020  1.479
 HCX  P    O2P   single  1.604  0.020  1.604
 HCX  P    O5'   single  1.601  0.020  1.601
 HCX  O2P  H2P   single  0.832  0.020  0.971
 HCX  O5'  C5'   single  1.433  0.020  1.433
 HCX  C4   C7    single  1.501  0.020  1.501
 HCX  C4   C4'   single  1.516  0.020  1.516
 HCX  C4   C1'   single  1.500  0.020  1.500
 HCX  C4   H4    single  0.970  0.020  1.090
 HCX  C7   C1'   single  1.499  0.020  1.499
 HCX  C7   H71   single  0.939  0.020  1.096
 HCX  C7   H72   single  0.939  0.020  1.096
 HCX  C2'  C1'   single  1.513  0.020  1.513
 HCX  C2'  C3'   single  1.533  0.020  1.533
 HCX  C2'  H2'1  single  0.939  0.020  1.096
 HCX  C2'  H2'2  single  0.939  0.020  1.096
 HCX  C5'  C4'   single  1.516  0.020  1.516
 HCX  C5'  H5'1  single  0.939  0.020  1.096
 HCX  C5'  H5'2  single  0.939  0.020  1.096
 HCX  C4'  C3'   single  1.549  0.020  1.549
 HCX  C4'  H4'   single  0.939  0.020  1.096
 HCX  C1'  H1'   single  0.939  0.020  1.096
 HCX  C3'  O3'   single  1.415  0.020  1.415
 HCX  C3'  H1    single  0.939  0.020  1.096
 HCX  O3'  H3'   single  0.832  0.020  0.971
 HCX  HP1  P     single  1.209  0.020  1.412

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
 HCX  HP1   P    O5'   105.06  3.000
 HCX  HP1   P    O2P    98.91  3.000
 HCX  O5'   P    O2P   107.20  3.000
 HCX  HP1   P    O1P   116.81  3.000
 HCX  O5'   P    O1P   110.64  3.000
 HCX  O2P   P    O1P   116.92  3.000
 HCX  H2P   O2P  P     114.77  3.000
 HCX  C5'   O5'  P     121.04  3.000
 HCX  H4    C4   C1'   121.13  3.000
 HCX  H4    C4   C4'   118.17  3.000
 HCX  C1'   C4   C4'   108.57  3.000
 HCX  H4    C4   C7    117.94  3.000
 HCX  C1'   C4   C7     59.93  3.000
 HCX  C4'   C4   C7    117.73  3.000
 HCX  H72   C7   H71   114.15  3.000
 HCX  H72   C7   C1'   119.56  3.000
 HCX  H71   C7   C1'   116.89  3.000
 HCX  H72   C7   C4    119.44  3.000
 HCX  H71   C7   C4    116.41  3.000
 HCX  C1'   C7   C4     60.00  3.000
 HCX  H2'2  C2'  H2'1  107.07  3.000
 HCX  H2'2  C2'  C3'   109.46  3.000
 HCX  H2'1  C2'  C3'   111.05  3.000
 HCX  H2'2  C2'  C1'   109.21  3.000
 HCX  H2'1  C2'  C1'   113.82  3.000
 HCX  C3'   C2'  C1'   106.20  3.000
 HCX  H5'2  C5'  H5'1  107.72  3.000
 HCX  H5'2  C5'  C4'   110.48  3.000
 HCX  H5'1  C5'  C4'   109.42  3.000
 HCX  H5'2  C5'  O5'   109.10  3.000
 HCX  H5'1  C5'  O5'   110.62  3.000
 HCX  C4'   C5'  O5'   109.47  3.000
 HCX  H4'   C4'  C3'   109.97  3.000
 HCX  H4'   C4'  C5'   105.32  3.000
 HCX  C3'   C4'  C5'   112.33  3.000
 HCX  H4'   C4'  C4    111.91  3.000
 HCX  C3'   C4'  C4    105.43  3.000
 HCX  C5'   C4'  C4    112.00  3.000
 HCX  H1'   C1'  C2'   118.19  3.000
 HCX  H1'   C1'  C7    118.31  3.000
 HCX  C2'   C1'  C7    117.84  3.000
 HCX  H1'   C1'  C4    120.82  3.000
 HCX  C2'   C1'  C4    108.08  3.000
 HCX  C7    C1'  C4     60.06  3.000
 HCX  H1    C3'  O3'   109.33  3.000
 HCX  H1    C3'  C4'   110.28  3.000
 HCX  O3'   C3'  C4'   112.55  3.000
 HCX  H1    C3'  C2'   110.57  3.000
 HCX  O3'   C3'  C2'   108.63  3.000
 HCX  C4'   C3'  C2'   105.41  3.000
 HCX  H3'   O3'  C3'   108.12  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
 HCX  Var_01  C2'  C1'  C7   C4     95.79  30.0  1
 HCX  Var_02  C3'  C2'  C1'  C4     15.65  30.0  1
 HCX  Var_03  C4'  C5'  O5'  P    -152.71  30.0  3
 HCX  Var_04  HP1  P    O5'  C5'    49.20  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
 HCX  chir_03  C4'  C4   C5'  C3'  positiv
 HCX  chir_05  C3'  O3'  C4'  C2'  positiv
 HCX  chir_06  P    O1P  O2P  O5'  both
 HCX  chir_07  C4   C7   C4'  C1'  both
 HCX  chir_08  C1'  C2'  C7   C4   both

