# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 03:25:08 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,4S,6S,7R)-6-(hydroxymethyl)-6-methyl-1,3,5,2,4-trioxadiphosphocane-2,4,7-triol 2,4-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CO)O[P@@](O)(=O)O[P@@](O)(=O)OC[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
 CDI  CDI  '(2R,4S,6S,7R)-6-(hydroxymethyl)-6-methyl-1,3,5,2,4-trioxadiphosphocane-2,4,7-triol 2,4-dioxide'  ligand  28  16  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CDI
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
 CDI  C4    C  CH2   0  -0.131  -0.3213  -0.5192  -3.0309
 CDI  C3    C  CT    0   0.177  -0.3292   0.1764  -1.6646
 CDI  OB4   O  O2    0  -0.593   0.8494  -0.3690  -1.0220
 CDI  PB    P  P     0   1.469   1.6601   0.0152   0.2674
 CDI  OB2   O  OH1   0  -0.706   2.8703  -0.9882   0.0765
 CDI  OB3   O  O     0  -0.686   1.9658   1.4243   0.5605
 CDI  PA    P  P     0   1.479  -0.3667  -0.0243   2.3106
 CDI  OA3   O  O2    0  -0.594  -1.0308   0.9557   1.2484
 CDI  OA1   O  OH1   0  -0.725  -1.3039  -1.2969   2.4551
 CDI  OA2   O  O     0  -0.665   0.0422   0.6768   3.5349
 CDI  C1    C  CH2   0  -0.222  -2.0262   0.6178   0.2782
 CDI  C2    C  CH1   0  -0.021  -1.5738  -0.2922  -0.8674
 CDI  O1    O  OH1   0  -0.658  -2.6661  -0.3284  -1.7571
 CDI  C5    C  CH3   0  -0.709  -0.2388   1.6832  -1.8315
 CDI  O2    O  OH1   0  -0.666   0.9169  -0.2808  -3.6513
 CDI  OB1   O  O2    0  -0.694   0.8346  -0.7116   1.4792
 CDI  HC41  H  HCH2  0   0.210  -0.4997  -1.5943  -2.8892
 CDI  HC42  H  HCH2  0   0.224  -1.1488  -0.1262  -3.6246
 CDI  HB2O  H  HOH1  0   0.511   3.6349  -0.7923   0.6359
 CDI  HA1O  H  HOH1  0   0.512  -1.8998  -1.2706   3.2170
 CDI  HC11  H  HCH2  0   0.271  -2.8817   0.1538   0.7743
 CDI  HC12  H  HCH2  0   0.268  -2.3559   1.5709  -0.1326
 CDI  HC2   H  HCH1  0   0.253  -1.3554  -1.3003  -0.4921
 CDI  HO1   H  HOH1  0   0.470  -3.2990  -0.9815  -1.4434
 CDI  HC51  H  HCH3  0   0.262   0.6141   1.9522  -2.4518
 CDI  HC52  H  HCH3  0   0.250  -1.1405   2.0390  -2.3316
 CDI  HC53  H  HCH3  0   0.255  -0.1506   2.2159  -0.8875
 CDI  HO2   H  HOH1  0   0.460   0.8061  -0.4244  -4.5946

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
 CDI  C4   C3    single  1.533  0.020  1.533
 CDI  C4   O2    single  1.405  0.020  1.405
 CDI  C4   HC41  single  0.970  0.020  1.090
 CDI  C4   HC42  single  0.970  0.020  1.090
 CDI  C3   OB4   single  1.449  0.020  1.449
 CDI  C3   C2    single  1.551  0.020  1.551
 CDI  C3   C5    single  1.519  0.020  1.519
 CDI  OB4  PB    single  1.571  0.020  1.571
 CDI  PB   OB2   single  1.584  0.020  1.584
 CDI  PB   OB3   double  1.471  0.020  1.471
 CDI  PB   OB1   single  1.636  0.020  1.636
 CDI  OB2  HB2O  single  0.850  0.020  0.980
