# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:24:51 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (2R,3aR,4S,5R,6S,7R,7aR)octahydro-1,2-benzoxaphosphole-2,4,5,6,7-pentol 2-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](O)[C@@H]2O[P@@](O)(=O)C[C@@H]2[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
 CIP  CIP  '(2R,3aR,4S,5R,6S,7R,7aR)octahydro-1,2-benzoxaphosphole-2,4,5,6,7-pentol 2-oxide'  ligand  28  15  .  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_CIP
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
 CIP  C1    C  CR15  0   0.006   0.4035  -1.0323  -0.2601
 CIP  C2    C  CR15  0  -0.350  -1.0688  -0.6452  -0.0514
 CIP  C3    C  CH1   0   0.060  -1.4400  -0.4816   1.4169
 CIP  C4    C  CH1   0  -0.004  -0.4420   0.3824   2.1770
 CIP  C5    C  CH1   0  -0.020   0.9631  -0.1879   2.0156
 CIP  C6    C  CH1   0   0.040   1.3644  -0.1703   0.5438
 CIP  C7    C  CH2   0  -0.759  -1.3023   0.5798  -0.9432
 CIP  O1    O  O     0  -0.596   0.6682  -0.8982  -1.6606
 CIP  O3    O  OH1   0  -0.668  -2.7423   0.0401   1.4742
 CIP  O4    O  OH1   0  -0.677  -0.8539   0.3883   3.5250
 CIP  O5    O  OH1   0  -0.678   1.9121   0.5853   2.7196
 CIP  O6    O  OH1   0  -0.670   2.6588  -0.6732   0.3486
 CIP  P     P  P     0   1.371  -0.3111   0.1677  -2.3996
 CIP  O1P   O  O     0  -0.699  -0.9617  -0.4019  -3.6033
 CIP  O2P   O  OH1   0  -0.739   0.5789   1.4719  -2.6781
 CIP  H1    H  HCR5  0   0.277   0.5654  -2.0819  -0.0006
 CIP  H2    H  HCR5  0   0.298  -1.6761  -1.4641  -0.4494
 CIP  H3    H  HCH1  0   0.225  -1.4059  -1.4858   1.8698
 CIP  H4    H  HCH1  0   0.216  -0.4590   1.4045   1.7692
 CIP  H5    H  HCH1  0   0.229   0.9713  -1.2283   2.3721
 CIP  H6    H  HCH1  0   0.211   1.2983   0.8731   0.1914
 CIP  H71   H  HCH2  0   0.292  -0.9467   1.5098  -0.4951
 CIP  H72   H  HCH2  0   0.315  -2.3474   0.7155  -1.2131
 CIP  HO3   H  HOH1  0   0.452  -2.9728   0.1617   2.4017
 CIP  HO4   H  HOH1  0   0.457  -0.4004   1.1020   3.9841
 CIP  HO5   H  HOH1  0   0.464   2.0545   0.1964   3.5866
 CIP  HO6   H  HOH1  0   0.450   3.2452  -0.2066   0.9549
 CIP  HOP2  H  HOH1  0   0.495   0.9487   1.5093  -3.5709

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
 CIP  C1   C2    single  1.537  0.020  1.537
 CIP  C1   C6    single  1.521  0.020  1.521
 CIP  C1   O1    single  1.432  0.020  1.432
 CIP  C1   H1    single  0.970  0.020  1.090
 CIP  C2   C3    single  1.523  0.020  1.523
 CIP  C2   C7    single  1.533  0.020  1.533
 CIP  C2   H2    single  0.970  0.020  1.090
 CIP  C3   C4    single  1.523  0.020  1.523
 CIP  C3   O3    single  1.404  0.020  1.404
 CIP  C3   H3    single  0.970  0.020  1.090
 CIP  C4   C5    single  1.525  0.020  1.525
 CIP  C4   O4    single  1.410  0.020  1.410
 CIP  C4   H4    single  0.970  0.020  1.090
 CIP  C5   C6    single  1.526  0.020  1.526
 CIP  C5   O5    single  1.412  0.020  1.412
 CIP  C5   H5    single  0.970  0.020  1.090
 CIP  C6   O6    single  1.402  0.020  1.402
