# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 04:57:22 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] (2E)-oct-2-enethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC/C=C/C(=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
 SOO  SOO  'S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (2E)-oct-2-enethioate'  ligand  66  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_SOO
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
 SOO  C1    C  C     0   0.226   -6.2398   0.0492   0.0607
 SOO  O1    O  O     0  -0.401   -5.8243   0.2845   1.1708
 SOO  S1    S  S2    0  -0.004   -5.2355  -0.6841  -1.2020
 SOO  C2    C  C1    0  -0.344   -7.6018   0.3246  -0.4180
 SOO  C3    C  C1    0  -0.124   -8.5273   0.8746   0.3720
 SOO  C4    C  CH2   0  -0.495   -9.9223   1.1778  -0.0460
 SOO  C5    C  CH2   0  -0.421  -10.9531   0.3846   0.7623
 SOO  C6    C  CH2   0  -0.409  -12.3826   0.7512   0.3837
 SOO  C7    C  CH2   0  -0.422  -13.4298  -0.0394   1.1581
 SOO  C8    C  CH3   0  -0.662  -14.8533   0.3398   0.7728
 SOO  O23   O  O     0  -0.712    8.1320   2.7426  -1.4262
 SOO  P24   P  P     0   1.453    8.5509   2.3039  -0.0821
 SOO  O26   O  OH1   0  -0.732    8.7543   3.4192   1.0387
 SOO  O27   O  O2    0  -0.588    7.5233   1.4008   0.7328
 SOO  O28   O  OH1   0  -0.742    9.9125   1.4717  -0.1953
 SOO  C29   C  CT    0  -0.162    6.2496  -0.5921   1.1613
 SOO  C30   C  CH3   0  -0.650    7.3015  -1.0960   2.1538
 SOO  C31   C  CH3   0  -0.671    5.1857   0.2066   1.9189
 SOO  C32   C  CH1   0  -0.035    5.6035  -1.8399   0.4953
 SOO  O33   O  OH1   0  -0.661    6.5371  -2.6274  -0.1923
 SOO  C34   C  C     0   0.521    4.4627  -1.4950  -0.4626
 SOO  O35   O  O     0  -0.499    4.7000  -1.2843  -1.6475
 SOO  N36   N  NH1   0  -0.639    3.2341  -1.4590   0.0540
 SOO  C37   C  CH2   0  -0.236    2.0619  -1.1421  -0.7378
 SOO  C38   C  CH2   0  -0.626    0.8072  -1.3669   0.0916
 SOO  C39   C  C     0   0.564   -0.4386  -1.0308  -0.6992
 SOO  O40   O  O     0  -0.495   -0.5171  -0.0193  -1.3813
 SOO  N41   N  NH1   0  -0.631   -1.4426  -1.9172  -0.5890
 SOO  C42   C  CH2   0  -0.291   -2.7292  -1.7309  -1.2137
 SOO  C43   C  CH2   0  -0.559   -3.6589  -0.9005  -0.3332
 SOO  H2    H  H     0   0.274   -7.8347   0.0671  -1.4461
 SOO  H3    H  H     0   0.270   -8.2677   1.1183   1.3987
 SOO  H4    H  HCH2  0   0.249  -10.1030   2.2474   0.1081
 SOO  H4A   H  HCH2  0   0.244  -10.0517   0.9801  -1.1127
 SOO  H5    H  HCH2  0   0.225  -10.7926  -0.6854   0.6008
 SOO  H5A   H  HCH2  0   0.224  -10.7999   0.5645   1.8309
 SOO  H6    H  HCH2  0   0.212  -12.5361   1.8226   0.5526
 SOO  H6A   H  HCH2  0   0.212  -12.5254   0.5879  -0.6900
 SOO  H7    H  HCH2  0   0.213  -13.2766  -1.1093   0.9866
