# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 11:20:25 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] decanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[PH](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
 PM8  PM8  'S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] decanethioate'  ligand  73  32  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PM8
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
 PM8  O23   O  OH1   0  -0.735    9.0211   3.7053   0.2687
 PM8  P24   P  P     0   1.134    8.5860   2.3777   1.0488
 PM8  O26   O  O     0  -0.711    7.7504   2.5597   2.2579
 PM8  O27   O  O2    0  -0.584    7.9135   1.6219  -0.1896
 PM8  C28   C  CH2   0  -0.148    7.5066   0.2579  -0.0318
 PM8  C29   C  CT    0  -0.161    7.2453  -0.3378  -1.4145
 PM8  C30   C  CH3   0  -0.672    6.1195   0.4248  -2.1171
 PM8  C31   C  CH3   0  -0.647    8.5108  -0.2591  -2.2734
 PM8  C32   C  CH1   0  -0.031    6.8671  -1.8400  -1.2745
 PM8  O33   O  OH1   0  -0.661    7.8922  -2.5986  -0.6924
 PM8  C34   C  C     0   0.515    5.5853  -2.0686  -0.4723
 PM8  O35   O  O     0  -0.498    5.6472  -2.2098   0.7447
 PM8  N36   N  NH1   0  -0.626    4.4451  -2.1244  -1.1631
 PM8  C37   C  CH2   0  -0.279    3.1474  -2.2843  -0.5406
 PM8  C38   C  CH2   0  -0.600    2.6063  -0.9654  -0.0041
 PM8  C39   C  C     0   0.568    1.2469  -1.1186   0.6445
 PM8  O40   O  O     0  -0.496    0.7394  -2.2091   0.8617
 PM8  N41   N  NH1   0  -0.633    0.6541   0.0407   0.9844
 PM8  C42   C  CH2   0  -0.289   -0.6257   0.1126   1.6440
 PM8  C43   C  CH2   0  -0.555   -1.7796   0.0894   0.6439
 PM8  S1    S  S2    0  -0.010   -3.3315   0.2078   1.5772
 PM8  C1    C  C     0   0.258   -4.5430   0.1736   0.2794
 PM8  O1    O  O     0  -0.385   -4.2443   0.0980  -0.8833
 PM8  C2    C  CH2   0  -0.538   -5.9504   0.2464   0.8105
 PM8  C3    C  CH2   0  -0.417   -7.0321   0.2477  -0.2587
 PM8  C4    C  CH2   0  -0.417   -8.4195   0.3284   0.3669
 PM8  C5    C  CH2   0  -0.414   -9.5457   0.3303  -0.6584
 PM8  C6    C  CH2   0  -0.412  -10.9247   0.4209  -0.0166
 PM8  C7    C  CH2   0  -0.412  -12.0673   0.4225  -1.0242
 PM8  C8    C  CH2   0  -0.406  -13.4385   0.5269  -0.3680
 PM8  C9    C  CH2   0  -0.419  -14.5915   0.5238  -1.3641
 PM8  C10   C  CH3   0  -0.662  -15.9514   0.6468  -0.6903
 PM8  H23   H  HOH1  0   0.500    9.1465   4.4683   0.8476
 PM8  H24   H  H     0   0.071    9.7679   1.6641   1.2949
 PM8  H281  H  HCH2  0   0.238    8.2931  -0.3078   0.4797
 PM8  H282  H  HCH2  0   0.249    6.6086   0.2273   0.5888
 PM8  H301  H  HCH3  0   0.249    6.4377   1.4367  -2.3644
 PM8  H302  H  HCH3  0   0.236    5.8495  -0.0625  -3.0560
 PM8  H303  H  HCH3  0   0.235    5.2186   0.5047  -1.5074
 PM8  H311  H  HCH3  0   0.236    9.3558  -0.7620  -1.8041
 PM8  H312  H  HCH3  0   0.230    8.3386  -0.7255  -3.2456
 PM8  H313  H  HCH3  0   0.240    8.7957   0.7762  -2.4578
 PM8  H32   H  HCH1  0   0.257    6.7228  -2.2155  -2.2946
