# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:37:32 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2~{S})-3-methyl-2-[(4-octoxyphenyl)carbonylamino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOc1ccc(cc1)C(=O)N[C@@H](C(C)C)C(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
 H8R  H8R  '(2~{S})-3-methyl-2-[(4-octoxyphenyl)carbonylamino]butanoic acid'  ligand  55  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H8R
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
 H8R  CG2  C  CH3    0  -0.657  -5.5396   2.7753  -0.5270
 H8R  CB   C  CH1    0  -0.279  -5.8788   1.9294   0.6992
 H8R  CG1  C  CH3    0  -0.646  -7.3184   2.1828   1.1316
 H8R  CA   C  CH1    0  -0.138  -5.5893   0.4284   0.5056
 H8R  C    C  C      0   0.411  -6.2766  -0.1402  -0.7603
 H8R  O    O  O      0  -0.605  -5.5888  -0.2241  -1.7925
 H8R  OXT  O  OC    -1  -0.610  -7.4819  -0.4353  -0.6324
 H8R  N    N  NH1    0  -0.652  -4.1556   0.2277   0.4859
 H8R  CAQ  C  C      0   0.533  -3.6137  -0.9981   0.5342
 H8R  OAR  O  O      0  -0.504  -4.2826  -2.0136   0.6966
 H8R  CAP  C  CR6    0  -0.066  -2.1293  -1.0704   0.4072
 H8R  CAA  C  CR16   0  -0.256  -1.5507  -2.2620  -0.0341
 H8R  CAB  C  CR16   0  -0.338  -0.1834  -2.3850  -0.1653
 H8R  CAO  C  CR16   0  -0.280  -1.2852  -0.0184   0.7450
 H8R  CAN  C  CR16   0  -0.372   0.0937  -0.1297   0.6329
 H8R  CAC  C  CR6    0   0.390   0.6562  -1.3162   0.1647
 H8R  OAD  O  O2     0  -0.471   1.9724  -1.5192   0.0040
 H8R  CAE  C  CH2    0  -0.173   2.8726  -0.4582   0.2957
 H8R  CAF  C  CH2    0  -0.455   4.2743  -0.8998  -0.0652
 H8R  CAG  C  CH2    0  -0.425   5.2880   0.2031   0.2181
 H8R  CAH  C  CH2    0  -0.412   6.7100  -0.1831  -0.1676
 H8R  CAI  C  CH2    0  -0.412   7.7206   0.9229   0.1096
 H8R  CAJ  C  CH2    0  -0.406   9.1440   0.5521  -0.2865
 H8R  CAK  C  CH2    0  -0.418  10.1532   1.6608  -0.0134
 H8R  CAL  C  CH3    0  -0.663  11.5730   1.2792  -0.4082
 H8R  H1   H  HCH3   0   0.222  -6.2110   2.5566  -1.3586
 H8R  H2   H  HCH3   0   0.226  -5.6433   3.8352  -0.2900
 H8R  H3   H  HCH3   0   0.221  -4.5188   2.6246  -0.8826
 H8R  H4   H  HCH1   0   0.227  -5.2313   2.2567   1.5220
 H8R  H5   H  HCH3   0   0.223  -8.0240   1.9262   0.3423
 H8R  H6   H  HCH3   0   0.220  -7.5801   1.5969   2.0144
 H8R  H7   H  HCH3   0   0.218  -7.4578   3.2365   1.3783
 H8R  H8   H  HCH1   0   0.228  -5.9875  -0.0953   1.3796
 H8R  H10  H  HNH1   0   0.393  -3.5849   0.9807   0.1365
 H8R  H11  H  HCR6   0   0.257  -2.1825  -3.1024  -0.2899
 H8R  H12  H  HCR6   0   0.265   0.2497  -3.3101  -0.5244
 H8R  H13  H  HCR6   0   0.259  -1.6854   0.9103   1.1321
 H8R  H14  H  HCR6   0   0.284   0.7057   0.7135   0.9213
 H8R  H15  H  HCH2   0   0.223   2.6003   0.4345  -0.2788
 H8R  H16  H  HCH2   0   0.223   2.8143  -0.1975   1.3589
 H8R  H17  H  HCH2   0   0.230   4.5393  -1.7977   0.5009
 H8R  H18  H  HCH2   0   0.229   4.3096  -1.1671  -1.1253
 H8R  H19  H  HCH2   0   0.216   4.9998   1.1098  -0.3248