 CIP  C6   H6    single  0.970  0.020  1.090
 CIP  C7   P     single  1.809  0.020  1.809
 CIP  C7   H71   single  0.970  0.020  1.090
 CIP  C7   H72   single  0.970  0.020  1.090
 CIP  O1   P     single  1.625  0.020  1.625
 CIP  O3   HO3   single  0.850  0.020  0.980
 CIP  O4   HO4   single  0.850  0.020  0.980
 CIP  O5   HO5   single  0.850  0.020  0.980
 CIP  O6   HO6   single  0.850  0.020  0.980
 CIP  P    O1P   double  1.482  0.020  1.482
 CIP  P    O2P   single  1.603  0.020  1.603
 CIP  O2P  HOP2  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
 CIP  H1    C1   O1   107.15  3.000
 CIP  H1    C1   C6   108.97  3.000
 CIP  O1    C1   C6   110.32  3.000
 CIP  H1    C1   C2   110.58  3.000
 CIP  O1    C1   C2   106.64  3.000
 CIP  C6    C1   C2   113.00  3.000
 CIP  H2    C2   C7   107.57  3.000
 CIP  H2    C2   C3   107.20  3.000
 CIP  C7    C2   C3   115.96  3.000
 CIP  H2    C2   C1   107.08  3.000
 CIP  C7    C2   C1   105.55  3.000
 CIP  C3    C2   C1   113.05  3.000
 CIP  H3    C3   O3   110.51  3.000
 CIP  H3    C3   C4   106.95  3.000
 CIP  O3    C3   C4   112.12  3.000
 CIP  H3    C3   C2   106.89  3.000
 CIP  O3    C3   C2   107.77  3.000
 CIP  C4    C3   C2   112.47  3.000
 CIP  H4    C4   O4   110.24  3.000
 CIP  H4    C4   C5   108.80  3.000
 CIP  O4    C4   C5   111.84  3.000
 CIP  H4    C4   C3   109.38  3.000
 CIP  O4    C4   C3   106.75  3.000
 CIP  C5    C4   C3   109.80  3.000
 CIP  H5    C5   O5   110.57  3.000
 CIP  H5    C5   C6   108.76  3.000
 CIP  O5    C5   C6   107.33  3.000
 CIP  H5    C5   C4   109.05  3.000
 CIP  O5    C5   C4   111.21  3.000
 CIP  C6    C5   C4   109.89  3.000
 CIP  H6    C6   O6   110.48  3.000
 CIP  H6    C6   C5   107.65  3.000
 CIP  O6    C6   C5   111.90  3.000
 CIP  H6    C6   C1   109.23  3.000
 CIP  O6    C6   C1   107.84  3.000
 CIP  C5    C6   C1   109.71  3.000
 CIP  H72   C7   H71  107.96  3.000
 CIP  H72   C7   P    110.79  3.000
 CIP  H71   C7   P    110.24  3.000
 CIP  H72   C7   C2   112.97  3.000
 CIP  H71   C7   C2   113.09  3.000
 CIP  P     C7   C2   101.70  3.000
 CIP  P     O1   C1   113.26  3.000
 CIP  HO3   O3   C3   107.94  3.000
 CIP  HO4   O4   C4   108.77  3.000
 CIP  HO5   O5   C5   109.14  3.000
 CIP  HO6   O6   C6   107.48  3.000
 CIP  O2P   P    O1P  114.53  3.000
 CIP  O2P   P    O1   106.14  3.000
 CIP  O1P   P    O1   112.44  3.000
 CIP  O2P   P    C7   104.99  3.000
 CIP  O1P   P    C7   120.06  3.000
 CIP  O1    P    C7    96.51  3.000
 CIP  HOP2  O2P  P    113.83  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
 CIP  Var_01  C7  P  O1  C1   -1.99  30.0  1
 CIP  Var_02  O1  P  C7  C2  -21.80  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
 CIP  chir_01  C1  C2  C6   O1   positiv
 CIP  chir_02  C2  C1  C3   C7   negativ
 CIP  chir_03  C3  O3  C2   C4   negativ
 CIP  chir_04  C4  O4  C3   C5   positiv
 CIP  chir_05  C5  O5  C4   C6   negativ
 CIP  chir_06  C6  O6  C5   C1   positiv
 CIP  chir_07  P   O1  O1P  O2P  both

