# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 16:03:23 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-(cyclohexylmethoxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(OCC2CCCCC2)cc1
#
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
 8C7  8C7  "4-(cyclohexylmethoxy)benzamide"
  ligand  36  17  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8C7
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
 8C7  C4   C  CR16  0  -0.339  15.0015  -15.1435   -8.3528
 8C7  C14  C  CR16  0  -0.264  14.9694  -15.1223  -11.1178
 8C7  C5   C  CR6   0   0.397  13.7838  -15.2662   -9.0293
 8C7  C6   C  CH2   0  -0.161  11.4106  -15.4320   -8.8827
 8C7  C11  C  CH2   0  -0.432   9.2727  -14.2483   -5.8663
 8C7  C7   C  CH1   0  -0.276  10.3473  -15.4611   -7.8028
 8C7  C8   C  CH2   0  -0.422   8.9709  -15.6075   -8.4535
 8C7  C9   C  CH2   0  -0.430   7.8569  -15.6370   -7.4124
 8C7  C10  C  CH2   0  -0.427   7.9014  -14.4066   -6.5129
 8C7  C12  C  CH2   0  -0.413  10.3850  -14.2206   -6.9097
 8C7  C13  C  CR16  0  -0.368  13.7769  -15.2628  -10.4234
 8C7  N1   N  NH2   0  -0.818  17.4584  -14.4477  -12.4361
 8C7  C3   C  CR16  0  -0.251  16.1783  -15.0156   -9.0584
 8C7  O1   O  O     0  -0.478  18.5456  -15.0862  -10.5723
 8C7  C2   C  CR6   0  -0.064  16.1847  -14.9872  -10.4548
 8C7  O2   O  O2    0  -0.467  12.6903  -15.3879   -8.2675
 8C7  H1   H  HCR6  0   0.263  15.0104  -15.1487   -7.2700
 8C7  H2   H  HCR6  0   0.257  14.9217  -15.1442  -12.1991
 8C7  H3   H  HCH2  0   0.219  11.2693  -14.5530   -9.5242
 8C7  H4   H  HCH2  0   0.232  11.3291  -16.3227   -9.5170
 8C7  H5   H  HCH2  0   0.209   9.4467  -15.0810   -5.1759
 8C7  H6   H  HCH2  0   0.226   9.3058  -13.3374   -5.2637
 8C7  H7   H  HCH1  0   0.225  10.5177  -16.3459   -7.1757
 8C7  H8   H  HCH2  0   0.211   8.8053  -14.7675   -9.1385
 8C7  H9   H  HCH2  0   0.229   8.9394  -16.5159   -9.0618
 8C7  H10  H  HCH2  0   0.227   6.8865  -15.7098   -7.9089
 8C7  H11  H  HCH2  0   0.210   7.9610  -16.5384   -6.7990
 8C7  H12  H  HCH2  0   0.208   7.6763  -13.5144   -7.1073
 8C7  H13  H  HCH2  0   0.225   7.1254  -14.4708   -5.7462
 8C7  H14  H  HCH2  0   0.231  11.3541  -14.1335   -6.4145
 8C7  H15  H  HCH2  0   0.206  10.2734  -13.3287   -7.5384
 8C7  H16  H  HCR6  0   0.284  12.8594  -15.3754  -10.9841
 8C7  H17  H  HNH2  0   0.400  18.3238  -14.3153  -12.9332
 8C7  H18  H  HNH2  0   0.409  16.6269  -14.0958  -12.8771
 8C7  H19  H  HCR6  0   0.259  17.1097  -14.9233   -8.5159
 8C7  C1   C  C     0   0.483  17.4943  -14.8460  -11.1520

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
 8C7  N1   C1   single    1.345  0.020  1.345
 8C7  C1   C2   single    1.490  0.020  1.490
 8C7  C1   O1   double    1.224  0.020  1.224
 8C7  C14  C2   aromatic  1.391  0.020  1.391
 8C7  C14  C13  aromatic  1.387  0.020  1.387
 8C7  C2   C3   aromatic  1.397  0.020  1.397
 8C7  C13  C5   aromatic  1.394  0.020  1.394
 8C7  C3   C4   aromatic  1.378  0.020  1.378
 8C7  C5   C4   aromatic  1.398  0.020  1.398
 8C7  C5   O2   single    1.338  0.020  1.338
 8C7  C6   O2   single    1.421  0.020  1.421
 8C7  C6   C7   single    1.516  0.020  1.516
 8C7  C8   C7   single    1.529  0.020  1.529
 8C7  C8   C9   single    1.525  0.020  1.525
 8C7  C7   C12  single    1.529  0.020  1.529
 8C7  C9   C10  single    1.525  0.020  1.525