 H8R  H20  H  HCH2   0   0.217   5.2577   0.4629   1.2814
 H8R  H21  H  HCH2   0   0.210   7.0040  -1.0884   0.3748
 H8R  H22  H  HCH2   0   0.210   6.7395  -0.4436  -1.2310
 H8R  H23  H  HCH2   0   0.207   7.4185   1.8300  -0.4258
 H8R  H24  H  HCH2   0   0.207   7.6946   1.1782   1.1746
 H8R  H25  H  HCH2   0   0.206   9.4484  -0.3535   0.2504
 H8R  H26  H  HCH2   0   0.206   9.1699   0.2943  -1.3511
 H8R  H27  H  HCH2   0   0.210   9.8503   2.5646  -0.5514
 H8R  H28  H  HCH2   0   0.210  10.1262   1.9195   1.0496
 H8R  H29  H  HCH3   0   0.216  11.9107   0.3988   0.1418
 H8R  H30  H  HCH3   0   0.215  11.6390   1.0463  -1.4728
 H8R  H31  H  HCH3   0   0.226  12.2780   2.0855  -0.2024

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
 H8R  CAI  CAJ  single    1.523  0.020  1.523
 H8R  CAI  CAH  single    1.524  0.020  1.524
 H8R  CAL  CAK  single    1.522  0.020  1.522
 H8R  CAK  CAJ  single    1.524  0.020  1.524
 H8R  CAG  CAH  single    1.523  0.020  1.523
 H8R  CAG  CAF  single    1.525  0.020  1.525
 H8R  CAF  CAE  single    1.513  0.020  1.513
 H8R  CAE  OAD  single    1.422  0.020  1.422
 H8R  OAD  CAC  single    1.341  0.020  1.341
 H8R  CAC  CAB  aromatic  1.399  0.020  1.399
 H8R  CAC  CAN  aromatic  1.394  0.020  1.394
 H8R  CAB  CAA  aromatic  1.379  0.020  1.379
 H8R  CAN  CAO  aromatic  1.388  0.020  1.388
 H8R  CAA  CAP  aromatic  1.396  0.020  1.396
 H8R  CAO  CAP  aromatic  1.390  0.020  1.390
 H8R  CAP  CAQ  single    1.492  0.020  1.492
 H8R  CAQ  OAR  double    1.227  0.020  1.227
 H8R  CAQ  N    single    1.341  0.020  1.341
 H8R  N    CA   single    1.448  0.020  1.448
 H8R  CG2  CB   single    1.528  0.020  1.528
 H8R  CA   CB   single    1.541  0.020  1.541
 H8R  CA   C    single    1.549  0.020  1.549
 H8R  CB   CG1  single    1.524  0.020  1.524
 H8R  C    O    deloc     1.243  0.020  1.243
 H8R  C    OXT  deloc     1.247  0.020  1.247
 H8R  CG2  H1   single    0.970  0.020  1.090
 H8R  CG2  H2   single    0.970  0.020  1.090
 H8R  CG2  H3   single    0.970  0.020  1.090
 H8R  CB   H4   single    0.970  0.020  1.090
 H8R  CG1  H5   single    0.970  0.020  1.090
 H8R  CG1  H6   single    0.970  0.020  1.090
 H8R  CG1  H7   single    0.970  0.020  1.090
 H8R  CA   H8   single    0.970  0.020  1.090
 H8R  N    H10  single    0.890  0.020  1.040
 H8R  CAA  H11  single    0.930  0.020  1.080
 H8R  CAB  H12  single    0.930  0.020  1.080
 H8R  CAO  H13  single    0.930  0.020  1.080
 H8R  CAN  H14  single    0.930  0.020  1.080
 H8R  CAE  H15  single    0.970  0.020  1.090
 H8R  CAE  H16  single    0.970  0.020  1.090
 H8R  CAF  H17  single    0.970  0.020  1.090
 H8R  CAF  H18  single    0.970  0.020  1.090
 H8R  CAG  H19  single    0.970  0.020  1.090
 H8R  CAG  H20  single    0.970  0.020  1.090
 H8R  CAH  H21  single    0.970  0.020  1.090
 H8R  CAH  H22  single    0.970  0.020  1.090
 H8R  CAI  H23  single    0.970  0.020  1.090
 H8R  CAI  H24  single    0.970  0.020  1.090
 H8R  CAJ  H25  single    0.970  0.020  1.090
