# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:24:34 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{R})-2-[[(2~{R})-5-chloranyl-1-methyl-2,3-dihydroindol-2-yl]carbonylamino]-2-cyclohexyl-ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H](Cc2cc(Cl)ccc12)C(=O)N[C@H](C3CCCCC3)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
 E0N  E0N  '(2~{R})-2-[[(2~{R})-5-chloranyl-1-methyl-2,3-dihydroindol-2-yl]carbonylamino]-2-cyclohexyl-ethanoic acid'  ligand  47  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E0N
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
 E0N  C10   C   CH2   0  -0.492   1.4274   0.1634  -0.9109
 E0N  C15   C   CH1   0  -0.111  -2.6619  -0.0881   0.8984
 E0N  C20   C   CH2   0  -0.418  -5.2121  -0.1536   0.7884
 E0N  C21   C   CH2   0  -0.434  -6.4043  -0.6172  -0.0441
 E0N  C22   C   CH2   0  -0.431  -6.4297   0.0656  -1.4078
 E0N  C24   C   CH2   0  -0.427  -3.9240   0.3269  -1.3136
 E0N  C01   C   CH3   0  -0.544   1.9150  -2.6770   1.4525
 E0N  C03   C   CR56  0   0.418   3.1672  -1.0534   0.1072
 E0N  C04   C   CR16  0  -0.351   4.4644  -1.4919   0.3361
 E0N  C05   C   CR16  0  -0.218   5.4956  -0.9528  -0.4307
 E0N  C06   C   CR6   0  -0.064   5.2218  -0.0075  -1.4034
 E0N  C08   C   CR16  0  -0.287   3.9185   0.4256  -1.6480
 E0N  C09   C   CR56  0  -0.006   2.9028  -0.1112  -0.8915
 E0N  C11   C   CR15  0  -0.186   0.8745  -0.9912  -0.0426
 E0N  C12   C   C     0   0.551  -0.2724  -0.5044   0.8261
 E0N  C16   C   C     0   0.537  -2.4818   1.4021   1.1465
 E0N  C19   C   CH1   0  -0.307  -3.9030  -0.3926   0.0366
 E0N  C23   C   CH2   0  -0.430  -5.1136  -0.1347  -2.1512
 E0N  N02   N   NR5   0  -0.520   2.0073  -1.4222   0.7522
 E0N  N14   N   NH1   0  -0.656  -1.4829  -0.6124   0.2595
 E0N  O13   O   O     0  -0.479  -0.1029  -0.0040   1.9254
 E0N  O17   O   O     0  -0.434  -1.8632   2.1424   0.4272
 E0N  O18   O   OH1   0  -0.587  -3.1192   1.7964   2.2402
 E0N  CL7   CL  CL    0  -0.149   6.5233   0.6466  -2.3547
 E0N  H102  H   HCH2  0   0.273   1.2090   1.1376  -0.4637
 E0N  H101  H   HCH2  0   0.276   0.9957   0.1601  -1.9102
 E0N  H151  H   HCH1  0   0.286  -2.8051  -0.5814   1.8652
 E0N  H202  H   HCH2  0   0.221  -5.3318   0.9101   1.0148
 E0N  H201  H   HCH2  0   0.234  -5.1933  -0.6820   1.7451
 E0N  H212  H   HCH2  0   0.213  -6.3509  -1.7027  -0.1802
 E0N  H211  H   HCH2  0   0.231  -7.3321  -0.4170   0.4965
 E0N  H221  H   HCH2  0   0.229  -7.2625  -0.3138  -2.0046
 E0N  H222  H   HCH2  0   0.211  -6.6076   1.1378  -1.2711
 E0N  H241  H   HCH2  0   0.223  -3.9977   1.4078  -1.1580
 E0N  H242  H   HCH2  0   0.231  -2.9977   0.1574  -1.8692
 E0N  H011  H   HCH3  0   0.225   1.9693  -3.5425   0.7813
 E0N  H012  H   HCH3  0   0.252   2.7145  -2.7609   2.1874