 PM8  H33   H  HOH1  0   0.446    7.7249  -2.6370   0.2584
 PM8  H36   H  HNH1  0   0.408    4.4759  -2.0158  -2.1638
 PM8  H371  H  HCH2  0   0.264    2.4775  -2.6952  -1.2938
 PM8  H372  H  HCH2  0   0.254    3.2264  -3.0205   0.2578
 PM8  H381  H  HCH2  0   0.282    3.2948  -0.5529   0.7392
 PM8  H382  H  HCH2  0   0.273    2.5475  -0.2268  -0.8085
 PM8  H41   H  HNH1  0   0.406    1.1053   0.9080   0.7425
 PM8  H421  H  HCH2  0   0.258   -0.7179  -0.7161   2.3464
 PM8  H422  H  HCH2  0   0.268   -0.6503   1.0345   2.2251
 PM8  H431  H  HCH2  0   0.284   -1.7058   0.9305  -0.0448
 PM8  H432  H  HCH2  0   0.286   -1.7722  -0.8378   0.0720
 PM8  H21   H  HCH2  0   0.279   -6.0907  -0.5964   1.4952
 PM8  H22   H  HCH2  0   0.278   -6.0281   1.1421   1.4354
 PM8  H31   H  HCH2  0   0.228   -6.8868   1.0929  -0.9367
 PM8  H32A  H  HCH2  0   0.228   -6.9562  -0.6570  -0.8680
 PM8  H41A  H  HCH2  0   0.214   -8.5570  -0.5138   1.0539
 PM8  H42   H  HCH2  0   0.213   -8.4883   1.2328   0.9815
 PM8  H51   H  HCH2  0   0.209   -9.4096   1.1700  -1.3487
 PM8  H52   H  HCH2  0   0.209   -9.4852  -0.5772  -1.2693
 PM8  H61   H  HCH2  0   0.207  -11.0559  -0.4166   0.6776
 PM8  H62   H  HCH2  0   0.207  -10.9799   1.3291   0.5941
 PM8  H71   H  HCH2  0   0.206  -11.9350   1.2558  -1.7232
 PM8  H72   H  HCH2  0   0.206  -12.0207  -0.4899  -1.6295
 PM8  H81   H  HCH2  0   0.206  -13.5676  -0.3025   0.3364
 PM8  H82   H  HCH2  0   0.205  -13.4832   1.4419   0.2338
 PM8  H91   H  HCH2  0   0.210  -14.4587   1.3464  -2.0736
 PM8  H92   H  HCH2  0   0.210  -14.5555  -0.3957  -1.9568
 PM8  H101  H  HCH3  0   0.215  -16.0260   1.5778  -0.1248
 PM8  H102  H  HCH3  0   0.226  -16.7648   0.6351  -1.4166
 PM8  H103  H  HCH3  0   0.215  -16.1206  -0.1747   0.0090

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
 PM8  O23  P24   single  1.600  0.020  1.600
 PM8  O23  H23   single  0.832  0.020  0.971
 PM8  P24  O26   double  1.481  0.020  1.481
 PM8  P24  O27   single  1.599  0.020  1.599
 PM8  P24  H24   single  1.209  0.020  1.412
 PM8  O27  C28   single  1.432  0.020  1.432
 PM8  C28  C29   single  1.528  0.020  1.528
 PM8  C28  H281  single  0.970  0.020  1.090
 PM8  C28  H282  single  0.970  0.020  1.090
 PM8  C29  C30   single  1.531  0.020  1.531
 PM8  C29  C31   single  1.532  0.020  1.532
 PM8  C29  C32   single  1.555  0.020  1.555
 PM8  C30  H301  single  0.970  0.020  1.090
 PM8  C30  H302  single  0.970  0.020  1.090
 PM8  C30  H303  single  0.970  0.020  1.090
 PM8  C31  H311  single  0.970  0.020  1.090
 PM8  C31  H312  single  0.970  0.020  1.090
 PM8  C31  H313  single  0.970  0.020  1.090
 PM8  C32  O33   single  1.402  0.020  1.402
 PM8  C32  C34   single  1.529  0.020  1.529
 PM8  C32  H32   single  0.970  0.020  1.090
 PM8  O33  H33   single  0.850  0.020  0.980
 PM8  C34  O35   double  1.227  0.020  1.227
 PM8  C34  N36   single  1.334  0.020  1.334
 PM8  N36  C37   single  1.448  0.020  1.448
 PM8  N36  H36   single  0.860  0.020  1.020
 PM8  C37  C38   single  1.523  0.020  1.523
