# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 02:26:35 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-{2-[(3,5-dioxohexyl)sulfanyl]ethyl}-N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CC(=O)CCSCCNC(=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
 SXD  SXD  N-{2-[(3,5-dioxohexyl)sulfanyl]ethyl}-N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide  ligand  61  30  .  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_SXD
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
 SXD  O25   O  OH1   0  -0.743    9.1164   1.5567  -0.9406
 SXD  P24   P  P     0   1.455    7.7474   2.3330  -0.6548
 SXD  O26   O  OH1   0  -0.732    8.0772   3.5746   0.2887
 SXD  O23   O  O     0  -0.712    7.0582   2.5994  -1.9312
 SXD  O27   O  O2    0  -0.587    6.9453   1.4824   0.4271
 SXD  C28   C  CH2   0  -0.151    6.3515   0.2339   0.0465
 SXD  C29   C  CT    0  -0.166    5.7543  -0.4213   1.2912
 SXD  C30   C  CH3   0  -0.646    6.8399  -0.6357   2.3500
 SXD  C31   C  CH3   0  -0.670    4.6501   0.4596   1.8792
 SXD  C32   C  CH1   0  -0.032    5.1773  -1.8168   0.9180
 SXD  O33   O  OH1   0  -0.661    6.1599  -2.6984   0.4477
 SXD  C34   C  C     0   0.517    4.0562  -1.7403  -0.1204
 SXD  O35   O  O     0  -0.498    4.3279  -1.7899  -1.3154
 SXD  N36   N  NH1   0  -0.639    2.8104  -1.6285   0.3435
 SXD  C37   C  CH2   0  -0.240    1.6652  -1.4393  -0.5250
 SXD  C38   C  CH2   0  -0.625    0.3782  -1.6222   0.2634
 SXD  C39   C  C     0   0.564   -0.8353  -1.3158  -0.5893
 SXD  O40   O  O     0  -0.497   -0.8615  -0.3602  -1.3520
 SXD  N41   N  NH1   0  -0.630   -1.8710  -2.1570  -0.4372
 SXD  C42   C  CH2   0  -0.288   -3.1433  -1.9654  -1.0923
 SXD  C43   C  CH2   0  -0.547   -4.0637  -1.0565  -0.2852
 SXD  S1    S  S2    0  -0.035   -5.6154  -0.8077  -1.1926
 SXD  C1    C  CH2   0  -0.547   -6.5477   0.1093   0.0656
 SXD  C2    C  CH2   0  -0.566   -7.9121   0.4677  -0.4917
 SXD  C3    C  C     0   0.426   -8.7735   1.2388   0.4698
 SXD  O3    O  O     0  -0.388   -8.3770   1.6150   1.5470
 SXD  C4    C  CH2   0  -0.682  -10.1879   1.5163   0.0145
 SXD  C5    C  C     0   0.399  -11.1291   0.4054   0.4363
 SXD  O5    O  O     0  -0.393  -10.7168  -0.6024   0.9617
 SXD  C6    C  CH3   0  -0.767  -12.5816   0.6547   0.1623
 SXD  H28   H  HCH2  0   0.250    5.5844   0.4198  -0.7081
 SXD  H28A  H  HCH2  0   0.238    7.1149  -0.4149  -0.3924
 SXD  H30   H  HCH3  0   0.231    6.4360  -1.1814   3.2054
 SXD  H30A  H  HCH3  0   0.236    7.6847  -1.2045   1.9616
 SXD  H30B  H  HCH3  0   0.240    7.2175   0.3160   2.7219
 SXD  H31   H  HCH3  0   0.250    5.0622   1.3983   2.2479
 SXD  H31A  H  HCH3  0   0.234    3.8766   0.7036   1.1496
 SXD  H31B  H  HCH3  0   0.236    4.1685  -0.0349   2.7262
 SXD  H32   H  HCH1  0   0.259    4.7806  -2.2406   1.8475
 SXD  HO33  H  HOH1  0   0.446    6.1884  -2.6225  -0.5147
 SXD  HN36  H  HNH1  0   0.408    2.6657  -1.5921   1.3404
 SXD  H37   H  HCH2  0   0.250    1.6923  -0.4442  -0.9730
 SXD  H37A  H  HCH2  0   0.255    1.7088  -2.1645  -1.3392
 SXD  H38   H  HCH2  0   0.271    0.3288  -2.6307   0.6785
 SXD  H38A  H  HCH2  0   0.283    0.3594  -0.9285   1.1109
