# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 02:30:05 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCc1ccc2OCOc2c1
#
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
 SH3  SH3  N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide  ligand  57  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_SH3
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
 SH3  OAC  O  OH1   0  -0.693  -7.7904  -2.8901  -1.3299
 SH3  PAB  P  P     0   1.441  -7.3241  -2.1895   0.0202
 SH3  OAD  O  OH1   0  -0.727  -8.6320  -1.6138   0.7399
 SH3  OAA  O  O     0  -0.783  -6.5335  -2.9829   0.9783
 SH3  OAE  O  O2    0  -0.603  -6.5763  -0.9552  -0.6556
 SH3  CAF  C  CH2   0  -0.164  -5.8121  -0.0575   0.1565
 SH3  CAG  C  CT    0  -0.158  -5.2294   1.0335  -0.7422
 SH3  CAH  C  CH3   0  -0.719  -4.3191   0.4072  -1.8005
 SH3  CAI  C  CH3   0  -0.649  -6.3516   1.8118  -1.4340
 SH3  CAJ  C  CH1   0  -0.017  -4.4215   2.0407   0.1229
 SH3  OAK  O  OH1   0  -0.653  -5.2021   2.6399   1.1230
 SH3  CAL  C  C     0   0.456  -3.1863   1.4245   0.7803
 SH3  OAM  O  O     0  -0.554  -3.2786   0.8794   1.8746
 SH3  NAN  N  NH1   0  -0.580  -2.0359   1.5318   0.1132
 SH3  CAO  C  CH2   0  -0.243  -0.7871   0.9827   0.6043
 SH3  CAP  C  CH2   0  -0.628   0.3047   1.1724  -0.4368
 SH3  CAQ  C  C     0   0.613   1.6131   0.5591   0.0302
 SH3  OAR  O  O     0  -0.535   1.6498  -0.5314   0.5746
 SH3  NAS  N  NH1   0  -0.584   2.7045   1.3081  -0.2039
 SH3  CAT  C  CH2   0  -0.241   4.0471   0.8815   0.1192
 SH3  CAU  C  CH2   0  -0.581   4.7129   0.0803  -1.0016
 SH3  CAV  C  CR6   0   0.154   6.1284  -0.2781  -0.6434
 SH3  CBD  C  CR16  0  -0.419   7.1581   0.6433  -0.8989
 SH3  CBC  C  CR56  0   0.303   8.4278   0.3019  -0.5092
 SH3  OBB  O  O     0  -0.557   9.5776   1.0017  -0.6683
 SH3  CBA  C  CH2   0   0.063  10.5843   0.2795   0.0251
 SH3  OAZ  O  O     0  -0.499  10.0369  -0.9850   0.3641
 SH3  CAY  C  CR56  0   0.343   8.7057  -0.9025   0.1171
 SH3  CAX  C  CR16  0  -0.315   7.7203  -1.8198   0.3790
 SH3  CAW  C  CR16  0  -0.307   6.4193  -1.4812  -0.0145
 SH3  H1   H  HOH1  0   0.534  -8.3310  -3.6813  -1.2090
 SH3  H2   H  HOH1  0   0.477  -9.2542  -1.1544   0.1612
 SH3  H3   H  HCH2  0   0.242  -6.4586   0.3846   0.9203
 SH3  H4   H  HCH2  0   0.279  -5.0181  -0.6146   0.6581
 SH3  H5   H  HCH3  0   0.248  -4.8978  -0.1821  -2.5108
 SH3  H6   H  HCH3  0   0.282  -3.7995   1.1734  -2.3800
 SH3  H7   H  HCH3  0   0.218  -3.5669  -0.2529  -1.3669
