# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 01:12:00 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(3-oxooctyl)sulfanyl]ethyl}-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=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
 SYO  SYO  N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(3-oxooctyl)sulfanyl]ethyl}-beta-alaninamide  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_SYO
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
 SYO  C1    C  CH2   0  -0.545   5.9684  -0.8512   0.1763
 SYO  S1    S  S2    0  -0.037   4.9870  -1.6587   1.4729
 SYO  C2    C  CH2   0  -0.551   7.3648  -0.5735   0.7014
 SYO  C3    C  C     0   0.414   8.2655   0.0903  -0.3155
 SYO  O3    O  O     0  -0.406   7.8790   0.3590  -1.4300
 SYO  C4    C  CH2   0  -0.555   9.6661   0.3939   0.1505
 SYO  C5    C  CH2   0  -0.415  10.5566   1.0524  -0.8910
 SYO  C6    C  CH2   0  -0.409  11.9538   1.3425  -0.3567
 SYO  C7    C  CH2   0  -0.420  12.8573   2.0000  -1.3933
 SYO  C8    C  CH3   0  -0.662  14.2513   2.3008  -0.8609
 SYO  O23   O  O     0  -0.713  -6.9209   3.3263   1.3773
 SYO  P24   P  P     0   1.456  -7.6567   3.0295   0.1339
 SYO  O26   O  OH1   0  -0.732  -7.7546   4.1805  -0.9647
 SYO  O27   O  O2    0  -0.587  -7.0398   1.9111  -0.8178
 SYO  C29   C  CT    0  -0.168  -6.1047  -0.2297  -1.3937
 SYO  O29   O  OH1   0  -0.744  -9.1451   2.5678   0.4936
 SYO  C30   C  CH3   0  -0.646  -7.1165  -0.3939  -2.5317
 SYO  C31   C  CH3   0  -0.667  -4.8304   0.4128  -1.9471
 SYO  C32   C  CH1   0  -0.034  -5.7847  -1.6485  -0.8417
 SYO  O33   O  OH1   0  -0.660  -6.9216  -2.3102  -0.3578
 SYO  C34   C  C     0   0.520  -4.7214  -1.6368   0.2568
 SYO  O35   O  O     0  -0.498  -5.0475  -1.4787   1.4284
 SYO  N36   N  NH1   0  -0.639  -3.4582  -1.8121  -0.1327
 SYO  C37   C  CH2   0  -0.236  -2.3398  -1.7564   0.7881
 SYO  C38   C  CH2   0  -0.630  -1.0444  -2.0081   0.0340
 SYO  C39   C  C     0   0.564   0.1660  -1.8245   0.9250
 SYO  O40   O  O     0  -0.496   0.2404  -0.9055   1.7281
 SYO  N41   N  NH1   0  -0.630   1.1446  -2.7283   0.7517
 SYO  C42   C  CH2   0  -0.289   2.4303  -2.6373   1.4023
 SYO  C43   C  CH2   0  -0.547   3.4058  -1.7909   0.5923
 SYO  H1    H  HCH2  0   0.269   6.0050  -1.5044  -0.6966
 SYO  H1A   H  HCH2  0   0.269   5.4737   0.0759  -0.1159
 SYO  H2    H  HCH2  0   0.279   7.3269   0.0658   1.5893
 SYO  H2A   H  HCH2  0   0.278   7.8508  -1.4982   1.0294
 SYO  H4    H  HCH2  0   0.265   9.5898   1.0213   1.0461
 SYO  H4A   H  HCH2  0   0.265  10.1116  -0.5432   0.5035
 SYO  H5    H  HCH2  0   0.221  10.6315   0.4079  -1.7710
 SYO  H5A   H  HCH2  0   0.221  10.0987   1.9852  -1.2314
 SYO  H6    H  HCH2  0   0.210  11.8821   1.9906   0.5237
 SYO  H6A   H  HCH2  0   0.210  12.4165   0.4115  -0.0112
