# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:18:22 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R)-N-(3-{[2-(1,3-benzodioxol-5-yl)ethyl]amino}-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[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
 SH2  SH2  (2R)-N-(3-{[2-(1,3-benzodioxol-5-yl)ethyl]amino}-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide  ligand  52  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SH2
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
 SH2  CAZ  C  CR16  0  -0.390  -5.1688  -0.5983   0.1733
 SH2  CAY  C  CR56  0   0.311  -6.5033  -0.5755  -0.1447
 SH2  OAX  O  O     0  -0.488  -7.2976  -1.6019  -0.5393
 SH2  CAW  C  CH2   0   0.069  -8.6244  -1.0919  -0.5400
 SH2  OAV  O  O     0  -0.488  -8.5235   0.3241  -0.4903
 SH2  CAU  C  CR56  0   0.282  -7.2470   0.5933  -0.1140
 SH2  CAT  C  CR16  0  -0.329  -6.6845   1.7940   0.2388
 SH2  CAS  C  CR16  0  -0.323  -5.3232   1.7818   0.5686
 SH2  CAR  C  CR6   0   0.106  -4.5673   0.6165   0.5435
 SH2  CAQ  C  CH2   0  -0.519  -3.0981   0.6476   0.8604
 SH2  CAP  C  CH2   0  -0.281  -2.2629   0.8877  -0.4015
 SH2  NAO  N  NH1   0  -0.634  -0.8422   0.9016  -0.1407
 SH2  CAM  C  C     0   0.564  -0.0885  -0.2098  -0.1078
 SH2  OAN  O  O     0  -0.504  -0.5452  -1.3260  -0.3175
 SH2  CAL  C  CH2   0  -0.591   1.3826   0.0197   0.1685
 SH2  CAK  C  CH2   0  -0.276   2.0537  -1.2084   0.7753
 SH2  NAJ  N  NH1   0  -0.624   3.4688  -1.0071   0.9876
 SH2  CAH  C  C     0   0.520   4.3790  -1.2056   0.0260
 SH2  OAI  O  O     0  -0.496   4.0831  -1.5795  -1.1018
 SH2  CAF  C  CH1   0  -0.029   5.8405  -0.9588   0.4150
 SH2  OAG  O  OH1   0  -0.666   6.0180  -1.0308   1.8127
 SH2  CAB  C  CT    0  -0.201   6.4247   0.3404  -0.2026
 SH2  CAA  C  CH3   0  -0.642   6.3018   0.3193  -1.7285
 SH2  CAC  C  CH3   0  -0.669   5.7104   1.5788   0.3480
 SH2  CAD  C  CH2   0  -0.105   7.9159   0.3652   0.1717
 SH2  OAE  O  OH1   0  -0.669   8.5254   1.5070  -0.3808
 SH2  H1   H  HCR6  0   0.265  -4.5969  -1.5177   0.1480
 SH2  H2   H  HCH2  0   0.245  -9.1358  -1.3949  -1.4533
 SH2  H3   H  HCR6  0   0.270  -7.2605   2.7093   0.2629
 SH2  H4   H  HCR6  0   0.251  -4.8521   2.7124   0.8601
 SH2  H5   H  HCH2  0   0.248  -2.8856   1.4372   1.5845
 SH2  H6   H  HCH2  0   0.251  -2.7920  -0.2969   1.3153
 SH2  H7   H  HCH2  0   0.246  -2.4821   0.1209  -1.1453
 SH2  H8   H  HCH2  0   0.256  -2.5318   1.8482  -0.8419
 SH2  H9   H  HNH1  0   0.400  -0.4178   1.7832   0.0968
 SH2  H10  H  HCH2  0   0.280   1.8680   0.2685  -0.7802
 SH2  H11  H  HCH2  0   0.259   1.5184   0.8837   0.8228
 SH2  H12  H  HCH2  0   0.259   1.6059  -1.4462   1.7396
 SH2  H13  H  HCH2  0   0.247   1.9090  -2.0724   0.1288
 SH2  H14  H  HNH1  0   0.395   3.7808  -0.7537   1.9095
 SH2  H15  H  HCH1  0   0.260   6.3957  -1.8015  -0.0140
 SH2  H16  H  HOH1  0   0.453   6.0116  -0.1460   2.1917