 CDI  PA   OA3   single  1.591  0.020  1.591
 CDI  PA   OA1   single  1.587  0.020  1.587
 CDI  PA   OA2   double  1.469  0.020  1.469
 CDI  PA   OB1   single  1.615  0.020  1.615
 CDI  OA3  C1    single  1.430  0.020  1.430
 CDI  OA1  HA1O  single  0.850  0.020  0.980
 CDI  C1   C2    single  1.531  0.020  1.531
 CDI  C1   HC11  single  0.970  0.020  1.090
 CDI  C1   HC12  single  0.970  0.020  1.090
 CDI  C2   O1    single  1.409  0.020  1.409
 CDI  C2   HC2   single  0.970  0.020  1.090
 CDI  O1   HO1   single  0.850  0.020  0.980
 CDI  C5   HC51  single  0.970  0.020  1.090
 CDI  C5   HC52  single  0.970  0.020  1.090
 CDI  C5   HC53  single  0.970  0.020  1.090
 CDI  O2   HO2   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
 CDI  HC42  C4   HC41  107.42  3.000
 CDI  HC42  C4   O2    111.52  3.000
 CDI  HC41  C4   O2    111.46  3.000
 CDI  HC42  C4   C3    108.51  3.000
 CDI  HC41  C4   C3    109.15  3.000
 CDI  O2    C4   C3    108.72  3.000
 CDI  C5    C3   C2    113.84  3.000
 CDI  C5    C3   OB4   111.95  3.000
 CDI  C2    C3   OB4   108.13  3.000
 CDI  C5    C3   C4    110.60  3.000
 CDI  C2    C3   C4    108.98  3.000
 CDI  OB4   C3   C4    102.72  3.000
 CDI  PB    OB4  C3    133.77  3.000
 CDI  OB1   PB   OB3   112.50  3.000
 CDI  OB1   PB   OB2   101.15  3.000
 CDI  OB3   PB   OB2   118.17  3.000
 CDI  OB1   PB   OB4   103.82  3.000
 CDI  OB3   PB   OB4   120.33  3.000
 CDI  OB2   PB   OB4    98.07  3.000
 CDI  HB2O  OB2  PB    113.95  3.000
 CDI  OB1   PA   OA2   115.16  3.000
 CDI  OB1   PA   OA1    98.34  3.000
 CDI  OA2   PA   OA1   118.12  3.000
 CDI  OB1   PA   OA3   103.24  3.000
 CDI  OA2   PA   OA3   112.25  3.000
 CDI  OA1   PA   OA3   107.96  3.000
 CDI  C1    OA3  PA    126.72  3.000
 CDI  HA1O  OA1  PA    114.43  3.000
 CDI  HC12  C1   HC11  107.82  3.000
 CDI  HC12  C1   C2    109.10  3.000
 CDI  HC11  C1   C2    108.59  3.000
 CDI  HC12  C1   OA3   105.05  3.000
 CDI  HC11  C1   OA3   109.71  3.000
 CDI  C2    C1   OA3   116.24  3.000
 CDI  HC2   C2   O1    110.27  3.000
 CDI  HC2   C2   C1    110.41  3.000
 CDI  O1    C2   C1    104.99  3.000
 CDI  HC2   C2   C3    107.07  3.000
 CDI  O1    C2   C3    107.78  3.000
 CDI  C1    C2   C3    116.25  3.000
 CDI  HO1   O1   C2    108.75  3.000
 CDI  HC53  C5   HC52  107.77  3.000
 CDI  HC53  C5   HC51  108.06  3.000
 CDI  HC52  C5   HC51  107.81  3.000
 CDI  HC53  C5   C3    113.29  3.000
 CDI  HC52  C5   C3    108.95  3.000
 CDI  HC51  C5   C3    110.76  3.000
 CDI  HO2   O2   C4    107.85  3.000
 CDI  PA    OB1  PB    124.58  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
 CDI  chir_01  C3  OB4  C2   C5   negativ
 CDI  chir_04  C2  O1   C3   C1   negativ
 CDI  chir_05  PB  OB2  OB3  OB1  both
 CDI  chir_06  PA  OA2  OA1  OA3  both

