# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 11:04:02 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: S-[2-({N-[(2S)-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
 SXO  SXO  'S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate'  ligand  68  31  .  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_SXO
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
 SXO  O25   O  OH1   0  -0.744    9.4746   2.0808  -0.7258
 SXO  P24   P  P     0   1.456    8.0134   2.6438  -0.4004
 SXO  O26   O  OH1   0  -0.732    8.1771   3.8717   0.6031
 SXO  O23   O  O     0  -0.713    7.2844   2.8787  -1.6607
 SXO  O27   O  O2    0  -0.587    7.3470   1.6379   0.6395
 SXO  C28   C  CH2   0  -0.151    6.9218   0.3403   0.2022
 SXO  C29   C  CT    0  -0.168    6.3107  -0.3993   1.3915
 SXO  C30   C  CH3   0  -0.645    7.3342  -0.5216   2.5244
 SXO  C31   C  CH3   0  -0.666    5.0792   0.3462   1.9103
 SXO  C32   C  CH1   0  -0.033    5.9154  -1.8401   0.9569
 SXO  O33   O  OH1   0  -0.660    7.0192  -2.6020   0.5502
 SXO  C34   C  C     0   0.520    4.8712  -1.8673  -0.1598
 SXO  O35   O  O     0  -0.499    5.2288  -1.8569  -1.3331
 SXO  N36   N  NH1   0  -0.638    3.5921  -1.9062   0.2147
 SXO  C37   C  CH2   0  -0.235    2.4983  -1.9125  -0.7377
 SXO  C38   C  CH2   0  -0.636    1.1827  -1.7508   0.0013
 SXO  C39   C  C     0   0.575   -0.0061  -1.7587  -0.9376
 SXO  O40   O  O     0  -0.497    0.0747  -2.1049  -2.1071
 SXO  N41   N  NH1   0  -0.648   -1.1630  -1.3686  -0.3805
 SXO  C42   C  CH2   0  -0.238   -2.4065  -1.3478  -1.1198
 SXO  C43   C  CH2   0  -0.602   -3.5354  -0.9352  -0.1876
 SXO  S1    S  S2    0   0.007   -5.0739  -0.9017  -1.1445
 SXO  C1    C  C     0   0.259   -6.2302  -0.3384   0.0812
 SXO  O1    O  O     0  -0.383   -5.9015  -0.1001   1.2132
 SXO  C2    C  CH2   0  -0.538   -7.6276  -0.1991  -0.4632
 SXO  C3    C  CH2   0  -0.417   -8.6448   0.2889   0.5574
 SXO  C4    C  CH2   0  -0.416  -10.0328   0.4298  -0.0554
 SXO  C5    C  CH2   0  -0.413  -11.0723   0.9186   0.9451
 SXO  C6    C  CH2   0  -0.407  -12.4616   1.0756   0.3399
 SXO  C7    C  CH2   0  -0.419  -13.4990   1.5736   1.3389
 SXO  C8    C  CH3   0  -0.662  -14.8849   1.7309   0.7285
 SXO  H28   H  HCH2  0   0.248    6.1943   0.4554  -0.6038
 SXO  H28A  H  HCH2  0   0.239    7.7825  -0.2119  -0.1854
 SXO  H30   H  HCH3  0   0.231    6.9196  -1.1026   3.3510
 SXO  H30A  H  HCH3  0   0.235    8.2498  -1.0132   2.1961
 SXO  H30B  H  HCH3  0   0.240    7.6019   0.4578   2.9187
 SXO  H31   H  HCH3  0   0.234    4.5932  -0.2203   2.7082
 SXO  H31A  H  HCH3  0   0.248    5.3612   1.3114   2.3294
 SXO  H31B  H  HCH3  0   0.234    4.3381   0.5283   1.1309
 SXO  H32   H  HCH1  0   0.258    5.4998  -2.3239   1.8487
 SXO  HO33  H  HOH1  0   0.446    7.1167  -2.4937  -0.4046
