# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:28:51 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3-oxo-5-phenylpentyl)sulfanyl]ethyl}-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(COP(O)O)[C@H](O)C(=O)NCCC(=O)NCCSCCC(=O)CCc1ccccc1
#
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
 SXR  SXR  N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3-oxo-5-phenylpentyl)sulfanyl]ethyl}-beta-alaninamide  ligand  68  33  .  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_SXR
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
 SXR  P24   P  P     0   0.886   10.0574   2.1657  -0.3383
 SXR  O26   O  OH1   0  -0.771    9.7379   2.7378  -1.8451
 SXR  O23   O  OH1   0  -0.766   10.4041   3.5680   0.4308
 SXR  O27   O  O2    0  -0.605    8.5131   2.0852   0.2084
 SXR  C28   C  CH2   0  -0.148    7.7725   0.9012  -0.0616
 SXR  C29   C  CT    0  -0.139    7.3396   0.2329   1.2470
 SXR  C30   C  CH3   0  -0.654    8.5716  -0.0912   2.0986
 SXR  C31   C  CH3   0  -0.668    6.4228   1.1641   2.0422
 SXR  C32   C  CH1   0  -0.034    6.6093  -1.1063   0.9488
 SXR  O33   O  OH1   0  -0.662    7.4401  -2.0423   0.3146
 SXR  C34   C  C     0   0.517    5.3455  -0.9337   0.1053
 SXR  O35   O  O     0  -0.499    5.4183  -0.9643  -1.1188
 SXR  N36   N  NH1   0  -0.626    4.1996  -0.7636   0.7687
 SXR  C37   C  CH2   0  -0.283    2.9241  -0.5728   0.1124
 SXR  C38   C  CH2   0  -0.587    2.3021  -1.8915  -0.3401
 SXR  C39   C  C     0   0.564    0.9614  -1.6749  -1.0073
 SXR  O40   O  O     0  -0.501    0.7257  -0.6778  -1.6761
 SXR  N41   N  NH1   0  -0.632    0.0685  -2.6648  -0.8356
 SXR  C42   C  CH2   0  -0.287   -1.2610  -2.6365  -1.3977
 SXR  C43   C  CH2   0  -0.546   -2.2427  -1.9034  -0.4898
 SXR  S1    S  S2    0  -0.038   -3.8766  -1.8609  -1.2775
 SXR  C11   C  CR16  0  -0.311  -11.8229   0.0141   0.9559
 SXR  C10   C  CR16  0  -0.239  -13.1054   0.1943   0.4542
 SXR  C9    C  CR16  0  -0.273  -13.4087   1.3242  -0.2941
 SXR  C8    C  CR16  0  -0.239  -12.4213   2.2713  -0.5344
 SXR  C7    C  CR16  0  -0.308  -11.1410   2.0863  -0.0302
 SXR  C6    C  CR6   0   0.127  -10.8243   0.9565   0.7216
 SXR  C5    C  CH2   0  -0.508   -9.4265   0.7404   1.2322
 SXR  C4    C  CH2   0  -0.551   -8.5635   0.0459   0.1832
 SXR  C3    C  C     0   0.417   -7.1397  -0.2015   0.6121
 SXR  O3    O  O     0  -0.405   -6.7332   0.0942   1.7120
 SXR  C2    C  CH2   0  -0.552   -6.2495  -0.8423  -0.4269
 SXR  C1    C  CH2   0  -0.544   -4.8348  -1.0960   0.0612
 SXR  H1    H  HOH1  0   0.481   10.3594   2.3783  -2.4883
 SXR  H2    H  HOH1  0   0.486   11.2444   3.5058   0.8984
 SXR  H28A  H  HCH2  0   0.239    6.9084   1.1840  -0.6671
 SXR  H28B  H  HCH2  0   0.220    8.3657   0.1948  -0.6560
 SXR  H30A  H  HCH3  0   0.237    9.0575   0.8213   2.4442
 SXR  H30B  H  HCH3  0   0.231    8.2864  -0.6578   2.9877
 SXR  H30C  H  HCH3  0   0.233    9.3081  -0.6783   1.5498
 SXR  H31A  H  HCH3  0   0.233    5.5364   1.4645   1.4822
