# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 15:30:14 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-(cyclopentylmethoxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(OCC2CCCC2)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
 8CI  8CI  "4-(cyclopentylmethoxy)benzamide"
  ligand  33  16  .  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_8CI
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
 8CI  C4   C  CR16  0  -0.338  -14.8257  13.8419   -8.7547
 8CI  C5   C  CR6   0   0.396  -13.6493  14.4474   -9.2089
 8CI  C6   C  CH2   0  -0.188  -11.2831  14.6494   -9.0161
 8CI  C11  C  CH2   0  -0.449  -10.2180  14.6139   -6.6869
 8CI  C7   C  CH1   0  -0.253  -10.1758  14.0969   -8.1450
 8CI  C8   C  CH2   0  -0.448   -8.7988  14.5281   -8.6966
 8CI  C9   C  CH2   0  -0.443   -7.9702  14.8935   -7.4669
 8CI  C10  C  CH2   0  -0.437   -9.0015  15.5312   -6.5420
 8CI  C12  C  CR16  0  -0.368  -13.7143  15.3429  -10.2752
 8CI  C13  C  CR16  0  -0.264  -14.9344  15.6082  -10.8791
 8CI  N1   N  NH2   0  -0.817  -17.4529  15.7659  -12.2990
 8CI  C3   C  CR16  0  -0.251  -16.0316  14.1242   -9.3600
 8CI  O1   O  O     0  -0.478  -18.4741  15.0396  -10.4292
 8CI  C2   C  CR6   0  -0.064  -16.1077  15.0013  -10.4443
 8CI  O2   O  O2    0  -0.466  -12.5220  14.1166   -8.5662
 8CI  H1   H  HCR6  0   0.263  -14.7795  13.1489   -7.9240
 8CI  H2   H  HCH2  0   0.235  -11.1173  14.3739  -10.0645
 8CI  H3   H  HCH2  0   0.222  -11.2953  15.7451   -8.9575
 8CI  H4   H  HCH2  0   0.233  -11.1553  15.1187   -6.4449
 8CI  H5   H  HCH2  0   0.228  -10.1308  13.7734   -5.9954
 8CI  H6   H  HCH1  0   0.243  -10.2495  13.0061   -8.1575
 8CI  H7   H  HCH2  0   0.238   -8.3404  13.7534   -9.3122
 8CI  H8   H  HCH2  0   0.224   -8.9084  15.4130   -9.3324
 8CI  H9   H  HCH2  0   0.217   -7.5620  13.9914   -7.0020
 8CI  H10  H  HCH2  0   0.230   -7.1304  15.5491   -7.7009
 8CI  H11  H  HCH2  0   0.229   -8.6626  15.6243   -5.5092
 8CI  H12  H  HCH2  0   0.217   -9.2407  16.5380   -6.8971
 8CI  H13  H  HCR6  0   0.283  -12.8322  15.8463  -10.6457
 8CI  H14  H  HCR6  0   0.258  -14.9452  16.3259  -11.6896
 8CI  H15  H  HNH2  0   0.400  -18.3355  15.9322  -12.7545
 8CI  H16  H  HNH2  0   0.408  -16.6337  15.7973  -12.8801
 8CI  H17  H  HCR6  0   0.259  -16.9297  13.6463   -8.9918
 8CI  C1   C  C     0   0.481  -17.4438  15.2658  -11.0502

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
 8CI  N1   C1   single    1.345  0.020  1.345
 8CI  C1   C2   single    1.491  0.020  1.491
 8CI  C1   O1   double    1.224  0.020  1.224
 8CI  C13  C2   aromatic  1.391  0.020  1.391
 8CI  C13  C12  aromatic  1.387  0.020  1.387
 8CI  C2   C3   aromatic  1.397  0.020  1.397
 8CI  C12  C5   aromatic  1.394  0.020  1.394
 8CI  C3   C4   aromatic  1.378  0.020  1.378
 8CI  C5   C4   aromatic  1.399  0.020  1.399
 8CI  C5   O2   single    1.339  0.020  1.339
 8CI  C6   O2   single    1.422  0.020  1.422
 8CI  C6   C7   single    1.513  0.020  1.513
 8CI  C8   C7   single    1.545  0.020  1.545
 8CI  C8   C9   single    1.527  0.020  1.527
 8CI  C7   C11  single    1.548  0.020  1.548
 8CI  C9   C10  single    1.525  0.020  1.525
 8CI  C11  C10  single    1.530  0.020  1.530
 8CI  C4   H1   single    0.930  0.020  1.080
