# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 11:09:50 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-[[(2~{R},5~{S})-5-(hydroxymethyl)-3,3-bis(oxidanyl)-1,4-dioxa-3$l^{6}-phosphaspiro[2.2]pentan-2-yl]oxy]ethyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[P]12(O)(O)O[C@H]2OCCO[P](O)(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 I9X  I9X  "2-[[(2~{R},5~{S})-5-(hydroxymethyl)-3,3-bis(oxidanyl)-1,4-dioxa-3$l^{6}-phosphaspiro[2.2]pentan-2-yl]oxy]ethyl dihydrogen phosphate"  ligand  28  17  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I9X
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
 I9X  O15   O  O      0  -0.775  163.1049  164.2200  183.4994
 I9X  P08   P  P      2   1.521  166.8598  158.3320  181.7980
 I9X  P14   P  P      0   1.155  162.8197  162.9937  182.7117
 I9X  C01   C  CH2    0  -0.319  163.7097  160.5196  182.8344
 I9X  C02   C  CH2    0  -0.660  164.1975  159.5172  183.8488
 I9X  C04   C  CH1    0  -0.142  166.9603  157.9192  184.2238
 I9X  C05   C  CH1    0   0.206  166.6242  159.4297  184.0532
 I9X  O06   O  O2     0  -0.410  165.4248  159.8969  184.4747
 I9X  O07   O  OC2    0  -0.425  166.8307  159.6761  182.6177
 I9X  O10   O  OC2    0  -0.417  166.7518  157.2797  182.9434
 I9X  O12   O  OH1    0  -0.565  165.3248  156.1934  184.8432
 I9X  O13   O  O2     0  -0.656  163.6660  161.7952  183.4357
 I9X  O16   O  OP    -1  -0.924  161.3624  162.5038  182.5386
 I9X  O17   O  OP    -1  -0.850  163.1615  162.9633  181.1974
 I9X  H012  H  HCH2   0   0.289  164.3463  160.5255  181.9457
 I9X  H011  H  HCH2   0   0.270  162.7158  160.1843  182.5136
 I9X  H021  H  HCH2   0   1.958  165.6855  157.8886  185.9465
 I9X  H1    H  HCH2   0   0.447  164.2843  158.5313  183.3780
 I9X  H2    H  HCH2   0   0.455  166.9387  156.6535  185.9673
 I9X  H031  H  HCH2   0   0.352  163.4701  159.3986  184.6503
 I9X  H041  H  HCH1   0   0.388  168.0267  157.8774  184.4311
 I9X  H051  H  HCH1   0   0.221  167.3780  160.0191  184.5784
 I9X  H3    H  H      0   0.566  165.6837  158.4159  179.9578
 I9X  H111  H  H      0   0.502  168.4093  157.6762  180.3721
 I9X  H121  H  HOH1   0   0.514  164.4514  156.5753  184.7264
 I9X  O09   O  OP     0  -0.579  165.6329  158.0898  180.8747
 I9X  O11   O  OP     0  -0.660  168.2016  158.3781  181.0111
 I9X  C03   C  CH2    0  -1.461  166.2082  157.1588  185.3386

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
 I9X  O15  P14   deloc   1.485  0.020  1.485
 I9X  P08  C04   single  2.463  0.020  2.463
 I9X  P08  C05   single  2.519  0.020  2.519
 I9X  P08  O07   single  1.575  0.020  1.575
 I9X  P08  O09   single  1.554  0.020  1.554
 I9X  P08  O10   single  1.559  0.020  1.559
 I9X  P08  O11   single  1.556  0.020  1.556
 I9X  P14  O13   single  1.636  0.020  1.636
 I9X  P14  O16   deloc   1.547  0.020  1.547
 I9X  P14  O17   deloc   1.553  0.020  1.553
 I9X  C01  C02   single  1.507  0.020  1.507
