# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:45:14 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2R)-3-[(tetrahydroxy-lambda~5~-phosphanyl)oxy]propane-1,2-diyl dibutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)OC[C@H](CO[P](O)(O)(O)O)OC(=O)CCC
#
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
 HI5  HI5  '(2R)-3-[(tetrahydroxy-lambda~5~-phosphanyl)oxy]propane-1,2-diyl dibutanoate'  ligand  44  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HI5
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
 HI5  P     P  P     0    2.595   1.1978  -2.0004  -0.1908
 HI5  O1P   O  OH1   0   -0.723   1.1737  -1.5295  -1.7366
 HI5  O2P   O  OH1   0    0.873   2.5746  -2.9347  -0.5602
 HI5  O3P   O  O2    0  -19.633  -0.1465  -1.0425   0.0083
 HI5  O4P   O  OH1   0    0.474   1.9890  -1.1305   0.9334
 HI5  O5P   O  OH1   0    0.919   0.3449  -3.2931   0.3053
 HI5  C1    C  CH2   0   -4.395  -0.8272  -0.9121   1.2278
 HI5  C2    C  CH1   0   -3.602  -1.1955   0.5379   1.5022
 HI5  C3    C  CH2   0    1.105  -0.0256   1.4668   1.7418
 HI5  O3    O  O2    0   -0.357   0.7300   1.6162   0.5468
 HI5  C11   C  C     0    1.057   2.0412   1.7962   0.6293
 HI5  O11   O  O     0    1.335   2.6327   1.9615   1.6679
 HI5  C12   C  CH2   0    0.188   2.6783   1.8160  -0.7338
 HI5  C13   C  CH2   0    0.260   4.1674   1.5070  -0.7119
 HI5  C14   C  CH3   0    0.965   4.7788   1.5879  -2.1034
 HI5  O2    O  O2    0   -3.735  -1.9616   1.0888   0.4241
 HI5  C31   C  C     0   -2.148  -3.2772   0.8903   0.3941
 HI5  C32   C  CH2   0    0.867  -3.8951   1.5175  -0.8255
 HI5  C33   C  CH2   0    0.385  -5.4099   1.3967  -0.8774
 HI5  C34   C  CH3   0    0.792  -5.9777   2.0236  -2.1427
 HI5  O31   O  O     0    1.308  -3.8802   0.2797   1.2406
 HI5  H1P   H  HOH1  0    0.866   1.8937  -1.9313  -2.2375
 HI5  H2P   H  HOH1  0    0.834   2.9498  -3.4491   0.1631
 HI5  H4P   H  HOH1  0    0.828   2.9047  -1.4029   1.0591
 HI5  H5P   H  HOH1  0    0.839   0.8320  -4.1231   0.2456
 HI5  H1C1  H  HCH2  0    0.986  -0.2548  -1.2624   2.0930
 HI5  H1C2  H  HCH2  0    1.123  -1.7447  -1.5099   1.2056
 HI5  H2    H  HCH1  0    1.128  -1.7823   0.5468   2.4264
 HI5  H3C1  H  HCH2  0    0.885   0.5796   1.0554   2.5504
 HI5  H3C2  H  HCH2  0    0.911  -0.3883   2.4472   2.0620
 HI5  H121  H  HCH2  0    0.984   2.5112   2.8147  -1.1538
 HI5  H122  H  HCH2  0    0.853   2.1492   1.1239  -1.3913
 HI5  H131  H  HCH2  0    0.911   4.3264   0.5062  -0.3018
 HI5  H132  H  HCH2  0    0.988   4.6806   2.2002  -0.0433
 HI5  H141  H  HCH3  0    0.953   5.8449   1.3619  -2.0781
 HI5  H142  H  HCH3  0    0.931   4.3078   0.8802  -2.7881
 HI5  H143  H  HCH3  0    0.954   4.6613   2.5860  -2.5294
 HI5  H321  H  HCH2  0    0.982  -3.5900   2.5679  -0.8680
 HI5  H322  H  HCH2  0    0.791  -3.4451   1.0492  -1.7074
 HI5  H331  H  HCH2  0    0.937  -5.6978   0.3443  -0.8299
 HI5  H332  H  HCH2  0    0.965  -5.8495   1.8769  -0.0005