 SXR  H31B  H  HCH3  0   0.232    6.0895   0.6851   2.9654
 SXR  H31C  H  HCH3  0   0.245    6.9555   2.0719   2.3234
 SXR  H32A  H  HCH1  0   0.252    6.3318  -1.5318   1.9202
 SXR  H33A  H  HOH1  0   0.445    7.3280  -1.9392  -0.6389
 SXR  H36A  H  HNH1  0   0.407    4.2044  -0.8251   1.7738
 SXR  H37A  H  HCH2  0   0.265    2.2680  -0.0700   0.8217
 SXR  H37B  H  HCH2  0   0.254    3.0546   0.0967  -0.7359
 SXR  H38A  H  HCH2  0   0.283    2.9626  -2.3776  -1.0638
 SXR  H38B  H  HCH2  0   0.261    2.2118  -2.5734   0.5081
 SXR  H41A  H  HNH1  0   0.404    0.3050  -3.4333  -0.2297
 SXR  H42A  H  HCH2  0   0.252   -1.2247  -2.1610  -2.3781
 SXR  H42B  H  HCH2  0   0.263   -1.5875  -3.6655  -1.5478
 SXR  H43A  H  HCH2  0   0.266   -2.3196  -2.4159   0.4709
 SXR  H43B  H  HCH2  0   0.269   -1.8995  -0.8837  -0.3075
 SXR  H10A  H  HCR6  0   0.253  -13.8698  -0.5465   0.6521
 SXR  H9A   H  HCR6  0   0.253  -14.4081   1.4672  -0.6847
 SXR  H8A   H  HCR6  0   0.253  -12.6493   3.1576  -1.1129
 SXR  H7A   H  HCR6  0   0.246  -10.3772   2.8319  -0.2208
 SXR  H5A   H  HCH2  0   0.251   -8.9767   1.6983   1.5008
 SXR  H5B   H  HCH2  0   0.250   -9.4536   0.1378   2.1421
 SXR  H4A   H  HCH2  0   0.279   -9.0038  -0.9166  -0.0997
 SXR  H4B   H  HCH2  0   0.276   -8.5408   0.6291  -0.7433
 SXR  H2A   H  HCH2  0   0.280   -6.7251  -1.7731  -0.7527
 SXR  H2B   H  HCH2  0   0.281   -6.2424  -0.1948  -1.3098
 SXR  H1A   H  HCH2  0   0.270   -4.8362  -1.7595   0.9270
 SXR  H1B   H  HCH2  0   0.270   -4.3528  -0.1614   0.3509
 SXR  H11A  H  HCR6  0   0.246  -11.5951  -0.8683   1.5430

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
 SXR  P24  O26   single    1.643  0.020  1.643
 SXR  P24  O23   single    1.636  0.020  1.636
 SXR  P24  O27   single    1.640  0.020  1.640
 SXR  O27  C28   single    1.422  0.020  1.422
 SXR  C28  C29   single    1.532  0.020  1.532
 SXR  C29  C30   single    1.532  0.020  1.532
 SXR  C29  C31   single    1.530  0.020  1.530
 SXR  C29  C32   single    1.554  0.020  1.554
 SXR  C32  O33   single    1.403  0.020  1.403
 SXR  C32  C34   single    1.529  0.020  1.529
 SXR  C34  O35   double    1.227  0.020  1.227
 SXR  C34  N36   single    1.335  0.020  1.335
 SXR  N36  C37   single    1.447  0.020  1.447
 SXR  C37  C38   single    1.527  0.020  1.527
 SXR  C38  C39   single    1.513  0.020  1.513
 SXR  C39  O40   double    1.224  0.020  1.224
 SXR  C39  N41   single    1.344  0.020  1.344
 SXR  N41  C42   single    1.444  0.020  1.444
 SXR  C42  C43   single    1.525  0.020  1.525
 SXR  C43  S1    single    1.814  0.020  1.814
 SXR  S1   C1    single    1.815  0.020  1.815
 SXR  C11  C10   aromatic  1.389  0.020  1.389
 SXR  C11  C6    aromatic  1.393  0.020  1.393
 SXR  C10  C9    aromatic  1.389  0.020  1.389
 SXR  C9   C8    aromatic  1.389  0.020  1.389
 SXR  C8   C7    aromatic  1.388  0.020  1.388
 SXR  C7   C6    aromatic  1.394  0.020  1.394
 SXR  C6   C5    single    1.504  0.020  1.504
 SXR  C5   C4    single    1.526  0.020  1.526
