# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 30 19:18:38 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R)-2-{[(1R)-1-hydroxybutyl]oxy}-1-({[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}methyl)ethyl butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](O)OC[C@H](CO[P@@](O)(=O)O[C@@H]1[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@H](O[P](O)(O)=O)[C@H]1O)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
 3PI  3PI  '(1R)-2-{[(1R)-1-hydroxybutyl]oxy}-1-({[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}methyl)ethyl butanoate'  ligand  69  39  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3PI
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
 3PI  C1    C  CH1    0   0.018  -1.8023   0.0127  -1.4922
 3PI  C2    C  CH1    0  -0.042  -1.5345  -1.2380  -0.6488
 3PI  C3    C  CH1    0   0.079  -0.8690  -0.9094   0.6955
 3PI  C4    C  CH1    0  -0.010  -1.6559   0.1401   1.4749
 3PI  C5    C  CH1    0   0.069  -1.9212   1.3645   0.6205
 3PI  C6    C  CH1    0  -0.001  -2.5878   1.0576  -0.7061
 3PI  O1    O  O2     0  -0.601  -0.5824   0.5873  -1.9416
 3PI  O2    O  OH1    0  -0.671  -2.7391  -1.9434  -0.4727
 3PI  O3    O  O2     0  -0.605  -0.7406  -2.0327   1.5411
 3PI  O4    O  OH1    0  -0.669  -0.9701   0.5182   2.6524
 3PI  O5    O  O2     0  -0.615  -2.7475   2.2543   1.3428
 3PI  O6    O  OH1    0  -0.683  -2.7748   2.2352  -1.4488
 3PI  P1    P  P      0   1.377   0.0214   0.2373  -3.4213
 3PI  O11   O  OP    -1  -0.909   0.9755   1.3265  -3.7899
 3PI  O12   O  O      0  -0.873  -1.0994  -0.1495  -4.3406
 3PI  O13   O  O2     0  -0.457   0.8313  -1.1720  -3.1356
 3PI  P3    P  P      0   1.160  -0.3277  -3.5738   1.0003
 3PI  O31   O  O      0  -0.850  -1.5964  -4.0588   0.2504
 3PI  O32   O  OP    -1  -0.957   0.8928  -3.4318   0.1028
 3PI  O33   O  OP    -1  -0.955  -0.1001  -4.3090   2.3101
 3PI  P5    P  P      0   1.188  -2.0529   3.7670   1.6249
 3PI  O51   O  O      0  -0.857  -0.8354   3.4416   2.5010
 3PI  O52   O  OP    -1  -0.987  -1.7300   4.2738   0.2068
 3PI  O53   O  OP    -1  -0.894  -3.1597   4.5294   2.3307
 3PI  C7    C  CH2    0  -0.179   2.2257  -1.2896  -3.0327
 3PI  C8    C  CH1    0  -0.085   2.7889  -0.9987  -1.6492
 3PI  C9    C  CH2    0  -0.214   4.2369  -1.4595  -1.6215
 3PI  C10   C  CH1    0   0.272   6.1102  -1.6751  -0.2010
 3PI  C11   C  CH2    0  -0.454   6.4645  -1.4747   1.2616
 3PI  C12   C  CH2    0  -0.415   7.8313  -2.0326   1.6369
 3PI  C13   C  CH3    0  -0.657   8.1177  -1.8968   3.1261
 3PI  C15   C  CH2    0  -0.556   2.1587   2.4142  -0.3839
 3PI  C16   C  CH2    0  -0.431   2.2442   3.1585   0.9399
 3PI  C17   C  CH3    0  -0.669   1.9125   4.6330   0.7741
 3PI  O14   O  O2     0  -0.399   2.7166   0.4174  -1.4670