 SYO  H7    H  HCH2  0   0.212  12.9318   1.3498  -2.2704
 SYO  H7A   H  HCH2  0   0.212  12.3901   2.9262  -1.7417
 SYO  H8    H  HCH3  0   0.216  14.2094   2.9824  -0.0094
 SYO  H8A   H  HCH3  0   0.216  14.7526   1.3901  -0.5276
 SYO  H8B   H  HCH3  0   0.226  14.8797   2.7625  -1.6234
 SYO  HO26  H  HOH1  0   0.503  -7.9789   5.0491  -0.6056
 SYO  H28   H  HCH2  0   0.248  -5.9721   0.7644   0.5327
 SYO  H28A  H  HCH2  0   0.241  -7.5888   0.1556   0.1368
 SYO  HO29  H  HOH1  0   0.495  -9.7220   2.3872  -0.2608
 SYO  H30   H  HCH3  0   0.240  -7.3531   0.5661  -2.9893
 SYO  H30A  H  HCH3  0   0.230  -6.7043  -1.0339  -3.3147
 SYO  H30B  H  HCH3  0   0.235  -8.0486  -0.8427  -2.1888
 SYO  H31   H  HCH3  0   0.235  -4.0995   0.6347  -1.1681
 SYO  H31A  H  HCH3  0   0.235  -4.3526  -0.2453  -2.6765
 SYO  H31B  H  HCH3  0   0.249  -5.0604   1.3469  -2.4580
 SYO  H32   H  HCH1  0   0.258  -5.4126  -2.2306  -1.6935
 SYO  HO33  H  HOH1  0   0.447  -7.0169  -2.0935   0.5784
 SYO  HN36  H  HNH1  0   0.409  -3.2710  -1.9825  -1.1080
 SYO  H37   H  HCH2  0   0.250  -2.3089  -0.7799   1.2734
 SYO  H37A  H  HCH2  0   0.252  -2.4671  -2.5069   1.5714
 SYO  H38   H  HCH2  0   0.272  -1.0563  -3.0026  -0.4172
 SYO  H38A  H  HCH2  0   0.284  -0.9500  -1.2887  -0.7863
 SYO  HN41  H  HNH1  0   0.406   1.0287  -3.4380   0.0468
 SYO  H42   H  HCH2  0   0.255   2.2957  -2.2176   2.3990
 SYO  H42A  H  HCH2  0   0.264   2.8226  -3.6468   1.5249
 SYO  H43   H  HCH2  0   0.269   2.9949  -0.7932   0.4282
 SYO  H43A  H  HCH2  0   0.267   3.5808  -2.2522  -0.3817
 SYO  C28   C  CH2   0  -0.151  -6.6934   0.6294  -0.2758

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
 SYO  C1   S1    single  1.816  0.020  1.816
 SYO  C1   C2    single  1.518  0.020  1.518
 SYO  S1   C43   single  1.815  0.020  1.815
 SYO  C2   C3    single  1.512  0.020  1.512
 SYO  C3   O3    double  1.210  0.020  1.210
 SYO  C3   C4    single  1.507  0.020  1.507
 SYO  C4   C5    single  1.520  0.020  1.520
 SYO  C5   C6    single  1.524  0.020  1.524
 SYO  C6   C7    single  1.524  0.020  1.524
 SYO  C7   C8    single  1.522  0.020  1.522
 SYO  O23  P24   double  1.475  0.020  1.475
 SYO  P24  O26   single  1.594  0.020  1.594
 SYO  P24  O27   single  1.593  0.020  1.593
 SYO  P24  O29   single  1.599  0.020  1.599
 SYO  O27  C28   single  1.434  0.020  1.434
 SYO  C28  C29   single  1.528  0.020  1.528
 SYO  C29  C30   single  1.532  0.020  1.532
 SYO  C29  C31   single  1.531  0.020  1.531
 SYO  C29  C32   single  1.556  0.020  1.556
 SYO  C32  O33   single  1.402  0.020  1.402
 SYO  C32  C34   single  1.529  0.020  1.529
 SYO  C34  O35   double  1.226  0.020  1.226
 SYO  C34  N36   single  1.333  0.020  1.333
 SYO  N36  C37   single  1.450  0.020  1.450
