# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 12:46:54 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(3-oxobutyl)sulfanyl]ethyl}-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 SXV  SXV  N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(3-oxobutyl)sulfanyl]ethyl}-beta-alaninamide  ligand  56  27  .  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_SXV
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
 SXV  O25   O  O     0  -0.713  -5.4356   2.9102   1.4315
 SXV  P24   P  P     0   1.456  -6.1068   2.5968   0.1561
 SXV  O26   O  OH1   0  -0.743  -7.6251   2.1820   0.4395
 SXV  O23   O  OH1   0  -0.732  -6.1107   3.7168  -0.9783
 SXV  O27   O  O2    0  -0.588  -5.4648   1.4376  -0.7279
 SXV  C28   C  CH2   0  -0.149  -5.1488   0.1748  -0.1269
 SXV  C29   C  CT    0  -0.165  -4.5637  -0.7400  -1.2014
 SXV  C30   C  CH3   0  -0.647  -5.5820  -0.9716  -2.3215
 SXV  C31   C  CH3   0  -0.668  -3.2993  -0.1178  -1.7996
 SXV  C32   C  CH1   0  -0.033  -4.2322  -2.1250  -0.5748
 SXV  O33   O  OH1   0  -0.662  -5.3632  -2.7531  -0.0361
 SXV  C34   C  C     0   0.518  -3.1548  -2.0514   0.5089
 SXV  O35   O  O     0  -0.499  -3.4756  -1.8768   1.6798
 SXV  N36   N  NH1   0  -0.636  -1.8917  -2.1861   0.1047
 SXV  C37   C  CH2   0  -0.236  -0.7544  -2.0840   0.9984
 SXV  C38   C  CH2   0  -0.635   0.5081  -1.8854   0.1792
 SXV  C39   C  C     0   0.572   1.7451  -1.7453   1.0423
 SXV  O40   O  O     0  -0.498   1.7513  -2.0018   2.2376
 SXV  N41   N  NH1   0  -0.645   2.8366  -1.3227   0.3862
 SXV  C42   C  CH2   0  -0.238   4.1251  -1.1658   1.0266
 SXV  C43   C  CH2   0  -0.591   5.0894  -0.4954   0.0617
 SXV  S1    S  S2    0  -0.024   6.6976  -0.2838   0.8694
 SXV  C1    C  CH2   0  -0.544   7.6001   0.5182  -0.4857
 SXV  C2    C  CH2   0  -0.560   9.0064   0.8439  -0.0180
 SXV  C3    C  C     0   0.404   9.8441   1.5442  -1.0599
 SXV  O3    O  O     0  -0.404   9.3775   1.9266  -2.1090
 SXV  C4    C  CH3   0  -0.769  11.2960   1.7179  -0.7135
 SXV  H28   H  HCH2  0   0.248  -4.4327   0.3314   0.6825
 SXV  H28A  H  HCH2  0   0.241  -6.0564  -0.2651   0.2963
 SXV  H30   H  HCH3  0   0.240  -5.8479  -0.0347  -2.8102
 SXV  H30A  H  HCH3  0   0.231  -5.1599  -1.6286  -3.0848
 SXV  H30B  H  HCH3  0   0.236  -6.4991  -1.4315  -1.9533
 SXV  H31   H  HCH3  0   0.235  -2.5824   0.1913  -1.0379
 SXV  H31A  H  HCH3  0   0.233  -2.7974  -0.8244  -2.4651
 SXV  H31B  H  HCH3  0   0.249  -3.5473   0.7599  -2.3950
 SXV  H32   H  HCH1  0   0.257  -3.8687  -2.7525  -1.3985
 SXV  HO33  H  HOH1  0   0.446  -5.3968  -2.5410   0.9059
 SXV  HN36  H  HNH1  0   0.407  -1.7176  -2.4125  -0.8616
 SXV  H37   H  HCH2  0   0.251  -0.9058  -1.2406   1.6727
 SXV  H37A  H  HCH2  0   0.249  -0.6751  -2.9817   1.6150
 SXV  H38   H  HCH2  0   0.288   0.6565  -2.7352  -0.4956
 SXV  H38A  H  HCH2  0   0.278   0.4088  -1.0026  -0.4587