 SH2  H17  H  HCH3  0   0.235   5.2699   0.4137  -2.0596
 SH2  H18  H  HCH3  0   0.233   6.8598   1.1517  -2.1541
 SH2  H19  H  HCH3  0   0.223   6.7039  -0.6046  -2.1493
 SH2  H20  H  HCH3  0   0.220   5.8215   1.6945   1.4302
 SH2  H21  H  HCH3  0   0.253   6.1141   2.4850  -0.1009
 SH2  H22  H  HCH3  0   0.237   4.6419   1.5528   0.1280
 SH2  H23  H  HCH2  0   0.199   8.0325   0.3583   1.2617
 SH2  H24  H  HCH2  0   0.199   8.3807  -0.5588  -0.2041
 SH2  H25  H  HOH1  0   0.456   9.4418   1.5224  -0.0919
 SH2  H26  H  HCH2  0   0.231  -9.1633  -1.4581   0.3412

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
 SH2  OAX  CAW  single    1.421  0.020  1.421
 SH2  OAX  CAY  single    1.357  0.020  1.357
 SH2  CAZ  CAY  aromatic  1.372  0.020  1.372
 SH2  CAZ  CAR  aromatic  1.405  0.020  1.405
 SH2  CAW  OAV  single    1.420  0.020  1.420
 SH2  CAY  CAU  aromatic  1.386  0.020  1.386
 SH2  CAQ  CAR  single    1.503  0.020  1.503
 SH2  CAQ  CAP  single    1.532  0.020  1.532
 SH2  CAR  CAS  aromatic  1.389  0.020  1.389
 SH2  CAU  OAV  single    1.358  0.020  1.358
 SH2  CAU  CAT  aromatic  1.372  0.020  1.372
 SH2  CAS  CAT  aromatic  1.401  0.020  1.401
 SH2  CAP  NAO  single    1.444  0.020  1.444
 SH2  NAO  CAM  single    1.343  0.020  1.343
 SH2  OAN  CAM  double    1.224  0.020  1.224
 SH2  CAM  CAL  single    1.514  0.020  1.514
 SH2  OAI  CAH  double    1.224  0.020  1.224
 SH2  NAJ  CAH  single    1.339  0.020  1.339
 SH2  NAJ  CAK  single    1.445  0.020  1.445
 SH2  CAH  CAF  single    1.532  0.020  1.532
 SH2  CAL  CAK  single    1.525  0.020  1.525
 SH2  CAC  CAB  single    1.532  0.020  1.532
 SH2  CAA  CAB  single    1.531  0.020  1.531
 SH2  CAF  CAB  single    1.553  0.020  1.553
 SH2  CAF  OAG  single    1.411  0.020  1.411
 SH2  CAB  CAD  single    1.538  0.020  1.538
 SH2  CAD  OAE  single    1.407  0.020  1.407
 SH2  CAZ  H1   single    0.930  0.020  1.080
 SH2  CAW  H2   single    0.970  0.020  1.090
 SH2  CAT  H3   single    0.930  0.020  1.080
 SH2  CAS  H4   single    0.930  0.020  1.080
 SH2  CAQ  H5   single    0.970  0.020  1.090
 SH2  CAQ  H6   single    0.970  0.020  1.090
 SH2  CAP  H7   single    0.970  0.020  1.090
 SH2  CAP  H8   single    0.970  0.020  1.090
 SH2  NAO  H9   single    0.860  0.020  1.020
 SH2  CAL  H10  single    0.970  0.020  1.090
 SH2  CAL  H11  single    0.970  0.020  1.090
 SH2  CAK  H12  single    0.970  0.020  1.090
 SH2  CAK  H13  single    0.970  0.020  1.090
 SH2  NAJ  H14  single    0.860  0.020  1.020
 SH2  CAF  H15  single    0.970  0.020  1.090
 SH2  OAG  H16  single    0.850  0.020  0.980
 SH2  CAA  H17  single    0.970  0.020  1.090
 SH2  CAA  H18  single    0.970  0.020  1.090
 SH2  CAA  H19  single    0.970  0.020  1.090
 SH2  CAC  H20  single    0.970  0.020  1.090
 SH2  CAC  H21  single    0.970  0.020  1.090
 SH2  CAC  H22  single    0.970  0.020  1.090