 SXD  HN41  H  HNH1  0   0.406   -1.7958  -2.9069   0.2303
 SXD  H42   H  HCH2  0   0.254   -2.9732  -1.5489  -2.0852
 SXD  H42A  H  HCH2  0   0.264   -3.6062  -2.9430  -1.2251
 SXD  H43   H  HCH2  0   0.267   -4.2843  -1.5104   0.6829
 SXD  H43A  H  HCH2  0   0.270   -3.5860  -0.0912  -0.1106
 SXD  H1    H  HCH2  0   0.272   -6.6425  -0.5118   0.9575
 SXD  H1A   H  HCH2  0   0.271   -5.9932   1.0082   0.3373
 SXD  H2    H  HCH2  0   0.287   -7.8168   1.0733  -1.4002
 SXD  H2A   H  HCH2  0   0.283   -8.4611  -0.4278  -0.8006
 SXD  H4    H  HCH2  0   0.308  -10.5441   2.4604   0.4349
 SXD  H4A   H  HCH2  0   0.305  -10.2497   1.6140  -1.0738
 SXD  H6    H  HCH3  0   0.275  -12.9265   1.4913   0.7737
 SXD  H6A   H  HCH3  0   0.268  -12.7311   0.9460  -0.8782
 SXD  H6B   H  HCH3  0   0.266  -13.1854  -0.2215   0.3871
 SXD  HO25  H  HOH1  0   0.494    9.6729   1.3876  -0.1686
 SXD  HO26  H  HOH1  0   0.503    8.5302   4.3016  -0.1591

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
 SXD  P24   O25   single  1.599  0.020  1.599
 SXD  O25   HO25  single  0.850  0.020  0.980
 SXD  O23   P24   double  1.475  0.020  1.475
 SXD  O27   P24   single  1.593  0.020  1.593
 SXD  P24   O26   single  1.594  0.020  1.594
 SXD  O26   HO26  single  0.850  0.020  0.980
 SXD  O27   C28   single  1.434  0.020  1.434
 SXD  C29   C28   single  1.528  0.020  1.528
 SXD  C28   H28A  single  0.970  0.020  1.090
 SXD  C28   H28   single  0.970  0.020  1.090
 SXD  C31   C29   single  1.530  0.020  1.530
 SXD  C32   C29   single  1.556  0.020  1.556
 SXD  C29   C30   single  1.531  0.020  1.531
 SXD  H30   C30   single  0.970  0.020  1.090
 SXD  C30   H30B  single  0.970  0.020  1.090
 SXD  C30   H30A  single  0.970  0.020  1.090
 SXD  H31   C31   single  0.970  0.020  1.090
 SXD  H31B  C31   single  0.970  0.020  1.090
 SXD  C31   H31A  single  0.970  0.020  1.090
 SXD  H32   C32   single  0.970  0.020  1.090
 SXD  O33   C32   single  1.401  0.020  1.401
 SXD  C32   C34   single  1.530  0.020  1.530
 SXD  O33   HO33  single  0.850  0.020  0.980
 SXD  C34   O35   double  1.226  0.020  1.226
 SXD  C34   N36   single  1.334  0.020  1.334
 SXD  HN36  N36   single  0.860  0.020  1.020
 SXD  N36   C37   single  1.450  0.020  1.450
 SXD  H37A  C37   single  0.970  0.020  1.090
 SXD  C37   C38   single  1.520  0.020  1.520
 SXD  C37   H37   single  0.970  0.020  1.090
 SXD  C39   C38   single  1.514  0.020  1.514
 SXD  C38   H38   single  0.970  0.020  1.090
 SXD  C38   H38A  single  0.970  0.020  1.090
 SXD  N41   C39   single  1.343  0.020  1.343
 SXD  O40   C39   double  1.223  0.020  1.223
 SXD  C42   N41   single  1.444  0.020  1.444
 SXD  N41   HN41  single  0.860  0.020  1.020
 SXD  C43   C42   single  1.525  0.020  1.525
 SXD  H42A  C42   single  0.970  0.020  1.090
 SXD  H42   C42   single  0.970  0.020  1.090
 SXD  S1    C43   single  1.815  0.020  1.815
 SXD  C43   H43A  single  0.970  0.020  1.090
 SXD  C43   H43   single  0.970  0.020  1.090
 SXD  C1    S1    single  1.815  0.020  1.815
 SXD  H1    C1    single  0.970  0.020  1.090
 SXD  C1    C2    single  1.517  0.020  1.517
 SXD  C1    H1A   single  0.970  0.020  1.090
 SXD  C3    C2    single  1.504  0.020  1.504
