# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 04:26:46 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] hexanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=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
 SXH  SXH  'S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] hexanethioate'  ligand  62  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SXH
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
 SXH  O25   O  OH1   0  -0.743  -5.9076  -3.2664  -1.0258
 SXH  P24   P  P     0   1.454  -7.1381  -2.6050  -0.2473
 SXH  O26   O  O     0  -0.712  -8.1463  -2.1504  -1.2229
 SXH  O23   O  OH1   0  -0.732  -7.6038  -3.6255   0.8850
 SXH  O27   O  O2    0  -0.587  -6.5332  -1.4981   0.7260
 SXH  C28   C  CH2   0  -0.151  -6.0134  -0.2842   0.1671
 SXH  C29   C  CT    0  -0.164  -5.3938   0.5448   1.2908
 SXH  C30   C  CH3   0  -0.649  -6.4512   0.8971   2.3409
 SXH  C31   C  CH3   0  -0.672  -4.2601  -0.2304   1.9653
 SXH  C32   C  CH1   0  -0.033  -4.8528   1.8811   0.7068
 SXH  O33   O  OH1   0  -0.662  -5.8590   2.6511   0.1083
 SXH  C34   C  C     0   0.518  -3.7255   1.6838  -0.3091
 SXH  O35   O  O     0  -0.499  -3.9899   1.5762  -1.5021
 SXH  N36   N  NH1   0  -0.638  -2.4822   1.6535   0.1710
 SXH  C37   C  CH2   0  -0.237  -1.3211   1.4231  -0.6656
 SXH  C38   C  CH2   0  -0.627  -0.0548   1.6667   0.1399
 SXH  C39   C  C     0   0.565   1.1861   1.3711  -0.6749
 SXH  O40   O  O     0  -0.494   1.2660   0.3879  -1.3969
 SXH  N41   N  NH1   0  -0.631   2.1865   2.2571  -0.5332
 SXH  C42   C  CH2   0  -0.292   3.4816   2.0888  -1.1465
 SXH  C43   C  CH2   0  -0.557   4.3963   1.2363  -0.2717
 SXH  S1    S  S2    0  -0.005   6.0033   1.0643  -1.0980
 SXH  C1    C  C     0   0.259   6.9304   0.1825   0.1336
 SXH  O1    O  O     0  -0.385   6.4543  -0.1344   1.1919
 SXH  C2    C  CH2   0  -0.537   8.3411  -0.1201  -0.3003
 SXH  C3    C  CH2   0  -0.416   9.1927  -0.7595   0.7867
 SXH  C4    C  CH2   0  -0.411  10.6042  -1.0627   0.2992
 SXH  C5    C  CH2   0  -0.421  11.4723  -1.7031   1.3759
 SXH  C6    C  CH3   0  -0.662  12.8805  -2.0190   0.8913
 SXH  H28   H  HCH2  0   0.244  -5.2637  -0.5220  -0.5925
 SXH  H28A  H  HCH2  0   0.246  -6.8258   0.2662  -0.3138
 SXH  H30   H  HCH3  0   0.231  -6.0095   1.5076   3.1315
 SXH  H30A  H  HCH3  0   0.237  -7.2818   1.4575   1.9116
 SXH  H30B  H  HCH3  0   0.240  -6.8547  -0.0005   2.8087
 SXH  H31   H  HCH3  0   0.235  -3.5410  -0.6336   1.2506
 SXH  H31A  H  HCH3  0   0.234  -3.7168   0.4075   2.6666
 SXH  H31B  H  HCH3  0   0.250  -4.6565  -1.0679   2.5383
 SXH  H32   H  HCH1  0   0.259  -4.4683   2.4517   1.5608
 SXH  HO33  H  HOH1  0   0.446  -5.8564   2.4533  -0.8373
 SXH  HN36  H  HNH1  0   0.408  -2.3450   1.7586   1.1637
 SXH  H37   H  HCH2  0   0.251  -1.3315   0.4033  -1.0540
 SXH  H37A  H  HCH2  0   0.254  -1.3536   2.0994  -1.5220
 SXH  H38   H  HCH2  0   0.272  -0.0431   2.6895   0.5220
 SXH  H38A  H  HCH2  0   0.284  -0.0354   1.0019   1.0099
 SXH  HN41  H  HNH1  0   0.407   2.0659   3.0296   0.1013
 SXH  H42   H  HCH2  0   0.260   3.3559   1.6345  -2.1292
 SXH  H42A  H  HCH2  0   0.270   3.9149   3.0771  -1.2977