 PM8  C37  H371  single  0.970  0.020  1.090
 PM8  C37  H372  single  0.970  0.020  1.090
 PM8  C38  C39   single  1.514  0.020  1.514
 PM8  C38  H381  single  0.970  0.020  1.090
 PM8  C38  H382  single  0.970  0.020  1.090
 PM8  C39  O40   double  1.222  0.020  1.222
 PM8  C39  N41   single  1.346  0.020  1.346
 PM8  N41  C42   single  1.442  0.020  1.442
 PM8  N41  H41   single  0.860  0.020  1.020
 PM8  C42  C43   single  1.527  0.020  1.527
 PM8  C42  H421  single  0.970  0.020  1.090
 PM8  C42  H422  single  0.970  0.020  1.090
 PM8  C43  S1    single  1.815  0.020  1.815
 PM8  C43  H431  single  0.970  0.020  1.090
 PM8  C43  H432  single  0.970  0.020  1.090
 PM8  S1   C1    single  1.776  0.020  1.776
 PM8  C1   O1    double  1.203  0.020  1.203
 PM8  C1   C2    single  1.506  0.020  1.506
 PM8  C2   C3    single  1.521  0.020  1.521
 PM8  C2   H21   single  0.970  0.020  1.090
 PM8  C2   H22   single  0.970  0.020  1.090
 PM8  C3   C4    single  1.524  0.020  1.524
 PM8  C3   H31   single  0.970  0.020  1.090
 PM8  C3   H32A  single  0.970  0.020  1.090
 PM8  C4   C5    single  1.523  0.020  1.523
 PM8  C4   H41A  single  0.970  0.020  1.090
 PM8  C4   H42   single  0.970  0.020  1.090
 PM8  C5   C6    single  1.524  0.020  1.524
 PM8  C5   H51   single  0.970  0.020  1.090
 PM8  C5   H52   single  0.970  0.020  1.090
 PM8  C6   C7    single  1.523  0.020  1.523
 PM8  C6   H61   single  0.970  0.020  1.090
 PM8  C6   H62   single  0.970  0.020  1.090
 PM8  C7   C8    single  1.524  0.020  1.524
 PM8  C7   H71   single  0.970  0.020  1.090
 PM8  C7   H72   single  0.970  0.020  1.090
 PM8  C8   C9    single  1.524  0.020  1.524
 PM8  C8   H81   single  0.970  0.020  1.090
 PM8  C8   H82   single  0.970  0.020  1.090
 PM8  C9   C10   single  1.523  0.020  1.523
 PM8  C9   H91   single  0.970  0.020  1.090
 PM8  C9   H92   single  0.970  0.020  1.090
 PM8  C10  H101  single  0.970  0.020  1.090
 PM8  C10  H102  single  0.970  0.020  1.090
 PM8  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
 PM8  H23   O23  P24   113.48  3.000
 PM8  H24   P24  O27   104.46  3.000
 PM8  H24   P24  O26   113.26  3.000
 PM8  O27   P24  O26   116.94  3.000
 PM8  H24   P24  O23   106.18  3.000
 PM8  O27   P24  O23    97.41  3.000
 PM8  O26   P24  O23   116.71  3.000
 PM8  C28   O27  P24   118.97  3.000
 PM8  H282  C28  H281  108.09  3.000
 PM8  H282  C28  C29   111.26  3.000
 PM8  H281  C28  C29   110.12  3.000
 PM8  H282  C28  O27   108.85  3.000
 PM8  H281  C28  O27   109.83  3.000
 PM8  C29   C28  O27   108.68  3.000
 PM8  C32   C29  C31   107.52  3.000
 PM8  C32   C29  C30   110.10  3.000
 PM8  C31   C29  C30   108.95  3.000
 PM8  C32   C29  C28   109.68  3.000
 PM8  C31   C29  C28   110.25  3.000
 PM8  C30   C29  C28   110.30  3.000
 PM8  H303  C30  H302  108.01  3.000
 PM8  H303  C30  H301  107.47  3.000
 PM8  H302  C30  H301  106.95  3.000
 PM8  H303  C30  C29   112.80  3.000
 PM8  H302  C30  C29   110.75  3.000
 PM8  H301  C30  C29   110.62  3.000