 SXD  H2    C2    single  0.970  0.020  1.090
 SXD  C2    H2A   single  0.970  0.020  1.090
 SXD  C4    C3    single  1.512  0.020  1.512
 SXD  C3    O3    double  1.208  0.020  1.208
 SXD  H4A   C4    single  0.970  0.020  1.090
 SXD  H4    C4    single  0.970  0.020  1.090
 SXD  C4    C5    single  1.516  0.020  1.516
 SXD  C5    O5    double  1.209  0.020  1.209
 SXD  C5    C6    single  1.499  0.020  1.499
 SXD  H6B   C6    single  0.970  0.020  1.090
 SXD  H6    C6    single  0.970  0.020  1.090
 SXD  C6    H6A   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
 SXD  HO25  O25  P24   115.79  3.000
 SXD  O27   P24  O23   116.68  3.000
 SXD  O27   P24  O26    96.78  3.000
 SXD  O23   P24  O26   117.92  3.000
 SXD  O26   P24  O25   107.86  3.000
 SXD  O27   P24  O25   107.05  3.000
 SXD  O23   P24  O25   109.45  3.000
 SXD  HO26  O26  P24   114.12  3.000
 SXD  C28   O27  P24   119.55  3.000
 SXD  H28A  C28  H28   108.29  3.000
 SXD  H28   C28  C29   111.18  3.000
 SXD  H28A  C28  C29   110.20  3.000
 SXD  H28   C28  O27   109.03  3.000
 SXD  H28A  C28  O27   109.51  3.000
 SXD  C29   C28  O27   108.60  3.000
 SXD  C32   C29  C31   109.94  3.000
 SXD  C32   C29  C30   107.65  3.000
 SXD  C31   C29  C30   109.05  3.000
 SXD  C30   C29  C28   110.25  3.000
 SXD  C32   C29  C28   109.52  3.000
 SXD  C31   C29  C28   110.38  3.000
 SXD  H30B  C30  H30A  107.99  3.000
 SXD  H30A  C30  H30   107.75  3.000
 SXD  H30B  C30  H30   107.30  3.000
 SXD  H30A  C30  C29   112.09  3.000
 SXD  H30B  C30  C29   111.07  3.000
 SXD  H30   C30  C29   110.45  3.000
 SXD  H31B  C31  H31A  107.89  3.000
 SXD  H31A  C31  H31   107.57  3.000
 SXD  H31B  C31  H31   107.12  3.000
 SXD  H31A  C31  C29   112.55  3.000
 SXD  H31B  C31  C29   110.82  3.000
 SXD  H31   C31  C29   110.68  3.000
 SXD  H32   C32  C34   109.26  3.000
 SXD  C34   C32  O33   108.51  3.000
 SXD  H32   C32  O33   107.17  3.000
 SXD  C34   C32  C29   112.94  3.000
 SXD  O33   C32  C29   112.63  3.000
 SXD  H32   C32  C29   106.13  3.000
 SXD  HO33  O33  C32   107.80  3.000
 SXD  N36   C34  O35   123.30  3.000
 SXD  N36   C34  C32   116.90  3.000
 SXD  O35   C34  C32   119.80  3.000
 SXD  HN36  N36  C37   118.32  3.000
 SXD  C37   N36  C34   122.71  3.000
 SXD  HN36  N36  C34   118.75  3.000
 SXD  H37A  C37  H37   107.37  3.000
 SXD  H37   C37  C38   110.09  3.000
 SXD  H37A  C37  C38   109.93  3.000
 SXD  H37   C37  N36   110.19  3.000
 SXD  C38   C37  N36   110.02  3.000
 SXD  H37A  C37  N36   109.19  3.000
 SXD  H38A  C38  H38   106.86  3.000
 SXD  H38A  C38  C39   107.09  3.000
 SXD  H38   C38  C39   111.39  3.000
 SXD  H38A  C38  C37   109.85  3.000
 SXD  H38   C38  C37   110.27  3.000
 SXD  C39   C38  C37   111.22  3.000
 SXD  N41   C39  O40   122.93  3.000
 SXD  O40   C39  C38   121.76  3.000
 SXD  N41   C39  C38   115.31  3.000
 SXD  HN41  N41  C42   117.74  3.000
 SXD  HN41  N41  C39   118.95  3.000
 SXD  C42   N41  C39   123.03  3.000
 SXD  H42A  C42  H42   107.34  3.000
 SXD  H42   C42  C43   110.40  3.000
 SXD  H42A  C42  C43   110.06  3.000
 SXD  H42   C42  N41   109.05  3.000
 SXD  H42A  C42  N41   108.09  3.000
 SXD  C43   C42  N41   111.77  3.000
