# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 00:03:57 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (1S,3R,4R,5S)-1,3,4-trihydroxy-5-(phosphonomethyl)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)(C[C@H](C[P](O)(O)=O)[C@H]1O)C(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
 CRB  CRB  '(1S,3R,4R,5S)-1,3,4-trihydroxy-5-(phosphonomethyl)cyclohexanecarboxylic acid'  ligand  29  17  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CRB
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
 CRB  C1   C  C      0   0.420  -1.9118  -0.2421   2.5517
 CRB  O11  O  OC    -1  -0.590  -2.0413  -1.4517   2.7922
 CRB  O12  O  O      0  -0.612  -2.7141   0.6754   2.8523
 CRB  C2   C  CT     0   0.078  -0.6381   0.2287   1.8046
 CRB  O2   O  OH1    0  -0.717  -0.7103   1.6341   1.6713
 CRB  C3   C  CH2    0  -0.468   0.6096  -0.1490   2.6075
 CRB  C4   C  CH1    0   0.030   1.8778   0.2308   1.8594
 CRB  O4   O  OH1    0  -0.689   3.0465  -0.1724   2.5613
 CRB  C5   C  CH1    0   0.091   1.9282  -0.4387   0.4910
 CRB  O5   O  OH1    0  -0.686   3.1055  -0.0612  -0.1951
 CRB  C6   C  CH1    0  -0.249   0.7068  -0.0745  -0.3517
 CRB  C7   C  CH2    0  -0.709   0.7185  -0.7490  -1.7244
 CRB  C8   C  CH2    0  -0.427  -0.5620  -0.4276   0.4251
 CRB  P1   P  P      0   1.165  -0.3841   0.0162  -3.0182
 CRB  O91  O  O      0  -0.914   0.0422   1.4916  -3.0760
 CRB  O92  O  OP    -1  -0.919  -0.0505  -0.7680  -4.2989
 CRB  O93  O  OP    -1  -0.904  -1.8401  -0.1793  -2.5622
 CRB  HO2  H  HOH1   0   0.421  -1.5689   1.8274   2.0972
 CRB  H31  H  HCH2   0   0.216   0.6095  -1.2267   2.7923
 CRB  H32  H  HCH2   0   0.222   0.5917   0.3442   3.5857
 CRB  H4   H  HCH1   0   0.194   1.8933   1.3187   1.7037
 CRB  HO4  H  HOH1   0   0.450   3.1761   0.4257   3.3028
 CRB  H5   H  HCH1   0   0.164   1.9163  -1.5322   0.6538
 CRB  HO5  H  HOH1   0   0.438   3.8414  -0.1904   0.4126
 CRB  H6   H  HCH1   0   0.196   0.7249   1.0099  -0.5143
 CRB  H71  H  HCH2   0   0.195   1.7345  -0.7273  -2.1298
 CRB  H72  H  HCH2   0   0.173   0.4698  -1.8114  -1.5997
 CRB  H81  H  HCH2   0   0.192  -0.6075  -1.5146   0.5525
 CRB  H82  H  HCH2   0   0.237  -1.4257  -0.1525  -0.1825

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
 CRB  C1  O11  deloc   1.240  0.020  1.240
 CRB  C1  O12  deloc   1.255  0.020  1.255
 CRB  C1  C2   single  1.550  0.020  1.550
 CRB  C2  O2   single  1.414  0.020  1.414
 CRB  C2  C3   single  1.531  0.020  1.531
 CRB  C2  C8   single  1.530  0.020  1.530
 CRB  O2  HO2  single  0.850  0.020  0.980
 CRB  C3  C4   single  1.521  0.020  1.521
 CRB  C3  H31  single  0.970  0.020  1.090
 CRB  C3  H32  single  0.970  0.020  1.090
 CRB  C4  O4   single  1.422  0.020  1.422
 CRB  C4  C5   single  1.524  0.020  1.524
 CRB  C4  H4   single  0.970  0.020  1.090
 CRB  O4  HO4  single  0.850  0.020  0.980
 CRB  C5  O5   single  1.414  0.020  1.414
 CRB  C5  C6   single  1.528  0.020  1.528
 CRB  C5  H5   single  0.970  0.020  1.090
 CRB  O5  HO5  single  0.850  0.020  0.980
 CRB  C6  C7   single  1.529  0.020  1.529
 CRB  C6  C8   single  1.529  0.020  1.529
 CRB  C6  H6   single  0.970  0.020  1.090
 CRB  C7  P1   single  1.864  0.020  1.864
 CRB  C7  H71  single  0.970  0.020  1.090
 CRB  C7  H72  single  0.970  0.020  1.090
 CRB  C8  H81  single  0.970  0.020  1.090
 CRB  C8  H82  single  0.970  0.020  1.090
 CRB  P1  O91  deloc   1.537  0.020  1.537
 CRB  P1  O92  deloc   1.538  0.020  1.538
 CRB  P1  O93  deloc   1.538  0.020  1.538