 SXR  C4   C3    single    1.507  0.020  1.507
 SXR  C3   O3    double    1.209  0.020  1.209
 SXR  C3   C2    single    1.511  0.020  1.511
 SXR  C2   C1    single    1.518  0.020  1.518
 SXR  O26  H1    single    0.850  0.020  0.980
 SXR  O23  H2    single    0.850  0.020  0.980
 SXR  C28  H28A  single    0.970  0.020  1.090
 SXR  C28  H28B  single    0.970  0.020  1.090
 SXR  C30  H30A  single    0.970  0.020  1.090
 SXR  C30  H30B  single    0.970  0.020  1.090
 SXR  C30  H30C  single    0.970  0.020  1.090
 SXR  C31  H31A  single    0.970  0.020  1.090
 SXR  C31  H31B  single    0.970  0.020  1.090
 SXR  C31  H31C  single    0.970  0.020  1.090
 SXR  C32  H32A  single    0.970  0.020  1.090
 SXR  O33  H33A  single    0.850  0.020  0.980
 SXR  N36  H36A  single    0.860  0.020  1.020
 SXR  C37  H37A  single    0.970  0.020  1.090
 SXR  C37  H37B  single    0.970  0.020  1.090
 SXR  C38  H38A  single    0.970  0.020  1.090
 SXR  C38  H38B  single    0.970  0.020  1.090
 SXR  N41  H41A  single    0.860  0.020  1.020
 SXR  C42  H42A  single    0.970  0.020  1.090
 SXR  C42  H42B  single    0.970  0.020  1.090
 SXR  C43  H43A  single    0.970  0.020  1.090
 SXR  C43  H43B  single    0.970  0.020  1.090
 SXR  C11  H11A  single    0.930  0.020  1.080
 SXR  C10  H10A  single    0.930  0.020  1.080
 SXR  C9   H9A   single    0.930  0.020  1.080
 SXR  C8   H8A   single    0.930  0.020  1.080
 SXR  C7   H7A   single    0.930  0.020  1.080
 SXR  C5   H5A   single    0.970  0.020  1.090
 SXR  C5   H5B   single    0.970  0.020  1.090
 SXR  C4   H4A   single    0.970  0.020  1.090
 SXR  C4   H4B   single    0.970  0.020  1.090
 SXR  C2   H2A   single    0.970  0.020  1.090
 SXR  C2   H2B   single    0.970  0.020  1.090
 SXR  C1   H1A   single    0.970  0.020  1.090
 SXR  C1   H1B   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
 SXR  O27   P24  O23    94.87  3.000
 SXR  O27   P24  O26    98.03  3.000
 SXR  O23   P24  O26   100.01  3.000
 SXR  H1    O26  P24   110.90  3.000
 SXR  H2    O23  P24   110.95  3.000
 SXR  C28   O27  P24   117.89  3.000
 SXR  H28B  C28  H28A  107.10  3.000
 SXR  H28B  C28  C29   109.55  3.000
 SXR  H28A  C28  C29   111.28  3.000
 SXR  H28B  C28  O27   110.93  3.000
 SXR  H28A  C28  O27   107.56  3.000
 SXR  C29   C28  O27   110.37  3.000
 SXR  C32   C29  C31   110.04  3.000
 SXR  C32   C29  C30   107.59  3.000
 SXR  C31   C29  C30   108.77  3.000
 SXR  C32   C29  C28   110.17  3.000
 SXR  C31   C29  C28   110.36  3.000
 SXR  C30   C29  C28   109.87  3.000
 SXR  H30C  C30  H30B  107.87  3.000
 SXR  H30C  C30  H30A  108.02  3.000
 SXR  H30B  C30  H30A  107.01  3.000
 SXR  H30C  C30  C29   112.17  3.000
 SXR  H30B  C30  C29   110.62  3.000
 SXR  H30A  C30  C29   110.95  3.000
 SXR  H31C  C31  H31B  107.24  3.000
 SXR  H31C  C31  H31A  107.48  3.000
 SXR  H31B  C31  H31A  107.87  3.000
 SXR  H31C  C31  C29   110.39  3.000
 SXR  H31B  C31  C29   110.81  3.000
 SXR  H31A  C31  C29   112.82  3.000
 SXR  H32A  C32  C34   108.87  3.000