 SXD  H43A  C43  H43   108.33  3.000
 SXD  H43   C43  S1    109.12  3.000
 SXD  H43A  C43  S1    109.45  3.000
 SXD  H43   C43  C42   110.09  3.000
 SXD  H43A  C43  C42   110.36  3.000
 SXD  S1    C43  C42   109.46  3.000
 SXD  C1    S1   C43    99.32  3.000
 SXD  H1A   C1   H1    108.04  3.000
 SXD  H1A   C1   C2    110.74  3.000
 SXD  H1    C1   C2    110.90  3.000
 SXD  H1A   C1   S1    109.14  3.000
 SXD  C2    C1   S1    109.08  3.000
 SXD  H1    C1   S1    108.89  3.000
 SXD  H2A   C2   H2    105.17  3.000
 SXD  H2A   C2   C3    108.21  3.000
 SXD  H2    C2   C3    107.24  3.000
 SXD  H2A   C2   C1    111.19  3.000
 SXD  H2    C2   C1    110.92  3.000
 SXD  C3    C2   C1    113.67  3.000
 SXD  C4    C3   O3    121.24  3.000
 SXD  O3    C3   C2    122.81  3.000
 SXD  C4    C3   C2    115.95  3.000
 SXD  H4A   C4   H4    106.67  3.000
 SXD  H4    C4   C5    108.88  3.000
 SXD  H4A   C4   C5    107.89  3.000
 SXD  C5    C4   C3    111.26  3.000
 SXD  H4    C4   C3    110.34  3.000
 SXD  H4A   C4   C3    111.64  3.000
 SXD  C6    C5   O5    123.26  3.000
 SXD  C6    C5   C4    115.39  3.000
 SXD  O5    C5   C4    121.34  3.000
 SXD  H6B   C6   H6A   109.65  3.000
 SXD  H6A   C6   H6    106.63  3.000
 SXD  H6B   C6   H6    109.03  3.000
 SXD  H6A   C6   C5    110.59  3.000
 SXD  H6    C6   C5    109.33  3.000
 SXD  H6B   C6   C5    111.48  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
 SXD  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SXD  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SXD  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SXD  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SXD  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SXD  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SXD  Var_01    C29   C28  O27  P24   175.24  30.0  3
 SXD  Var_02    C31   C29  C28  O27    62.12  30.0  1
 SXD  Var_03    C38   C37  N36  C34   168.89  30.0  3
 SXD  Var_04    C39   C38  C37  N36   175.20  30.0  3
 SXD  Var_05    N41   C39  C38  C37   138.61  30.0  1
 SXD  Var_06    C43   C42  N41  C39   -86.31  30.0  1
 SXD  Var_07    S1    C43  C42  N41   177.85  30.0  1
 SXD  Var_08    C2    C1   S1   C43   178.72  30.0  1
 SXD  Var_09    C3    C2   C1   S1   -179.78  30.0  3
 SXD  Var_10    C4    C3   C2   C1   -174.75  30.0  1
 SXD  Var_11    C5    C4   C3   C2     89.94  30.0  1
 SXD  Var_12    O5    C5   C4   C3     -6.01  30.0  3
 SXD  Var_13    H31   C31  C29  C28   -65.44  30.0  3
 SXD  Var_14    H30   C30  C29  C28  -175.09  30.0  3
 SXD  Var_15    H6B   C6   C5   C4    173.73  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
 SXD  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
 SXD  plan-1  C32   0.020
 SXD  plan-1  C34   0.020
 SXD  plan-1  O35   0.020
 SXD  plan-1  N36   0.020
 SXD  plan-1  C37   0.020
 SXD  plan-1  HN36  0.020
 SXD  plan-2  C38   0.020
 SXD  plan-2  C39   0.020
 SXD  plan-2  O40   0.020
 SXD  plan-2  N41   0.020
 SXD  plan-2  C42   0.020
 SXD  plan-2  HN41  0.020
 SXD  plan-3  C2    0.020
 SXD  plan-3  C3    0.020
 SXD  plan-3  O3    0.020
 SXD  plan-3  C4    0.020
 SXD  plan-4  C4    0.020
 SXD  plan-4  C5    0.020
 SXD  plan-4  O5    0.020
 SXD  plan-4  C6    0.020