 SXH  H43   H  HCH2  0   0.284   4.5451   1.7111   0.6976
 SXH  H43A  H  HCH2  0   0.286   3.9644   0.2485  -0.1160
 SXH  H2    H  HCH2  0   0.281   8.2818  -0.7739  -1.1771
 SXH  H2A   H  HCH2  0   0.275   8.8001   0.8074  -0.6568
 SXH  H3    H  HCH2  0   0.227   9.2418  -0.0954   1.6537
 SXH  H3A   H  HCH2  0   0.227   8.7211  -1.6841   1.1287
 SXH  H4    H  HCH2  0   0.213  10.5556  -1.7276  -0.5700
 SXH  H4A   H  HCH2  0   0.213  11.0803  -0.1396  -0.0488
 SXH  H5    H  HCH2  0   0.213  11.5238  -1.0361   2.2420
 SXH  H5A   H  HCH2  0   0.213  10.9907  -2.6207   1.7272
 SXH  H6    H  HCH3  0   0.217  12.8619  -2.7156   0.0514
 SXH  H6A   H  HCH3  0   0.216  13.3957  -1.1162   0.5578
 SXH  H6B   H  HCH3  0   0.227  13.4831  -2.4691   1.6810
 SXH  HO25  H  HOH1  0   0.494  -5.2213  -3.6636  -0.4733
 SXH  HO23  H  HOH1  0   0.504  -8.1142  -4.3751   0.5504

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
 SXH  P24   O25   single  1.599  0.020  1.599
 SXH  O25   HO25  single  0.850  0.020  0.980
 SXH  O26   P24   double  1.475  0.020  1.475
 SXH  P24   O27   single  1.593  0.020  1.593
 SXH  P24   O23   single  1.594  0.020  1.594
 SXH  O23   HO23  single  0.850  0.020  0.980
 SXH  O27   C28   single  1.434  0.020  1.434
 SXH  C28   H28A  single  0.970  0.020  1.090
 SXH  C28   C29   single  1.528  0.020  1.528
 SXH  C28   H28   single  0.970  0.020  1.090
 SXH  C31   C29   single  1.530  0.020  1.530
 SXH  C32   C29   single  1.556  0.020  1.556
 SXH  C29   C30   single  1.531  0.020  1.531
 SXH  C30   H30B  single  0.970  0.020  1.090
 SXH  C30   H30A  single  0.970  0.020  1.090
 SXH  C30   H30   single  0.970  0.020  1.090
 SXH  H31B  C31   single  0.970  0.020  1.090
 SXH  C31   H31   single  0.970  0.020  1.090
 SXH  C31   H31A  single  0.970  0.020  1.090
 SXH  O33   C32   single  1.401  0.020  1.401
 SXH  C32   C34   single  1.530  0.020  1.530
 SXH  C32   H32   single  0.970  0.020  1.090
 SXH  HO33  O33   single  0.850  0.020  0.980
 SXH  O35   C34   double  1.227  0.020  1.227
 SXH  C34   N36   single  1.333  0.020  1.333
 SXH  N36   C37   single  1.450  0.020  1.450
 SXH  N36   HN36  single  0.860  0.020  1.020
 SXH  H37   C37   single  0.970  0.020  1.090
 SXH  H37A  C37   single  0.970  0.020  1.090
 SXH  C37   C38   single  1.520  0.020  1.520
 SXH  C38   H38   single  0.970  0.020  1.090
 SXH  C38   C39   single  1.514  0.020  1.514
 SXH  C38   H38A  single  0.970  0.020  1.090
 SXH  N41   C39   single  1.344  0.020  1.344
 SXH  C39   O40   double  1.222  0.020  1.222
 SXH  HN41  N41   single  0.860  0.020  1.020
 SXH  N41   C42   single  1.443  0.020  1.443
 SXH  C43   C42   single  1.526  0.020  1.526
 SXH  C42   H42   single  0.970  0.020  1.090
 SXH  C42   H42A  single  0.970  0.020  1.090
 SXH  S1    C43   single  1.815  0.020  1.815
 SXH  C43   H43   single  0.970  0.020  1.090
 SXH  C43   H43A  single  0.970  0.020  1.090
 SXH  C1    S1    single  1.776  0.020  1.776
 SXH  C2    C1    single  1.507  0.020  1.507
 SXH  C1    O1    double  1.203  0.020  1.203
 SXH  C3    C2    single  1.522  0.020  1.522
 SXH  H2    C2    single  0.970  0.020  1.090
 SXH  H2A   C2    single  0.970  0.020  1.090
 SXH  H3    C3    single  0.970  0.020  1.090