 SYO  C37  C38   single  1.520  0.020  1.520
 SYO  C38  C39   single  1.514  0.020  1.514
 SYO  C39  O40   double  1.223  0.020  1.223
 SYO  C39  N41   single  1.343  0.020  1.343
 SYO  N41  C42   single  1.444  0.020  1.444
 SYO  C42  C43   single  1.525  0.020  1.525
 SYO  C1   H1    single  0.970  0.020  1.090
 SYO  C1   H1A   single  0.970  0.020  1.090
 SYO  C2   H2    single  0.970  0.020  1.090
 SYO  C2   H2A   single  0.970  0.020  1.090
 SYO  C4   H4    single  0.970  0.020  1.090
 SYO  C4   H4A   single  0.970  0.020  1.090
 SYO  C5   H5    single  0.970  0.020  1.090
 SYO  C5   H5A   single  0.970  0.020  1.090
 SYO  C6   H6    single  0.970  0.020  1.090
 SYO  C6   H6A   single  0.970  0.020  1.090
 SYO  C7   H7    single  0.970  0.020  1.090
 SYO  C7   H7A   single  0.970  0.020  1.090
 SYO  C8   H8    single  0.970  0.020  1.090
 SYO  C8   H8A   single  0.970  0.020  1.090
 SYO  C8   H8B   single  0.970  0.020  1.090
 SYO  O26  HO26  single  0.850  0.020  0.980
 SYO  C28  H28   single  0.970  0.020  1.090
 SYO  C28  H28A  single  0.970  0.020  1.090
 SYO  O29  HO29  single  0.850  0.020  0.980
 SYO  C30  H30   single  0.970  0.020  1.090
 SYO  C30  H30A  single  0.970  0.020  1.090
 SYO  C30  H30B  single  0.970  0.020  1.090
 SYO  C31  H31   single  0.970  0.020  1.090
 SYO  C31  H31A  single  0.970  0.020  1.090
 SYO  C31  H31B  single  0.970  0.020  1.090
 SYO  C32  H32   single  0.970  0.020  1.090
 SYO  O33  HO33  single  0.850  0.020  0.980
 SYO  N36  HN36  single  0.860  0.020  1.020
 SYO  C37  H37   single  0.970  0.020  1.090
 SYO  C37  H37A  single  0.970  0.020  1.090
 SYO  C38  H38   single  0.970  0.020  1.090
 SYO  C38  H38A  single  0.970  0.020  1.090
 SYO  N41  HN41  single  0.860  0.020  1.020
 SYO  C42  H42   single  0.970  0.020  1.090
 SYO  C42  H42A  single  0.970  0.020  1.090
 SYO  C43  H43   single  0.970  0.020  1.090
 SYO  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
 SYO  H1A   C1   H1    108.05  3.000
 SYO  H1A   C1   C2    110.76  3.000
 SYO  H1    C1   C2    110.83  3.000
 SYO  H1A   C1   S1    108.92  3.000
 SYO  H1    C1   S1    108.86  3.000
 SYO  C2    C1   S1    109.37  3.000
 SYO  C43   S1   C1     99.02  3.000
 SYO  H2A   C2   H2    105.40  3.000
 SYO  H2A   C2   C3    107.93  3.000
 SYO  H2    C2   C3    108.05  3.000
 SYO  H2A   C2   C1    110.95  3.000
 SYO  H2    C2   C1    110.83  3.000
 SYO  C3    C2   C1    113.32  3.000
 SYO  C4    C3   O3    122.48  3.000
 SYO  C4    C3   C2    115.74  3.000
 SYO  O3    C3   C2    121.78  3.000
 SYO  H4A   C4   H4    104.74  3.000
 SYO  H4A   C4   C5    110.67  3.000
 SYO  H4    C4   C5    110.65  3.000
 SYO  H4A   C4   C3    107.76  3.000
 SYO  H4    C4   C3    107.65  3.000
 SYO  C5    C4   C3    114.82  3.000
 SYO  H5A   C5   H5    106.32  3.000
