# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:35:04 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: (2S)-3-hydroxypropane-1,2-diyl didecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCCCC
#
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
 DDR  DDR  '(2S)-3-hydroxypropane-1,2-diyl didecanoate'  ligand  72  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DDR
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
 DDR  O21   O  O     0  -0.451   -3.3127  -3.3330  -0.1411
 DDR  C21   C  C     0   0.612   -2.7112  -2.2962  -0.0126
 DDR  C22   C  CH2   0  -0.584   -3.3471  -0.9355   0.0776
 DDR  C23   C  CH2   0  -0.417   -4.8532  -0.9597  -0.1255
 DDR  C24   C  CH2   0  -0.416   -5.4879   0.4123   0.0643
 DDR  C25   C  CH2   0  -0.412   -6.9961   0.3872  -0.1472
 DDR  C26   C  CH2   0  -0.412   -7.6681   1.7335   0.0895
 DDR  C27   C  CH2   0  -0.411   -9.1745   1.6936  -0.1349
 DDR  C28   C  CH2   0  -0.407   -9.8633   3.0258   0.1308
 DDR  C29   C  CH2   0  -0.418  -11.3677   2.9833  -0.1085
 DDR  C30   C  CH3   0  -0.662  -12.0514   4.3132   0.1769
 DDR  O52   O  O2    0  -0.466   -1.3858  -2.2239   0.0869
 DDR  C52   C  CH1   0  -0.051   -0.6263  -3.4384   0.0958
 DDR  C53   C  CH2   0  -0.174   -0.3855  -3.9571  -1.3120
 DDR  O53   O  OH1   0  -0.658    0.1630  -2.9566  -2.1289
 DDR  C51   C  CH2   0  -0.193    0.6115  -3.1902   0.9258
 DDR  O51   O  O2    0  -0.448    1.4312  -2.2020   0.3084
 DDR  C1    C  C     0   0.610    2.5962  -1.9296   0.8858
 DDR  O1    O  O     0  -0.456    2.9589  -2.4454   1.9141
 DDR  C2    C  CH2   0  -0.583    3.3891  -0.9260   0.0934
 DDR  C3    C  CH2   0  -0.417    4.7256  -0.5777   0.7290
 DDR  C4    C  CH2   0  -0.416    5.5613   0.3517  -0.1413
 DDR  C5    C  CH2   0  -0.412    6.8963   0.7024   0.5042
 DDR  C6    C  CH2   0  -0.412    7.7849   1.5816  -0.3652
 DDR  C7    C  CH2   0  -0.411    9.1120   1.9256   0.3006
 DDR  C8    C  CH2   0  -0.407   10.0210   2.7889  -0.5637
 DDR  C9    C  CH2   0  -0.418   11.3449   3.1294   0.1107
 DDR  C10   C  CH3   0  -0.664   12.2500   3.9899  -0.7590
 DDR  H221  H  HCH2  0   0.274   -3.0997  -0.5175   1.0591
 DDR  H222  H  HCH2  0   0.273   -2.8663  -0.2751  -0.6503
 DDR  H231  H  HCH2  0   0.224   -5.0827  -1.3321  -1.1279
 DDR  H232  H  HCH2  0   0.224   -5.3087  -1.6633   0.5760
 DDR  H241  H  HCH2  0   0.212   -5.2683   0.7798   1.0727
 DDR  H242  H  HCH2  0   0.212   -5.0336   1.1312  -0.6262
 DDR  H251  H  HCH2  0   0.209   -7.2108   0.0460  -1.1659
 DDR  H252  H  HCH2  0   0.208   -7.4414  -0.3594   0.5199
 DDR  H261  H  HCH2  0   0.207   -7.4632   2.0672   1.1128
 DDR  H262  H  HCH2  0   0.207   -7.2218   2.4871  -0.5688
 DDR  H271  H  HCH2  0   0.206   -9.3772   1.3765  -1.1640
 DDR  H272  H  HCH2  0   0.206   -9.6157   0.9242   0.5088
 DDR  H281  H  HCH2  0   0.205   -9.6714   3.3351   1.1645
