# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:14:33 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  46  24  .  2021-08-08  2021-08-08  
;
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  -0.488   1.5006   0.3559  -0.6050
 E0N  C15   C   CH1    0  -0.152  -2.6296   0.0603   0.8937
 E0N  C20   C   CH2    0  -0.414  -5.1837  -0.0278   0.8906
 E0N  C21   C   CH2    0  -0.432  -6.4044  -0.6022   0.1779
 E0N  C22   C   CH2    0  -0.428  -6.4840  -0.1136  -1.2648
 E0N  C24   C   CH2    0  -0.431  -3.9771   0.1663  -1.2961
 E0N  C01   C   CH3    0  -0.542   1.7813  -2.9619   1.0663
 E0N  C03   C   CR56   0   0.416   3.1475  -1.1637   0.1160
 E0N  C04   C   CR16   0  -0.354   4.4133  -1.7190   0.2479
 E0N  C05   C   CR16   0  -0.219   5.4872  -1.0884  -0.3780
 E0N  C06   C   CR6    0  -0.064   5.2854   0.0608  -1.1214
 E0N  C08   C   CR16   0  -0.291   4.0137   0.6164  -1.2680
 E0N  C09   C   CR56   0  -0.006   2.9554  -0.0089  -0.6511
 E0N  C11   C   CR15   0  -0.196   0.8656  -0.9337  -0.0359
 E0N  C12   C   C      0   0.544  -0.2836  -0.5871   0.8969
 E0N  C16   C   C      0   0.409  -2.4166   1.5969   0.8998
 E0N  C19   C   CH1    0  -0.263  -3.8987  -0.3667   0.1367
 E0N  C23   C   CH2    0  -0.428  -5.1927  -0.4032  -2.0227
 E0N  N02   N   NR5    0  -0.518   1.9567  -1.5936   0.6559
 E0N  N14   N   NH1    0  -0.634  -1.4902  -0.6252   0.3200
 E0N  O13   O   O      0  -0.496  -0.0927  -0.2708   2.0614
 E0N  O17   O   O      0  -0.594  -1.5724   2.0568   0.1108
 E0N  O18   O   OC    -1  -0.605  -3.1339   2.2383   1.6932
 E0N  CL7   CL  CL     0  -0.152   6.6386   0.8260  -1.9040
 E0N  H102  H   HCH2   0   0.271   1.3351   1.2031   0.0656
 E0N  H101  H   HCH2   0   0.269   1.0800   0.6196  -1.5736
 E0N  H151  H   HCH1   0   0.234  -2.7414  -0.2773   1.9279
 E0N  H202  H   HCH2   0   0.217  -5.2865   1.0566   0.9756
 E0N  H201  H   HCH2   0   0.217  -5.1243  -0.4154   1.9117
 E0N  H212  H   HCH2   0   0.205  -6.3523  -1.6967   0.1908
 E0N  H211  H   HCH2   0   0.223  -7.3151  -0.3296   0.7173
 E0N  H221  H   HCH2   0   0.223  -7.3341  -0.5735  -1.7753
 E0N  H222  H   HCH2   0   0.207  -6.6679   0.9665  -1.2688
 E0N  H241  H   HCH2   0   0.216  -4.0450   1.2589  -1.2790
 E0N  H242  H   HCH2   0   0.221  -3.0720  -0.0751  -1.8618
 E0N  H011  H   HCH3   0   0.223   1.8184  -3.6653   0.2258
 E0N  H012  H   HCH3   0   0.250   2.5507  -3.2438   1.7839
 E0N  H013  H   HCH3   0   0.253   0.8203  -3.0750   1.5650
 E0N  H041  H   HCR6   0   0.267   4.5845  -2.6234   0.8166
 E0N  H051  H   HCR6   0   0.272   6.4791  -1.5098  -0.2848
 E0N  H081  H   HCR6   0   0.270   3.8652   1.5101  -1.8605
 E0N  H111  H   HCR5   0   0.260   0.5057  -1.5589  -0.8672
 E0N  H191  H   HCH1   0   0.216  -3.8498  -1.4633   0.0751
 E0N  H231  H   HCH2   0   0.208  -5.0707  -1.4866  -2.1327
 E0N  H232  H   HCH2   0   0.225  -5.2498   0.0050  -3.0350
 E0N  H141  H   HNH1   0   0.390  -1.5118  -0.7983  -0.6731

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    1.531  0.020  1.531
 E0N  C20  C19   single    1.528  0.020  1.528
 E0N  C19  C15   single    1.538  0.020  1.538
 E0N  C15  N14   single    1.448  0.020  1.448
 E0N  C15  C16   single    1.551  0.020  1.551
 E0N  O17  C16   deloc     1.244  0.020  1.244
 E0N  N14  C12   single    1.338  0.020  1.338
 E0N  C16  O18   deloc     1.247  0.020  1.247
 E0N  C10  C11   single    1.546  0.020  1.546
 E0N  C10  C09   single    1.501  0.020  1.501
 E0N  C12  C11   single    1.520  0.020  1.520
 E0N  C12  O13   double    1.222  0.020  1.222
 E0N  C08  C09   aromatic  1.375  0.020  1.375
 E0N  C08  C06   aromatic  1.395  0.020  1.395
 E0N  C11  N02   single    1.451  0.020  1.451
 E0N  C09  C03   aromatic  1.400  0.020  1.400
 E0N  CL7  C06   single    1.740  0.020  1.740
 E0N  C06  C05   aromatic  1.383  0.020  1.383
 E0N  N02  C03   single    1.376  0.020  1.376
 E0N  N02  C01   single    1.439  0.020  1.439
 E0N  C03  C04   aromatic  1.389  0.020  1.389
