# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:10:41 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)COP(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
 SDO  SDO  N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide  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_SDO
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
 SDO  P24   P  P     0   0.891   -9.3774   2.4939   0.5440
 SDO  O26   O  OH1   0  -0.774   -8.7041   2.8203   2.0080
 SDO  O23   O  OH1   0  -0.765   -9.3755   3.9855  -0.1273
 SDO  O27   O  O2    0  -0.605   -8.0243   2.0129  -0.2465
 SDO  C28   C  CH2   0  -0.137   -7.5353   0.7060   0.0249
 SDO  C29   C  CT    0  -0.151   -6.9643   0.0969  -1.2582
 SDO  C30   C  CH3   0  -0.647   -8.0552   0.0225  -2.3298
 SDO  C31   C  CH3   0  -0.670   -5.8110   0.9543  -1.7844
 SDO  C32   C  CH1   0  -0.034   -6.4662  -1.3510  -0.9885
 SDO  O33   O  OH1   0  -0.661   -7.4950  -2.2108  -0.5773
 SDO  C34   C  C     0   0.520   -5.3408  -1.4174   0.0453
 SDO  O35   O  O     0  -0.499   -5.6087  -1.5264   1.2371
 SDO  N36   N  NH1   0  -0.640   -4.0915  -1.3657  -0.4217
 SDO  C37   C  CH2   0  -0.239   -2.9312  -1.3272   0.4458
 SDO  C38   C  CH2   0  -0.623   -1.6671  -1.5762  -0.3624
 SDO  C39   C  C     0   0.562   -0.4316  -1.4367   0.5022
 SDO  O40   O  O     0  -0.497   -0.3068  -0.5203   1.3024
 SDO  N41   N  NH1   0  -0.630    0.5052  -2.3813   0.3204
 SDO  C42   C  CH2   0  -0.288    1.7774  -2.3744   1.0020
 SDO  C43   C  CH2   0  -0.546    2.8204  -1.5495   0.2555
 SDO  S1    S  S2    0  -0.038    4.3623  -1.5323   1.2122
 SDO  C1    C  CH2   0  -0.545    5.4678  -0.7533   0.0015
 SDO  C2    C  CH2   0  -0.552    6.8417  -0.5955   0.6266
 SDO  C3    C  C     0   0.414    7.8648   0.0177  -0.3005
 SDO  O3    O  O     0  -0.405    7.6043   0.2991  -1.4477
 SDO  C4    C  CH2   0  -0.555    9.2245   0.2534   0.3052
 SDO  C5    C  CH2   0  -0.419   10.2788   0.7550  -0.6686
 SDO  C6    C  CH2   0  -0.562   11.6078   0.9619   0.0387
 SDO  C7    C  C     0   0.395   12.7270   1.4603  -0.8388
 SDO  O7    O  O     0  -0.408   12.5543   1.7624  -1.9987
 SDO  C8    C  CH3   0  -0.768   14.0781   1.5437  -0.1820
 SDO  H1    H  HOH1  0   0.481   -9.2897   2.5492   2.7243
 SDO  H2    H  HOH1  0   0.485  -10.2732   4.2795  -0.3182
 SDO  H28A  H  HCH2  0   0.235   -6.7712   0.7721   0.8034
 SDO  H28B  H  HCH2  0   0.217   -8.3405   0.0656   0.4082
 SDO  H30A  H  HCH3  0   0.238   -8.3774   1.0201  -2.6251
 SDO  H30B  H  HCH3  0   0.227   -7.6820  -0.4778  -3.2260
 SDO  H30C  H  HCH3  0   0.232   -8.9327  -0.5241  -1.9838
 SDO  H31A  H  HCH3  0   0.233   -5.0222   1.0978  -1.0444
 SDO  H31B  H  HCH3  0   0.232   -5.3621   0.5034  -2.6728