 SXR  H32A  C32  O33   106.95  3.000
 SXR  C34   C32  O33   108.38  3.000
 SXR  H32A  C32  C29   106.46  3.000
 SXR  C34   C32  C29   113.38  3.000
 SXR  O33   C32  C29   112.54  3.000
 SXR  H33A  O33  C32   107.84  3.000
 SXR  N36   C34  O35   123.36  3.000
 SXR  N36   C34  C32   116.72  3.000
 SXR  O35   C34  C32   119.91  3.000
 SXR  H36A  N36  C37   117.71  3.000
 SXR  H36A  N36  C34   118.95  3.000
 SXR  C37   N36  C34   123.23  3.000
 SXR  H37B  C37  H37A  107.20  3.000
 SXR  H37B  C37  C38   110.43  3.000
 SXR  H37A  C37  C38   110.27  3.000
 SXR  H37B  C37  N36   109.20  3.000
 SXR  H37A  C37  N36   107.25  3.000
 SXR  C38   C37  N36   112.31  3.000
 SXR  H38B  C38  H38A  106.64  3.000
 SXR  H38B  C38  C39   111.02  3.000
 SXR  H38A  C38  C39   107.88  3.000
 SXR  H38B  C38  C37   110.05  3.000
 SXR  H38A  C38  C37   109.51  3.000
 SXR  C39   C38  C37   111.60  3.000
 SXR  N41   C39  O40   122.83  3.000
 SXR  N41   C39  C38   115.27  3.000
 SXR  O40   C39  C38   121.89  3.000
 SXR  H41A  N41  C42   117.75  3.000
 SXR  H41A  N41  C39   118.88  3.000
 SXR  C42   N41  C39   123.20  3.000
 SXR  H42B  C42  H42A  107.34  3.000
 SXR  H42B  C42  C43   110.06  3.000
 SXR  H42A  C42  C43   110.31  3.000
 SXR  H42B  C42  N41   108.12  3.000
 SXR  H42A  C42  N41   109.15  3.000
 SXR  C43   C42  N41   111.74  3.000
 SXR  H43B  C43  H43A  108.29  3.000
 SXR  H43B  C43  S1    109.51  3.000
 SXR  H43A  C43  S1    109.25  3.000
 SXR  H43B  C43  C42   110.26  3.000
 SXR  H43A  C43  C42   110.09  3.000
 SXR  S1    C43  C42   109.42  3.000
 SXR  C1    S1   C43    99.50  3.000
 SXR  H11A  C11  C6    119.41  3.000
 SXR  H11A  C11  C10   119.69  3.000
 SXR  C6    C11  C10   120.90  3.000
 SXR  H10A  C10  C9    120.06  3.000
 SXR  H10A  C10  C11   119.81  3.000
 SXR  C9    C10  C11   120.12  3.000
 SXR  H9A   C9   C8    120.25  3.000
 SXR  H9A   C9   C10   120.23  3.000
 SXR  C8    C9   C10   119.52  3.000
 SXR  H8A   C8   C7    119.82  3.000
 SXR  H8A   C8   C9    120.06  3.000
 SXR  C7    C8   C9    120.12  3.000
 SXR  H7A   C7   C6    119.49  3.000
 SXR  H7A   C7   C8    119.61  3.000
 SXR  C6    C7   C8    120.90  3.000
 SXR  C5    C6   C7    120.73  3.000
 SXR  C5    C6   C11   120.80  3.000
 SXR  C7    C6   C11   118.45  3.000
 SXR  H5B   C5   H5A   106.83  3.000
 SXR  H5B   C5   C4    109.63  3.000
 SXR  H5A   C5   C4    109.61  3.000
 SXR  H5B   C5   C6    109.83  3.000
 SXR  H5A   C5   C6    109.90  3.000
 SXR  C4    C5   C6    110.96  3.000
 SXR  H4B   C4   H4A   104.94  3.000
 SXR  H4B   C4   C3    107.97  3.000
 SXR  H4A   C4   C3    107.99  3.000
 SXR  H4B   C4   C5    110.55  3.000
 SXR  H4A   C4   C5    110.49  3.000
 SXR  C3    C4   C5    114.42  3.000
 SXR  C2    C3   O3    122.09  3.000
 SXR  C2    C3   C4    115.49  3.000
 SXR  O3    C3   C4    122.42  3.000
 SXR  H2B   C2   H2A   105.41  3.000
 SXR  H2B   C2   C1    110.62  3.000
 SXR  H2A   C2   C1    111.00  3.000
 SXR  H2B   C2   C3    107.91  3.000
 SXR  H2A   C2   C3    108.01  3.000