 3PI  O15   O  O2     0  -0.504   4.8294  -1.1459  -0.3864
 3PI  O16   O  OH1    0  -0.675   7.0506  -1.1129  -1.0726
 3PI  O17   O  O      0  -0.534   2.4179   0.3131   0.7499
 3PI  H1    H  HCH1   0   0.270  -2.4019  -0.2965  -2.3545
 3PI  H2    H  HCH1   0   0.217  -0.8167  -1.8502  -1.2088
 3PI  H3    H  HCH1   0   0.226   0.1191  -0.4980   0.4689
 3PI  H4    H  HCH1   0   0.146  -2.6261  -0.3048   1.7506
 3PI  H5    H  HCH1   0   0.230  -0.9443   1.8220   0.4019
 3PI  H6    H  HCH1   0   0.226  -3.5697   0.6074  -0.4903
 3PI  HO2   H  HOH1   0   0.441  -2.4088  -2.8527  -0.1889
 3PI  HO4   H  HOH1   0   0.420  -0.8535   1.4897   2.6437
 3PI  HO6   H  HOH1   0   0.419  -2.3724   2.9791  -0.9483
 3PI  H71   H  HCH2   0   0.164   2.7349  -0.6577  -3.7681
 3PI  H72   H  HCH2   0   0.238   2.4694  -2.3268  -3.2797
 3PI  H8    H  HCH1   0   0.278   2.1999  -1.5231  -0.8904
 3PI  H91   H  HCH2   0   0.226   4.7828  -0.9971  -2.4542
 3PI  H92   H  HCH2   0   0.281   4.2566  -2.5451  -1.7937
 3PI  H10   H  HCH1   0   0.236   6.1121  -2.7477  -0.4463
 3PI  H121  H  HCH2   0   0.229   8.6126  -1.5216   1.0698
 3PI  H122  H  HCH2   0   0.218   7.8879  -3.0880   1.3519
 3PI  H131  H  HCH3   0   0.185   8.0757  -0.8531   3.4439
 3PI  H132  H  HCH3   0   0.260   7.3906  -2.4513   3.7220
 3PI  H133  H  HCH3   0   0.217   9.1081  -2.2786   3.3757
 3PI  H151  H  HCH2   0   0.242   2.8112   2.8630  -1.1379
 3PI  H152  H  HCH2   0   0.297   1.1434   2.4967  -0.7853
 3PI  H161  H  HCH2   0   0.248   1.5267   2.7303   1.6410
 3PI  H162  H  HCH2   0   0.247   3.2435   3.0402   1.3693
 3PI  H171  H  HCH3   0   0.176   2.0385   5.1709   1.7151
 3PI  H172  H  HCH3   0   0.235   2.5563   5.1133   0.0329
 3PI  H173  H  HCH3   0   0.236   0.8723   4.7460   0.4672
 3PI  H16   H  HOH1   0   0.423   7.2202  -0.2012  -0.8060
 3PI  C14   C  C      0   0.614   2.4532   0.9423  -0.2754
 3PI  H111  H  HCH2   0   0.239   5.6949  -1.9579   1.8699
 3PI  H112  H  HCH2   0   0.158   6.4197  -0.4045   1.4987

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
 3PI  C1   C2    single  1.532  0.020  1.532
 3PI  C1   C6    single  1.525  0.020  1.525
 3PI  C1   O1    single  1.421  0.020  1.421
 3PI  C1   H1    single  0.970  0.020  1.090
 3PI  C2   C3    single  1.535  0.020  1.535
 3PI  C2   O2    single  1.407  0.020  1.407
 3PI  C2   H2    single  0.970  0.020  1.090
 3PI  C3   C4    single  1.526  0.020  1.526
 3PI  C3   O3    single  1.412  0.020  1.412
 3PI  C3   H3    single  0.970  0.020  1.090
 3PI  C4   C5    single  1.516  0.020  1.516
 3PI  C4   O4    single  1.414  0.020  1.414
 3PI  C4   H4    single  0.970  0.020  1.090
 3PI  C5   C6    single  1.516  0.020  1.516
 3PI  C5   O5    single  1.413  0.020  1.413