 8C7  C12  C11  single    1.525  0.020  1.525
 8C7  C10  C11  single    1.524  0.020  1.524
 8C7  C4   H1   single    0.930  0.020  1.080
 8C7  C14  H2   single    0.930  0.020  1.080
 8C7  C6   H3   single    0.970  0.020  1.090
 8C7  C6   H4   single    0.970  0.020  1.090
 8C7  C11  H5   single    0.970  0.020  1.090
 8C7  C11  H6   single    0.970  0.020  1.090
 8C7  C7   H7   single    0.970  0.020  1.090
 8C7  C8   H8   single    0.970  0.020  1.090
 8C7  C8   H9   single    0.970  0.020  1.090
 8C7  C9   H10  single    0.970  0.020  1.090
 8C7  C9   H11  single    0.970  0.020  1.090
 8C7  C10  H12  single    0.970  0.020  1.090
 8C7  C10  H13  single    0.970  0.020  1.090
 8C7  C12  H14  single    0.970  0.020  1.090
 8C7  C12  H15  single    0.970  0.020  1.090
 8C7  C13  H16  single    0.930  0.020  1.080
 8C7  N1   H17  single    0.860  0.020  1.020
 8C7  N1   H18  single    0.860  0.020  1.020
 8C7  C3   H19  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
 8C7  H1   C4   C3   120.36  3.000
 8C7  H1   C4   C5   119.37  3.000
 8C7  C3   C4   C5   120.27  3.000
 8C7  H2   C14  C2   121.10  3.000
 8C7  H2   C14  C13  117.39  3.000
 8C7  C2   C14  C13  121.50  3.000
 8C7  O2   C5   C13  124.43  3.000
 8C7  O2   C5   C4   116.37  3.000
 8C7  C13  C5   C4   119.20  3.000
 8C7  H4   C6   H3   107.63  3.000
 8C7  H4   C6   O2   110.04  3.000
 8C7  H3   C6   O2   110.14  3.000
 8C7  H4   C6   C7   110.14  3.000
 8C7  H3   C6   C7   109.97  3.000
 8C7  O2   C6   C7   108.91  3.000
 8C7  H6   C11  H5   106.34  3.000
 8C7  H6   C11  C12  109.88  3.000
 8C7  H5   C11  C12  109.21  3.000
 8C7  H6   C11  C10  110.35  3.000
 8C7  H5   C11  C10  109.34  3.000
 8C7  C12  C11  C10  111.58  3.000
 8C7  H7   C7   C12  108.45  3.000
 8C7  H7   C7   C8   107.79  3.000
 8C7  C12  C7   C8   110.38  3.000
 8C7  H7   C7   C6   108.27  3.000
 8C7  C12  C7   C6   112.54  3.000
 8C7  C8   C7   C6   109.27  3.000
 8C7  H9   C8   H8   106.52  3.000
 8C7  H9   C8   C9   110.04  3.000
 8C7  H8   C8   C9   109.33  3.000
 8C7  H9   C8   C7   110.00  3.000
 8C7  H8   C8   C7   109.17  3.000
 8C7  C9   C8   C7   111.64  3.000
 8C7  H11  C9   H10  106.51  3.000
 8C7  H11  C9   C10  109.33  3.000
 8C7  H10  C9   C10  110.35  3.000
 8C7  H11  C9   C8   109.19  3.000
 8C7  H10  C9   C8   109.87  3.000
 8C7  C10  C9   C8   111.46  3.000
 8C7  H13  C10  H12  106.42  3.000
 8C7  H13  C10  C9   110.23  3.000
 8C7  H12  C10  C9   109.33  3.000
 8C7  H13  C10  C11  110.32  3.000
 8C7  H12  C10  C11  109.29  3.000
 8C7  C9   C10  C11  111.12  3.000
 8C7  H15  C12  H14  106.59  3.000
 8C7  H15  C12  C7   108.81  3.000
 8C7  H14  C12  C7   110.58  3.000
 8C7  H15  C12  C11  109.43  3.000
 8C7  H14  C12  C11  109.78  3.000
 8C7  C7   C12  C11  111.52  3.000
 8C7  H16  C13  C5   121.50  3.000
 8C7  H16  C13  C14  118.73  3.000
 8C7  C5   C13  C14  119.77  3.000
 8C7  H18  N1   H17  116.65  3.000
 8C7  H18  N1   C1   123.02  3.000
 8C7  H17  N1   C1   119.17  3.000
 8C7  H19  C3   C2   119.72  3.000
 8C7  H19  C3   C4   119.10  3.000
 8C7  C2   C3   C4   121.18  3.000
 8C7  C1   C2   C3   118.27  3.000
 8C7  C3   C2   C14  118.07  3.000
 8C7  C1   C2   C14  123.64  3.000
 8C7  C6   O2   C5   119.50  3.000
 8C7  C2   C1   O1   120.96  3.000
 8C7  O1   C1   N1   122.22  3.000