 SOO  H7A   H  HCH2  0   0.213  -13.2855   0.1202   2.2311
 SOO  H8    H  HCH3  0   0.217  -15.0449   1.3967   0.9661
 SOO  H8A   H  HCH3  0   0.216  -15.0341   0.1613  -0.2887
 SOO  H8B   H  HCH3  0   0.227  -15.5888  -0.2372   1.3344
 SOO  HO26  H  HOH1  0   0.504    9.2882   4.1725   0.7528
 SOO  H28   H  HCH2  0   0.251    6.1665   0.6490  -0.6239
 SOO  H28A  H  HCH2  0   0.241    7.6535  -0.3004  -0.4597
 SOO  HO28  H  HOH1  0   0.494   10.3020   1.1861   0.6417
 SOO  H30   H  HCH3  0   0.240    7.7821  -0.2676   2.6731
 SOO  H30A  H  HCH3  0   0.232    6.8338  -1.7300   2.9100
 SOO  H30B  H  HCH3  0   0.236    8.0767  -1.6826   1.6606
 SOO  H31   H  HCH3  0   0.236    4.4946   0.7229   1.2518
 SOO  H31A  H  HCH3  0   0.234    4.6000  -0.4449   2.5710
 SOO  H31B  H  HCH3  0   0.249    5.6506   0.9591   2.5548
 SOO  H32   H  HCH1  0   0.258    5.2083  -2.4497   1.3160
 SOO  HO33  H  HOH1  0   0.447    6.5498  -2.3351  -1.1129
 SOO  HN36  H  HNH1  0   0.409    3.1110  -1.6738   1.0310
 SOO  H37   H  HCH2  0   0.251    2.1065  -0.1075  -1.0813
 SOO  H37A  H  HCH2  0   0.252    2.0424  -1.7804  -1.6237
 SOO  H38   H  HCH2  0   0.270    0.7775  -2.3955   0.4568
 SOO  H38A  H  HCH2  0   0.285    0.8213  -0.7156   0.9715
 SOO  HN41  H  HNH1  0   0.408   -1.3231  -2.7182   0.0093
 SOO  H42   H  HCH2  0   0.260   -2.5890  -1.2529  -2.1832
 SOO  H42A  H  HCH2  0   0.271   -3.1622  -2.7141  -1.3956
 SOO  H43   H  HCH2  0   0.288   -3.2240   0.0774  -0.1291
 SOO  H43A  H  HCH2  0   0.287   -3.8422  -1.4074   0.6137
 SOO  C28   C  CH2   0  -0.151    6.9042   0.2775   0.0899

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
 SOO  C1   O1    double  1.208  0.020  1.208
 SOO  C1   S1    single  1.772  0.020  1.772
 SOO  C1   C2    single  1.470  0.020  1.470
 SOO  S1   C43   single  1.813  0.020  1.813
 SOO  C2   C3    double  1.335  0.020  1.335
 SOO  C3   C4    single  1.488  0.020  1.488
 SOO  C4   C5    single  1.531  0.020  1.531
 SOO  C5   C6    single  1.524  0.020  1.524
 SOO  C6   C7    single  1.524  0.020  1.524
 SOO  C7   C8    single  1.523  0.020  1.523
 SOO  O23  P24   double  1.475  0.020  1.475
 SOO  P24  O26   single  1.594  0.020  1.594
 SOO  P24  O27   single  1.592  0.020  1.592
 SOO  P24  O28   single  1.600  0.020  1.600
 SOO  O27  C28   single  1.435  0.020  1.435
 SOO  C28  C29   single  1.527  0.020  1.527
 SOO  C29  C30   single  1.531  0.020  1.531
 SOO  C29  C31   single  1.531  0.020  1.531
 SOO  C29  C32   single  1.555  0.020  1.555
 SOO  C32  O33   single  1.402  0.020  1.402
 SOO  C32  C34   single  1.529  0.020  1.529
 SOO  C34  O35   double  1.227  0.020  1.227
 SOO  C34  N36   single  1.333  0.020  1.333
 SOO  N36  C37   single  1.450  0.020  1.450