 H8R  CAJ  H26  single    0.970  0.020  1.090
 H8R  CAK  H27  single    0.970  0.020  1.090
 H8R  CAK  H28  single    0.970  0.020  1.090
 H8R  CAL  H29  single    0.970  0.020  1.090
 H8R  CAL  H30  single    0.970  0.020  1.090
 H8R  CAL  H31  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
 H8R  H3   CG2  H2   107.08  3.000
 H8R  H3   CG2  H1   107.44  3.000
 H8R  H2   CG2  H1   107.57  3.000
 H8R  H3   CG2  CB   113.12  3.000
 H8R  H2   CG2  CB   110.02  3.000
 H8R  H1   CG2  CB   111.36  3.000
 H8R  H4   CB   CA   105.90  3.000
 H8R  H4   CB   CG1  107.16  3.000
 H8R  CA   CB   CG1  112.03  3.000
 H8R  H4   CB   CG2  107.80  3.000
 H8R  CG1  CB   CG2  110.20  3.000
 H8R  CA   CB   CG2  113.38  3.000
 H8R  H7   CG1  H6   107.75  3.000
 H8R  H7   CG1  H5   107.97  3.000
 H8R  H6   CG1  H5   107.72  3.000
 H8R  H7   CG1  CB   110.20  3.000
 H8R  H6   CG1  CB   111.51  3.000
 H8R  H5   CG1  CB   111.53  3.000
 H8R  H8   CA   N    107.76  3.000
 H8R  H8   CA   C    108.40  3.000
 H8R  N    CA   C    112.17  3.000
 H8R  H8   CA   CB   107.31  3.000
 H8R  C    CA   CB   112.14  3.000
 H8R  N    CA   CB   108.84  3.000
 H8R  OXT  C    O    127.13  3.000
 H8R  OXT  C    CA   115.59  3.000
 H8R  O    C    CA   117.26  3.000
 H8R  H10  N    CAQ  117.83  3.000
 H8R  H10  N    CA   117.52  3.000
 H8R  CAQ  N    CA   121.76  3.000
 H8R  CAP  CAQ  OAR  120.92  3.000
 H8R  OAR  CAQ  N    122.75  3.000
 H8R  CAP  CAQ  N    116.32  3.000
 H8R  CAO  CAP  CAA  118.10  3.000
 H8R  CAO  CAP  CAQ  123.15  3.000
 H8R  CAA  CAP  CAQ  118.73  3.000
 H8R  H11  CAA  CAB  119.16  3.000
 H8R  H11  CAA  CAP  119.71  3.000
 H8R  CAB  CAA  CAP  121.13  3.000
 H8R  H12  CAB  CAC  119.41  3.000
 H8R  H12  CAB  CAA  120.28  3.000
 H8R  CAC  CAB  CAA  120.30  3.000
 H8R  H13  CAO  CAN  117.70  3.000
 H8R  H13  CAO  CAP  120.76  3.000
 H8R  CAN  CAO  CAP  121.52  3.000
 H8R  H14  CAN  CAC  121.67  3.000
 H8R  H14  CAN  CAO  118.58  3.000
 H8R  CAC  CAN  CAO  119.75  3.000
 H8R  OAD  CAC  CAN  124.40  3.000
 H8R  CAN  CAC  CAB  119.17  3.000
 H8R  OAD  CAC  CAB  116.43  3.000
 H8R  CAE  OAD  CAC  118.93  3.000
 H8R  H16  CAE  H15  107.55  3.000
 H8R  H16  CAE  CAF  110.49  3.000
 H8R  H15  CAE  CAF  110.05  3.000
 H8R  H16  CAE  OAD  110.04  3.000
 H8R  H15  CAE  OAD  110.06  3.000
 H8R  CAF  CAE  OAD  108.65  3.000
 H8R  H18  CAF  H17  107.04  3.000
 H8R  H18  CAF  CAG  109.60  3.000
 H8R  H17  CAF  CAG  109.66  3.000
 H8R  H18  CAF  CAE  109.42  3.000
 H8R  H17  CAF  CAE  109.91  3.000
 H8R  CAG  CAF  CAE  111.12  3.000
 H8R  H20  CAG  H19  106.12  3.000
 H8R  H20  CAG  CAH  109.38  3.000
 H8R  H19  CAG  CAH  109.27  3.000
 H8R  H20  CAG  CAF  109.50  3.000
 H8R  H19  CAG  CAF  109.38  3.000
 H8R  CAH  CAG  CAF  112.97  3.000
 H8R  H22  CAH  H21  106.08  3.000
 H8R  H22  CAH  CAI  109.35  3.000
 H8R  H21  CAH  CAI  109.38  3.000
 H8R  H22  CAH  CAG  109.35  3.000
 H8R  H21  CAH  CAG  109.55  3.000
 H8R  CAI  CAH  CAG  112.90  3.000