 SYO  H5A   C5   C6    109.32  3.000
 SYO  H5    C5   C6    109.37  3.000
 SYO  H5A   C5   C4    109.72  3.000
 SYO  H5    C5   C4    109.65  3.000
 SYO  C6    C5   C4    112.29  3.000
 SYO  H6A   C6   H6    106.08  3.000
 SYO  H6A   C6   C7    109.31  3.000
 SYO  H6    C6   C7    109.28  3.000
 SYO  H6A   C6   C5    109.64  3.000
 SYO  H6    C6   C5    109.54  3.000
 SYO  C7    C6   C5    112.78  3.000
 SYO  H7A   C7   H7    106.07  3.000
 SYO  H7A   C7   C8    109.57  3.000
 SYO  H7    C7   C8    109.60  3.000
 SYO  H7A   C7   C6    109.18  3.000
 SYO  H7    C7   C6    109.22  3.000
 SYO  C8    C7   C6    112.97  3.000
 SYO  H8B   C8   H8A   107.58  3.000
 SYO  H8B   C8   H8    107.65  3.000
 SYO  H8A   C8   H8    107.48  3.000
 SYO  H8B   C8   C7    111.51  3.000
 SYO  H8A   C8   C7    111.25  3.000
 SYO  H8    C8   C7    111.17  3.000
 SYO  O29   P24  O27   106.98  3.000
 SYO  O29   P24  O26   107.84  3.000
 SYO  O27   P24  O26    96.83  3.000
 SYO  O29   P24  O23   109.44  3.000
 SYO  O27   P24  O23   116.86  3.000
 SYO  O26   P24  O23   117.80  3.000
 SYO  HO26  O26  P24   114.03  3.000
 SYO  C28   O27  P24   119.69  3.000
 SYO  C32   C29  C31   109.87  3.000
 SYO  C32   C29  C30   107.56  3.000
 SYO  C31   C29  C30   109.05  3.000
 SYO  C32   C29  C28   109.42  3.000
 SYO  C31   C29  C28   110.44  3.000
 SYO  C30   C29  C28   110.45  3.000
 SYO  HO29  O29  P24   115.71  3.000
 SYO  H30B  C30  H30A  107.88  3.000
 SYO  H30B  C30  H30   108.02  3.000
 SYO  H30A  C30  H30   107.29  3.000
 SYO  H30B  C30  C29   112.05  3.000
 SYO  H30A  C30  C29   110.25  3.000
 SYO  H30   C30  C29   111.17  3.000
 SYO  H31B  C31  H31A  107.21  3.000
 SYO  H31B  C31  H31   107.57  3.000
 SYO  H31A  C31  H31   107.83  3.000
 SYO  H31B  C31  C29   110.72  3.000
 SYO  H31A  C31  C29   110.65  3.000
 SYO  H31   C31  C29   112.65  3.000
 SYO  H32   C32  C34   109.03  3.000
 SYO  H32   C32  O33   107.03  3.000
 SYO  C34   C32  O33   108.64  3.000
 SYO  H32   C32  C29   106.15  3.000
 SYO  C34   C32  C29   113.02  3.000
 SYO  O33   C32  C29   112.72  3.000
 SYO  HO33  O33  C32   107.99  3.000
 SYO  N36   C34  O35   123.22  3.000
 SYO  N36   C34  C32   116.61  3.000
 SYO  O35   C34  C32   120.16  3.000
 SYO  HN36  N36  C37   118.55  3.000
 SYO  HN36  N36  C34   118.75  3.000
 SYO  C37   N36  C34   122.70  3.000
 SYO  H37A  C37  H37   107.42  3.000
 SYO  H37A  C37  C38   109.96  3.000
 SYO  H37   C37  C38   110.18  3.000
 SYO  H37A  C37  N36   109.82  3.000
 SYO  H37   C37  N36   109.80  3.000
 SYO  C38   C37  N36   109.63  3.000
 SYO  H38A  C38  H38   106.84  3.000
 SYO  H38A  C38  C39   106.99  3.000
 SYO  H38   C38  C39   111.24  3.000
 SYO  H38A  C38  C37   109.65  3.000
 SYO  H38   C38  C37   110.27  3.000
 SYO  C39   C38  C37   111.67  3.000