 SH2  CAD  H23  single    0.970  0.020  1.090
 SH2  CAD  H24  single    0.970  0.020  1.090
 SH2  OAE  H25  single    0.850  0.020  0.980
 SH2  CAW  H26  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
 SH2  H1   CAZ  CAR  120.93  3.000
 SH2  H1   CAZ  CAY  121.48  3.000
 SH2  CAR  CAZ  CAY  117.58  3.000
 SH2  CAU  CAY  OAX  109.30  3.000
 SH2  CAU  CAY  CAZ  122.07  3.000
 SH2  OAX  CAY  CAZ  128.63  3.000
 SH2  CAW  OAX  CAY  105.97  3.000
 SH2  H26  CAW  H2   110.50  3.000
 SH2  H26  CAW  OAV  109.87  3.000
 SH2  H2   CAW  OAV  109.86  3.000
 SH2  H26  CAW  OAX  109.80  3.000
 SH2  H2   CAW  OAX  109.80  3.000
 SH2  OAV  CAW  OAX  106.94  3.000
 SH2  CAU  OAV  CAW  105.91  3.000
 SH2  CAT  CAU  OAV  129.06  3.000
 SH2  CAT  CAU  CAY  121.59  3.000
 SH2  OAV  CAU  CAY  109.34  3.000
 SH2  H3   CAT  CAS  121.31  3.000
 SH2  H3   CAT  CAU  121.87  3.000
 SH2  CAS  CAT  CAU  116.83  3.000
 SH2  H4   CAS  CAR  119.27  3.000
 SH2  H4   CAS  CAT  118.59  3.000
 SH2  CAR  CAS  CAT  122.14  3.000
 SH2  CAQ  CAR  CAS  120.71  3.000
 SH2  CAS  CAR  CAZ  119.80  3.000
 SH2  CAQ  CAR  CAZ  119.46  3.000
 SH2  H6   CAQ  H5   107.13  3.000
 SH2  H6   CAQ  CAP  109.01  3.000
 SH2  H5   CAQ  CAP  109.07  3.000
 SH2  H6   CAQ  CAR  110.11  3.000
 SH2  H5   CAQ  CAR  110.17  3.000
 SH2  CAP  CAQ  CAR  111.25  3.000
 SH2  H8   CAP  H7   107.12  3.000
 SH2  H8   CAP  NAO  107.88  3.000
 SH2  H7   CAP  NAO  109.13  3.000
 SH2  H8   CAP  CAQ  109.65  3.000
 SH2  H7   CAP  CAQ  110.00  3.000
 SH2  NAO  CAP  CAQ  112.89  3.000
 SH2  H9   NAO  CAM  118.82  3.000
 SH2  H9   NAO  CAP  117.75  3.000
 SH2  CAM  NAO  CAP  123.25  3.000
 SH2  CAL  CAM  OAN  122.13  3.000
 SH2  CAL  CAM  NAO  115.10  3.000
 SH2  OAN  CAM  NAO  122.74  3.000
 SH2  H11  CAL  H10  106.52  3.000
 SH2  H11  CAL  CAK  110.11  3.000
 SH2  H10  CAL  CAK  109.43  3.000
 SH2  H11  CAL  CAM  110.49  3.000
 SH2  H10  CAL  CAM  107.89  3.000
 SH2  CAK  CAL  CAM  112.21  3.000
 SH2  H13  CAK  H12  107.32  3.000
 SH2  H13  CAK  NAJ  109.15  3.000
 SH2  H12  CAK  NAJ  107.63  3.000
 SH2  H13  CAK  CAL  110.13  3.000
 SH2  H12  CAK  CAL  110.30  3.000
 SH2  NAJ  CAK  CAL  112.16  3.000
 SH2  H14  NAJ  CAH  119.00  3.000
 SH2  H14  NAJ  CAK  118.27  3.000
 SH2  CAH  NAJ  CAK  122.66  3.000
 SH2  CAF  CAH  OAI  120.90  3.000
 SH2  CAF  CAH  NAJ  116.24  3.000
 SH2  OAI  CAH  NAJ  122.85  3.000
 SH2  H15  CAF  CAB  107.27  3.000
 SH2  H15  CAF  OAG  106.54  3.000
 SH2  CAB  CAF  OAG  112.92  3.000
 SH2  H15  CAF  CAH  105.06  3.000
 SH2  OAG  CAF  CAH  111.30  3.000
 SH2  CAB  CAF  CAH  113.12  3.000
 SH2  H16  OAG  CAF  110.02  3.000
 SH2  CAD  CAB  CAC  110.59  3.000
 SH2  CAD  CAB  CAA  108.71  3.000
 SH2  CAC  CAB  CAA  109.39  3.000
 SH2  CAD  CAB  CAF  106.35  3.000
 SH2  CAA  CAB  CAF  110.77  3.000
 SH2  CAC  CAB  CAF  110.98  3.000
 SH2  H19  CAA  H18  107.91  3.000
 SH2  H19  CAA  H17  107.79  3.000