 DDR  H282  H  HCH2  0   0.206   -9.4172   3.8010  -0.5025
 DDR  H291  H  HCH2  0   0.210  -11.5588   2.6858  -1.1441
 DDR  H292  H  HCH2  0   0.210  -11.8099   2.2010   0.5164
 DDR  H301  H  HCH3  0   0.215  -11.9131   4.6119   1.2181
 DDR  H302  H  HCH3  0   0.215  -11.6421   5.1087  -0.4488
 DDR  H303  H  HCH3  0   0.225  -13.1244   4.2632  -0.0120
 DDR  H52   H  HCH1  0   0.269   -1.1765  -4.2216   0.6272
 DDR  H531  H  HCH2  0   0.207    0.2704  -4.8347  -1.2234
 DDR  H532  H  HCH2  0   0.222   -1.3380  -4.3223  -1.7104
 DDR  HO53  H  HOH1  0   0.457    0.1264  -3.2706  -3.0366
 DDR  H511  H  HCH2  0   0.255    0.3212  -2.8722   1.9304
 DDR  H512  H  HCH2  0   0.246    1.1533  -4.1344   1.0195
 DDR  H21   H  HCH2  0   0.272    3.5364  -1.3331  -0.9125
 DDR  H22   H  HCH2  0   0.273    2.7785  -0.0282  -0.0428
 DDR  H31   H  HCH2  0   0.224    4.5594  -0.1116   1.7042
 DDR  H32   H  HCH2  0   0.224    5.2925  -1.4928   0.9187
 DDR  H41   H  HCH2  0   0.212    5.7399  -0.1222  -1.1129
 DDR  H42   H  HCH2  0   0.212    5.0034   1.2708  -0.3497
 DDR  H51   H  HCH2  0   0.209    6.7130   1.2040   1.4609
 DDR  H52A  H  HCH2  0   0.208    7.4313  -0.2224   0.7478
 DDR  H61   H  HCH2  0   0.207    7.9769   1.0752  -1.3177
 DDR  H62   H  HCH2  0   0.207    7.2535   2.5062  -0.6169
 DDR  H71   H  HCH2  0   0.206    8.9170   2.4392   1.2487
 DDR  H72   H  HCH2  0   0.206    9.6347   0.9990   0.5635
 DDR  H81   H  HCH2  0   0.206   10.2197   2.2741  -1.5105
 DDR  H82   H  HCH2  0   0.206    9.5008   3.7162  -0.8290
 DDR  H91   H  HCH2  0   0.210   11.1457   3.6444   1.0557
 DDR  H92   H  HCH2  0   0.210   11.8627   2.2023   0.3768
 DDR  H101  H  HCH3  0   0.216   12.4928   3.4851  -1.6960
 DDR  H102  H  HCH3  0   0.216   11.7684   4.9362  -1.0126
 DDR  H103  H  HCH3  0   0.226   13.1895   4.2217  -0.2562

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
 DDR  C30  C29   single  1.522  0.020  1.522
 DDR  C29  C28   single  1.524  0.020  1.524
 DDR  C8   C9    single  1.524  0.020  1.524
 DDR  C8   C7    single  1.523  0.020  1.523
 DDR  C10  C9    single  1.522  0.020  1.522
 DDR  C28  C27   single  1.523  0.020  1.523
 DDR  C7   C6    single  1.524  0.020  1.524
 DDR  C6   C5    single  1.523  0.020  1.523
 DDR  C27  C26   single  1.524  0.020  1.524
 DDR  C5   C4    single  1.524  0.020  1.524
 DDR  C26  C25   single  1.523  0.020  1.523
 DDR  C4   C3    single  1.523  0.020  1.523
 DDR  C25  C24   single  1.523  0.020  1.523
 DDR  C3   C2    single  1.520  0.020  1.520
 DDR  C2   C1    single  1.505  0.020  1.505
 DDR  C24  C23   single  1.524  0.020  1.524
 DDR  C23  C22   single  1.520  0.020  1.520
 DDR  C1   O1    double  1.206  0.020  1.206
 DDR  C1   O51   single  1.328  0.020  1.328
 DDR  O21  C21   double  1.205  0.020  1.205
 DDR  C22  C21   single  1.505  0.020  1.505
 DDR  O51  C51   single  1.425  0.020  1.425