 SXO  HN36  H  HNH1  0   0.408    3.3786  -2.0068   1.1942
 SXO  H37   H  HCH2  0   0.250    2.6355  -1.0957  -1.4477
 SXO  H37A  H  HCH2  0   0.249    2.5031  -2.8429  -1.3089
 SXO  H38   H  HCH2  0   0.289    1.0527  -2.5644   0.7225
 SXO  H38A  H  HCH2  0   0.278    1.1832  -0.8235   0.5809
 SXO  HN41  H  HNH1  0   0.408   -1.1698  -1.0869   0.5871
 SXO  H42   H  HCH2  0   0.250   -2.3371  -0.6471  -1.9558
 SXO  H42A  H  HCH2  0   0.251   -2.6098  -2.3360  -1.5393
 SXO  H43   H  HCH2  0   0.292   -3.6362  -1.6457   0.6330
 SXO  H43A  H  HCH2  0   0.292   -3.3513   0.0572   0.2246
 SXO  H2    H  HCH2  0   0.279   -7.5853   0.4806  -1.3208
 SXO  H2A   H  HCH2  0   0.279   -7.9275  -1.1692  -0.8731
 SXO  H3    H  HCH2  0   0.228   -8.6861  -0.4063   1.3999
 SXO  H3A   H  HCH2  0   0.228   -8.3272   1.2528   0.9635
 SXO  H4    H  HCH2  0   0.214   -9.9884   1.1240  -0.9016
 SXO  H4A   H  HCH2  0   0.214  -10.3501  -0.5339  -0.4681
 SXO  H5    H  HCH2  0   0.209  -11.1206   0.2207   1.7882
 SXO  H5A   H  HCH2  0   0.209  -10.7487   1.8783   1.3629
 SXO  H6    H  HCH2  0   0.207  -12.4128   1.7698  -0.5066
 SXO  H6A   H  HCH2  0   0.207  -12.7888   0.1153  -0.0741
 SXO  H7    H  HCH2  0   0.210  -13.5483   0.8811   2.1851
 SXO  H7A   H  HCH2  0   0.210  -13.1706   2.5329   1.7511
 SXO  H8    H  HCH3  0   0.215  -14.8718   2.4385  -0.1026
 SXO  H8A   H  HCH3  0   0.216  -15.2581   0.7801   0.3437
 SXO  H8B   H  HCH3  0   0.225  -15.6055   2.0957   1.4616
 SXO  HO25  H  HOH1  0   0.495   10.0500   1.9423   0.0385
 SXO  HO26  H  HOH1  0   0.503    8.4646   4.6911   0.1790

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
 SXO  P24   O25   single  1.599  0.020  1.599
 SXO  O25   HO25  single  0.850  0.020  0.980
 SXO  O23   P24   double  1.475  0.020  1.475
 SXO  P24   O27   single  1.593  0.020  1.593
 SXO  P24   O26   single  1.594  0.020  1.594
 SXO  O26   HO26  single  0.850  0.020  0.980
 SXO  O27   C28   single  1.434  0.020  1.434
 SXO  C28   H28A  single  0.970  0.020  1.090
 SXO  C28   C29   single  1.528  0.020  1.528
 SXO  C28   H28   single  0.970  0.020  1.090
 SXO  C31   C29   single  1.530  0.020  1.530
 SXO  C29   C32   single  1.556  0.020  1.556
 SXO  C29   C30   single  1.532  0.020  1.532
 SXO  H30   C30   single  0.970  0.020  1.090
 SXO  C30   H30B  single  0.970  0.020  1.090
 SXO  C30   H30A  single  0.970  0.020  1.090
 SXO  H31   C31   single  0.970  0.020  1.090
 SXO  H31A  C31   single  0.970  0.020  1.090
 SXO  C31   H31B  single  0.970  0.020  1.090
 SXO  O33   C32   single  1.402  0.020  1.402
 SXO  C32   C34   single  1.529  0.020  1.529
 SXO  C32   H32   single  0.970  0.020  1.090
 SXO  HO33  O33   single  0.850  0.020  0.980
 SXO  O35   C34   double  1.227  0.020  1.227
