# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 03:05:55 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[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
 66S  66S  'S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate'  ligand  68  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_66S
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
 66S  P24   P  P     0   1.454  -7.5583  -3.0158   0.2157
 66S  O26   O  O     0  -0.711  -6.5415  -3.4089   1.2091
 66S  O23   O  OH1   0  -0.745  -8.8976  -2.5744   0.9698
 66S  O27   O  O2    0  -0.586  -7.1773  -1.8355  -0.7835
 66S  C28   C  CH2   0  -0.151  -6.7694  -0.5620  -0.2667
 66S  C29   C  CT    0  -0.166  -6.1739   0.2608  -1.4082
 66S  C30   C  CH3   0  -0.669  -4.9359  -0.4353  -1.9792
 66S  C31   C  CH3   0  -0.647  -7.2025   0.4457  -2.5278
 66S  C32   C  CH1   0  -0.034  -5.7928   1.6745  -0.8833
 66S  O33   O  OH1   0  -0.661  -6.8959   2.3796  -0.3828
 66S  C34   C  C     0   0.519  -4.7071   1.6406   0.1932
 66S  O35   O  O     0  -0.498  -5.0166   1.5346   1.3752
 66S  N36   N  NH1   0  -0.639  -3.4459   1.7432  -0.2268
 66S  C37   C  CH2   0  -0.236  -2.3099   1.6593   0.6700
 66S  C38   C  CH2   0  -0.631  -1.0272   1.9000  -0.1090
 66S  C39   C  C     0   0.566   0.1979   1.7130   0.7600
 66S  O40   O  O     0  -0.494   0.2803   0.8042   1.5733
 66S  N41   N  NH1   0  -0.631   1.1821   2.6053   0.5567
 66S  C42   C  CH2   0  -0.292   2.4703   2.5212   1.2009
 66S  C43   C  CH2   0  -0.557   3.4200   1.6248   0.4108
 66S  S1    S  S2    0  -0.005   5.0201   1.5692   1.2654
 66S  C1    C  C     0   0.261   5.9901   0.6149   0.1260
 66S  O1    O  O     0  -0.386   5.5487   0.2163  -0.9200
 66S  C2    C  CH2   0  -0.538   7.3878   0.3555   0.6246
 66S  C3    C  CH2   0  -0.417   8.3391  -0.1500  -0.4504
 66S  C4    C  CH2   0  -0.416   9.7295  -0.4301   0.1066
 66S  C5    C  CH2   0  -0.413  10.6950  -0.9399  -0.9559
 66S  C6    C  CH2   0  -0.407  12.0848  -1.2473  -0.4126
 66S  C7    C  CH2   0  -0.419  13.0425  -1.7679  -1.4776
 66S  C8    C  CH3   0  -0.662  14.4283  -2.0823  -0.9310
 66S  H1    H  HOH1  0   0.495  -9.6440  -2.3481   0.3988
 66S  H28   H  HCH2  0   0.242  -7.6402  -0.0555   0.1579
 66S  H28A  H  HCH2  0   0.246  -6.0351  -0.7081   0.5292
 66S  H30   H  HCH3  0   0.250  -5.2121  -1.3637  -2.4774
 66S  H30A  H  HCH3  0   0.235  -4.4475   0.1970  -2.7244
 66S  H30B  H  HCH3  0   0.235  -4.1999  -0.6784  -1.2115
 66S  H31   H  HCH3  0   0.236  -8.1113   0.9320  -2.1731
 66S  H31A  H  HCH3  0   0.231  -6.7842   1.0611  -3.3272
 66S  H31B  H  HCH3  0   0.240  -7.4819  -0.5109  -2.9678
 66S  H32   H  HCH1  0   0.259  -5.4187   2.2316  -1.7507
 66S  HO33  H  HOH1  0   0.446  -6.9519   2.2077   0.5660
 66S  HN36  H  HNH1  0   0.409  -3.2729   1.8603  -1.2125
 66S  H37   H  HCH2  0   0.253  -2.4114   2.4045   1.4617
 66S  H37A  H  HCH2  0   0.250  -2.2829   0.6781   1.1465
 66S  H38   H  HCH2  0   0.285  -0.9524   1.1780  -0.9291
 66S  H38A  H  HCH2  0   0.272  -1.0415   2.8932  -0.5627
 66S  HN41  H  HNH1  0   0.407   1.0604   3.3104  -0.1518
 66S  H42   H  HCH2  0   0.270   2.8766   3.5296   1.2771
 66S  H42A  H  HCH2  0   0.261   2.3399   2.1450   2.2152
 66S  H43   H  HCH2  0   0.286   3.0179   0.6151   0.3347
 66S  H43A  H  HCH2  0   0.285   3.5684   2.0208  -0.5933
 66S  H2    H  HCH2  0   0.270   7.7738   1.2672   1.0901
 66S  H2A   H  HCH2  0   0.285   7.3047  -0.3763   1.4364