 DDR  C21  O52   single  1.331  0.020  1.331
 DDR  O52  C52   single  1.432  0.020  1.432
 DDR  C51  C52   single  1.511  0.020  1.511
 DDR  C52  C53   single  1.520  0.020  1.520
 DDR  C53  O53   single  1.403  0.020  1.403
 DDR  C22  H221  single  0.970  0.020  1.090
 DDR  C22  H222  single  0.970  0.020  1.090
 DDR  C23  H231  single  0.970  0.020  1.090
 DDR  C23  H232  single  0.970  0.020  1.090
 DDR  C24  H241  single  0.970  0.020  1.090
 DDR  C24  H242  single  0.970  0.020  1.090
 DDR  C25  H251  single  0.970  0.020  1.090
 DDR  C25  H252  single  0.970  0.020  1.090
 DDR  C26  H261  single  0.970  0.020  1.090
 DDR  C26  H262  single  0.970  0.020  1.090
 DDR  C27  H271  single  0.970  0.020  1.090
 DDR  C27  H272  single  0.970  0.020  1.090
 DDR  C28  H281  single  0.970  0.020  1.090
 DDR  C28  H282  single  0.970  0.020  1.090
 DDR  C29  H291  single  0.970  0.020  1.090
 DDR  C29  H292  single  0.970  0.020  1.090
 DDR  C30  H301  single  0.970  0.020  1.090
 DDR  C30  H302  single  0.970  0.020  1.090
 DDR  C30  H303  single  0.970  0.020  1.090
 DDR  C52  H52   single  0.970  0.020  1.090
 DDR  C53  H531  single  0.970  0.020  1.090
 DDR  C53  H532  single  0.970  0.020  1.090
 DDR  O53  HO53  single  0.850  0.020  0.980
 DDR  C51  H511  single  0.970  0.020  1.090
 DDR  C51  H512  single  0.970  0.020  1.090
 DDR  C2   H21   single  0.970  0.020  1.090
 DDR  C2   H22   single  0.970  0.020  1.090
 DDR  C3   H31   single  0.970  0.020  1.090
 DDR  C3   H32   single  0.970  0.020  1.090
 DDR  C4   H41   single  0.970  0.020  1.090
 DDR  C4   H42   single  0.970  0.020  1.090
 DDR  C5   H51   single  0.970  0.020  1.090
 DDR  C5   H52A  single  0.970  0.020  1.090
 DDR  C6   H61   single  0.970  0.020  1.090
 DDR  C6   H62   single  0.970  0.020  1.090
 DDR  C7   H71   single  0.970  0.020  1.090
 DDR  C7   H72   single  0.970  0.020  1.090
 DDR  C8   H81   single  0.970  0.020  1.090
 DDR  C8   H82   single  0.970  0.020  1.090
 DDR  C9   H91   single  0.970  0.020  1.090
 DDR  C9   H92   single  0.970  0.020  1.090
 DDR  C10  H101  single  0.970  0.020  1.090
 DDR  C10  H102  single  0.970  0.020  1.090
 DDR  C10  H103  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
 DDR  O52   C21  C22   111.54  3.000
 DDR  O52   C21  O21   123.47  3.000
 DDR  C22   C21  O21   124.98  3.000
 DDR  H222  C22  H221  105.47  3.000
 DDR  H222  C22  C23   110.87  3.000
 DDR  H221  C22  C23   110.47  3.000
 DDR  H222  C22  C21   108.67  3.000
 DDR  H221  C22  C21   107.66  3.000
 DDR  C23   C22  C21   113.35  3.000
 DDR  H232  C23  H231  106.36  3.000
 DDR  H232  C23  C24   109.04  3.000
 DDR  H231  C23  C24   109.47  3.000
 DDR  H232  C23  C22   109.72  3.000
 DDR  H231  C23  C22   109.62  3.000
 DDR  C24   C23  C22   112.45  3.000
 DDR  H242  C24  H241  106.08  3.000
 DDR  H242  C24  C25   109.51  3.000
 DDR  H241  C24  C25   109.37  3.000