 SOO  C37  C38   single  1.521  0.020  1.521
 SOO  C38  C39   single  1.513  0.020  1.513
 SOO  C39  O40   double  1.223  0.020  1.223
 SOO  C39  N41   single  1.344  0.020  1.344
 SOO  N41  C42   single  1.442  0.020  1.442
 SOO  C42  C43   single  1.526  0.020  1.526
 SOO  C2   H2    single  0.930  0.020  1.080
 SOO  C3   H3    single  0.930  0.020  1.080
 SOO  C4   H4    single  0.970  0.020  1.090
 SOO  C4   H4A   single  0.970  0.020  1.090
 SOO  C5   H5    single  0.970  0.020  1.090
 SOO  C5   H5A   single  0.970  0.020  1.090
 SOO  C6   H6    single  0.970  0.020  1.090
 SOO  C6   H6A   single  0.970  0.020  1.090
 SOO  C7   H7    single  0.970  0.020  1.090
 SOO  C7   H7A   single  0.970  0.020  1.090
 SOO  C8   H8    single  0.970  0.020  1.090
 SOO  C8   H8A   single  0.970  0.020  1.090
 SOO  C8   H8B   single  0.970  0.020  1.090
 SOO  O26  HO26  single  0.850  0.020  0.980
 SOO  C28  H28   single  0.970  0.020  1.090
 SOO  C28  H28A  single  0.970  0.020  1.090
 SOO  O28  HO28  single  0.850  0.020  0.980
 SOO  C30  H30   single  0.970  0.020  1.090
 SOO  C30  H30A  single  0.970  0.020  1.090
 SOO  C30  H30B  single  0.970  0.020  1.090
 SOO  C31  H31   single  0.970  0.020  1.090
 SOO  C31  H31A  single  0.970  0.020  1.090
 SOO  C31  H31B  single  0.970  0.020  1.090
 SOO  C32  H32   single  0.970  0.020  1.090
 SOO  O33  HO33  single  0.850  0.020  0.980
 SOO  N36  HN36  single  0.860  0.020  1.020
 SOO  C37  H37   single  0.970  0.020  1.090
 SOO  C37  H37A  single  0.970  0.020  1.090
 SOO  C38  H38   single  0.970  0.020  1.090
 SOO  C38  H38A  single  0.970  0.020  1.090
 SOO  N41  HN41  single  0.860  0.020  1.020
 SOO  C42  H42   single  0.970  0.020  1.090
 SOO  C42  H42A  single  0.970  0.020  1.090
 SOO  C43  H43   single  0.970  0.020  1.090
 SOO  C43  H43A  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
 SOO  C2    C1   S1    111.75  3.000
 SOO  C2    C1   O1    125.54  3.000
 SOO  S1    C1   O1    122.71  3.000
 SOO  C43   S1   C1    101.58  3.000
 SOO  H2    C2   C3    120.63  3.000
 SOO  H2    C2   C1    117.58  3.000
 SOO  C3    C2   C1    121.79  3.000
 SOO  H3    C3   C4    116.35  3.000
 SOO  H3    C3   C2    119.06  3.000
 SOO  C4    C3   C2    124.59  3.000
 SOO  H4A   C4   H4    107.12  3.000
 SOO  H4A   C4   C5    109.99  3.000
 SOO  H4    C4   C5    108.69  3.000
 SOO  H4A   C4   C3    110.40  3.000
 SOO  H4    C4   C3    108.31  3.000
 SOO  C5    C4   C3    112.17  3.000
 SOO  H5A   C5   H5    106.52  3.000
 SOO  H5A   C5   C6    109.54  3.000
 SOO  H5    C5   C6    109.65  3.000
 SOO  H5A   C5   C4    109.63  3.000
 SOO  H5    C5   C4    109.27  3.000
 SOO  C6    C5   C4    112.07  3.000
 SOO  H6A   C6   H6    106.18  3.000