 66S  H3    H  HCH2  0   0.228   7.9392  -1.0627  -0.8985
 66S  H3A   H  HCH2  0   0.228   8.4102   0.5867  -1.2552
 66S  H4    H  HCH2  0   0.214  10.1336   0.4814   0.5599
 66S  H4A   H  HCH2  0   0.214   9.6558  -1.1655   0.9151
 66S  H5    H  HCH2  0   0.208  10.2805  -1.8429  -1.4173
 66S  H5A   H  HCH2  0   0.210  10.7753  -0.1992  -1.7590
 66S  H6    H  HCH2  0   0.207  12.5054  -0.3446   0.0442
 66S  H6A   H  HCH2  0   0.207  12.0041  -1.9850   0.3936
 66S  H7    H  HCH2  0   0.210  12.6186  -2.6677  -1.9344
 66S  H7A   H  HCH2  0   0.211  13.1244  -1.0307  -2.2824
 66S  H8    H  HCH3  0   0.216  14.3784  -2.8346  -0.1418
 66S  H8A   H  HCH3  0   0.225  15.0883  -2.4647  -1.7106
 66S  H8B   H  HCH3  0   0.215  14.8986  -1.1930  -0.5075
 66S  OP3   O  OH1   0  -0.732  -7.9537  -4.0878  -0.8963
 66S  HOP3  H  HOH1  0   0.503  -8.0244  -4.9910  -0.5598

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
 66S  P24  O26   double  1.475  0.020  1.475
 66S  P24  O23   single  1.599  0.020  1.599
 66S  P24  O27   single  1.593  0.020  1.593
 66S  O27  C28   single  1.434  0.020  1.434
 66S  C28  C29   single  1.528  0.020  1.528
 66S  C29  C30   single  1.531  0.020  1.531
 66S  C29  C31   single  1.531  0.020  1.531
 66S  C29  C32   single  1.555  0.020  1.555
 66S  C32  O33   single  1.402  0.020  1.402
 66S  C32  C34   single  1.529  0.020  1.529
 66S  C34  O35   double  1.226  0.020  1.226
 66S  C34  N36   single  1.333  0.020  1.333
 66S  N36  C37   single  1.450  0.020  1.450
 66S  C37  C38   single  1.520  0.020  1.520
 66S  C38  C39   single  1.514  0.020  1.514
 66S  C39  O40   double  1.222  0.020  1.222
 66S  C39  N41   single  1.344  0.020  1.344
 66S  N41  C42   single  1.443  0.020  1.443
 66S  C42  C43   single  1.526  0.020  1.526
 66S  C43  S1    single  1.815  0.020  1.815
 66S  S1   C1    single  1.775  0.020  1.775
 66S  C1   O1    double  1.203  0.020  1.203
 66S  C1   C2    single  1.506  0.020  1.506
 66S  C2   C3    single  1.522  0.020  1.522
 66S  C3   C4    single  1.524  0.020  1.524
 66S  C4   C5    single  1.523  0.020  1.523
 66S  C5   C6    single  1.524  0.020  1.524
 66S  C6   C7    single  1.524  0.020  1.524
 66S  C7   C8    single  1.523  0.020  1.523
 66S  O23  H1    single  0.850  0.020  0.980
 66S  C28  H28   single  0.970  0.020  1.090
 66S  C28  H28A  single  0.970  0.020  1.090
 66S  C30  H30   single  0.970  0.020  1.090
 66S  C30  H30A  single  0.970  0.020  1.090
 66S  C30  H30B  single  0.970  0.020  1.090
 66S  C31  H31   single  0.970  0.020  1.090
 66S  C31  H31A  single  0.970  0.020  1.090
 66S  C31  H31B  single  0.970  0.020  1.090
 66S  C32  H32   single  0.970  0.020  1.090
 66S  O33  HO33  single  0.850  0.020  0.980
 66S  N36  HN36  single  0.860  0.020  1.020
 66S  C37  H37   single  0.970  0.020  1.090
 66S  C37  H37A  single  0.970  0.020  1.090
 66S  C38  H38   single  0.970  0.020  1.090
 66S  C38  H38A  single  0.970  0.020  1.090
 66S  N41  HN41  single  0.860  0.020  1.020
 66S  C42  H42   single  0.970  0.020  1.090
 66S  C42  H42A  single  0.970  0.020  1.090
 66S  C43  H43   single  0.970  0.020  1.090
 66S  C43  H43A  single  0.970  0.020  1.090
 66S  C2   H2    single  0.970  0.020  1.090
 66S  C2   H2A   single  0.970  0.020  1.090
 66S  C3   H3    single  0.970  0.020  1.090
 66S  C3   H3A   single  0.970  0.020  1.090
 66S  C4   H4    single  0.970  0.020  1.090
 66S  C4   H4A   single  0.970  0.020  1.090
 66S  C5   H5    single  0.970  0.020  1.090