 DDR  H242  C24  C23   109.86  3.000
 DDR  H241  C24  C23   109.46  3.000
 DDR  C25   C24  C23   112.36  3.000
 DDR  H252  C25  H251  105.91  3.000
 DDR  H252  C25  C26   109.17  3.000
 DDR  H251  C25  C26   109.47  3.000
 DDR  H252  C25  C24   109.22  3.000
 DDR  H251  C25  C24   109.16  3.000
 DDR  C26   C25  C24   113.62  3.000
 DDR  H262  C26  H261  105.99  3.000
 DDR  H262  C26  C27   109.41  3.000
 DDR  H261  C26  C27   109.29  3.000
 DDR  H262  C26  C25   109.57  3.000
 DDR  H261  C26  C25   109.38  3.000
 DDR  C27   C26  C25   112.97  3.000
 DDR  H272  C27  H271  105.91  3.000
 DDR  H272  C27  C28   109.24  3.000
 DDR  H271  C27  C28   109.47  3.000
 DDR  H272  C27  C26   109.26  3.000
 DDR  H271  C27  C26   109.20  3.000
 DDR  C28   C27  C26   113.49  3.000
 DDR  H282  C28  H281  105.91  3.000
 DDR  H282  C28  C29   109.32  3.000
 DDR  H281  C28  C29   109.21  3.000
 DDR  H282  C28  C27   109.50  3.000
 DDR  H281  C28  C27   109.40  3.000
 DDR  C29   C28  C27   113.24  3.000
 DDR  H292  C29  H291  105.99  3.000
 DDR  H292  C29  C30   109.62  3.000
 DDR  H291  C29  C30   109.66  3.000
 DDR  H292  C29  C28   109.22  3.000
 DDR  H291  C29  C28   109.18  3.000
 DDR  C30   C29  C28   112.92  3.000
 DDR  H303  C30  H302  107.63  3.000
 DDR  H303  C30  H301  107.59  3.000
 DDR  H302  C30  H301  107.44  3.000
 DDR  H303  C30  C29   111.67  3.000
 DDR  H302  C30  C29   111.15  3.000
 DDR  H301  C30  C29   111.16  3.000
 DDR  C52   O52  C21   118.84  3.000
 DDR  H52   C52  C51   105.22  3.000
 DDR  H52   C52  C53   106.57  3.000
 DDR  C51   C52  C53   115.80  3.000
 DDR  H52   C52  O52   110.06  3.000
 DDR  C53   C52  O52   111.58  3.000
 DDR  C51   C52  O52   107.36  3.000
 DDR  H532  C53  H531  106.39  3.000
 DDR  H532  C53  O53   111.47  3.000
 DDR  H531  C53  O53   112.51  3.000
 DDR  H532  C53  C52   108.24  3.000
 DDR  H531  C53  C52   107.00  3.000
 DDR  O53   C53  C52   110.97  3.000
 DDR  HO53  O53  C53   107.57  3.000
 DDR  H512  C51  H511  107.72  3.000
 DDR  H512  C51  O51   110.56  3.000
 DDR  H511  C51  O51   110.45  3.000
 DDR  H512  C51  C52   108.14  3.000
 DDR  H511  C51  C52   109.58  3.000
 DDR  O51   C51  C52   110.32  3.000
 DDR  C1    O51  C51   117.28  3.000
 DDR  C2    C1   O1    125.15  3.000
 DDR  O1    C1   O51   123.13  3.000
 DDR  C2    C1   O51   111.72  3.000
 DDR  H22   C2   H21   105.41  3.000
 DDR  H22   C2   C3    110.77  3.000
 DDR  H21   C2   C3    110.55  3.000
 DDR  H22   C2   C1    108.59  3.000
 DDR  H21   C2   C1    107.85  3.000
 DDR  C3    C2   C1    113.32  3.000
 DDR  H32   C3   H31   106.31  3.000
 DDR  H32   C3   C4    108.99  3.000
 DDR  H31   C3   C4    109.44  3.000
 DDR  H32   C3   C2    109.68  3.000
 DDR  H31   C3   C2    109.69  3.000
 DDR  C4    C3   C2    112.53  3.000
 DDR  H42   C4   H41   106.10  3.000
 DDR  H42   C4   C5    109.50  3.000