 E0N  H013  H   HCH3  0   0.254   0.9742  -2.7260   1.9979
 E0N  H041  H   HCR6  0   0.268   4.6899  -2.2380   1.0867
 E0N  H051  H   HCR6  0   0.274   6.5116  -1.2858  -0.2662
 E0N  H081  H   HCR6  0   0.271   3.7145   1.1565  -2.4200
 E0N  H111  H   HCR5  0   0.269   0.5259  -1.8078  -0.6922
 E0N  H191  H   HCH1  0   0.250  -3.8431  -1.4717  -0.1583
 E0N  H231  H   HCH2  0   0.214  -4.9916  -1.1940  -2.4013
 E0N  H232  H   HCH2  0   0.231  -5.1277   0.4084  -3.0989
 E0N  H141  H   HNH1  0   0.408  -1.5736  -1.0655  -0.6362
 E0N  H1    H   HOH1  0   0.481  -3.0330   2.7558   2.3485

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
 E0N  C22  C21   single    1.525  0.020  1.525
 E0N  C22  C23   single    1.525  0.020  1.525
 E0N  C21  C20   single    1.526  0.020  1.526
 E0N  C23  C24   single    1.526  0.020  1.526
 E0N  C24  C19   single    1.530  0.020  1.530
 E0N  C20  C19   single    1.528  0.020  1.528
 E0N  C19  C15   single    1.541  0.020  1.541
 E0N  C15  N14   single    1.440  0.020  1.440
 E0N  C15  C16   single    1.521  0.020  1.521
 E0N  O17  C16   double    1.203  0.020  1.203
 E0N  N14  C12   single    1.341  0.020  1.341
 E0N  C16  O18   single    1.326  0.020  1.326
 E0N  C10  C11   single    1.547  0.020  1.547
 E0N  C10  C09   single    1.501  0.020  1.501
 E0N  C12  C11   single    1.519  0.020  1.519
 E0N  C12  O13   double    1.220  0.020  1.220
 E0N  C08  C09   aromatic  1.376  0.020  1.376
 E0N  C08  C06   aromatic  1.395  0.020  1.395
 E0N  C11  N02   single    1.449  0.020  1.449
 E0N  C09  C03   aromatic  1.398  0.020  1.398
 E0N  CL7  C06   single    1.740  0.020  1.740
 E0N  C06  C05   aromatic  1.384  0.020  1.384
 E0N  N02  C03   single    1.377  0.020  1.377
 E0N  N02  C01   single    1.440  0.020  1.440
 E0N  C03  C04   aromatic  1.388  0.020  1.388
 E0N  C05  C04   aromatic  1.393  0.020  1.393
 E0N  C10  H102  single    0.970  0.020  1.090
 E0N  C10  H101  single    0.970  0.020  1.090
 E0N  C15  H151  single    0.970  0.020  1.090
 E0N  C20  H202  single    0.970  0.020  1.090
 E0N  C20  H201  single    0.970  0.020  1.090
 E0N  C21  H212  single    0.970  0.020  1.090
 E0N  C21  H211  single    0.970  0.020  1.090
 E0N  C22  H221  single    0.970  0.020  1.090
 E0N  C22  H222  single    0.970  0.020  1.090
 E0N  C24  H241  single    0.970  0.020  1.090
 E0N  C24  H242  single    0.970  0.020  1.090
 E0N  C01  H011  single    0.970  0.020  1.090
 E0N  C01  H012  single    0.970  0.020  1.090
 E0N  C01  H013  single    0.970  0.020  1.090
 E0N  C04  H041  single    0.930  0.020  1.080
 E0N  C05  H051  single    0.930  0.020  1.080
 E0N  C08  H081  single    0.930  0.020  1.080
 E0N  C11  H111  single    0.970  0.020  1.090
 E0N  C19  H191  single    0.970  0.020  1.090
 E0N  C23  H231  single    0.970  0.020  1.090