 SXO  C34   N36   single  1.333  0.020  1.333
 SXO  N36   C37   single  1.450  0.020  1.450
 SXO  N36   HN36  single  0.860  0.020  1.020
 SXO  H37   C37   single  0.970  0.020  1.090
 SXO  C37   H37A  single  0.970  0.020  1.090
 SXO  C37   C38   single  1.518  0.020  1.518
 SXO  C39   C38   single  1.515  0.020  1.515
 SXO  C38   H38A  single  0.970  0.020  1.090
 SXO  C38   H38   single  0.970  0.020  1.090
 SXO  N41   C39   single  1.342  0.020  1.342
 SXO  C39   O40   double  1.222  0.020  1.222
 SXO  HN41  N41   single  0.860  0.020  1.020
 SXO  C42   N41   single  1.447  0.020  1.447
 SXO  C43   C42   single  1.521  0.020  1.521
 SXO  H42   C42   single  0.970  0.020  1.090
 SXO  C42   H42A  single  0.970  0.020  1.090
 SXO  S1    C43   single  1.812  0.020  1.812
 SXO  H43A  C43   single  0.970  0.020  1.090
 SXO  C43   H43   single  0.970  0.020  1.090
 SXO  C1    S1    single  1.777  0.020  1.777
 SXO  C2    C1    single  1.506  0.020  1.506
 SXO  C1    O1    double  1.203  0.020  1.203
 SXO  C3    C2    single  1.521  0.020  1.521
 SXO  H2    C2    single  0.970  0.020  1.090
 SXO  C2    H2A   single  0.970  0.020  1.090
 SXO  H3A   C3    single  0.970  0.020  1.090
 SXO  H3    C3    single  0.970  0.020  1.090
 SXO  C3    C4    single  1.524  0.020  1.524
 SXO  C5    C4    single  1.523  0.020  1.523
 SXO  C4    H4    single  0.970  0.020  1.090
 SXO  C4    H4A   single  0.970  0.020  1.090
 SXO  H5A   C5    single  0.970  0.020  1.090
 SXO  H5    C5    single  0.970  0.020  1.090
 SXO  C5    C6    single  1.523  0.020  1.523
 SXO  H6    C6    single  0.970  0.020  1.090
 SXO  C6    C7    single  1.524  0.020  1.524
 SXO  C6    H6A   single  0.970  0.020  1.090
 SXO  C8    C7    single  1.523  0.020  1.523
 SXO  C7    H7    single  0.970  0.020  1.090
 SXO  C7    H7A   single  0.970  0.020  1.090
 SXO  H8A   C8    single  0.970  0.020  1.090
 SXO  H8    C8    single  0.970  0.020  1.090
 SXO  C8    H8B   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
 SXO  HO25  O25  P24   115.68  3.000
 SXO  O27   P24  O23   116.85  3.000
 SXO  O27   P24  O26    96.80  3.000
 SXO  O23   P24  O26   117.78  3.000
 SXO  O26   P24  O25   107.78  3.000
 SXO  O27   P24  O25   107.02  3.000
 SXO  O23   P24  O25   109.50  3.000
 SXO  HO26  O26  P24   114.04  3.000
 SXO  C28   O27  P24   119.76  3.000
 SXO  H28A  C28  H28   108.42  3.000
 SXO  H28   C28  C29   111.05  3.000
 SXO  H28A  C28  C29   110.26  3.000
 SXO  H28   C28  O27   109.11  3.000
 SXO  C29   C28  O27   108.62  3.000
 SXO  H28A  C28  O27   109.37  3.000
 SXO  C32   C29  C31   109.96  3.000
 SXO  C32   C29  C30   107.60  3.000
 SXO  C31   C29  C30   109.02  3.000
 SXO  C30   C29  C28   110.31  3.000
 SXO  C32   C29  C28   109.41  3.000
 SXO  C31   C29  C28   110.48  3.000