 SDO  H31C  H  HCH3  0   0.247   -6.1708   1.9414  -2.0727
 SDO  H32A  H  HCH1  0   0.255   -6.0946  -1.7324  -1.9465
 SDO  H33A  H  HOH1  0   0.445   -7.5434  -2.1727   0.3863
 SDO  H36A  H  HNH1  0   0.407   -3.9491  -1.2778  -1.4155
 SDO  H37A  H  HCH2  0   0.249   -2.8706  -0.3611   0.9507
 SDO  H37B  H  HCH2  0   0.254   -3.0359  -2.0921   1.2167
 SDO  H38A  H  HCH2  0   0.270   -1.7104  -2.5582  -0.8378
 SDO  H38B  H  HCH2  0   0.282   -1.5873  -0.8360  -1.1654
 SDO  H41A  H  HNH1  0   0.406    0.3516  -3.0910  -0.3770
 SDO  H42A  H  HCH2  0   0.254    1.6377  -1.9860   2.0111
 SDO  H42B  H  HCH2  0   0.264    2.1165  -3.4059   1.0953
 SDO  H43A  H  HCH2  0   0.267    3.0128  -1.9873  -0.7259
 SDO  H43B  H  HCH2  0   0.269    2.4657  -0.5277   0.1117
 SDO  H1A   H  HCH2  0   0.270    5.5150  -1.3797  -0.8901
 SDO  H1B   H  HCH2  0   0.270    5.0575   0.2157  -0.2859
 SDO  H2A   H  HCH2  0   0.278    6.7904   0.0173   1.5322
 SDO  H2B   H  HCH2  0   0.281    7.2321  -1.5650   0.9546
 SDO  H4A   H  HCH2  0   0.272    9.0943   0.9618   1.1318
 SDO  H4B   H  HCH2  0   0.266    9.5471  -0.6781   0.7831
 SDO  H5A   H  HCH2  0   0.236   10.3997   0.0383  -1.4833
 SDO  H5B   H  HCH2  0   0.236    9.9506   1.6922  -1.1211
 SDO  H6A   H  HCH2  0   0.270   11.5006   1.6778   0.8621
 SDO  H6B   H  HCH2  0   0.264   11.9455   0.0363   0.5185
 SDO  H8A   H  HCH3  0   0.269   14.4724   0.5333  -0.0487
 SDO  H8B   H  HCH3  0   0.259   14.7828   2.1148  -0.7829
 SDO  H8C   H  HCH3  0   0.257   14.0051   1.9836   0.8131

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
 SDO  P24  O26   single  1.644  0.020  1.644
 SDO  P24  O23   single  1.636  0.020  1.636
 SDO  P24  O27   single  1.639  0.020  1.639
 SDO  O27  C28   single  1.422  0.020  1.422
 SDO  C28  C29   single  1.531  0.020  1.531
 SDO  C29  C30   single  1.531  0.020  1.531
 SDO  C29  C31   single  1.530  0.020  1.530
 SDO  C29  C32   single  1.555  0.020  1.555
 SDO  C32  O33   single  1.402  0.020  1.402
 SDO  C32  C34   single  1.530  0.020  1.530
 SDO  C34  O35   double  1.226  0.020  1.226
 SDO  C34  N36   single  1.335  0.020  1.335
 SDO  N36  C37   single  1.449  0.020  1.449
 SDO  C37  C38   single  1.521  0.020  1.521
 SDO  C38  C39   single  1.514  0.020  1.514
 SDO  C39  O40   double  1.223  0.020  1.223
 SDO  C39  N41   single  1.343  0.020  1.343
 SDO  N41  C42   single  1.443  0.020  1.443
 SDO  C42  C43   single  1.525  0.020  1.525
 SDO  C43  S1    single  1.815  0.020  1.815
 SDO  S1   C1    single  1.815  0.020  1.815
 SDO  C1   C2    single  1.518  0.020  1.518
 SDO  C2   C3    single  1.511  0.020  1.511
 SDO  C3   O3    double  1.210  0.020  1.210