 SXH  C3    C4    single  1.524  0.020  1.524
 SXH  C3    H3A   single  0.970  0.020  1.090
 SXH  C5    C4    single  1.524  0.020  1.524
 SXH  H4A   C4    single  0.970  0.020  1.090
 SXH  C4    H4    single  0.970  0.020  1.090
 SXH  C6    C5    single  1.522  0.020  1.522
 SXH  C5    H5    single  0.970  0.020  1.090
 SXH  C5    H5A   single  0.970  0.020  1.090
 SXH  H6B   C6    single  0.970  0.020  1.090
 SXH  H6A   C6    single  0.970  0.020  1.090
 SXH  H6    C6    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
 SXH  HO25  O25  P24   115.98  3.000
 SXH  O27   P24  O23    97.00  3.000
 SXH  O23   P24  O26   117.87  3.000
 SXH  O27   P24  O26   116.71  3.000
 SXH  O23   P24  O25   107.81  3.000
 SXH  O27   P24  O25   107.02  3.000
 SXH  O26   P24  O25   109.35  3.000
 SXH  HO23  O23  P24   113.89  3.000
 SXH  C28   O27  P24   119.19  3.000
 SXH  H28A  C28  H28   108.27  3.000
 SXH  H28   C28  C29   110.55  3.000
 SXH  H28A  C28  C29   110.60  3.000
 SXH  H28   C28  O27   109.59  3.000
 SXH  C29   C28  O27   108.65  3.000
 SXH  H28A  C28  O27   109.17  3.000
 SXH  C32   C29  C31   110.06  3.000
 SXH  C32   C29  C30   107.46  3.000
 SXH  C31   C29  C30   109.02  3.000
 SXH  C30   C29  C28   110.44  3.000
 SXH  C32   C29  C28   109.33  3.000
 SXH  C31   C29  C28   110.47  3.000
 SXH  H30B  C30  H30A  108.09  3.000
 SXH  H30A  C30  H30   107.81  3.000
 SXH  H30B  C30  H30   107.42  3.000
 SXH  H30   C30  C29   110.23  3.000
 SXH  H30A  C30  C29   111.99  3.000
 SXH  H30B  C30  C29   111.14  3.000
 SXH  H31B  C31  H31A  106.99  3.000
 SXH  H31A  C31  H31   107.96  3.000
 SXH  H31B  C31  H31   107.47  3.000
 SXH  H31A  C31  C29   110.83  3.000
 SXH  H31   C31  C29   112.76  3.000
 SXH  H31B  C31  C29   110.60  3.000
 SXH  H32   C32  C34   109.02  3.000
 SXH  H32   C32  O33   107.37  3.000
 SXH  C34   C32  O33   108.44  3.000
 SXH  H32   C32  C29   106.05  3.000
 SXH  C34   C32  C29   113.25  3.000
 SXH  O33   C32  C29   112.50  3.000
 SXH  HO33  O33  C32   107.68  3.000
 SXH  N36   C34  O35   123.32  3.000
 SXH  N36   C34  C32   116.80  3.000
 SXH  O35   C34  C32   119.88  3.000
 SXH  HN36  N36  C37   118.43  3.000
 SXH  HN36  N36  C34   118.65  3.000
 SXH  C37   N36  C34   122.88  3.000
 SXH  H37A  C37  H37   107.42  3.000
 SXH  H37A  C37  C38   109.95  3.000
 SXH  H37   C37  C38   110.26  3.000
 SXH  C38   C37  N36   109.63  3.000
 SXH  H37A  C37  N36   109.30  3.000
 SXH  H37   C37  N36   110.26  3.000
 SXH  H38A  C38  H38   106.88  3.000
 SXH  H38A  C38  C39   107.13  3.000
 SXH  H38   C38  C39   111.26  3.000
 SXH  H38A  C38  C37   109.78  3.000
 SXH  C39   C38  C37   111.49  3.000
 SXH  H38   C38  C37   110.15  3.000
 SXH  N41   C39  O40   122.95  3.000
 SXH  O40   C39  C38   121.91  3.000
 SXH  N41   C39  C38   115.13  3.000
 SXH  HN41  N41  C42   117.71  3.000
 SXH  C42   N41  C39   123.12  3.000
 SXH  HN41  N41  C39   118.89  3.000
 SXH  H42A  C42  H42   107.39  3.000
 SXH  H42A  C42  C43   110.35  3.000
 SXH  H42   C42  C43   110.68  3.000
 SXH  H42A  C42  N41   108.06  3.000
 SXH  H42   C42  N41   109.17  3.000
 SXH  C43   C42  N41   111.07  3.000
 SXH  H43A  C43  H43   108.79  3.000