 SH3  H8   H  HCH3  0   0.228  -7.0065   2.3079  -0.7180
 SH3  H9   H  HCH3  0   0.246  -5.9345   2.5778  -2.0906
 SH3  H10  H  HCH3  0   0.241  -6.9645   1.1550  -2.0501
 SH3  H11  H  HCH1  0   0.277  -4.1033   2.8426  -0.5533
 SH3  H12  H  HOH1  0   0.430  -5.1109   2.1129   1.9269
 SH3  H13  H  HNH1  0   0.429  -2.0221   2.0574  -0.7462
 SH3  H14  H  HCH2  0   0.284  -0.5039   1.4764   1.5375
 SH3  H15  H  HCH2  0   0.264  -0.9124  -0.0771   0.8249
 SH3  H16  H  HCH2  0   0.220   0.0176   0.6761  -1.3691
 SH3  H17  H  HCH2  0   0.296   0.4282   2.2341  -0.6643
 SH3  H18  H  HNH1  0   0.404   2.5941   2.1871  -0.6813
 SH3  H19  H  HCH2  0   0.236   4.6356   1.7721   0.3435
 SH3  H20  H  HCH2  0   0.204   4.0175   0.2853   1.0312
 SH3  H21  H  HCH2  0   0.286   4.1294  -0.8236  -1.1872
 SH3  H22  H  HCH2  0   0.251   4.6971   0.6657  -1.9246
 SH3  H23  H  HCR6  0   0.256   6.9569   1.5839  -1.3967
 SH3  H24  H  HCH2  0   0.268  11.4535   0.1452  -0.6202
 SH3  H25  H  HCH2  0   0.243  10.8695   0.8191   0.9355
 SH3  H26  H  HCR6  0   0.247   7.9346  -2.7632   0.8624
 SH3  H27  H  HCR6  0   0.243   5.6189  -2.1847   0.1796

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
 SH3  CBA  OBB  single    1.420  0.020  1.420
 SH3  CBA  OAZ  single    1.419  0.020  1.419
 SH3  OBB  CBC  single    1.355  0.020  1.355
 SH3  CAI  CAG  single    1.531  0.020  1.531
 SH3  OAA  PAB  double    1.474  0.020  1.474
 SH3  CAF  CAG  single    1.529  0.020  1.529
 SH3  CAF  OAE  single    1.432  0.020  1.432
 SH3  OAZ  CAY  single    1.356  0.020  1.356
 SH3  CBC  CAY  aromatic  1.386  0.020  1.386
 SH3  CBC  CBD  aromatic  1.371  0.020  1.371
 SH3  CAG  CAH  single    1.530  0.020  1.530
 SH3  CAG  CAJ  single    1.554  0.020  1.554
 SH3  OAE  PAB  single    1.594  0.020  1.594
 SH3  CAY  CAX  aromatic  1.371  0.020  1.371
 SH3  PAB  OAC  single    1.591  0.020  1.591
 SH3  PAB  OAD  single    1.600  0.020  1.600
 SH3  CBD  CAV  aromatic  1.405  0.020  1.405
 SH3  OAK  CAJ  single    1.403  0.020  1.403
 SH3  CAP  CAQ  single    1.519  0.020  1.519
 SH3  CAP  CAO  single    1.521  0.020  1.521
 SH3  CAJ  CAL  single    1.529  0.020  1.529
 SH3  CAX  CAW  aromatic  1.401  0.020  1.401
 SH3  NAS  CAQ  single    1.344  0.020  1.344
 SH3  NAS  CAT  single    1.445  0.020  1.445
 SH3  NAN  CAL  single    1.334  0.020  1.334
 SH3  NAN  CAO  single    1.450  0.020  1.450
 SH3  CAL  OAM  double    1.226  0.020  1.226