 SDO  C3   C4    single  1.507  0.020  1.507
 SDO  C4   C5    single  1.520  0.020  1.520
 SDO  C5   C6    single  1.520  0.020  1.520
 SDO  C6   C7    single  1.507  0.020  1.507
 SDO  C7   O7    double  1.211  0.020  1.211
 SDO  C7   C8    single  1.505  0.020  1.505
 SDO  O26  H1    single  0.850  0.020  0.980
 SDO  O23  H2    single  0.850  0.020  0.980
 SDO  C28  H28A  single  0.970  0.020  1.090
 SDO  C28  H28B  single  0.970  0.020  1.090
 SDO  C30  H30A  single  0.970  0.020  1.090
 SDO  C30  H30B  single  0.970  0.020  1.090
 SDO  C30  H30C  single  0.970  0.020  1.090
 SDO  C31  H31A  single  0.970  0.020  1.090
 SDO  C31  H31B  single  0.970  0.020  1.090
 SDO  C31  H31C  single  0.970  0.020  1.090
 SDO  C32  H32A  single  0.970  0.020  1.090
 SDO  O33  H33A  single  0.850  0.020  0.980
 SDO  N36  H36A  single  0.860  0.020  1.020
 SDO  C37  H37A  single  0.970  0.020  1.090
 SDO  C37  H37B  single  0.970  0.020  1.090
 SDO  C38  H38A  single  0.970  0.020  1.090
 SDO  C38  H38B  single  0.970  0.020  1.090
 SDO  N41  H41A  single  0.860  0.020  1.020
 SDO  C42  H42A  single  0.970  0.020  1.090
 SDO  C42  H42B  single  0.970  0.020  1.090
 SDO  C43  H43A  single  0.970  0.020  1.090
 SDO  C43  H43B  single  0.970  0.020  1.090
 SDO  C1   H1A   single  0.970  0.020  1.090
 SDO  C1   H1B   single  0.970  0.020  1.090
 SDO  C2   H2A   single  0.970  0.020  1.090
 SDO  C2   H2B   single  0.970  0.020  1.090
 SDO  C4   H4A   single  0.970  0.020  1.090
 SDO  C4   H4B   single  0.970  0.020  1.090
 SDO  C5   H5A   single  0.970  0.020  1.090
 SDO  C5   H5B   single  0.970  0.020  1.090
 SDO  C6   H6A   single  0.970  0.020  1.090
 SDO  C6   H6B   single  0.970  0.020  1.090
 SDO  C8   H8A   single  0.970  0.020  1.090
 SDO  C8   H8B   single  0.970  0.020  1.090
 SDO  C8   H8C   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
 SDO  O27   P24  O23    93.94  3.000
 SDO  O27   P24  O26    98.60  3.000
 SDO  O23   P24  O26   100.60  3.000
 SDO  H1    O26  P24   110.91  3.000
 SDO  H2    O23  P24   111.00  3.000
 SDO  C28   O27  P24   117.50  3.000
 SDO  H28B  C28  H28A  107.41  3.000
 SDO  H28B  C28  C29   109.52  3.000
 SDO  H28A  C28  C29   111.12  3.000
 SDO  H28B  C28  O27   110.53  3.000
 SDO  H28A  C28  O27   108.72  3.000
 SDO  C29   C28  O27   109.52  3.000
 SDO  C32   C29  C31   109.88  3.000
 SDO  C32   C29  C30   107.73  3.000
 SDO  C31   C29  C30   108.87  3.000
 SDO  C32   C29  C28   110.16  3.000
 SDO  C31   C29  C28   110.26  3.000
 SDO  C30   C29  C28   109.89  3.000
 SDO  H30C  C30  H30B  107.81  3.000
 SDO  H30C  C30  H30A  107.89  3.000
 SDO  H30B  C30  H30A  107.35  3.000
 SDO  H30C  C30  C29   112.07  3.000
 SDO  H30B  C30  C29   110.68  3.000