 E0N  C23  H232  single    0.970  0.020  1.090
 E0N  N14  H141  single    0.860  0.020  1.020
 E0N  O18  H1    single    0.850  0.020  0.980

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
 E0N  H101  C10  H102  107.38  3.000
 E0N  H101  C10  C11   111.80  3.000
 E0N  H102  C10  C11   111.34  3.000
 E0N  H101  C10  C09   113.64  3.000
 E0N  H102  C10  C09   110.73  3.000
 E0N  C11   C10  C09   101.98  3.000
 E0N  H151  C15  N14   109.57  3.000
 E0N  H151  C15  C19   107.42  3.000
 E0N  N14   C15  C19   109.83  3.000
 E0N  H151  C15  C16   108.23  3.000
 E0N  N14   C15  C16   109.40  3.000
 E0N  C19   C15  C16   112.33  3.000
 E0N  H201  C20  H202  106.90  3.000
 E0N  H201  C20  C19   109.88  3.000
 E0N  H202  C20  C19   110.33  3.000
 E0N  H201  C20  C21   110.12  3.000
 E0N  H202  C20  C21   108.83  3.000
 E0N  C19   C20  C21   110.69  3.000
 E0N  H211  C21  H212  106.53  3.000
 E0N  H211  C21  C22   110.26  3.000
 E0N  H212  C21  C22   109.48  3.000
 E0N  H211  C21  C20   109.74  3.000
 E0N  H212  C21  C20   109.31  3.000
 E0N  C22   C21  C20   111.39  3.000
 E0N  H222  C22  H221  106.51  3.000
 E0N  H222  C22  C23   109.25  3.000
 E0N  H221  C22  C23   110.24  3.000
 E0N  H222  C22  C21   109.22  3.000
 E0N  H221  C22  C21   110.22  3.000
 E0N  C23   C22  C21   111.27  3.000
 E0N  H242  C24  H241  106.41  3.000
 E0N  H242  C24  C23   109.54  3.000
 E0N  H241  C24  C23   108.91  3.000
 E0N  H242  C24  C19   111.34  3.000
 E0N  H241  C24  C19   109.87  3.000
 E0N  C23   C24  C19   110.65  3.000
 E0N  H013  C01  H012  107.03  3.000
 E0N  H013  C01  H011  108.30  3.000
 E0N  H012  C01  H011  108.41  3.000
 E0N  H013  C01  N02   109.77  3.000
 E0N  H012  C01  N02   110.38  3.000
 E0N  H011  C01  N02   112.77  3.000
 E0N  N02   C03  C09   110.83  3.000
 E0N  N02   C03  C04   128.69  3.000
 E0N  C09   C03  C04   120.48  3.000
 E0N  H041  C04  C05   119.62  3.000
 E0N  H041  C04  C03   121.79  3.000
 E0N  C05   C04  C03   118.59  3.000
 E0N  H051  C05  C06   120.20  3.000
 E0N  H051  C05  C04   119.49  3.000
 E0N  C06   C05  C04   120.31  3.000
 E0N  CL7   C06  C08   119.10  3.000
 E0N  CL7   C06  C05   119.55  3.000
 E0N  C08   C06  C05   121.35  3.000
 E0N  H081  C08  C09   121.10  3.000
 E0N  H081  C08  C06   120.71  3.000
 E0N  C09   C08  C06   118.18  3.000
 E0N  C08   C09  C03   121.07  3.000
 E0N  C03   C09  C10   108.57  3.000
 E0N  C08   C09  C10   130.35  3.000
 E0N  H111  C11  N02   110.53  3.000
 E0N  H111  C11  C12   109.66  3.000
 E0N  N02   C11  C12   111.83  3.000
 E0N  H111  C11  C10   109.63  3.000
 E0N  N02   C11  C10   104.50  3.000
 E0N  C12   C11  C10   110.59  3.000
 E0N  O13   C12  N14   122.65  3.000
 E0N  O13   C12  C11   122.82  3.000
 E0N  N14   C12  C11   114.46  3.000
 E0N  O18   C16  O17   123.87  3.000
 E0N  O18   C16  C15   111.65  3.000