 8C7  C2   C1   N1   116.82  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
 8C7  CONST_01  C14  C2   C3   C4      0.00   0.0  0
 8C7  CONST_02  C14  C13  C5   C4      0.00   0.0  0
 8C7  CONST_03  C2   C14  C13  C5      0.00   0.0  0
 8C7  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 8C7  CONST_05  C3   C2   C14  C13     0.00   0.0  0
 8C7  CONST_06  C3   C4   C5   C13     0.00   0.0  0
 8C7  CONST_07  C1   C2   C3   C4    180.00   0.0  0
 8C7  CONST_08  O2   C5   C13  C14   180.00   0.0  0
 8C7  CONST_09  C1   C2   C14  C13   180.00   0.0  0
 8C7  CONST_10  O2   C5   C4   C3    180.00   0.0  0
 8C7  CONST_11  H16  C13  C5   C4    180.00   0.0  0
 8C7  CONST_12  H19  C3   C2   C14   180.00   0.0  0
 8C7  CONST_13  H2   C14  C13  C5    180.00   0.0  0
 8C7  CONST_14  H19  C3   C4   C5    180.00   0.0  0
 8C7  CONST_15  H1   C4   C5   C13   180.00   0.0  0
 8C7  CONST_16  H2   C14  C2   C3    180.00   0.0  0
 8C7  CONST_17  H16  C13  C14  C2    180.00   0.0  0
 8C7  CONST_18  H1   C4   C3   C2    180.00   0.0  0
 8C7  CONST_19  H17  N1   C1   C2    180.00   0.0  0
 8C7  CONST_20  H18  N1   C1   C2      0.00   0.0  0
 8C7  CONST_21  H17  N1   C1   O1      0.00   0.0  0
 8C7  CONST_22  H18  N1   C1   O1    180.00   0.0  0
 8C7  Var_01    C8   C9   C10  C11   -54.72  30.0  1
 8C7  Var_02    C10  C9   C8   C7     55.55  30.0  1
 8C7  Var_03    C10  C11  C12  C7    -55.57  30.0  1
 8C7  Var_04    C12  C11  C10  C9     54.79  30.0  1
 8C7  Var_05    H10  C9   C10  C11  -177.09  30.0  1
 8C7  Var_06    H11  C9   C10  C11    66.09  30.0  1
 8C7  Var_07    H10  C9   C8   C7    178.19  30.0  1
 8C7  Var_08    H11  C9   C8   C7    -65.34  30.0  1
 8C7  Var_09    H5   C11  C12  C7     65.42  30.0  1
 8C7  Var_10    H6   C11  C12  C7   -178.30  30.0  1
 8C7  Var_11    H12  C10  C9   C8     66.00  30.0  1
 8C7  Var_12    H13  C10  C9   C8   -177.35  30.0  1
 8C7  Var_13    H5   C11  C10  C9    -66.12  30.0  1
 8C7  Var_14    H6   C11  C10  C9    177.25  30.0  1
 8C7  Var_15    H8   C8   C9   C10   -65.35  30.0  1
 8C7  Var_16    H9   C8   C9   C10   177.99  30.0  1
 8C7  Var_17    H14  C12  C11  C10  -178.48  30.0  1
 8C7  Var_18    H15  C12  C11  C10    64.87  30.0  1
 8C7  Var_19    H12  C10  C11  C12   -65.96  30.0  1
 8C7  Var_20    H13  C10  C11  C12   177.36  30.0  1
 8C7  Var_21    C6   O2   C5   C4    176.05  30.0  2
 8C7  Var_22    N1   C1   C2   C14    19.65  30.0  2
 8C7  Var_23    O1   C1   C2   C14  -160.24  30.0  2
 8C7  Var_24    C7   C6   O2   C5   -175.56  30.0  1
 8C7  Var_25    C13  C5   O2   C6     -4.33  30.0  1
 8C7  Var_26    C3   C2   C1   N1   -161.82  30.0  2
 8C7  Var_27    O1   C1   C2   C3     18.28  30.0  2
 8C7  Var_28    H3   C6   O2   C5    -54.89  30.0  1
 8C7  Var_29    H4   C6   O2   C5     63.61  30.0  1

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
 8C7  chir_01  C7  C6  C8  C12  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
 8C7  plan-1  C4   0.020
 8C7  plan-1  C14  0.020
 8C7  plan-1  C5   0.020
 8C7  plan-1  C13  0.020
 8C7  plan-1  C3   0.020
 8C7  plan-1  C2   0.020
 8C7  plan-1  O2   0.020
 8C7  plan-1  H1   0.020
 8C7  plan-1  H2   0.020
 8C7  plan-1  H16  0.020
 8C7  plan-1  H19  0.020
 8C7  plan-1  C1   0.020
 8C7  plan-2  N1   0.020
 8C7  plan-2  O1   0.020
 8C7  plan-2  C2   0.020
 8C7  plan-2  H17  0.020
 8C7  plan-2  H18  0.020
 8C7  plan-2  C1   0.020