 I9X  C01  O13   single  1.411  0.020  1.411
 I9X  C02  O06   single  1.429  0.020  1.429
 I9X  C03  C04   single  1.545  0.020  1.545
 I9X  C03  O12   single  1.399  0.020  1.399
 I9X  C04  O10   single  1.446  0.020  1.446
 I9X  C05  O06   single  1.354  0.020  1.354
 I9X  C05  O07   single  1.471  0.020  1.471
 I9X  C01  H012  single  0.970  0.020  1.090
 I9X  C01  H011  single  0.970  0.020  1.090
 I9X  C02  H021  single  0.970  0.020  1.090
 I9X  C02  H1    single  0.970  0.020  1.090
 I9X  C03  H2    single  0.970  0.020  1.090
 I9X  C03  H031  single  0.970  0.020  1.090
 I9X  C04  H041  single  0.970  0.020  1.090
 I9X  C05  H051  single  0.970  0.020  1.090
 I9X  O09  H3    single  0.850  0.020  0.980
 I9X  O11  H111  single  0.850  0.020  0.980
 I9X  O12  H121  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
 I9X  O11   P08  O10   116.82  3.000
 I9X  O11   P08  O09   112.63  3.000
 I9X  O10   P08  O09   106.05  3.000
 I9X  O11   P08  O07   104.71  3.000
 I9X  O10   P08  O07   101.10  3.000
 I9X  O09   P08  O07   115.31  3.000
 I9X  O11   P08  C05   121.36  3.000
 I9X  O10   P08  C05    68.28  3.000
 I9X  O09   P08  C05   121.72  3.000
 I9X  O07   P08  C05    32.89  3.000
 I9X  O11   P08  C04   117.90  3.000
 I9X  O10   P08  C04    33.50  3.000
 I9X  O09   P08  C04   126.24  3.000
 I9X  O07   P08  C04    68.35  3.000
 I9X  C05   P08  C04    36.40  3.000
 I9X  O17   P14  O16    95.28  3.000
 I9X  O17   P14  O13   107.66  3.000
 I9X  O16   P14  O13   107.74  3.000
 I9X  O17   P14  O15   119.42  3.000
 I9X  O16   P14  O15   120.11  3.000
 I9X  O13   P14  O15   105.71  3.000
 I9X  H011  C01  H012  106.94  3.000
 I9X  H011  C01  O13   111.90  3.000
 I9X  H012  C01  O13   111.08  3.000
 I9X  H011  C01  C02   106.67  3.000
 I9X  H012  C01  C02   111.24  3.000
 I9X  O13   C01  C02   108.94  3.000
 I9X  H1    C02  H021   77.06  3.000
 I9X  H1    C02  O06   111.05  3.000
 I9X  H021  C02  O06    54.59  3.000
 I9X  H1    C02  C01   109.56  3.000
 I9X  H021  C02  C01   167.90  3.000
 I9X  O06   C02  C01   113.33  3.000
 I9X  H041  C04  O10   107.04  3.000
 I9X  H041  C04  C03   108.73  3.000
 I9X  O10   C04  C03   110.55  3.000
 I9X  H041  C04  P08   103.55  3.000
 I9X  O10   C04  P08    36.51  3.000
 I9X  C03   C04  P08   140.66  3.000
 I9X  H051  C05  O07   106.39  3.000
 I9X  H051  C05  O06   106.00  3.000
 I9X  O07   C05  O06   111.73  3.000
 I9X  H051  C05  P08   126.97  3.000
 I9X  O07   C05  P08    35.54  3.000
 I9X  O06   C05  P08   120.78  3.000
 I9X  C05   O06  C02   122.18  3.000
 I9X  C05   O07  P08   111.57  3.000
 I9X  C04   O10  P08   109.99  3.000
 I9X  H121  O12  C03   110.05  3.000
 I9X  C01   O13  P14   119.32  3.000
 I9X  H3    O09  P08   117.75  3.000
 I9X  H111  O11  P08   119.69  3.000
 I9X  H031  C03  H2    155.36  3.000
 I9X  H031  C03  O12    83.19  3.000
 I9X  H2    C03  O12   107.94  3.000
 I9X  H031  C03  C04    85.77  3.000
 I9X  H2    C03  C04   108.58  3.000