 SH3  CAQ  OAR  double    1.219  0.020  1.219
 SH3  CAV  CAW  aromatic  1.388  0.020  1.388
 SH3  CAV  CAU  single    1.503  0.020  1.503
 SH3  CAT  CAU  single    1.530  0.020  1.530
 SH3  OAC  H1   single    0.850  0.020  0.980
 SH3  OAD  H2   single    0.850  0.020  0.980
 SH3  CAF  H3   single    0.970  0.020  1.090
 SH3  CAF  H4   single    0.970  0.020  1.090
 SH3  CAH  H5   single    0.970  0.020  1.090
 SH3  CAH  H6   single    0.970  0.020  1.090
 SH3  CAH  H7   single    0.970  0.020  1.090
 SH3  CAI  H8   single    0.970  0.020  1.090
 SH3  CAI  H9   single    0.970  0.020  1.090
 SH3  CAI  H10  single    0.970  0.020  1.090
 SH3  CAJ  H11  single    0.970  0.020  1.090
 SH3  OAK  H12  single    0.850  0.020  0.980
 SH3  NAN  H13  single    0.860  0.020  1.020
 SH3  CAO  H14  single    0.970  0.020  1.090
 SH3  CAO  H15  single    0.970  0.020  1.090
 SH3  CAP  H16  single    0.970  0.020  1.090
 SH3  CAP  H17  single    0.970  0.020  1.090
 SH3  NAS  H18  single    0.860  0.020  1.020
 SH3  CAT  H19  single    0.970  0.020  1.090
 SH3  CAT  H20  single    0.970  0.020  1.090
 SH3  CAU  H21  single    0.970  0.020  1.090
 SH3  CAU  H22  single    0.970  0.020  1.090
 SH3  CBD  H23  single    0.930  0.020  1.080
 SH3  CBA  H24  single    0.970  0.020  1.090
 SH3  CBA  H25  single    0.970  0.020  1.090
 SH3  CAX  H26  single    0.930  0.020  1.080
 SH3  CAW  H27  single    0.930  0.020  1.080

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
 SH3  H1   OAC  PAB  114.75  3.000
 SH3  OAE  PAB  OAA  116.16  3.000
 SH3  OAE  PAB  OAD  107.20  3.000
 SH3  OAA  PAB  OAD  109.86  3.000
 SH3  OAD  PAB  OAC  107.50  3.000
 SH3  OAE  PAB  OAC   96.82  3.000
 SH3  OAA  PAB  OAC  118.15  3.000
 SH3  H2   OAD  PAB  115.35  3.000
 SH3  CAF  OAE  PAB  119.71  3.000
 SH3  H4   CAF  H3   108.37  3.000
 SH3  H4   CAF  CAG  110.91  3.000
 SH3  H3   CAF  CAG  110.32  3.000
 SH3  H4   CAF  OAE  109.20  3.000
 SH3  H3   CAF  OAE  109.51  3.000
 SH3  CAG  CAF  OAE  108.51  3.000
 SH3  CAJ  CAG  CAI  107.64  3.000
 SH3  CAJ  CAG  CAH  109.94  3.000
 SH3  CAI  CAG  CAH  109.37  3.000
 SH3  CAJ  CAG  CAF  109.47  3.000
 SH3  CAH  CAG  CAF  109.95  3.000
 SH3  CAI  CAG  CAF  110.43  3.000
 SH3  H7   CAH  H6   107.90  3.000
 SH3  H7   CAH  H5   107.35  3.000
 SH3  H6   CAH  H5   106.64  3.000
 SH3  H7   CAH  CAG  112.52  3.000
 SH3  H6   CAH  CAG  111.28  3.000
 SH3  H5   CAH  CAG  110.88  3.000
 SH3  H10  CAI  H9   107.33  3.000
 SH3  H10  CAI  H8   107.94  3.000