 3PI  C5   H5    single  0.970  0.020  1.090
 3PI  C6   O6    single  1.405  0.020  1.405
 3PI  C6   H6    single  0.970  0.020  1.090
 3PI  O1   P1    single  1.636  0.020  1.636
 3PI  O2   HO2   single  0.850  0.020  0.980
 3PI  O3   P3    single  1.685  0.020  1.685
 3PI  O4   HO4   single  0.850  0.020  0.980
 3PI  O5   P5    single  1.688  0.020  1.688
 3PI  O6   HO6   single  0.850  0.020  0.980
 3PI  P1   O11   deloc   1.494  0.020  1.494
 3PI  P1   O12   deloc   1.500  0.020  1.500
 3PI  P1   O13   single  1.650  0.020  1.650
 3PI  O13  C7    single  1.403  0.020  1.403
 3PI  P3   O31   deloc   1.552  0.020  1.552
 3PI  P3   O32   deloc   1.522  0.020  1.522
 3PI  P3   O33   deloc   1.519  0.020  1.519
 3PI  P5   O51   deloc   1.535  0.020  1.535
 3PI  P5   O52   deloc   1.540  0.020  1.540
 3PI  P5   O53   deloc   1.518  0.020  1.518
 3PI  C7   C8    single  1.522  0.020  1.522
 3PI  C7   H71   single  0.970  0.020  1.090
 3PI  C7   H72   single  0.970  0.020  1.090
 3PI  C8   C9    single  1.520  0.020  1.520
 3PI  C8   O14   single  1.430  0.020  1.430
 3PI  C8   H8    single  0.970  0.020  1.090
 3PI  C9   O15   single  1.405  0.020  1.405
 3PI  C9   H91   single  0.970  0.020  1.090
 3PI  C9   H92   single  0.970  0.020  1.090
 3PI  C10  C11   single  1.518  0.020  1.518
 3PI  C10  O15   single  1.398  0.020  1.398
 3PI  C10  O16   single  1.400  0.020  1.400
 3PI  C10  H10   single  0.970  0.020  1.090
 3PI  C11  C12   single  1.523  0.020  1.523
 3PI  C11  H111  single  0.970  0.020  1.090
 3PI  C11  H112  single  0.970  0.020  1.090
 3PI  C12  C13   single  1.522  0.020  1.522
 3PI  C12  H121  single  0.970  0.020  1.090
 3PI  C12  H122  single  0.970  0.020  1.090
 3PI  C13  H131  single  0.970  0.020  1.090
 3PI  C13  H132  single  0.970  0.020  1.090
 3PI  C13  H133  single  0.970  0.020  1.090
 3PI  C14  C15   single  1.505  0.020  1.505
 3PI  C14  O14   single  1.329  0.020  1.329
 3PI  C14  O17   double  1.203  0.020  1.203
 3PI  C15  C16   single  1.521  0.020  1.521
 3PI  C15  H151  single  0.970  0.020  1.090
 3PI  C15  H152  single  0.970  0.020  1.090
 3PI  C16  C17   single  1.520  0.020  1.520
 3PI  C16  H161  single  0.970  0.020  1.090
 3PI  C16  H162  single  0.970  0.020  1.090
 3PI  C17  H171  single  0.970  0.020  1.090
 3PI  C17  H172  single  0.970  0.020  1.090
 3PI  C17  H173  single  0.970  0.020  1.090
 3PI  O16  H16   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
 3PI  H1    C1   O1    109.59  3.000
 3PI  H1    C1   C6    108.50  3.000
 3PI  O1    C1   C6    109.15  3.000
 3PI  H1    C1   C2    107.39  3.000
 3PI  O1    C1   C2    110.73  3.000
 3PI  C6    C1   C2    111.44  3.000
 3PI  H2    C2   O2    110.14  3.000
 3PI  H2    C2   C3    106.43  3.000
 3PI  O2    C2   C3    111.64  3.000