 H8R  H24  CAI  H23  105.99  3.000
 H8R  H24  CAI  CAJ  109.38  3.000
 H8R  H23  CAI  CAJ  109.40  3.000
 H8R  H24  CAI  CAH  109.29  3.000
 H8R  H23  CAI  CAH  109.21  3.000
 H8R  CAJ  CAI  CAH  113.32  3.000
 H8R  H26  CAJ  H25  105.96  3.000
 H8R  H26  CAJ  CAK  109.25  3.000
 H8R  H25  CAJ  CAK  109.23  3.000
 H8R  H26  CAJ  CAI  109.39  3.000
 H8R  H25  CAJ  CAI  109.47  3.000
 H8R  CAK  CAJ  CAI  113.27  3.000
 H8R  H28  CAK  H27  105.99  3.000
 H8R  H28  CAK  CAL  109.53  3.000
 H8R  H27  CAK  CAL  109.73  3.000
 H8R  H28  CAK  CAJ  109.25  3.000
 H8R  H27  CAK  CAJ  109.23  3.000
 H8R  CAL  CAK  CAJ  112.88  3.000
 H8R  H31  CAL  H30  107.62  3.000
 H8R  H31  CAL  H29  107.53  3.000
 H8R  H30  CAL  H29  107.49  3.000
 H8R  H31  CAL  CAK  111.63  3.000
 H8R  H30  CAL  CAK  111.27  3.000
 H8R  H29  CAL  CAK  111.10  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
 H8R  CONST_01  CAC  CAB  CAA  CAP     0.00   0.0  0
 H8R  CONST_02  CAC  CAN  CAO  CAP     0.00   0.0  0
 H8R  CONST_03  CAN  CAC  CAB  CAA     0.00   0.0  0
 H8R  CONST_04  CAN  CAO  CAP  CAA     0.00   0.0  0
 H8R  CONST_05  CAO  CAN  CAC  CAB     0.00   0.0  0
 H8R  CONST_06  CAO  CAP  CAA  CAB     0.00   0.0  0
 H8R  CONST_07  CAB  CAA  CAP  CAQ   180.00   0.0  0
 H8R  CONST_08  CAN  CAO  CAP  CAQ   180.00   0.0  0
 H8R  CONST_09  OAD  CAC  CAB  CAA   180.00   0.0  0
 H8R  CONST_10  OAD  CAC  CAN  CAO   180.00   0.0  0
 H8R  CONST_11  H12  CAB  CAA  CAP   180.00   0.0  0
 H8R  CONST_12  H14  CAN  CAO  CAP   180.00   0.0  0
 H8R  CONST_13  H13  CAO  CAP  CAA   180.00   0.0  0
 H8R  CONST_14  H11  CAA  CAP  CAO   180.00   0.0  0
 H8R  CONST_15  CAP  CAQ  N    CA    180.00   0.0  0
 H8R  CONST_17  OAR  CAQ  N    CA      0.00   0.0  0
 H8R  Var_01    CAA  CAP  CAQ  N    -156.91  30.0  2
 H8R  Var_02    CAF  CAE  OAD  CAC  -175.67  30.0  2
 H8R  Var_03    CAG  CAF  CAE  OAD   179.65  30.0  2
 H8R  Var_04    CAH  CAG  CAF  CAE  -178.36  30.0  1
 H8R  Var_05    CAI  CAH  CAG  CAF   179.71  30.0  3
 H8R  Var_06    CAJ  CAI  CAH  CAG  -179.39  30.0  1
 H8R  Var_07    CAK  CAJ  CAI  CAH   179.80  30.0  3
 H8R  Var_08    CAL  CAK  CAJ  CAI   179.81  30.0  2
 H8R  Var_09    H5   CG1  CB   CG2    60.18  30.0  3
 H8R  Var_10    H1   CG2  CB   CG1   -58.44  30.0  3
 H8R  Var_11    H29  CAL  CAK  CAJ   -59.86  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
 H8R  chir_01  CA  N  CB  C  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
 H8R  plan-1  CAQ  0.020
 H8R  plan-1  CAP  0.020
 H8R  plan-1  CAA  0.020
 H8R  plan-1  CAB  0.020
 H8R  plan-1  CAO  0.020
 H8R  plan-1  CAN  0.020
 H8R  plan-1  CAC  0.020
 H8R  plan-1  OAD  0.020
 H8R  plan-1  H11  0.020
 H8R  plan-1  H12  0.020
 H8R  plan-1  H13  0.020
 H8R  plan-1  H14  0.020
 H8R  plan-2  CA   0.020
 H8R  plan-2  N    0.020
 H8R  plan-2  CAQ  0.020
 H8R  plan-2  OAR  0.020
 H8R  plan-2  CAP  0.020
 H8R  plan-2  H10  0.020
 H8R  plan-3  CA   0.020
 H8R  plan-3  C    0.020
 H8R  plan-3  O    0.020
 H8R  plan-3  OXT  0.020