 SOO  H6A   C6   C7    109.35  3.000
 SOO  H6    C6   C7    109.44  3.000
 SOO  H6A   C6   C5    109.27  3.000
 SOO  H6    C6   C5    109.18  3.000
 SOO  C7    C6   C5    113.19  3.000
 SOO  H7A   C7   H7    106.13  3.000
 SOO  H7A   C7   C8    109.57  3.000
 SOO  H7    C7   C8    109.56  3.000
 SOO  H7A   C7   C6    109.39  3.000
 SOO  H7    C7   C6    109.36  3.000
 SOO  C8    C7   C6    112.63  3.000
 SOO  H8B   C8   H8A   107.62  3.000
 SOO  H8B   C8   H8    107.63  3.000
 SOO  H8A   C8   H8    107.55  3.000
 SOO  H8B   C8   C7    111.62  3.000
 SOO  H8A   C8   C7    111.11  3.000
 SOO  H8    C8   C7    111.13  3.000
 SOO  O28   P24  O27   106.89  3.000
 SOO  O28   P24  O26   107.76  3.000
 SOO  O27   P24  O26    96.85  3.000
 SOO  O28   P24  O23   109.39  3.000
 SOO  O27   P24  O23   116.86  3.000
 SOO  O26   P24  O23   117.96  3.000
 SOO  HO26  O26  P24   114.07  3.000
 SOO  C28   O27  P24   119.55  3.000
 SOO  HO28  O28  P24   115.81  3.000
 SOO  C32   C29  C31   109.99  3.000
 SOO  C32   C29  C30   107.40  3.000
 SOO  C31   C29  C30   109.16  3.000
 SOO  C32   C29  C28   109.54  3.000
 SOO  C31   C29  C28   110.36  3.000
 SOO  C30   C29  C28   110.34  3.000
 SOO  H30B  C30  H30A  107.79  3.000
 SOO  H30B  C30  H30   108.13  3.000
 SOO  H30A  C30  H30   107.48  3.000
 SOO  H30B  C30  C29   111.86  3.000
 SOO  H30A  C30  C29   110.22  3.000
 SOO  H30   C30  C29   111.20  3.000
 SOO  H31B  C31  H31A  107.00  3.000
 SOO  H31B  C31  H31   107.49  3.000
 SOO  H31A  C31  H31   107.93  3.000
 SOO  H31B  C31  C29   110.65  3.000
 SOO  H31A  C31  C29   110.91  3.000
 SOO  H31   C31  C29   112.62  3.000
 SOO  H32   C32  C34   109.00  3.000
 SOO  H32   C32  O33   107.15  3.000
 SOO  C34   C32  O33   108.44  3.000
 SOO  H32   C32  C29   106.00  3.000
 SOO  C34   C32  C29   113.41  3.000
 SOO  O33   C32  C29   112.59  3.000
 SOO  HO33  O33  C32   107.84  3.000
 SOO  N36   C34  O35   123.23  3.000
 SOO  N36   C34  C32   116.79  3.000
 SOO  O35   C34  C32   119.97  3.000
 SOO  HN36  N36  C37   118.51  3.000
 SOO  HN36  N36  C34   118.85  3.000
 SOO  C37   N36  C34   122.64  3.000
 SOO  H37A  C37  H37   107.43  3.000
 SOO  H37A  C37  C38   109.96  3.000
 SOO  H37   C37  C38   110.22  3.000
 SOO  H37A  C37  N36   109.25  3.000
 SOO  H37   C37  N36   110.26  3.000
 SOO  C38   C37  N36   109.69  3.000
 SOO  H38A  C38  H38   106.98  3.000
 SOO  H38A  C38  C39   107.37  3.000
 SOO  H38   C38  C39   111.19  3.000
 SOO  H38A  C38  C37   109.86  3.000
 SOO  H38   C38  C37   110.13  3.000
 SOO  C39   C38  C37   111.18  3.000
 SOO  N41   C39  O40   122.93  3.000
 SOO  N41   C39  C38   115.20  3.000
 SOO  O40   C39  C38   121.88  3.000
 SOO  HN41  N41  C42   117.77  3.000
 SOO  HN41  N41  C39   119.00  3.000