 3PI  H2    C2   C1    106.79  3.000
 3PI  O2    C2   C1    109.17  3.000
 3PI  C3    C2   C1    112.52  3.000
 3PI  H3    C3   O3    109.94  3.000
 3PI  H3    C3   C4    108.23  3.000
 3PI  O3    C3   C4    106.75  3.000
 3PI  H3    C3   C2    106.89  3.000
 3PI  O3    C3   C2    113.17  3.000
 3PI  C4    C3   C2    111.77  3.000
 3PI  H4    C4   O4    109.05  3.000
 3PI  H4    C4   C5    108.23  3.000
 3PI  O4    C4   C5    109.76  3.000
 3PI  H4    C4   C3    107.70  3.000
 3PI  O4    C4   C3    111.05  3.000
 3PI  C5    C4   C3    110.96  3.000
 3PI  H5    C5   O5    111.03  3.000
 3PI  H5    C5   C6    107.49  3.000
 3PI  O5    C5   C6    108.52  3.000
 3PI  H5    C5   C4    106.99  3.000
 3PI  O5    C5   C4    108.83  3.000
 3PI  C6    C5   C4    113.98  3.000
 3PI  H6    C6   O6    109.12  3.000
 3PI  H6    C6   C5    107.65  3.000
 3PI  O6    C6   C5    110.58  3.000
 3PI  H6    C6   C1    106.26  3.000
 3PI  O6    C6   C1    111.73  3.000
 3PI  C5    C6   C1    111.30  3.000
 3PI  P1    O1   C1    121.08  3.000
 3PI  HO2   O2   C2    101.94  3.000
 3PI  P3    O3   C3    123.91  3.000
 3PI  HO4   O4   C4    108.41  3.000
 3PI  P5    O5   C5    114.15  3.000
 3PI  HO6   O6   C6    108.10  3.000
 3PI  O13   P1   O12   104.63  3.000
 3PI  O13   P1   O11   110.60  3.000
 3PI  O12   P1   O11   120.92  3.000
 3PI  O13   P1   O1    101.96  3.000
 3PI  O12   P1   O1    109.49  3.000
 3PI  O11   P1   O1    107.63  3.000
 3PI  C7    O13  P1    124.89  3.000
 3PI  O33   P3   O32   115.69  3.000
 3PI  O33   P3   O31   112.83  3.000
 3PI  O32   P3   O31   113.58  3.000
 3PI  O33   P3   O3    101.69  3.000
 3PI  O32   P3   O3    107.49  3.000
 3PI  O31   P3   O3    103.93  3.000
 3PI  O53   P5   O52   114.56  3.000
 3PI  O53   P5   O51   114.80  3.000
 3PI  O52   P5   O51   115.41  3.000
 3PI  O53   P5   O5    103.16  3.000
 3PI  O52   P5   O5    103.13  3.000
 3PI  O51   P5   O5    103.40  3.000
 3PI  H72   C7   H71   106.97  3.000
 3PI  H72   C7   C8    107.70  3.000
 3PI  H71   C7   C8    109.15  3.000
 3PI  H72   C7   O13   106.52  3.000
 3PI  H71   C7   O13   111.38  3.000
 3PI  C8    C7   O13   114.74  3.000
 3PI  H8    C8   O14   111.04  3.000
 3PI  H8    C8   C9    110.78  3.000
 3PI  O14   C8   C9    110.26  3.000
 3PI  H8    C8   C7    109.85  3.000
 3PI  O14   C8   C7    106.65  3.000
 3PI  C9    C8   C7    108.14  3.000
 3PI  H92   C9   H91   106.75  3.000
 3PI  H92   C9   O15   110.52  3.000
 3PI  H91   C9   O15   111.29  3.000
 3PI  H92   C9   C8    108.28  3.000
 3PI  H91   C9   C8    109.40  3.000
 3PI  O15   C9   C8    110.49  3.000
 3PI  H10   C10  O16   104.57  3.000
 3PI  H10   C10  O15   109.93  3.000
 3PI  O16   C10  O15   112.38  3.000
 3PI  H10   C10  C11   110.07  3.000
 3PI  O16   C10  C11   112.96  3.000