 SXV  HN41  H  HNH1  0   0.406   2.7742  -1.1637  -0.6071
 SXV  H42   H  HCH2  0   0.248   4.0161  -0.5557   1.9255
 SXV  H42A  H  HCH2  0   0.245   4.5221  -2.1361   1.3381
 SXV  H43   H  HCH2  0   0.274   5.2152  -1.1057  -0.8354
 SXV  H43A  H  HCH2  0   0.275   4.7049   0.4811  -0.2397
 SXV  H1    H  HCH2  0   0.271   7.6247  -0.1526  -1.3459
 SXV  H1A   H  HCH2  0   0.271   7.0691   1.4251  -0.7770
 SXV  H2    H  HCH2  0   0.284   8.9807   1.4903   0.8664
 SXV  H2A   H  HCH2  0   0.277   9.5371  -0.0592   0.2998
 SXV  H4    H  HCH3  0   0.259  11.4291   1.9793   0.3361
 SXV  H4A   H  HCH3  0   0.273  11.8100   0.7660  -0.8693
 SXV  H4B   H  HCH3  0   0.262  11.7678   2.4701  -1.3422
 SXV  HO26  H  HOH1  0   0.495  -8.1646   2.0040  -0.3425
 SXV  HO23  H  HOH1  0   0.503  -6.3592   4.5960  -0.6631

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
 SXV  O25   P24   double  1.475  0.020  1.475
 SXV  O26   P24   single  1.599  0.020  1.599
 SXV  P24   O27   single  1.593  0.020  1.593
 SXV  P24   O23   single  1.594  0.020  1.594
 SXV  O26   HO26  single  0.850  0.020  0.980
 SXV  O23   HO23  single  0.850  0.020  0.980
 SXV  O27   C28   single  1.434  0.020  1.434
 SXV  H28   C28   single  0.970  0.020  1.090
 SXV  C29   C28   single  1.528  0.020  1.528
 SXV  C28   H28A  single  0.970  0.020  1.090
 SXV  C31   C29   single  1.531  0.020  1.531
 SXV  C29   C30   single  1.531  0.020  1.531
 SXV  C29   C32   single  1.556  0.020  1.556
 SXV  H30B  C30   single  0.970  0.020  1.090
 SXV  H30A  C30   single  0.970  0.020  1.090
 SXV  C30   H30   single  0.970  0.020  1.090
 SXV  H31B  C31   single  0.970  0.020  1.090
 SXV  H31A  C31   single  0.970  0.020  1.090
 SXV  H31   C31   single  0.970  0.020  1.090
 SXV  O33   C32   single  1.401  0.020  1.401
 SXV  C34   C32   single  1.530  0.020  1.530
 SXV  C32   H32   single  0.970  0.020  1.090
 SXV  O33   HO33  single  0.850  0.020  0.980
 SXV  N36   C34   single  1.333  0.020  1.333
 SXV  C34   O35   double  1.227  0.020  1.227
 SXV  C37   N36   single  1.450  0.020  1.450
 SXV  HN36  N36   single  0.860  0.020  1.020
 SXV  C38   C37   single  1.518  0.020  1.518
 SXV  H37A  C37   single  0.970  0.020  1.090
 SXV  C37   H37   single  0.970  0.020  1.090
 SXV  H38A  C38   single  0.970  0.020  1.090
 SXV  H38   C38   single  0.970  0.020  1.090
 SXV  C38   C39   single  1.515  0.020  1.515
 SXV  N41   C39   single  1.342  0.020  1.342
 SXV  C39   O40   double  1.223  0.020  1.223
 SXV  HN41  N41   single  0.860  0.020  1.020
 SXV  N41   C42   single  1.447  0.020  1.447
 SXV  C43   C42   single  1.520  0.020  1.520
 SXV  H42A  C42   single  0.970  0.020  1.090
 SXV  C42   H42   single  0.970  0.020  1.090
 SXV  H43A  C43   single  0.970  0.020  1.090
 SXV  S1    C43   single  1.812  0.020  1.812
 SXV  C43   H43   single  0.970  0.020  1.090
 SXV  C1    S1    single  1.815  0.020  1.815