 SH2  H18  CAA  H17  107.50  3.000
 SH2  H19  CAA  CAB  111.48  3.000
 SH2  H18  CAA  CAB  109.75  3.000
 SH2  H17  CAA  CAB  112.23  3.000
 SH2  H22  CAC  H21  107.44  3.000
 SH2  H22  CAC  H20  107.54  3.000
 SH2  H21  CAC  H20  106.39  3.000
 SH2  H22  CAC  CAB  111.40  3.000
 SH2  H21  CAC  CAB  110.59  3.000
 SH2  H20  CAC  CAB  113.18  3.000
 SH2  H24  CAD  H23  106.82  3.000
 SH2  H24  CAD  OAE  111.36  3.000
 SH2  H23  CAD  OAE  110.45  3.000
 SH2  H24  CAD  CAB  108.24  3.000
 SH2  H23  CAD  CAB  110.19  3.000
 SH2  OAE  CAD  CAB  109.72  3.000
 SH2  H25  OAE  CAD  107.94  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
 SH2  CONST_01  CAT  CAU  CAY  CAZ     0.00   0.0  0
 SH2  CONST_02  CAT  CAS  CAR  CAZ     0.00   0.0  0
 SH2  CONST_03  CAS  CAR  CAZ  CAY     0.00   0.0  0
 SH2  CONST_04  CAS  CAT  CAU  CAY     0.00   0.0  0
 SH2  CONST_05  CAR  CAZ  CAY  CAU     0.00   0.0  0
 SH2  CONST_06  CAR  CAS  CAT  CAU     0.00   0.0  0
 SH2  CONST_07  CAQ  CAR  CAZ  CAY   180.00   0.0  0
 SH2  CONST_08  CAQ  CAR  CAS  CAT   180.00   0.0  0
 SH2  CONST_09  H4   CAS  CAR  CAZ   180.00   0.0  0
 SH2  CONST_10  H3   CAT  CAU  CAY   180.00   0.0  0
 SH2  CONST_11  H1   CAZ  CAY  OAX     0.00   0.0  0
 SH2  CONST_12  OAN  CAM  NAO  CAP     0.00   0.0  0
 SH2  CONST_13  CAL  CAM  NAO  CAP   180.00   0.0  0
 SH2  CONST_14  OAI  CAH  NAJ  CAK     0.00   0.0  0
 SH2  CONST_15  CAF  CAH  NAJ  CAK   180.00   0.0  0
 SH2  CONST_16  H9   NAO  CAM  OAN   180.00   0.0  0
 SH2  CONST_17  H14  NAJ  CAH  OAI   180.00   0.0  0
 SH2  Var_01    OAV  CAW  OAX  CAY    15.50  30.0  1
 SH2  Var_02    CAU  CAY  OAX  CAW    -9.66  30.0  1
 SH2  Var_03    CAT  CAU  OAV  CAW  -171.11  30.0  1
 SH2  Var_04    CAP  CAQ  CAR  CAZ    88.14  30.0  2
 SH2  Var_05    NAO  CAP  CAQ  CAR  -179.02  30.0  3
 SH2  Var_06    CAM  NAO  CAP  CAQ    85.74  30.0  3
 SH2  Var_07    CAK  CAL  CAM  NAO   155.42  30.0  3
 SH2  Var_08    NAJ  CAK  CAL  CAM   177.62  30.0  3
 SH2  Var_09    CAH  NAJ  CAK  CAL   -84.80  30.0  2
 SH2  Var_10    OAE  CAD  CAB  CAF   178.74  30.0  3
 SH2  Var_11    H20  CAC  CAB  CAF    61.64  30.0  3
 SH2  Var_12    H17  CAA  CAB  CAF    69.91  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
 SH2  chir_01  CAF  CAH  CAB  OAG  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
 SH2  plan-1  CAP  0.020
 SH2  plan-1  NAO  0.020
 SH2  plan-1  CAM  0.020
 SH2  plan-1  OAN  0.020
 SH2  plan-1  CAL  0.020
 SH2  plan-1  H9   0.020
 SH2  plan-2  CAZ  0.020
 SH2  plan-2  CAY  0.020
 SH2  plan-2  OAX  0.020
 SH2  plan-2  OAV  0.020
 SH2  plan-2  CAU  0.020
 SH2  plan-2  CAT  0.020
 SH2  plan-2  CAS  0.020
 SH2  plan-2  CAR  0.020
 SH2  plan-2  CAQ  0.020
 SH2  plan-2  H1   0.020
 SH2  plan-2  H3   0.020
 SH2  plan-2  H4   0.020
 SH2  plan-3  CAK  0.020
 SH2  plan-3  NAJ  0.020
 SH2  plan-3  CAH  0.020
 SH2  plan-3  OAI  0.020
 SH2  plan-3  CAF  0.020
 SH2  plan-3  H14  0.020