 SDO  H30A  C30  C29   110.86  3.000
 SDO  H31C  C31  H31B  107.12  3.000
 SDO  H31C  C31  H31A  107.40  3.000
 SDO  H31B  C31  H31A  107.98  3.000
 SDO  H31C  C31  C29   110.47  3.000
 SDO  H31B  C31  C29   110.97  3.000
 SDO  H31A  C31  C29   112.66  3.000
 SDO  H32A  C32  C34   109.04  3.000
 SDO  H32A  C32  O33   106.96  3.000
 SDO  C34   C32  O33   108.35  3.000
 SDO  H32A  C32  C29   106.32  3.000
 SDO  C34   C32  C29   113.17  3.000
 SDO  O33   C32  C29   112.76  3.000
 SDO  H33A  O33  C32   107.77  3.000
 SDO  N36   C34  O35   123.22  3.000
 SDO  N36   C34  C32   116.77  3.000
 SDO  O35   C34  C32   120.00  3.000
 SDO  H36A  N36  C37   118.34  3.000
 SDO  H36A  N36  C34   118.73  3.000
 SDO  C37   N36  C34   122.75  3.000
 SDO  H37B  C37  H37A  107.39  3.000
 SDO  H37B  C37  C38   109.91  3.000
 SDO  H37A  C37  C38   110.15  3.000
 SDO  H37B  C37  N36   109.12  3.000
 SDO  H37A  C37  N36   110.17  3.000
 SDO  C38   C37  N36   110.06  3.000
 SDO  H38B  C38  H38A  106.95  3.000
 SDO  H38B  C38  C39   107.27  3.000
 SDO  H38A  C38  C39   111.33  3.000
 SDO  H38B  C38  C37   109.85  3.000
 SDO  H38A  C38  C37   110.23  3.000
 SDO  C39   C38  C37   111.07  3.000
 SDO  N41   C39  O40   123.00  3.000
 SDO  N41   C39  C38   115.28  3.000
 SDO  O40   C39  C38   121.72  3.000
 SDO  H41A  N41  C42   117.70  3.000
 SDO  H41A  N41  C39   118.90  3.000
 SDO  C42   N41  C39   123.21  3.000
 SDO  H42B  C42  H42A  107.33  3.000
 SDO  H42B  C42  C43   109.94  3.000
 SDO  H42A  C42  C43   110.36  3.000
 SDO  H42B  C42  N41   108.07  3.000
 SDO  H42A  C42  N41   109.02  3.000
 SDO  C43   C42  N41   111.98  3.000
 SDO  H43B  C43  H43A  108.32  3.000
 SDO  H43B  C43  S1    109.68  3.000
 SDO  H43A  C43  S1    109.14  3.000
 SDO  H43B  C43  C42   110.41  3.000
 SDO  H43A  C43  C42   110.10  3.000
 SDO  S1    C43  C42   109.16  3.000
 SDO  C1    S1   C43    99.79  3.000
 SDO  H1B   C1   H1A   108.12  3.000
 SDO  H1B   C1   C2    110.90  3.000
 SDO  H1A   C1   C2    110.93  3.000
 SDO  H1B   C1   S1    109.14  3.000
 SDO  H1A   C1   S1    108.97  3.000
 SDO  C2    C1   S1    108.74  3.000
 SDO  H2B   C2   H2A   105.34  3.000
 SDO  H2B   C2   C3    107.56  3.000
 SDO  H2A   C2   C3    108.19  3.000
 SDO  H2B   C2   C1    110.73  3.000
 SDO  H2A   C2   C1    110.88  3.000
 SDO  C3    C2   C1    113.74  3.000
 SDO  C4    C3   O3    122.63  3.000
 SDO  C4    C3   C2    115.33  3.000
 SDO  O3    C3   C2    122.04  3.000
 SDO  H4B   C4   H4A   104.81  3.000
 SDO  H4B   C4   C5    110.84  3.000
 SDO  H4A   C4   C5    110.62  3.000
 SDO  H4B   C4   C3    107.94  3.000
 SDO  H4A   C4   C3    107.27  3.000
 SDO  C5    C4   C3    114.82  3.000