 E0N  C05  C04   aromatic  1.394  0.020  1.394
 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    0.890  0.020  1.040

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  107.43  3.000
 E0N  H101  C10  C11   111.77  3.000
 E0N  H102  C10  C11   111.01  3.000
 E0N  H101  C10  C09   113.97  3.000
 E0N  H102  C10  C09   110.73  3.000
 E0N  C11   C10  C09   101.93  3.000
 E0N  H151  C15  N14   107.99  3.000
 E0N  H151  C15  C19   107.18  3.000
 E0N  N14   C15  C19   108.83  3.000
 E0N  H151  C15  C16   108.43  3.000
 E0N  N14   C15  C16   111.25  3.000
 E0N  C19   C15  C16   112.97  3.000
 E0N  H201  C20  H202  106.51  3.000
 E0N  H201  C20  C19   109.65  3.000
 E0N  H202  C20  C19   109.74  3.000
 E0N  H201  C20  C21   110.25  3.000
 E0N  H202  C20  C21   109.56  3.000
 E0N  C19   C20  C21   111.03  3.000
 E0N  H211  C21  H212  106.44  3.000
 E0N  H211  C21  C22   110.08  3.000
 E0N  H212  C21  C22   109.48  3.000
 E0N  H211  C21  C20   110.01  3.000
 E0N  H212  C21  C20   109.42  3.000
 E0N  C22   C21  C20   111.28  3.000
 E0N  H222  C22  H221  106.42  3.000
 E0N  H222  C22  C23   109.12  3.000
 E0N  H221  C22  C23   110.27  3.000
 E0N  H222  C22  C21   109.15  3.000
 E0N  H221  C22  C21   110.34  3.000
 E0N  C23   C22  C21   111.41  3.000
 E0N  H242  C24  H241  106.23  3.000
 E0N  H242  C24  C23   109.29  3.000
 E0N  H241  C24  C23   109.29  3.000
 E0N  H242  C24  C19   111.39  3.000
 E0N  H241  C24  C19   109.64  3.000
 E0N  C23   C24  C19   110.88  3.000
 E0N  H013  C01  H012  107.15  3.000
 E0N  H013  C01  H011  108.32  3.000
 E0N  H012  C01  H011  108.36  3.000
 E0N  H013  C01  N02   109.69  3.000
 E0N  H012  C01  N02   110.36  3.000
 E0N  H011  C01  N02   112.78  3.000
 E0N  N02   C03  C09   110.73  3.000
 E0N  N02   C03  C04   128.80  3.000
 E0N  C09   C03  C04   120.47  3.000
 E0N  H041  C04  C05   119.49  3.000
 E0N  H041  C04  C03   121.90  3.000
 E0N  C05   C04  C03   118.61  3.000
 E0N  H051  C05  C06   120.24  3.000
 E0N  H051  C05  C04   119.44  3.000
 E0N  C06   C05  C04   120.32  3.000
 E0N  CL7   C06  C08   119.09  3.000
 E0N  CL7   C06  C05   119.57  3.000
 E0N  C08   C06  C05   121.34  3.000
 E0N  H081  C08  C09   121.02  3.000
 E0N  H081  C08  C06   120.74  3.000
 E0N  C09   C08  C06   118.24  3.000
 E0N  C08   C09  C03   121.02  3.000
 E0N  C03   C09  C10   108.47  3.000
 E0N  C08   C09  C10   130.49  3.000
 E0N  H111  C11  N02   110.35  3.000
 E0N  H111  C11  C12   110.22  3.000
 E0N  N02   C11  C12   112.31  3.000
 E0N  H111  C11  C10   109.28  3.000
 E0N  N02   C11  C10   104.25  3.000
 E0N  C12   C11  C10   110.26  3.000
 E0N  O13   C12  N14   124.01  3.000
 E0N  O13   C12  C11   121.72  3.000
 E0N  N14   C12  C11   114.25  3.000
 E0N  O18   C16  O17   127.15  3.000
 E0N  O18   C16  C15   115.65  3.000
 E0N  O17   C16  C15   117.19  3.000
 E0N  H191  C19  C24   107.29  3.000
 E0N  H191  C19  C20   106.64  3.000
 E0N  C24   C19  C20   109.97  3.000
 E0N  H191  C19  C15   105.54  3.000
 E0N  C20   C19  C15   112.93  3.000
 E0N  C24   C19  C15   113.97  3.000
 E0N  H232  C23  H231  106.38  3.000
 E0N  H232  C23  C24   110.07  3.000
 E0N  H231  C23  C24   109.15  3.000
 E0N  H232  C23  C22   110.19  3.000
 E0N  H231  C23  C22   109.39  3.000
 E0N  C24   C23  C22   111.52  3.000
 E0N  C11   N02  C03   108.75  3.000
 E0N  C03   N02  C01   120.95  3.000
 E0N  C11   N02  C01   118.48  3.000
 E0N  H141  N14  C12   116.67  3.000
 E0N  H141  N14  C15   117.04  3.000
 E0N  C12   N14  C15   121.69  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_13  H141  N14  C12  C11     0.00   0.0  0
 E0N  Var_01    C23   C22  C21  C20    54.30  30.0  1
 E0N  Var_02    C24   C23  C22  C21   -54.23  30.0  1
 E0N  Var_03    C19   C20  C21  C22   -56.35  30.0  1
 E0N  Var_04    C19   C24  C23  C22    55.97  30.0  1
 E0N  Var_05    C11   C10  C09  C03   -14.33  30.0  1
 E0N  Var_06    C11   N02  C03  C04  -164.56  30.0  1
 E0N  Var_07    H011  C01  N02  C03   -65.44  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