 HI5  H341  H  HCH3  0    0.935  -7.0619   1.9182  -2.1808
 HI5  H342  H  HCH3  0    0.947  -5.7475   3.0890  -2.1975
 HI5  H343  H  HCH3  0    0.935  -5.5670   1.5517  -3.0371

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
 HI5  P    O1P   single  1.616  0.020  1.616
 HI5  P    O2P   single  1.704  0.020  1.704
 HI5  P    O3P   single  1.663  0.020  1.663
 HI5  P    O4P   single  1.627  0.020  1.627
 HI5  P    O5P   single  1.626  0.020  1.626
 HI5  O1P  H1P   single  0.850  0.020  0.980
 HI5  O2P  H2P   single  0.850  0.020  0.980
 HI5  O3P  C1    single  1.403  0.020  1.403
 HI5  O4P  H4P   single  0.850  0.020  0.980
 HI5  O5P  H5P   single  0.850  0.020  0.980
 HI5  C1   C2    single  1.521  0.020  1.521
 HI5  C1   H1C1  single  0.970  0.020  1.090
 HI5  C1   H1C2  single  0.970  0.020  1.090
 HI5  C2   C3    single  1.513  0.020  1.513
 HI5  C2   O2    single  1.433  0.020  1.433
 HI5  C2   H2    single  0.970  0.020  1.090
 HI5  C3   O3    single  1.422  0.020  1.422
 HI5  C3   H3C1  single  0.970  0.020  1.090
 HI5  C3   H3C2  single  0.970  0.020  1.090
 HI5  O3   C11   single  1.326  0.020  1.326
 HI5  C11  O11   double  1.207  0.020  1.207
 HI5  C11  C12   single  1.505  0.020  1.505
 HI5  C12  C13   single  1.521  0.020  1.521
 HI5  C12  H121  single  0.970  0.020  1.090
 HI5  C12  H122  single  0.970  0.020  1.090
 HI5  C13  C14   single  1.522  0.020  1.522
 HI5  C13  H131  single  0.970  0.020  1.090
 HI5  C13  H132  single  0.970  0.020  1.090
 HI5  C14  H141  single  0.970  0.020  1.090
 HI5  C14  H142  single  0.970  0.020  1.090
 HI5  C14  H143  single  0.970  0.020  1.090
 HI5  O2   C31   single  1.331  0.020  1.331
 HI5  C31  C32   single  1.504  0.020  1.504
 HI5  C31  O31   double  1.205  0.020  1.205
 HI5  C32  C33   single  1.520  0.020  1.520
 HI5  C32  H321  single  0.970  0.020  1.090
 HI5  C32  H322  single  0.970  0.020  1.090
 HI5  C33  C34   single  1.522  0.020  1.522
 HI5  C33  H331  single  0.970  0.020  1.090
 HI5  C33  H332  single  0.970  0.020  1.090
 HI5  C34  H341  single  0.970  0.020  1.090
 HI5  C34  H342  single  0.970  0.020  1.090
 HI5  C34  H343  single  0.970  0.020  1.090

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
 HI5  O5P   P    O4P   117.99  3.000
 HI5  O5P   P    O3P    89.85  3.000
 HI5  O4P   P    O3P    90.14  3.000
 HI5  O5P   P    O2P    93.10  3.000
 HI5  O4P   P    O2P    92.87  3.000
 HI5  O3P   P    O2P   174.21  3.000
 HI5  O5P   P    O1P   121.04  3.000
 HI5  O4P   P    O1P   120.82  3.000
 HI5  O3P   P    O1P    86.25  3.000
 HI5  O2P   P    O1P    87.96  3.000
 HI5  H1P   O1P  P     111.35  3.000
 HI5  H2P   O2P  P     116.39  3.000
 HI5  C1    O3P  P     123.37  3.000
 HI5  H4P   O4P  P     113.65  3.000
 HI5  H5P   O5P  P     113.61  3.000
 HI5  H1C2  C1   H1C1  106.21  3.000
 HI5  H1C2  C1   C2    108.74  3.000
 HI5  H1C1  C1   C2    106.80  3.000
 HI5  H1C2  C1   O3P   109.76  3.000
 HI5  H1C1  C1   O3P   113.80  3.000
 HI5  C2    C1   O3P   111.29  3.000