 66S  C5   H5A   single  0.970  0.020  1.090
 66S  C6   H6    single  0.970  0.020  1.090
 66S  C6   H6A   single  0.970  0.020  1.090
 66S  C7   H7    single  0.970  0.020  1.090
 66S  C7   H7A   single  0.970  0.020  1.090
 66S  C8   H8    single  0.970  0.020  1.090
 66S  C8   H8A   single  0.970  0.020  1.090
 66S  C8   H8B   single  0.970  0.020  1.090
 66S  P24  OP3   single  1.594  0.020  1.594
 66S  OP3  HOP3  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
 66S  OP3   P24  O27    96.90  3.000
 66S  OP3   P24  O23   107.86  3.000
 66S  O27   P24  O23   106.96  3.000
 66S  OP3   P24  O26   117.49  3.000
 66S  O27   P24  O26   117.07  3.000
 66S  O23   P24  O26   109.47  3.000
 66S  H1    O23  P24   115.64  3.000
 66S  C28   O27  P24   120.02  3.000
 66S  H28A  C28  H28   108.32  3.000
 66S  H28A  C28  C29   110.75  3.000
 66S  H28   C28  C29   110.56  3.000
 66S  H28A  C28  O27   109.57  3.000
 66S  H28   C28  O27   108.96  3.000
 66S  C29   C28  O27   108.66  3.000
 66S  C32   C29  C31   107.55  3.000
 66S  C32   C29  C30   109.94  3.000
 66S  C31   C29  C30   108.99  3.000
 66S  C32   C29  C28   109.43  3.000
 66S  C31   C29  C28   110.45  3.000
 66S  C30   C29  C28   110.43  3.000
 66S  H30B  C30  H30A  107.89  3.000
 66S  H30B  C30  H30   107.64  3.000
 66S  H30A  C30  H30   107.14  3.000
 66S  H30B  C30  C29   112.62  3.000
 66S  H30A  C30  C29   110.66  3.000
 66S  H30   C30  C29   110.68  3.000
 66S  H31B  C31  H31A  107.30  3.000
 66S  H31B  C31  H31   108.01  3.000
 66S  H31A  C31  H31   107.82  3.000
 66S  H31B  C31  C29   111.19  3.000
 66S  H31A  C31  C29   110.24  3.000
 66S  H31   C31  C29   112.09  3.000
 66S  H32   C32  C34   109.01  3.000
 66S  H32   C32  O33   107.18  3.000
 66S  C34   C32  O33   108.57  3.000
 66S  H32   C32  C29   106.16  3.000
 66S  C34   C32  C29   113.04  3.000
 66S  O33   C32  C29   112.64  3.000
 66S  HO33  O33  C32   107.87  3.000
 66S  N36   C34  O35   123.30  3.000
 66S  N36   C34  C32   116.62  3.000
 66S  O35   C34  C32   120.07  3.000
 66S  HN36  N36  C37   118.51  3.000
 66S  HN36  N36  C34   118.66  3.000
 66S  C37   N36  C34   122.81  3.000
 66S  H37A  C37  H37   107.43  3.000
 66S  H37A  C37  C38   110.20  3.000
 66S  H37   C37  C38   110.00  3.000
 66S  H37A  C37  N36   109.97  3.000
 66S  H37   C37  N36   109.64  3.000
 66S  C38   C37  N36   109.57  3.000
 66S  H38A  C38  H38   106.82  3.000
 66S  H38A  C38  C39   111.19  3.000
 66S  H38   C38  C39   107.05  3.000
 66S  H38A  C38  C37   110.24  3.000
 66S  H38   C38  C37   109.70  3.000
 66S  C39   C38  C37   111.67  3.000
 66S  N41   C39  O40   123.02  3.000
 66S  N41   C39  C38   115.08  3.000
 66S  O40   C39  C38   121.90  3.000
 66S  HN41  N41  C42   117.57  3.000
 66S  HN41  N41  C39   118.87  3.000
 66S  C42   N41  C39   123.21  3.000
 66S  H42A  C42  H42   107.40  3.000
 66S  H42A  C42  C43   110.70  3.000
 66S  H42   C42  C43   110.34  3.000
 66S  H42A  C42  N41   109.20  3.000
 66S  H42   C42  N41   108.07  3.000
 66S  C43   C42  N41   111.02  3.000
 66S  H43A  C43  H43   108.82  3.000
 66S  H43A  C43  S1    108.97  3.000
 66S  H43   C43  S1    109.26  3.000
 66S  H43A  C43  C42   110.39  3.000
 66S  H43   C43  C42   110.54  3.000
 66S  S1    C43  C42   108.83  3.000
 66S  C1    S1   C43   101.30  3.000
 66S  C2    C1   O1    124.82  3.000
 66S  C2    C1   S1    112.78  3.000
 66S  O1    C1   S1    122.40  3.000
 66S  H2A   C2   H2    105.54  3.000