 PM8  H313  C31  H312  107.25  3.000
 PM8  H313  C31  H311  107.98  3.000
 PM8  H312  C31  H311  107.98  3.000
 PM8  H313  C31  C29   111.09  3.000
 PM8  H312  C31  C29   110.30  3.000
 PM8  H311  C31  C29   112.06  3.000
 PM8  H32   C32  C34   109.06  3.000
 PM8  H32   C32  O33   107.29  3.000
 PM8  C34   C32  O33   108.31  3.000
 PM8  H32   C32  C29   106.20  3.000
 PM8  C34   C32  C29   113.29  3.000
 PM8  O33   C32  C29   112.47  3.000
 PM8  H33   O33  C32   107.67  3.000
 PM8  N36   C34  O35   123.50  3.000
 PM8  N36   C34  C32   116.80  3.000
 PM8  O35   C34  C32   119.69  3.000
 PM8  H36   N36  C37   117.80  3.000
 PM8  H36   N36  C34   118.93  3.000
 PM8  C37   N36  C34   123.22  3.000
 PM8  H372  C37  H371  107.27  3.000
 PM8  H372  C37  C38   110.67  3.000
 PM8  H371  C37  C38   110.61  3.000
 PM8  H372  C37  N36   108.95  3.000
 PM8  H371  C37  N36   107.20  3.000
 PM8  C38   C37  N36   111.97  3.000
 PM8  H382  C38  H381  106.20  3.000
 PM8  H382  C38  C39   109.58  3.000
 PM8  H381  C38  C39   108.19  3.000
 PM8  H382  C38  C37   110.17  3.000
 PM8  H381  C38  C37   110.01  3.000
 PM8  C39   C38  C37   112.47  3.000
 PM8  N41   C39  O40   122.74  3.000
 PM8  N41   C39  C38   114.62  3.000
 PM8  O40   C39  C38   122.63  3.000
 PM8  H41   N41  C42   117.69  3.000
 PM8  H41   N41  C39   118.94  3.000
 PM8  C42   N41  C39   123.34  3.000
 PM8  H422  C42  H421  107.31  3.000
 PM8  H422  C42  C43   110.17  3.000
 PM8  H421  C42  C43   110.27  3.000
 PM8  H422  C42  N41   107.83  3.000
 PM8  H421  C42  N41   109.39  3.000
 PM8  C43   C42  N41   111.74  3.000
 PM8  H432  C43  H431  108.95  3.000
 PM8  H432  C43  S1    109.34  3.000
 PM8  H431  C43  S1    109.42  3.000
 PM8  H432  C43  C42   110.59  3.000
 PM8  H431  C43  C42   110.55  3.000
 PM8  S1    C43  C42   107.96  3.000
 PM8  C1    S1   C43   101.91  3.000
 PM8  C2    C1   O1    125.17  3.000
 PM8  C2    C1   S1    112.26  3.000
 PM8  O1    C1   S1    122.56  3.000
 PM8  H22   C2   H21   105.29  3.000
 PM8  H22   C2   C3    110.49  3.000
 PM8  H21   C2   C3    110.43  3.000
 PM8  H22   C2   C1    107.89  3.000
 PM8  H21   C2   C1    107.65  3.000
 PM8  C3    C2   C1    114.62  3.000
 PM8  H32A  C3   H31   106.55  3.000
 PM8  H32A  C3   C4    109.62  3.000
 PM8  H31   C3   C4    109.54  3.000
 PM8  H32A  C3   C2    109.99  3.000
 PM8  H31   C3   C2    110.01  3.000
 PM8  C4    C3   C2    111.03  3.000
 PM8  H42   C4   H41A  105.96  3.000
 PM8  H42   C4   C5    109.28  3.000
 PM8  H41A  C4   C5    109.29  3.000
 PM8  H42   C4   C3    109.34  3.000
 PM8  H41A  C4   C3    109.33  3.000
 PM8  C5    C4   C3    113.38  3.000
 PM8  H52   C5   H51   106.07  3.000
 PM8  H52   C5   C6    109.51  3.000
 PM8  H51   C5   C6    109.41  3.000
 PM8  H52   C5   C4    109.48  3.000
 PM8  H51   C5   C4    109.47  3.000
 PM8  C6    C5   C4    112.69  3.000
 PM8  H62   C6   H61   105.92  3.000
 PM8  H62   C6   C7    109.27  3.000
 PM8  H61   C6   C7    109.27  3.000
 PM8  H62   C6   C5    109.24  3.000