 E0N  O17   C16  C15   124.47  3.000
 E0N  H191  C19  C24   107.83  3.000
 E0N  H191  C19  C20   106.72  3.000
 E0N  C24   C19  C20   110.41  3.000
 E0N  H191  C19  C15   104.44  3.000
 E0N  C20   C19  C15   112.57  3.000
 E0N  C24   C19  C15   114.30  3.000
 E0N  H232  C23  H231  106.51  3.000
 E0N  H232  C23  C24   109.62  3.000
 E0N  H231  C23  C24   109.32  3.000
 E0N  H232  C23  C22   110.28  3.000
 E0N  H231  C23  C22   109.54  3.000
 E0N  C24   C23  C22   111.44  3.000
 E0N  C11   N02  C03   108.77  3.000
 E0N  C03   N02  C01   120.99  3.000
 E0N  C11   N02  C01   118.41  3.000
 E0N  H141  N14  C12   119.54  3.000
 E0N  H141  N14  C15   118.97  3.000
 E0N  C12   N14  C15   121.49  3.000
 E0N  H1    O18  C16   110.11  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
 E0N  CONST_01  C06   C08  C09  C03     0.00   0.0  0
 E0N  CONST_02  C06   C05  C04  C03     0.00   0.0  0
 E0N  CONST_03  C08   C09  C03  C04     0.00   0.0  0
 E0N  CONST_04  C08   C06  C05  C04     0.00   0.0  0
 E0N  CONST_05  C09   C08  C06  C05     0.00   0.0  0
 E0N  CONST_06  C09   C03  C04  C05     0.00   0.0  0
 E0N  CONST_07  CL7   C06  C05  C04   180.00   0.0  0
 E0N  CONST_08  CL7   C06  C08  C09   180.00   0.0  0
 E0N  CONST_09  H081  C08  C09  C10     0.00   0.0  0
 E0N  CONST_10  H051  C05  C04  C03   180.00   0.0  0
 E0N  CONST_11  H041  C04  C05  C06   180.00   0.0  0
 E0N  CONST_12  C11   C12  N14  C15   180.00   0.0  0
 E0N  CONST_13  H141  N14  C12  C11     0.00   0.0  0
 E0N  CONST_14  O13   C12  N14  C15     0.00   0.0  0
 E0N  CONST_15  H1    O18  C16  C15   180.00   0.0  0
 E0N  Var_01    C23   C22  C21  C20    54.76  30.0  1
 E0N  Var_02    C24   C23  C22  C21   -54.74  30.0  1
 E0N  Var_03    C19   C20  C21  C22   -56.22  30.0  1
 E0N  Var_04    C19   C24  C23  C22    56.12  30.0  1
 E0N  Var_05    C11   C10  C09  C03   -13.31  30.0  1
 E0N  Var_06    C11   N02  C03  C04  -164.89  30.0  1
 E0N  Var_07    H011  C01  N02  C03   -66.41  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
 E0N  chir_01  C15  C19  N14  C16  negativ
 E0N  chir_02  C11  N02  C12  C10  negativ
 E0N  chir_03  C19  C24  C20  C15  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
 E0N  plan-1  C15   0.020
 E0N  plan-1  C11   0.020
 E0N  plan-1  C12   0.020
 E0N  plan-1  N14   0.020
 E0N  plan-1  O13   0.020
 E0N  plan-1  H141  0.020
 E0N  plan-2  C10   0.020
 E0N  plan-2  C03   0.020
 E0N  plan-2  C04   0.020
 E0N  plan-2  C05   0.020
 E0N  plan-2  C06   0.020
 E0N  plan-2  C08   0.020
 E0N  plan-2  C09   0.020
 E0N  plan-2  N02   0.020
 E0N  plan-2  CL7   0.020
 E0N  plan-2  H041  0.020
 E0N  plan-2  H051  0.020
 E0N  plan-2  H081  0.020
 E0N  plan-3  C15   0.020
 E0N  plan-3  C16   0.020
 E0N  plan-3  O17   0.020
 E0N  plan-3  O18   0.020
 E0N  plan-3  H1    0.020