 SOO  C42   N41  C39   123.07  3.000
 SOO  H42A  C42  H42   107.36  3.000
 SOO  H42A  C42  C43   110.19  3.000
 SOO  H42   C42  C43   110.66  3.000
 SOO  H42A  C42  N41   108.08  3.000
 SOO  H42   C42  N41   109.10  3.000
 SOO  C43   C42  N41   111.33  3.000
 SOO  H43A  C43  H43   108.78  3.000
 SOO  H43A  C43  C42   110.53  3.000
 SOO  H43   C43  C42   110.68  3.000
 SOO  H43A  C43  S1    109.01  3.000
 SOO  H43   C43  S1    109.25  3.000
 SOO  C42   C43  S1    108.56  3.000
 SOO  H28A  C28  H28   108.30  3.000
 SOO  H28A  C28  C29   110.19  3.000
 SOO  H28   C28  C29   111.28  3.000
 SOO  H28A  C28  O27   110.07  3.000
 SOO  H28   C28  O27   108.55  3.000
 SOO  C29   C28  O27   108.44  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
 SOO  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SOO  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SOO  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SOO  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SOO  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SOO  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SOO  Var_01    C4    C3   C2   C1   -179.90   0.0  2
 SOO  Var_02    C42   C43  S1   C1    171.10  30.0  3
 SOO  Var_03    C3    C2   C1   O1     -0.30  30.0  2
 SOO  Var_04    N41   C42  C43  S1    178.83  30.0  1
 SOO  Var_05    C5    C4   C3   C2    117.43  30.0  3
 SOO  Var_06    C6    C5   C4   C3    176.96  30.0  3
 SOO  Var_07    C7    C6   C5   C4    179.11  30.0  3
 SOO  Var_08    C8    C7   C6   C5    179.83  30.0  3
 SOO  Var_09    C29   C28  O27  P24   166.51  30.0  3
 SOO  Var_10    C30   C29  C28  O27   -60.42  30.0  3
 SOO  Var_11    O28   P24  O27  C28   -75.03  30.0  2
 SOO  Var_12    C38   C37  N36  C34   172.41  30.0  3
 SOO  Var_13    C39   C38  C37  N36   179.37  30.0  3
 SOO  Var_14    O40   C39  C38  C37   -44.53  30.0  3
 SOO  Var_15    C43   C42  N41  C39   -85.97  30.0  3
 SOO  Var_16    H8    C8   C7   C6    -60.00  30.0  3
 SOO  Var_17    H30   C30  C29  C28    61.78  30.0  3
 SOO  Var_18    H31   C31  C29  C28    49.59  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
 SOO  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
 SOO  plan-1  C32   0.020
 SOO  plan-1  C34   0.020
 SOO  plan-1  O35   0.020
 SOO  plan-1  N36   0.020
 SOO  plan-1  C37   0.020
 SOO  plan-1  HN36  0.020
 SOO  plan-2  C38   0.020
 SOO  plan-2  C39   0.020
 SOO  plan-2  O40   0.020
 SOO  plan-2  N41   0.020
 SOO  plan-2  C42   0.020
 SOO  plan-2  HN41  0.020
 SOO  plan-3  C1    0.020
 SOO  plan-3  O1    0.020
 SOO  plan-3  S1    0.020
 SOO  plan-3  C2    0.020
 SOO  plan-4  C1    0.020
 SOO  plan-4  C2    0.020
 SOO  plan-4  C3    0.020
 SOO  plan-4  C4    0.020
 SOO  plan-4  H2    0.020
 SOO  plan-4  H3    0.020