 SXR  C1    C2   C3    113.51  3.000
 SXR  H1B   C1   H1A   108.12  3.000
 SXR  H1B   C1   C2    110.74  3.000
 SXR  H1A   C1   C2    110.84  3.000
 SXR  H1B   C1   S1    108.88  3.000
 SXR  H1A   C1   S1    109.25  3.000
 SXR  C2    C1   S1    108.98  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
 SXR  CONST_01  C8    C9   C10  C11     0.00   0.0  0
 SXR  CONST_02  C8    C7   C6   C11     0.00   0.0  0
 SXR  CONST_03  C7    C6   C11  C10     0.00   0.0  0
 SXR  CONST_04  C7    C8   C9   C10     0.00   0.0  0
 SXR  CONST_05  C6    C11  C10  C9      0.00   0.0  0
 SXR  CONST_06  C6    C7   C8   C9      0.00   0.0  0
 SXR  CONST_07  C5    C6   C11  C10   180.00   0.0  0
 SXR  CONST_08  C5    C6   C7   C8    180.00   0.0  0
 SXR  CONST_09  H9A   C9   C10  C11   180.00   0.0  0
 SXR  CONST_10  H7A   C7   C6   C11   180.00   0.0  0
 SXR  CONST_11  H8A   C8   C9   C10   180.00   0.0  0
 SXR  CONST_12  H11A  C11  C10  C9    180.00   0.0  0
 SXR  CONST_13  H10A  C10  C9   C8    180.00   0.0  0
 SXR  CONST_14  C37   N36  C34  C32   180.00   0.0  0
 SXR  CONST_15  C37   N36  C34  O35     0.00   0.0  0
 SXR  CONST_16  C42   N41  C39  C38   180.00   0.0  0
 SXR  CONST_17  C42   N41  C39  O40     0.00   0.0  0
 SXR  CONST_18  H36A  N36  C34  C32     0.00   0.0  0
 SXR  CONST_19  H41A  N41  C39  C38     0.00   0.0  0
 SXR  Var_01    C4    C5   C6   C11    92.15  30.0  2
 SXR  Var_02    C3    C4   C5   C6    179.62  30.0  3
 SXR  Var_03    C29   C28  O27  P24   119.61  30.0  3
 SXR  Var_04    C30   C29  C28  O27   -58.06  30.0  3
 SXR  Var_05    C38   C37  N36  C34    81.40  30.0  3
 SXR  Var_06    C39   C38  C37  N36   179.24  30.0  3
 SXR  Var_07    O40   C39  C38  C37    33.55  30.0  3
 SXR  Var_08    C43   C42  N41  C39   -86.08  30.0  3
 SXR  Var_09    S1    C43  C42  N41   178.28  30.0  3
 SXR  Var_10    C2    C1   S1   C43   175.03  30.0  3
 SXR  Var_11    C3    C2   C1   S1   -179.89  30.0  2
 SXR  Var_12    O3    C3   C4   C5      2.01  30.0  3
 SXR  Var_13    C1    C2   C3   C4   -178.85  30.0  3
 SXR  Var_14    H30A  C30  C29  C28    67.10  30.0  3
 SXR  Var_15    H31A  C31  C29  C28    57.52  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
 SXR  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
 SXR  plan-1  C11   0.020
 SXR  plan-1  C10   0.020
 SXR  plan-1  C9    0.020
 SXR  plan-1  C8    0.020
 SXR  plan-1  C7    0.020
 SXR  plan-1  C6    0.020
 SXR  plan-1  C5    0.020
 SXR  plan-1  H10A  0.020
 SXR  plan-1  H9A   0.020
 SXR  plan-1  H8A   0.020
 SXR  plan-1  H7A   0.020
 SXR  plan-1  H11A  0.020
 SXR  plan-2  C32   0.020
 SXR  plan-2  C34   0.020
 SXR  plan-2  O35   0.020
 SXR  plan-2  N36   0.020
 SXR  plan-2  C37   0.020
 SXR  plan-2  H36A  0.020
 SXR  plan-3  C38   0.020
 SXR  plan-3  C39   0.020
 SXR  plan-3  O40   0.020
 SXR  plan-3  N41   0.020
 SXR  plan-3  C42   0.020
 SXR  plan-3  H41A  0.020
 SXR  plan-4  C4    0.020
 SXR  plan-4  C3    0.020
 SXR  plan-4  O3    0.020
 SXR  plan-4  C2    0.020