 3PI  O15   C10  C11   106.95  3.000
 3PI  H112  C11  H111  106.38  3.000
 3PI  H112  C11  C12   109.92  3.000
 3PI  H111  C11  C12   109.43  3.000
 3PI  H112  C11  C10   109.11  3.000
 3PI  H111  C11  C10   108.26  3.000
 3PI  C12   C11  C10   113.48  3.000
 3PI  H122  C12  H121  106.19  3.000
 3PI  H122  C12  C13   109.33  3.000
 3PI  H121  C12  C13   109.37  3.000
 3PI  H122  C12  C11   109.59  3.000
 3PI  H121  C12  C11   110.03  3.000
 3PI  C13   C12  C11   112.15  3.000
 3PI  H133  C13  H132  107.59  3.000
 3PI  H133  C13  H131  107.63  3.000
 3PI  H132  C13  H131  107.52  3.000
 3PI  H133  C13  C12   111.32  3.000
 3PI  H132  C13  C12   111.31  3.000
 3PI  H131  C13  C12   111.27  3.000
 3PI  H152  C15  H151  105.65  3.000
 3PI  H152  C15  C16   109.52  3.000
 3PI  H151  C15  C16   111.45  3.000
 3PI  H152  C15  C14   106.36  3.000
 3PI  H151  C15  C14   109.54  3.000
 3PI  C16   C15  C14   113.88  3.000
 3PI  H162  C16  H161  107.82  3.000
 3PI  H162  C16  C17   110.30  3.000
 3PI  H161  C16  C17   107.90  3.000
 3PI  H162  C16  C15   109.87  3.000
 3PI  H161  C16  C15   109.29  3.000
 3PI  C17   C16  C15   111.56  3.000
 3PI  H173  C17  H172  108.99  3.000
 3PI  H173  C17  H171  107.56  3.000
 3PI  H172  C17  H171  107.47  3.000
 3PI  H173  C17  C16   109.84  3.000
 3PI  H172  C17  C16   111.82  3.000
 3PI  H171  C17  C16   111.03  3.000
 3PI  C14   O14  C8    121.04  3.000
 3PI  C10   O15  C9    114.73  3.000
 3PI  H16   O16  C10   108.99  3.000
 3PI  O17   C14  O14   124.29  3.000
 3PI  O17   C14  C15   124.55  3.000
 3PI  O14   C14  C15   111.13  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
 3PI  Var_01  O11   P1   O1   C1    159.47  30.0  3
 3PI  Var_02  O31   P3   O3   C3    -71.96  30.0  3
 3PI  Var_03  O51   P5   O5   C5    -63.18  30.0  3
 3PI  Var_04  C8    C7   O13  P1     85.11  30.0  3
 3PI  Var_05  C15   C14  O14  C8   -168.67  30.0  2
 3PI  Var_06  C13   C12  C11  C10  -176.29  30.0  3
 3PI  Var_07  C17   C16  C15  C14  -178.94  30.0  3
 3PI  Var_08  O14   C14  C15  C16  -163.29  30.0  1
 3PI  Var_09  H91   C9   O15  C10   -65.78  30.0  1
 3PI  Var_10  H131  C13  C12  C11   -58.60  30.0  3
 3PI  Var_11  H171  C17  C16  C15  -176.36  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
 3PI  chir_01  C1   C2   C6   O1   negativ
 3PI  chir_02  C2   O2   C1   C3   negativ
 3PI  chir_03  C3   O3   C4   C2   positiv
 3PI  chir_04  C4   O4   C3   C5   positiv
 3PI  chir_05  C5   O5   C6   C4   positiv
 3PI  chir_06  C6   O6   C5   C1   positiv
 3PI  chir_08  C8   O14  C7   C9   negativ
 3PI  chir_09  C10  O15  O16  C11  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
 3PI  plan-1  C15  0.020
 3PI  plan-1  O14  0.020
 3PI  plan-1  O17  0.020
 3PI  plan-1  C14  0.020