 SYO  N41   C39  O40   123.10  3.000
 SYO  N41   C39  C38   115.14  3.000
 SYO  O40   C39  C38   121.76  3.000
 SYO  HN41  N41  C42   117.54  3.000
 SYO  HN41  N41  C39   118.73  3.000
 SYO  C42   N41  C39   123.24  3.000
 SYO  H42A  C42  H42   107.35  3.000
 SYO  H42A  C42  C43   110.10  3.000
 SYO  H42   C42  C43   110.56  3.000
 SYO  H42A  C42  N41   108.23  3.000
 SYO  H42   C42  N41   109.05  3.000
 SYO  C43   C42  N41   111.43  3.000
 SYO  H43A  C43  H43   108.21  3.000
 SYO  H43A  C43  C42   110.00  3.000
 SYO  H43   C43  C42   110.27  3.000
 SYO  H43A  C43  S1    108.91  3.000
 SYO  H43   C43  S1    109.54  3.000
 SYO  C42   C43  S1    109.89  3.000
 SYO  H28A  C28  H28   108.36  3.000
 SYO  H28A  C28  C29   110.35  3.000
 SYO  H28   C28  C29   110.90  3.000
 SYO  H28A  C28  O27   109.39  3.000
 SYO  H28   C28  O27   109.20  3.000
 SYO  C29   C28  O27   108.61  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
 SYO  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SYO  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SYO  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SYO  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SYO  CONST_05  HN36  N36  C34  C32     0.00   0.0  0
 SYO  CONST_06  HN41  N41  C39  C38     0.00   0.0  0
 SYO  Var_01    C42   C43  S1   C1    171.66  30.0  3
 SYO  Var_02    O3    C3   C2   C1     -0.04  30.0  3
 SYO  Var_03    C3    C2   C1   S1    179.49  30.0  3
 SYO  Var_04    N41   C42  C43  S1    178.12  30.0  1
 SYO  Var_05    C5    C4   C3   C2    179.60  30.0  3
 SYO  Var_06    C6    C5   C4   C3    179.59  30.0  3
 SYO  Var_07    C7    C6   C5   C4    179.86  30.0  3
 SYO  Var_08    C8    C7   C6   C5    179.58  30.0  3
 SYO  Var_09    C29   C28  O27  P24  -178.93  30.0  3
 SYO  Var_10    C30   C29  C28  O27   -59.10  30.0  3
 SYO  Var_11    O29   P24  O27  C28   -71.55  30.0  1
 SYO  Var_12    C38   C37  N36  C34   179.49  30.0  3
 SYO  Var_13    C39   C38  C37  N36   174.33  30.0  3
 SYO  Var_14    O40   C39  C38  C37   -41.39  30.0  3
 SYO  Var_15    C43   C42  N41  C39   -87.11  30.0  3
 SYO  Var_16    H8    C8   C7   C6    -60.34  30.0  3
 SYO  Var_17    H30   C30  C29  C28    62.90  30.0  3
 SYO  Var_18    H31   C31  C29  C28    53.60  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
 SYO  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
 SYO  plan-1  C32   0.020
 SYO  plan-1  C34   0.020
 SYO  plan-1  O35   0.020
 SYO  plan-1  N36   0.020
 SYO  plan-1  C37   0.020
 SYO  plan-1  HN36  0.020
 SYO  plan-2  C38   0.020
 SYO  plan-2  C39   0.020
 SYO  plan-2  O40   0.020
 SYO  plan-2  N41   0.020
 SYO  plan-2  C42   0.020
 SYO  plan-2  HN41  0.020
 SYO  plan-3  C2    0.020
 SYO  plan-3  C3    0.020
 SYO  plan-3  O3    0.020
 SYO  plan-3  C4    0.020