 SXO  H30B  C30  H30A  107.95  3.000
 SXO  H30A  C30  H30   107.88  3.000
 SXO  H30B  C30  H30   107.32  3.000
 SXO  H30A  C30  C29   112.00  3.000
 SXO  H30B  C30  C29   111.11  3.000
 SXO  H30   C30  C29   110.40  3.000
 SXO  H31B  C31  H31A  107.63  3.000
 SXO  H31B  C31  H31   107.82  3.000
 SXO  H31A  C31  H31   107.08  3.000
 SXO  H31B  C31  C29   112.70  3.000
 SXO  H31A  C31  C29   110.72  3.000
 SXO  H31   C31  C29   110.67  3.000
 SXO  H32   C32  C34   109.10  3.000
 SXO  H32   C32  O33   107.14  3.000
 SXO  C34   C32  O33   108.43  3.000
 SXO  H32   C32  C29   106.12  3.000
 SXO  C34   C32  C29   113.20  3.000
 SXO  O33   C32  C29   112.61  3.000
 SXO  HO33  O33  C32   107.79  3.000
 SXO  N36   C34  O35   123.27  3.000
 SXO  N36   C34  C32   116.78  3.000
 SXO  O35   C34  C32   119.95  3.000
 SXO  HN36  N36  C37   118.56  3.000
 SXO  HN36  N36  C34   118.64  3.000
 SXO  C37   N36  C34   122.63  3.000
 SXO  H37A  C37  H37   107.27  3.000
 SXO  H37A  C37  C38   110.45  3.000
 SXO  H37   C37  C38   110.25  3.000
 SXO  C38   C37  N36   109.48  3.000
 SXO  H37A  C37  N36   110.12  3.000
 SXO  H37   C37  N36   109.22  3.000
 SXO  H38A  C38  H38   106.33  3.000
 SXO  H38   C38  C39   108.13  3.000
 SXO  H38A  C38  C39   109.47  3.000
 SXO  H38   C38  C37   110.15  3.000
 SXO  H38A  C38  C37   110.37  3.000
 SXO  C39   C38  C37   112.20  3.000
 SXO  N41   C39  O40   122.44  3.000
 SXO  O40   C39  C38   122.86  3.000
 SXO  N41   C39  C38   114.69  3.000
 SXO  HN41  N41  C42   118.75  3.000
 SXO  C42   N41  C39   122.20  3.000
 SXO  HN41  N41  C39   119.05  3.000
 SXO  H42A  C42  H42   107.33  3.000
 SXO  H42A  C42  C43   110.03  3.000
 SXO  H42   C42  C43   109.99  3.000
 SXO  H42A  C42  N41   110.07  3.000
 SXO  H42   C42  N41   110.22  3.000
 SXO  C43   C42  N41   109.18  3.000
 SXO  H43A  C43  H43   108.92  3.000
 SXO  H43   C43  S1    109.33  3.000
 SXO  H43A  C43  S1    109.04  3.000
 SXO  H43   C43  C42   110.68  3.000
 SXO  H43A  C43  C42   110.69  3.000
 SXO  S1    C43  C42   108.15  3.000
 SXO  C1    S1   C43   101.19  3.000
 SXO  C2    C1   O1    125.13  3.000
 SXO  O1    C1   S1    122.30  3.000
 SXO  C2    C1   S1    112.57  3.000
 SXO  H2A   C2   H2    105.50  3.000
 SXO  H2A   C2   C3    110.62  3.000
 SXO  H2    C2   C3    110.62  3.000
 SXO  H2A   C2   C1    107.90  3.000
 SXO  H2    C2   C1    107.74  3.000
 SXO  C3    C2   C1    114.05  3.000
 SXO  H3A   C3   H3    106.59  3.000
 SXO  H3    C3   C4    109.53  3.000
 SXO  H3A   C3   C4    109.42  3.000
 SXO  C4    C3   C2    111.65  3.000
 SXO  H3    C3   C2    109.78  3.000
 SXO  H3A   C3   C2    109.74  3.000
 SXO  H4A   C4   H4    106.16  3.000
 SXO  H4A   C4   C5    109.39  3.000
 SXO  H4    C4   C5    109.37  3.000
 SXO  H4A   C4   C3    109.51  3.000