 SH3  H9   CAI  H8   107.78  3.000
 SH3  H10  CAI  CAG  111.19  3.000
 SH3  H9   CAI  CAG  110.39  3.000
 SH3  H8   CAI  CAG  112.03  3.000
 SH3  H11  CAJ  CAL  109.00  3.000
 SH3  H11  CAJ  OAK  106.78  3.000
 SH3  CAL  CAJ  OAK  108.37  3.000
 SH3  H11  CAJ  CAG  106.36  3.000
 SH3  CAL  CAJ  CAG  113.46  3.000
 SH3  OAK  CAJ  CAG  112.60  3.000
 SH3  H12  OAK  CAJ  107.93  3.000
 SH3  NAN  CAL  OAM  123.16  3.000
 SH3  OAM  CAL  CAJ  120.14  3.000
 SH3  NAN  CAL  CAJ  116.70  3.000
 SH3  H13  NAN  CAO  118.34  3.000
 SH3  H13  NAN  CAL  118.71  3.000
 SH3  CAO  NAN  CAL  122.88  3.000
 SH3  H15  CAO  H14  107.23  3.000
 SH3  H15  CAO  CAP  110.03  3.000
 SH3  H14  CAO  CAP  110.01  3.000
 SH3  H15  CAO  NAN  109.75  3.000
 SH3  H14  CAO  NAN  109.95  3.000
 SH3  CAP  CAO  NAN  109.84  3.000
 SH3  H17  CAP  H16  107.02  3.000
 SH3  H17  CAP  CAQ  111.04  3.000
 SH3  H16  CAP  CAQ  107.75  3.000
 SH3  H17  CAP  CAO  110.17  3.000
 SH3  H16  CAP  CAO  109.77  3.000
 SH3  CAQ  CAP  CAO  110.96  3.000
 SH3  NAS  CAQ  OAR  123.48  3.000
 SH3  OAR  CAQ  CAP  121.63  3.000
 SH3  NAS  CAQ  CAP  114.89  3.000
 SH3  H18  NAS  CAT  117.76  3.000
 SH3  H18  NAS  CAQ  118.70  3.000
 SH3  CAT  NAS  CAQ  123.42  3.000
 SH3  H20  CAT  H19  106.81  3.000
 SH3  H20  CAT  CAU  109.77  3.000
 SH3  H19  CAT  CAU  110.08  3.000
 SH3  H20  CAT  NAS  108.86  3.000
 SH3  H19  CAT  NAS  107.83  3.000
 SH3  CAU  CAT  NAS  113.27  3.000
 SH3  H22  CAU  H21  106.99  3.000
 SH3  H22  CAU  CAV  110.03  3.000
 SH3  H21  CAU  CAV  110.26  3.000
 SH3  H22  CAU  CAT  109.38  3.000
 SH3  H21  CAU  CAT  108.99  3.000
 SH3  CAV  CAU  CAT  111.10  3.000
 SH3  CAW  CAV  CBD  119.80  3.000
 SH3  CAW  CAV  CAU  120.78  3.000
 SH3  CBD  CAV  CAU  119.36  3.000
 SH3  H23  CBD  CBC  121.24  3.000
 SH3  H23  CBD  CAV  121.13  3.000
 SH3  CBC  CBD  CAV  117.62  3.000
 SH3  CAY  CBC  OBB  109.37  3.000
 SH3  CAY  CBC  CBD  122.04  3.000
 SH3  OBB  CBC  CBD  128.58  3.000
 SH3  CBA  OBB  CBC  106.35  3.000
 SH3  H25  CBA  H24  110.16  3.000
 SH3  H25  CBA  OAZ  109.92  3.000
 SH3  H24  CBA  OAZ  109.82  3.000
 SH3  H25  CBA  OBB  109.86  3.000
 SH3  H24  CBA  OBB  109.79  3.000
 SH3  OAZ  CBA  OBB  107.24  3.000
 SH3  CAY  OAZ  CBA  106.32  3.000
 SH3  CAX  CAY  OAZ  129.03  3.000
 SH3  CAX  CAY  CBC  121.57  3.000
 SH3  OAZ  CAY  CBC  109.39  3.000
 SH3  H26  CAX  CAW  121.36  3.000
 SH3  H26  CAX  CAY  121.76  3.000
 SH3  CAW  CAX  CAY  116.87  3.000