 66S  H2A   C2   C3    110.41  3.000
 66S  H2    C2   C3    110.90  3.000
 66S  H2A   C2   C1    106.84  3.000
 66S  H2    C2   C1    108.95  3.000
 66S  C3    C2   C1    113.79  3.000
 66S  H3A   C3   H3    106.54  3.000
 66S  H3A   C3   C4    109.48  3.000
 66S  H3    C3   C4    109.29  3.000
 66S  H3A   C3   C2    109.68  3.000
 66S  H3    C3   C2    109.78  3.000
 66S  C4    C3   C2    111.92  3.000
 66S  H4A   C4   H4    106.15  3.000
 66S  H4A   C4   C5    109.44  3.000
 66S  H4    C4   C5    109.47  3.000
 66S  H4A   C4   C3    109.38  3.000
 66S  H4    C4   C3    109.57  3.000
 66S  C5    C4   C3    112.63  3.000
 66S  H5A   C5   H5    106.04  3.000
 66S  H5A   C5   C6    109.33  3.000
 66S  H5    C5   C6    109.21  3.000
 66S  H5A   C5   C4    109.36  3.000
 66S  H5    C5   C4    109.25  3.000
 66S  C6    C5   C4    113.38  3.000
 66S  H6A   C6   H6    106.04  3.000
 66S  H6A   C6   C7    109.30  3.000
 66S  H6    C6   C7    109.36  3.000
 66S  H6A   C6   C5    109.34  3.000
 66S  H6    C6   C5    109.43  3.000
 66S  C7    C6   C5    113.14  3.000
 66S  H7A   C7   H7    106.01  3.000
 66S  H7A   C7   C8    109.57  3.000
 66S  H7    C7   C8    109.43  3.000
 66S  H7A   C7   C6    109.32  3.000
 66S  H7    C7   C6    109.21  3.000
 66S  C8    C7   C6    113.06  3.000
 66S  H8B   C8   H8A   107.59  3.000
 66S  H8B   C8   H8    107.50  3.000
 66S  H8A   C8   H8    107.63  3.000
 66S  H8B   C8   C7    111.30  3.000
 66S  H8A   C8   C7    111.51  3.000
 66S  H8    C8   C7    111.12  3.000
 66S  HOP3  OP3  P24   113.80  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
 66S  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 66S  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 66S  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 66S  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 66S  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 66S  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 66S  Var_01    C29   C28  O27  P24   167.50  30.0  3
 66S  Var_02    C30   C29  C28  O27   -61.77  30.0  3
 66S  Var_03    OP3   P24  O27  C28   178.16  30.0  1
 66S  Var_04    C38   C37  N36  C34  -176.52  30.0  3
 66S  Var_05    C39   C38  C37  N36  -175.40  30.0  3
 66S  Var_06    O40   C39  C38  C37    40.83  30.0  3
 66S  Var_07    C43   C42  N41  C39    86.15  30.0  3
 66S  Var_08    S1    C43  C42  N41   179.66  30.0  3
 66S  Var_09    O1    C1   S1   C43     1.71  30.0  3
 66S  Var_10    C3    C2   C1   S1   -165.70  30.0  3
 66S  Var_11    C4    C3   C2   C1   -178.62  30.0  3
 66S  Var_12    C5    C4   C3   C2    179.89  30.0  3
 66S  Var_13    C6    C5   C4   C3   -179.05  30.0  3
 66S  Var_14    C7    C6   C5   C4    179.51  30.0  3
 66S  Var_15    C8    C7   C6   C5   -179.66  30.0  3
 66S  Var_16    H30   C30  C29  C28    67.23  30.0  3
 66S  Var_17    H31   C31  C29  C28    58.07  30.0  3
 66S  Var_18    H8    C8   C7   C6     59.18  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
 66S  chir_01  C32  C29  O33  C34  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
 66S  plan-1  C32   0.020
 66S  plan-1  C34   0.020
 66S  plan-1  O35   0.020
 66S  plan-1  N36   0.020
 66S  plan-1  C37   0.020
 66S  plan-1  HN36  0.020
 66S  plan-2  C38   0.020
 66S  plan-2  C39   0.020
 66S  plan-2  O40   0.020
 66S  plan-2  N41   0.020
 66S  plan-2  C42   0.020
 66S  plan-2  HN41  0.020
 66S  plan-3  S1    0.020
 66S  plan-3  C1    0.020
 66S  plan-3  O1    0.020
 66S  plan-3  C2    0.020