 SXO  H4    C4   C3    109.41  3.000
 SXO  C5    C4   C3    112.77  3.000
 SXO  H5A   C5   H5    106.11  3.000
 SXO  H5    C5   C6    109.34  3.000
 SXO  H5A   C5   C6    109.31  3.000
 SXO  C6    C5   C4    113.23  3.000
 SXO  H5    C5   C4    109.34  3.000
 SXO  H5A   C5   C4    109.27  3.000
 SXO  H6A   C6   H6    106.06  3.000
 SXO  H6A   C6   C7    109.31  3.000
 SXO  H6    C6   C7    109.25  3.000
 SXO  H6A   C6   C5    109.40  3.000
 SXO  C7    C6   C5    113.20  3.000
 SXO  H6    C6   C5    109.36  3.000
 SXO  H7A   C7   H7    106.07  3.000
 SXO  H7A   C7   C8    109.48  3.000
 SXO  H7    C7   C8    109.53  3.000
 SXO  H7A   C7   C6    109.21  3.000
 SXO  H7    C7   C6    109.32  3.000
 SXO  C8    C7   C6    112.99  3.000
 SXO  H8B   C8   H8A   107.60  3.000
 SXO  H8B   C8   H8    107.63  3.000
 SXO  H8A   C8   H8    107.48  3.000
 SXO  H8B   C8   C7    111.50  3.000
 SXO  H8    C8   C7    111.18  3.000
 SXO  H8A   C8   C7    111.26  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
 SXO  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SXO  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SXO  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SXO  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SXO  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SXO  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SXO  Var_01    C29   C28  O27  P24  -179.38  30.0  3
 SXO  Var_02    C31   C29  C28  O27    61.96  30.0  3
 SXO  Var_03    C38   C37  N36  C34  -171.59  30.0  3
 SXO  Var_04    C39   C38  C37  N36  -179.61  30.0  3
 SXO  Var_05    N41   C39  C38  C37  -167.93  30.0  2
 SXO  Var_06    C43   C42  N41  C39   176.85  30.0  1
 SXO  Var_07    S1    C43  C42  N41   179.42  30.0  1
 SXO  Var_08    C2    C1   S1   C43   179.26  30.0  1
 SXO  Var_09    C3    C2   C1   S1   -179.69  30.0  1
 SXO  Var_10    C4    C3   C2   C1    179.15  30.0  1
 SXO  Var_11    C5    C4   C3   C2   -179.95  30.0  3
 SXO  Var_12    C6    C5   C4   C3    179.46  30.0  1
 SXO  Var_13    C7    C6   C5   C4   -179.61  30.0  3
 SXO  Var_14    C8    C7   C6   C5    179.91  30.0  3
 SXO  Var_15    H31   C31  C29  C28   175.46  30.0  3
 SXO  Var_16    H30   C30  C29  C28  -176.56  30.0  3
 SXO  Var_17    H8A   C8   C7   C6     60.34  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
 SXO  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
 SXO  plan-1  C32   0.020
 SXO  plan-1  C34   0.020
 SXO  plan-1  O35   0.020
 SXO  plan-1  N36   0.020
 SXO  plan-1  C37   0.020
 SXO  plan-1  HN36  0.020
 SXO  plan-2  C38   0.020
 SXO  plan-2  C39   0.020
 SXO  plan-2  O40   0.020
 SXO  plan-2  N41   0.020
 SXO  plan-2  C42   0.020
 SXO  plan-2  HN41  0.020
 SXO  plan-3  S1    0.020
 SXO  plan-3  C1    0.020
 SXO  plan-3  O1    0.020
 SXO  plan-3  C2    0.020