 SH3  H27  CAW  CAX  118.62  3.000
 SH3  H27  CAW  CAV  119.28  3.000
 SH3  CAX  CAW  CAV  122.10  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
 SH3  CONST_01  CAY  CBC  CBD  CAV     0.00   0.0  0
 SH3  CONST_02  CAY  CAX  CAW  CAV     0.00   0.0  0
 SH3  CONST_03  CAX  CAY  CBC  CBD     0.00   0.0  0
 SH3  CONST_04  CAX  CAW  CAV  CBD     0.00   0.0  0
 SH3  CONST_05  CAW  CAX  CAY  CBC     0.00   0.0  0
 SH3  CONST_06  CAW  CAV  CBD  CBC     0.00   0.0  0
 SH3  CONST_07  CBC  CBD  CAV  CAU   180.00   0.0  0
 SH3  CONST_08  CAX  CAW  CAV  CAU   180.00   0.0  0
 SH3  CONST_09  H26  CAX  CAW  CAV   180.00   0.0  0
 SH3  CONST_10  H27  CAW  CAV  CBD   180.00   0.0  0
 SH3  CONST_11  H23  CBD  CBC  OBB     0.00   0.0  0
 SH3  CONST_12  CAO  NAN  CAL  CAJ   180.00   0.0  0
 SH3  CONST_13  CAO  NAN  CAL  OAM     0.00   0.0  0
 SH3  CONST_14  CAT  NAS  CAQ  CAP   180.00   0.0  0
 SH3  CONST_15  CAT  NAS  CAQ  OAR     0.00   0.0  0
 SH3  CONST_16  H13  NAN  CAL  CAJ     0.00   0.0  0
 SH3  CONST_17  H18  NAS  CAQ  CAP     0.00   0.0  0
 SH3  Var_01    OAZ  CBA  OBB  CBC    11.24  30.0  1
 SH3  Var_02    CAY  CBC  OBB  CBA    -7.01  30.0  1
 SH3  Var_03    CAX  CAY  OAZ  CBA  -174.32  30.0  1
 SH3  Var_04    CBD  CAV  CAU  CAT   -85.22  30.0  3
 SH3  Var_05    CAV  CAU  CAT  NAS   177.12  30.0  3
 SH3  Var_06    CAG  CAF  OAE  PAB  -179.12  30.0  1
 SH3  Var_07    CAI  CAG  CAF  OAE    60.35  30.0  3
 SH3  Var_08    CAP  CAO  NAN  CAL   175.32  30.0  3
 SH3  Var_09    CAQ  CAP  CAO  NAN  -177.87  30.0  1
 SH3  Var_10    NAS  CAQ  CAP  CAO  -137.17  30.0  3
 SH3  Var_11    CAU  CAT  NAS  CAQ    87.87  30.0  3
 SH3  Var_12    H8   CAI  CAG  CAF    60.99  30.0  3
 SH3  Var_13    H5   CAH  CAG  CAF    68.15  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
 SH3  chir_01  CAJ  CAG  OAK  CAL  negativ

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
 SH3  plan-1  CAJ  0.020
 SH3  plan-1  CAL  0.020
 SH3  plan-1  OAM  0.020
 SH3  plan-1  NAN  0.020
 SH3  plan-1  CAO  0.020
 SH3  plan-1  H13  0.020
 SH3  plan-2  CAU  0.020
 SH3  plan-2  CAV  0.020
 SH3  plan-2  CBD  0.020
 SH3  plan-2  CBC  0.020
 SH3  plan-2  OBB  0.020
 SH3  plan-2  OAZ  0.020
 SH3  plan-2  CAY  0.020
 SH3  plan-2  CAX  0.020
 SH3  plan-2  CAW  0.020
 SH3  plan-2  H23  0.020
 SH3  plan-2  H26  0.020
 SH3  plan-2  H27  0.020
 SH3  plan-3  CAP  0.020
 SH3  plan-3  CAQ  0.020
 SH3  plan-3  OAR  0.020
 SH3  plan-3  NAS  0.020
 SH3  plan-3  CAT  0.020
 SH3  plan-3  H18  0.020