 SXH  H43A  C43  S1    109.28  3.000
 SXH  H43   C43  S1    108.99  3.000
 SXH  H43A  C43  C42   110.54  3.000
 SXH  H43   C43  C42   110.39  3.000
 SXH  S1    C43  C42   108.82  3.000
 SXH  C1    S1   C43   101.16  3.000
 SXH  C2    C1   O1    124.82  3.000
 SXH  O1    C1   S1    122.30  3.000
 SXH  C2    C1   S1    112.88  3.000
 SXH  H2A   C2   H2    105.54  3.000
 SXH  H2A   C2   C3    110.73  3.000
 SXH  H2    C2   C3    110.57  3.000
 SXH  H2A   C2   C1    108.43  3.000
 SXH  H2    C2   C1    107.44  3.000
 SXH  C3    C2   C1    113.74  3.000
 SXH  H3A   C3   H3    106.57  3.000
 SXH  H3A   C3   C4    109.36  3.000
 SXH  H3    C3   C4    109.45  3.000
 SXH  H3A   C3   C2    109.73  3.000
 SXH  C4    C3   C2    111.93  3.000
 SXH  H3    C3   C2    109.66  3.000
 SXH  H4A   C4   H4    106.18  3.000
 SXH  H4    C4   C5    109.32  3.000
 SXH  H4A   C4   C5    109.33  3.000
 SXH  H4    C4   C3    109.48  3.000
 SXH  H4A   C4   C3    109.66  3.000
 SXH  C5    C4   C3    112.66  3.000
 SXH  H5A   C5   H5    106.12  3.000
 SXH  H5A   C5   C6    109.59  3.000
 SXH  H5    C5   C6    109.57  3.000
 SXH  H5A   C5   C4    109.18  3.000
 SXH  H5    C5   C4    109.26  3.000
 SXH  C6    C5   C4    112.90  3.000
 SXH  H6B   C6   H6A   107.56  3.000
 SXH  H6A   C6   H6    107.50  3.000
 SXH  H6B   C6   H6    107.65  3.000
 SXH  H6    C6   C5    111.20  3.000
 SXH  H6A   C6   C5    111.24  3.000
 SXH  H6B   C6   C5    111.49  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
 SXH  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SXH  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SXH  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SXH  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SXH  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SXH  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SXH  Var_01    C29   C28  O27  P24  -175.29  30.0  3
 SXH  Var_02    C31   C29  C28  O27    59.99  30.0  3
 SXH  Var_03    C38   C37  N36  C34   171.11  30.0  3
 SXH  Var_04    C39   C38  C37  N36   177.17  30.0  3
 SXH  Var_05    N41   C39  C38  C37   137.99  30.0  3
 SXH  Var_06    C43   C42  N41  C39   -85.74  30.0  3
 SXH  Var_07    S1    C43  C42  N41  -179.99  30.0  1
 SXH  Var_08    C2    C1   S1   C43   179.35  30.0  1
 SXH  Var_09    C3    C2   C1   S1    174.61  30.0  1
 SXH  Var_10    C4    C3   C2   C1    179.32  30.0  1
 SXH  Var_11    C5    C4   C3   C2    179.96  30.0  3
 SXH  Var_12    C6    C5   C4   C3    179.53  30.0  1
 SXH  Var_13    H31B  C31  C29  C28   -69.94  30.0  3
 SXH  Var_14    H30B  C30  C29  C28    62.23  30.0  3
 SXH  Var_15    H6B   C6   C5   C4    179.58  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
 SXH  chir_01  C32  C29  O33  C34  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
 SXH  plan-1  C32   0.020
 SXH  plan-1  C34   0.020
 SXH  plan-1  O35   0.020
 SXH  plan-1  N36   0.020
 SXH  plan-1  C37   0.020
 SXH  plan-1  HN36  0.020
 SXH  plan-2  C38   0.020
 SXH  plan-2  C39   0.020
 SXH  plan-2  O40   0.020
 SXH  plan-2  N41   0.020
 SXH  plan-2  C42   0.020
 SXH  plan-2  HN41  0.020
 SXH  plan-3  S1    0.020
 SXH  plan-3  C1    0.020
 SXH  plan-3  O1    0.020
 SXH  plan-3  C2    0.020