 HI5  H2    C2   O2    110.21  3.000
 HI5  H2    C2   C3    106.01  3.000
 HI5  O2    C2   C3    107.25  3.000
 HI5  H2    C2   C1    106.85  3.000
 HI5  O2    C2   C1    111.12  3.000
 HI5  C3    C2   C1    115.26  3.000
 HI5  H3C2  C3   H3C1  107.77  3.000
 HI5  H3C2  C3   O3    109.16  3.000
 HI5  H3C1  C3   O3    111.59  3.000
 HI5  H3C2  C3   C2    109.90  3.000
 HI5  H3C1  C3   C2    108.35  3.000
 HI5  O3    C3   C2    110.02  3.000
 HI5  C11   O3   C3    119.18  3.000
 HI5  C12   C11  O11   124.77  3.000
 HI5  C12   C11  O3    111.35  3.000
 HI5  O11   C11  O3    123.84  3.000
 HI5  H122  C12  H121  105.84  3.000
 HI5  H122  C12  C13   110.75  3.000
 HI5  H121  C12  C13   109.87  3.000
 HI5  H122  C12  C11   109.40  3.000
 HI5  H121  C12  C11   107.13  3.000
 HI5  C13   C12  C11   113.50  3.000
 HI5  H132  C13  H131  106.46  3.000
 HI5  H132  C13  C14   109.72  3.000
 HI5  H131  C13  C14   109.47  3.000
 HI5  H132  C13  C12   109.88  3.000
 HI5  H131  C13  C12   109.50  3.000
 HI5  C14   C13  C12   111.67  3.000
 HI5  H143  C14  H142  107.56  3.000
 HI5  H143  C14  H141  107.69  3.000
 HI5  H142  C14  H141  107.58  3.000
 HI5  H143  C14  C13   111.24  3.000
 HI5  H142  C14  C13   111.45  3.000
 HI5  H141  C14  C13   111.13  3.000
 HI5  C31   O2   C2    119.22  3.000
 HI5  O31   C31  C32   125.11  3.000
 HI5  O31   C31  O2    123.66  3.000
 HI5  C32   C31  O2    111.23  3.000
 HI5  H322  C32  H321  105.34  3.000
 HI5  H322  C32  C33   110.36  3.000
 HI5  H321  C32  C33   110.65  3.000
 HI5  H322  C32  C31   107.80  3.000
 HI5  H321  C32  C31   108.49  3.000
 HI5  C33   C32  C31   113.81  3.000
 HI5  H332  C33  H331  106.42  3.000
 HI5  H332  C33  C34   109.65  3.000
 HI5  H331  C33  C34   109.56  3.000
 HI5  H332  C33  C32   109.79  3.000
 HI5  H331  C33  C32   109.74  3.000
 HI5  C34   C33  C32   111.55  3.000
 HI5  H343  C34  H342  107.56  3.000
 HI5  H343  C34  H341  107.69  3.000
 HI5  H342  C34  H341  107.60  3.000
 HI5  H343  C34  C33   111.27  3.000
 HI5  H342  C34  C33   111.41  3.000
 HI5  H341  C34  C33   111.12  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
 HI5  Var_01  C2    C1   O3P  P     136.77  30.0  3
 HI5  Var_02  C32   C31  O2   C2   -178.73  30.0  3
 HI5  Var_03  O11   C11  O3   C3     -6.85  30.0  3
 HI5  Var_04  C13   C12  C11  O3   -158.77  30.0  3
 HI5  Var_05  C14   C13  C12  C11  -177.92  30.0  3
 HI5  Var_06  C33   C32  C31  O2   -176.59  30.0  3
 HI5  Var_07  C34   C33  C32  C31  -178.91  30.0  3
 HI5  Var_08  H3C1  C3   O3   C11   -27.07  30.0  1
 HI5  Var_09  H141  C14  C13  C12  -179.82  30.0  3
 HI5  Var_10  H341  C34  C33  C32   179.04  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
 HI5  chir_01  C2  C1  C3  O2  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
 HI5  plan-1  O3   0.020
 HI5  plan-1  C11  0.020
 HI5  plan-1  O11  0.020
 HI5  plan-1  C12  0.020
 HI5  plan-2  O2   0.020
 HI5  plan-2  C31  0.020
 HI5  plan-2  C32  0.020
 HI5  plan-2  O31  0.020