 SXV  H1A   C1    single  0.970  0.020  1.090
 SXV  C2    C1    single  1.517  0.020  1.517
 SXV  C1    H1    single  0.970  0.020  1.090
 SXV  C3    C2    single  1.509  0.020  1.509
 SXV  H2    C2    single  0.970  0.020  1.090
 SXV  C2    H2A   single  0.970  0.020  1.090
 SXV  O3    C3    double  1.210  0.020  1.210
 SXV  C3    C4    single  1.503  0.020  1.503
 SXV  H4A   C4    single  0.970  0.020  1.090
 SXV  H4B   C4    single  0.970  0.020  1.090
 SXV  C4    H4    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
 SXV  O27   P24  O23    96.74  3.000
 SXV  O23   P24  O26   107.82  3.000
 SXV  O27   P24  O26   107.00  3.000
 SXV  O23   P24  O25   117.85  3.000
 SXV  O27   P24  O25   116.81  3.000
 SXV  O26   P24  O25   109.50  3.000
 SXV  HO26  O26  P24   115.74  3.000
 SXV  HO23  O23  P24   114.06  3.000
 SXV  C28   O27  P24   119.81  3.000
 SXV  H28A  C28  H28   108.36  3.000
 SXV  H28A  C28  C29   110.43  3.000
 SXV  H28   C28  C29   110.86  3.000
 SXV  H28A  C28  O27   109.49  3.000
 SXV  C29   C28  O27   108.48  3.000
 SXV  H28   C28  O27   109.20  3.000
 SXV  C32   C29  C31   110.07  3.000
 SXV  C32   C29  C30   107.56  3.000
 SXV  C31   C29  C30   108.96  3.000
 SXV  C32   C29  C28   109.36  3.000
 SXV  C30   C29  C28   110.50  3.000
 SXV  C31   C29  C28   110.35  3.000
 SXV  H30B  C30  H30A  107.90  3.000
 SXV  H30A  C30  H30   107.34  3.000
 SXV  H30B  C30  H30   108.00  3.000
 SXV  H30   C30  C29   111.12  3.000
 SXV  H30A  C30  C29   110.20  3.000
 SXV  H30B  C30  C29   112.10  3.000
 SXV  H31B  C31  H31A  107.02  3.000
 SXV  H31A  C31  H31   107.86  3.000
 SXV  H31B  C31  H31   107.64  3.000
 SXV  H31   C31  C29   112.65  3.000
 SXV  H31A  C31  C29   110.77  3.000
 SXV  H31B  C31  C29   110.67  3.000
 SXV  H32   C32  C34   109.03  3.000
 SXV  H32   C32  O33   107.43  3.000
 SXV  C34   C32  O33   108.52  3.000
 SXV  H32   C32  C29   106.10  3.000
 SXV  C34   C32  C29   113.11  3.000
 SXV  O33   C32  C29   112.45  3.000
 SXV  HO33  O33  C32   107.73  3.000
 SXV  N36   C34  O35   123.49  3.000
 SXV  O35   C34  C32   119.93  3.000
 SXV  N36   C34  C32   116.59  3.000
 SXV  HN36  N36  C37   118.12  3.000
 SXV  HN36  N36  C34   118.51  3.000
 SXV  C37   N36  C34   123.31  3.000
 SXV  H37A  C37  H37   107.26  3.000
 SXV  H37   C37  C38   110.36  3.000
 SXV  H37A  C37  C38   110.61  3.000
 SXV  H37   C37  N36   109.07  3.000
 SXV  H37A  C37  N36   110.31  3.000
 SXV  C38   C37  N36   109.20  3.000
 SXV  H38A  C38  H38   106.22  3.000
 SXV  H38   C38  C39   108.19  3.000
 SXV  H38A  C38  C39   109.38  3.000
 SXV  C39   C38  C37   112.56  3.000
 SXV  H38   C38  C37   110.10  3.000
 SXV  H38A  C38  C37   110.17  3.000
 SXV  N41   C39  O40   122.69  3.000
 SXV  O40   C39  C38   122.81  3.000
 SXV  N41   C39  C38   114.50  3.000
 SXV  HN41  N41  C42   118.30  3.000
 SXV  C42   N41  C39   122.81  3.000
 SXV  HN41  N41  C39   118.77  3.000