 PM8  H61   C6   C5    109.26  3.000
 PM8  C7    C6   C5    113.60  3.000
 PM8  H72   C7   H71   106.01  3.000
 PM8  H72   C7   C8    109.46  3.000
 PM8  H71   C7   C8    109.34  3.000
 PM8  H72   C7   C6    109.42  3.000
 PM8  H71   C7   C6    109.40  3.000
 PM8  C8    C7   C6    112.97  3.000
 PM8  H82   C8   H81   105.91  3.000
 PM8  H82   C8   C9    109.25  3.000
 PM8  H81   C8   C9    109.24  3.000
 PM8  H82   C8   C7    109.29  3.000
 PM8  H81   C8   C7    109.33  3.000
 PM8  C9    C8   C7    113.54  3.000
 PM8  H92   C9   H91   106.05  3.000
 PM8  H92   C9   C10   109.68  3.000
 PM8  H91   C9   C10   109.55  3.000
 PM8  H92   C9   C8    109.32  3.000
 PM8  H91   C9   C8    109.29  3.000
 PM8  C10   C9   C8    112.73  3.000
 PM8  H103  C10  H102  107.63  3.000
 PM8  H103  C10  H101  107.41  3.000
 PM8  H102  C10  H101  107.64  3.000
 PM8  H103  C10  C9    111.16  3.000
 PM8  H102  C10  C9    111.75  3.000
 PM8  H101  C10  C9    111.04  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
 PM8  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 PM8  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 PM8  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 PM8  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 PM8  CONST_05  H36   N36  C34  C32     0.00   0.0  0
 PM8  CONST_06  H41   N41  C39  C38     0.00   0.0  0
 PM8  Var_01    C29   C28  O27  P24  -165.34  30.0  3
 PM8  Var_02    C30   C29  C28  O27   -61.26  30.0  3
 PM8  Var_03    C38   C37  N36  C34    81.11  30.0  3
 PM8  Var_04    C39   C38  C37  N36   179.77  30.0  3
 PM8  Var_05    O40   C39  C38  C37     9.03  30.0  3
 PM8  Var_06    C43   C42  N41  C39   -86.36  30.0  3
 PM8  Var_07    S1    C43  C42  N41  -179.21  30.0  3
 PM8  Var_08    O1    C1   S1   C43    -0.48  30.0  3
 PM8  Var_09    C3    C2   C1   S1    178.89  30.0  3
 PM8  Var_10    C4    C3   C2   C1   -179.80  30.0  3
 PM8  Var_11    C5    C4   C3   C2   -179.88  30.0  3
 PM8  Var_12    C6    C5   C4   C3   -179.61  30.0  3
 PM8  Var_13    C7    C6   C5   C4   -179.92  30.0  3
 PM8  Var_14    C8    C7   C6   C5   -179.45  30.0  3
 PM8  Var_15    C9    C8   C7   C6   -179.76  30.0  3
 PM8  Var_16    C10   C9   C8   C7   -179.27  30.0  3
 PM8  Var_17    H24   P24  O27  C28    62.93  30.0  1
 PM8  Var_18    H301  C30  C29  C28    67.99  30.0  3
 PM8  Var_19    H311  C31  C29  C28    57.09  30.0  3
 PM8  Var_20    H101  C10  C9   C8     60.24  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
 PM8  chir_02  C32  C29  O33  C34  negativ
 PM8  chir_03  P24  O23  O26  O27  both

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
 PM8  plan-1  C32  0.020
 PM8  plan-1  C34  0.020
 PM8  plan-1  O35  0.020
 PM8  plan-1  N36  0.020
 PM8  plan-1  C37  0.020
 PM8  plan-1  H36  0.020
 PM8  plan-2  C38  0.020
 PM8  plan-2  C39  0.020
 PM8  plan-2  O40  0.020
 PM8  plan-2  N41  0.020
 PM8  plan-2  C42  0.020
 PM8  plan-2  H41  0.020
 PM8  plan-3  S1   0.020
 PM8  plan-3  C1   0.020
 PM8  plan-3  O1   0.020
 PM8  plan-3  C2   0.020