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
 CRB  C2   C1  O12  114.75  3.000
 CRB  C2   C1  O11  118.40  3.000
 CRB  O12  C1  O11  126.85  3.000
 CRB  C8   C2  C3   109.06  3.000
 CRB  C8   C2  O2   110.13  3.000
 CRB  C3   C2  O2   109.66  3.000
 CRB  C8   C2  C1   110.20  3.000
 CRB  C3   C2  C1   110.00  3.000
 CRB  O2   C2  C1   107.79  3.000
 CRB  HO2  O2  C2   101.55  3.000
 CRB  H32  C3  H31  107.02  3.000
 CRB  H32  C3  C4   109.90  3.000
 CRB  H31  C3  C4   109.23  3.000
 CRB  H32  C3  C2   110.11  3.000
 CRB  H31  C3  C2   109.37  3.000
 CRB  C4   C3  C2   111.11  3.000
 CRB  H4   C4  C5   107.89  3.000
 CRB  H4   C4  O4   109.82  3.000
 CRB  C5   C4  O4   106.95  3.000
 CRB  H4   C4  C3   109.18  3.000
 CRB  C5   C4  C3   111.07  3.000
 CRB  O4   C4  C3   111.83  3.000
 CRB  HO4  O4  C4   108.37  3.000
 CRB  H5   C5  C6   107.96  3.000
 CRB  H5   C5  O5   110.15  3.000
 CRB  C6   C5  O5   109.53  3.000
 CRB  H5   C5  C4   107.58  3.000
 CRB  C6   C5  C4   111.35  3.000
 CRB  O5   C5  C4   110.23  3.000
 CRB  HO5  O5  C5   107.11  3.000
 CRB  H6   C6  C8   108.50  3.000
 CRB  H6   C6  C7   107.64  3.000
 CRB  C8   C6  C7   111.12  3.000
 CRB  H6   C6  C5   107.71  3.000
 CRB  C8   C6  C5   109.15  3.000
 CRB  C7   C6  C5   112.57  3.000
 CRB  H72  C7  H71  105.76  3.000
 CRB  H72  C7  P1   109.99  3.000
 CRB  H71  C7  P1   106.49  3.000
 CRB  H72  C7  C6   108.85  3.000
 CRB  H71  C7  C6   109.33  3.000
 CRB  P1   C7  C6   115.93  3.000
 CRB  H82  C8  H81  106.39  3.000
 CRB  H82  C8  C6   108.40  3.000
 CRB  H81  C8  C6   108.83  3.000
 CRB  H82  C8  C2   110.77  3.000
 CRB  H81  C8  C2   108.59  3.000
 CRB  C6   C8  C2   113.60  3.000
 CRB  O93  P1  O92  112.79  3.000
 CRB  O93  P1  O91  113.31  3.000
 CRB  O92  P1  O91  113.45  3.000
 CRB  O93  P1  C7   107.57  3.000
 CRB  O92  P1  C7   103.90  3.000
 CRB  O91  P1  C7   104.84  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
 CRB  Var_01  O91  P1  C7  C6  54.93  30.0  3

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
 CRB  chir_01  C2  O2  C3  C8  positiv
 CRB  chir_02  C4  O4  C3  C5  positiv
 CRB  chir_03  C5  O5  C4  C6  negativ
 CRB  chir_04  C6  C5  C7  C8  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
 CRB  plan-1  C1   0.020
 CRB  plan-1  O11  0.020
 CRB  plan-1  O12  0.020
 CRB  plan-1  C2   0.020