 SXV  H42A  C42  H42   107.31  3.000
 SXV  H42   C42  C43   109.84  3.000
 SXV  H42A  C42  C43   109.98  3.000
 SXV  H42   C42  N41   109.63  3.000
 SXV  H42A  C42  N41   110.68  3.000
 SXV  C43   C42  N41   109.37  3.000
 SXV  H43A  C43  H43   108.27  3.000
 SXV  H43   C43  S1    109.22  3.000
 SXV  H43A  C43  S1    109.33  3.000
 SXV  H43   C43  C42   110.37  3.000
 SXV  S1    C43  C42   109.37  3.000
 SXV  H43A  C43  C42   110.26  3.000
 SXV  C1    S1   C43    99.22  3.000
 SXV  H1A   C1   H1    108.16  3.000
 SXV  H1    C1   C2    110.74  3.000
 SXV  H1A   C1   C2    110.80  3.000
 SXV  H1    C1   S1    109.16  3.000
 SXV  C2    C1   S1    109.00  3.000
 SXV  H1A   C1   S1    108.95  3.000
 SXV  H2A   C2   H2    105.29  3.000
 SXV  H2A   C2   C3    108.31  3.000
 SXV  H2    C2   C3    107.25  3.000
 SXV  H2A   C2   C1    111.20  3.000
 SXV  H2    C2   C1    110.71  3.000
 SXV  C3    C2   C1    113.66  3.000
 SXV  C4    C3   O3    122.40  3.000
 SXV  C4    C3   C2    115.52  3.000
 SXV  O3    C3   C2    122.08  3.000
 SXV  H4B   C4   H4A   108.41  3.000
 SXV  H4B   C4   H4    109.74  3.000
 SXV  H4A   C4   H4    106.78  3.000
 SXV  H4    C4   C3    111.57  3.000
 SXV  H4B   C4   C3    111.45  3.000
 SXV  H4A   C4   C3    108.71  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
 SXV  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SXV  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SXV  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SXV  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SXV  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SXV  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SXV  Var_01    C29   C28  O27  P24   179.49  30.0  3
 SXV  Var_02    C31   C29  C28  O27    59.60  30.0  1
 SXV  Var_03    C38   C37  N36  C34  -163.79  30.0  2
 SXV  Var_04    C39   C38  C37  N36   179.03  30.0  1
 SXV  Var_05    N41   C39  C38  C37  -168.18  30.0  3
 SXV  Var_06    C43   C42  N41  C39  -172.27  30.0  3
 SXV  Var_07    S1    C43  C42  N41   179.43  30.0  2
 SXV  Var_08    C2    C1   S1   C43   178.20  30.0  1
 SXV  Var_09    C3    C2   C1   S1   -178.77  30.0  1
 SXV  Var_10    O3    C3   C2   C1      7.33  30.0  1
 SXV  Var_11    H31B  C31  C29  C28   -69.44  30.0  3
 SXV  Var_12    H30B  C30  C29  C28   -59.61  30.0  3
 SXV  Var_13    H4A   C4   C3   C2     77.64  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
 SXV  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
 SXV  plan-1  C32   0.020
 SXV  plan-1  C34   0.020
 SXV  plan-1  O35   0.020
 SXV  plan-1  N36   0.020
 SXV  plan-1  C37   0.020
 SXV  plan-1  HN36  0.020
 SXV  plan-2  C38   0.020
 SXV  plan-2  C39   0.020
 SXV  plan-2  O40   0.020
 SXV  plan-2  N41   0.020
 SXV  plan-2  C42   0.020
 SXV  plan-2  HN41  0.020
 SXV  plan-3  C2    0.020
 SXV  plan-3  C3    0.020
 SXV  plan-3  O3    0.020
 SXV  plan-3  C4    0.020