 DDR  H41   C4   C5    109.41  3.000
 DDR  H42   C4   C3    109.96  3.000
 DDR  H41   C4   C3    109.41  3.000
 DDR  C5    C4   C3    112.28  3.000
 DDR  H52A  C5   H51   105.90  3.000
 DDR  H52A  C5   C6    109.23  3.000
 DDR  H51   C5   C6    109.38  3.000
 DDR  H52A  C5   C4    109.13  3.000
 DDR  H51   C5   C4    109.19  3.000
 DDR  C6    C5   C4    113.72  3.000
 DDR  H62   C6   H61   105.98  3.000
 DDR  H62   C6   C7    109.40  3.000
 DDR  H61   C6   C7    109.36  3.000
 DDR  H62   C6   C5    109.60  3.000
 DDR  H61   C6   C5    109.38  3.000
 DDR  C7    C6   C5    112.89  3.000
 DDR  H72   C7   H71   105.89  3.000
 DDR  H72   C7   C8    109.32  3.000
 DDR  H71   C7   C8    109.36  3.000
 DDR  H72   C7   C6    109.22  3.000
 DDR  H71   C7   C6    109.20  3.000
 DDR  C8    C7   C6    113.57  3.000
 DDR  H82   C8   H81   105.92  3.000
 DDR  H82   C8   C9    109.29  3.000
 DDR  H81   C8   C9    109.25  3.000
 DDR  H82   C8   C7    109.50  3.000
 DDR  H81   C8   C7    109.41  3.000
 DDR  C9    C8   C7    113.21  3.000
 DDR  H92   C9   H91   105.95  3.000
 DDR  H92   C9   C10   109.66  3.000
 DDR  H91   C9   C10   109.61  3.000
 DDR  H92   C9   C8    109.22  3.000
 DDR  H91   C9   C8    109.21  3.000
 DDR  C10   C9   C8    112.95  3.000
 DDR  H103  C10  H102  107.64  3.000
 DDR  H103  C10  H101  107.61  3.000
 DDR  H102  C10  H101  107.44  3.000
 DDR  H103  C10  C9    111.65  3.000
 DDR  H102  C10  C9    111.13  3.000
 DDR  H101  C10  C9    111.18  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
 DDR  Var_01  C23   C22  C21  O21   -4.83  30.0  1
 DDR  Var_02  C24   C23  C22  C21  176.08  30.0  1
 DDR  Var_03  C25   C24  C23  C22  179.69  30.0  1
 DDR  Var_04  C26   C25  C24  C23  177.72  30.0  1
 DDR  Var_05  C27   C26  C25  C24  179.62  30.0  1
 DDR  Var_06  C28   C27  C26  C25  178.62  30.0  1
 DDR  Var_07  C29   C28  C27  C26  179.43  30.0  1
 DDR  Var_08  C30   C29  C28  C27  179.24  30.0  1
 DDR  Var_09  C2    C1   O51  C51  176.97  30.0  1
 DDR  Var_10  C3    C2   C1   O51  179.47  30.0  2
 DDR  Var_11  C4    C3   C2   C1   175.38  30.0  1
 DDR  Var_12  C5    C4   C3   C2   179.72  30.0  1
 DDR  Var_13  C6    C5   C4   C3   177.47  30.0  1
 DDR  Var_14  C7    C6   C5   C4   179.76  30.0  1
 DDR  Var_15  C8    C7   C6   C5   179.20  30.0  1
 DDR  Var_16  C9    C8   C7   C6   179.93  30.0  1
 DDR  Var_17  C10   C9   C8   C7   179.89  30.0  3
 DDR  Var_18  H301  C30  C29  C28  -60.50  30.0  3
 DDR  Var_19  H511  C51  O51  C1    62.36  30.0  3
 DDR  Var_20  H101  C10  C9   C8   -59.89  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
 DDR  chir_01  C52  O52  C51  C53  positiv

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
 DDR  plan-1  O51  0.020
 DDR  plan-1  C1   0.020
 DDR  plan-1  O1   0.020
 DDR  plan-1  C2   0.020
 DDR  plan-2  O21  0.020
 DDR  plan-2  C21  0.020
 DDR  plan-2  C22  0.020
 DDR  plan-2  O52  0.020