 I9X  O12   C03  C04   113.05  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
 I9X  Var_01  O07   C05  P08  C04   162.30  30.0  3
 I9X  Var_02  C05   P08  O10  C04   -14.51  30.0  1
 I9X  Var_03  O07   P08  O10  C04   -12.18  30.0  1
 I9X  Var_04  O10   P08  O07  C05    -4.00  30.0  3
 I9X  Var_05  O06   C05  O07  P08  -112.94  30.0  1
 I9X  Var_06  C03   C04  O10  P08   151.88  30.0  1
 I9X  Var_07  C05   P08  C04  C03   112.76  30.0  1
 I9X  Var_08  O07   P08  C04  C03   123.00  30.0  1
 I9X  Var_09  O06   C05  P08  C04  -113.01  30.0  3
 I9X  Var_10  O09   P08  O10  C04  -132.83  30.0  1
 I9X  Var_11  O11   P08  O10  C04   100.72  30.0  1
 I9X  Var_12  O09   P08  O07  C05   109.85  30.0  3
 I9X  Var_13  O11   P08  O07  C05  -125.79  30.0  3
 I9X  Var_14  O10   P08  C05  O06   -99.53  30.0  3
 I9X  Var_15  H051  C05  O07  P08   131.82  30.0  1
 I9X  Var_16  H041  C04  O10  P08   -89.86  30.0  1
 I9X  Var_17  H051  C05  P08  C04    98.80  30.0  3
 I9X  Var_18  H041  C04  P08  C05  -102.66  30.0  1
 I9X  Var_19  H041  C04  P08  O07   -92.43  30.0  1
 I9X  Var_20  H051  C05  P08  O10   112.28  30.0  3
 I9X  Var_21  O12   C03  C04  P08    15.65  30.0  3
 I9X  Var_22  C02   O06  C05  P08    15.70  30.0  3
 I9X  Var_23  O07   C05  O06  C02    54.23  30.0  2
 I9X  Var_24  O09   P08  C04  C03    16.77  30.0  1
 I9X  Var_25  O11   P08  C04  C03  -141.32  30.0  1
 I9X  Var_26  O09   P08  C05  O06    -3.58  30.0  3
 I9X  Var_27  O11   P08  C05  O06   151.44  30.0  3
 I9X  Var_28  O12   C03  C04  O10   -10.61  30.0  3
 I9X  Var_29  H2    C03  C04  P08   135.40  30.0  3
 I9X  Var_30  H031  C03  C04  P08   -65.10  30.0  3
 I9X  Var_31  H041  C04  P08  O09   161.35  30.0  1
 I9X  Var_32  H051  C05  P08  O09  -151.77  30.0  3
 I9X  Var_33  H2    C03  C04  O10   109.14  30.0  3
 I9X  Var_34  H031  C03  C04  O10   -91.36  30.0  3
 I9X  Var_35  H041  C04  P08  O11     3.25  30.0  1
 I9X  Var_36  H051  C05  P08  O11     3.25  30.0  3
 I9X  Var_37  C05   O06  C02  C01   -97.07  30.0  3
 I9X  Var_38  H051  C05  O06  C02   169.71  30.0  2
 I9X  Var_39  H021  C02  O06  C05    82.14  30.0  1
 I9X  Var_40  H1    C02  O06  C05    26.76  30.0  1
 I9X  Var_41  H041  C04  C03  O12  -127.84  30.0  3
 I9X  Var_42  C01   O13  P14  O15  -173.56  30.0  3
 I9X  Var_43  C02   C01  O13  P14  -164.19  30.0  1
 I9X  Var_44  O16   P14  O13  C01    56.86  30.0  3
 I9X  Var_45  O17   P14  O13  C01   -44.88  30.0  3
 I9X  Var_46  O13   C01  C02  O06   -52.50  30.0  1
 I9X  Var_47  H012  C01  O13  P14    72.94  30.0  1
 I9X  Var_48  H011  C01  O13  P14   -46.50  30.0  1
 I9X  Var_49  H012  C01  C02  O06    70.27  30.0  1
 I9X  Var_50  H011  C01  C02  O06  -173.45  30.0  1
 I9X  Var_51  H021  C02  C01  O13   -55.58  30.0  3
 I9X  Var_52  H1    C02  C01  O13  -177.13  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
 I9X  chir_01  C04  P08  C03  O10  both
 I9X  chir_02  C05  P08  O07  O06  both