 SDO  H5B   C5   H5A   106.72  3.000
 SDO  H5B   C5   C6    109.82  3.000
 SDO  H5A   C5   C6    109.86  3.000
 SDO  H5B   C5   C4    109.90  3.000
 SDO  H5A   C5   C4    109.77  3.000
 SDO  C6    C5   C4    110.69  3.000
 SDO  H6B   C6   H6A   104.65  3.000
 SDO  H6B   C6   C7    107.78  3.000
 SDO  H6A   C6   C7    107.10  3.000
 SDO  H6B   C6   C5    111.00  3.000
 SDO  H6A   C6   C5    110.66  3.000
 SDO  C7    C6   C5    115.05  3.000
 SDO  C8    C7   O7    122.17  3.000
 SDO  C8    C7   C6    115.53  3.000
 SDO  O7    C7   C6    122.30  3.000
 SDO  H8C   C8   H8B   109.60  3.000
 SDO  H8C   C8   H8A   106.61  3.000
 SDO  H8B   C8   H8A   108.61  3.000
 SDO  H8C   C8   C7    111.14  3.000
 SDO  H8B   C8   C7    111.69  3.000
 SDO  H8A   C8   C7    109.03  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
 SDO  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 SDO  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 SDO  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 SDO  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 SDO  CONST_05  H36A  N36  C34  C32     0.00   0.0  0
 SDO  CONST_06  H41A  N41  C39  C38     0.00   0.0  0
 SDO  Var_01    C29   C28  O27  P24   143.79  30.0  3
 SDO  Var_02    C30   C29  C28  O27   -59.66  30.0  3
 SDO  Var_03    C38   C37  N36  C34   167.73  30.0  3
 SDO  Var_04    C39   C38  C37  N36   175.68  30.0  3
 SDO  Var_05    O40   C39  C38  C37   -43.61  30.0  3
 SDO  Var_06    C43   C42  N41  C39   -86.89  30.0  3
 SDO  Var_07    S1    C43  C42  N41   177.53  30.0  3
 SDO  Var_08    C2    C1   S1   C43   178.19  30.0  3
 SDO  Var_09    C3    C2   C1   S1    178.72  30.0  3
 SDO  Var_10    O3    C3   C2   C1     -2.80  30.0  3
 SDO  Var_11    C5    C4   C3   C2    174.83  30.0  3
 SDO  Var_12    C6    C5   C4   C3    179.93  30.0  3
 SDO  Var_13    C7    C6   C5   C4   -179.99  30.0  3
 SDO  Var_14    O7    C7   C6   C5      4.97  30.0  3
 SDO  Var_15    H30A  C30  C29  C28    65.19  30.0  3
 SDO  Var_16    H31A  C31  C29  C28    55.96  30.0  3
 SDO  Var_17    H8A   C8   C7   C6     73.00  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
 SDO  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
 SDO  plan-1  C32   0.020
 SDO  plan-1  C34   0.020
 SDO  plan-1  O35   0.020
 SDO  plan-1  N36   0.020
 SDO  plan-1  C37   0.020
 SDO  plan-1  H36A  0.020
 SDO  plan-2  C38   0.020
 SDO  plan-2  C39   0.020
 SDO  plan-2  O40   0.020
 SDO  plan-2  N41   0.020
 SDO  plan-2  C42   0.020
 SDO  plan-2  H41A  0.020
 SDO  plan-3  C2    0.020
 SDO  plan-3  C3    0.020
 SDO  plan-3  O3    0.020
 SDO  plan-3  C4    0.020
 SDO  plan-4  C6    0.020
 SDO  plan-4  C7    0.020
 SDO  plan-4  O7    0.020
 SDO  plan-4  C8    0.020