 8CI  C6   H2   single    0.970  0.020  1.090
 8CI  C6   H3   single    0.970  0.020  1.090
 8CI  C11  H4   single    0.970  0.020  1.090
 8CI  C11  H5   single    0.970  0.020  1.090
 8CI  C7   H6   single    0.970  0.020  1.090
 8CI  C8   H7   single    0.970  0.020  1.090
 8CI  C8   H8   single    0.970  0.020  1.090
 8CI  C9   H9   single    0.970  0.020  1.090
 8CI  C9   H10  single    0.970  0.020  1.090
 8CI  C10  H11  single    0.970  0.020  1.090
 8CI  C10  H12  single    0.970  0.020  1.090
 8CI  C12  H13  single    0.930  0.020  1.080
 8CI  C13  H14  single    0.930  0.020  1.080
 8CI  N1   H15  single    0.860  0.020  1.020
 8CI  N1   H16  single    0.860  0.020  1.020
 8CI  C3   H17  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
 8CI  H1   C4   C3   120.35  3.000
 8CI  H1   C4   C5   119.35  3.000
 8CI  C3   C4   C5   120.30  3.000
 8CI  O2   C5   C12  124.40  3.000
 8CI  O2   C5   C4   116.44  3.000
 8CI  C12  C5   C4   119.16  3.000
 8CI  H3   C6   H2   107.68  3.000
 8CI  H3   C6   O2   110.34  3.000
 8CI  H2   C6   O2   109.88  3.000
 8CI  H3   C6   C7   110.00  3.000
 8CI  H2   C6   C7   110.36  3.000
 8CI  O2   C6   C7   108.58  3.000
 8CI  H5   C11  H4   106.51  3.000
 8CI  H5   C11  C10  109.75  3.000
 8CI  H4   C11  C10  112.59  3.000
 8CI  H5   C11  C7   109.71  3.000
 8CI  H4   C11  C7   112.75  3.000
 8CI  C10  C11  C7   105.53  3.000
 8CI  H6   C7   C8   109.54  3.000
 8CI  H6   C7   C11  110.01  3.000
 8CI  C8   C7   C11  105.51  3.000
 8CI  H6   C7   C6   107.96  3.000
 8CI  C11  C7   C6   113.60  3.000
 8CI  C8   C7   C6   110.17  3.000
 8CI  H8   C8   H7   106.76  3.000
 8CI  H8   C8   C9   109.18  3.000
 8CI  H7   C8   C9   113.36  3.000
 8CI  H8   C8   C7   110.10  3.000
 8CI  H7   C8   C7   112.21  3.000
 8CI  C9   C8   C7   105.25  3.000
 8CI  H10  C9   H9   107.43  3.000
 8CI  H10  C9   C10  113.54  3.000
 8CI  H9   C9   C10  109.84  3.000
 8CI  H10  C9   C8   112.88  3.000
 8CI  H9   C9   C8   110.32  3.000
 8CI  C10  C9   C8   102.79  3.000
 8CI  H12  C10  H11  107.26  3.000
 8CI  H12  C10  C9   109.62  3.000
 8CI  H11  C10  C9   113.56  3.000
 8CI  H12  C10  C11  110.31  3.000
 8CI  H11  C10  C11  112.81  3.000
 8CI  C9   C10  C11  103.27  3.000
 8CI  H13  C12  C13  118.65  3.000
 8CI  H13  C12  C5   121.55  3.000
 8CI  C13  C12  C5   119.80  3.000
 8CI  H14  C13  C2   121.00  3.000
 8CI  H14  C13  C12  117.48  3.000
 8CI  C2   C13  C12  121.50  3.000
 8CI  H16  N1   H15  116.59  3.000
 8CI  H16  N1   C1   122.88  3.000
 8CI  H15  N1   C1   119.16  3.000
 8CI  H17  C3   C2   119.76  3.000
 8CI  H17  C3   C4   119.10  3.000
 8CI  C2   C3   C4   121.14  3.000
 8CI  C1   C2   C3   118.41  3.000
 8CI  C3   C2   C13  118.09  3.000
 8CI  C1   C2   C13  123.48  3.000
 8CI  C6   O2   C5   119.29  3.000
 8CI  C2   C1   O1   121.03  3.000
 8CI  O1   C1   N1   122.27  3.000
 8CI  C2   C1   N1   116.70  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
 8CI  CONST_01  C13  C2   C3   C4      0.00   0.0  0
 8CI  CONST_02  C13  C12  C5   C4      0.00   0.0  0
 8CI  CONST_03  C2   C13  C12  C5      0.00   0.0  0
 8CI  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 8CI  CONST_05  C3   C2   C13  C12     0.00   0.0  0
 8CI  CONST_06  C3   C4   C5   C12     0.00   0.0  0
 8CI  CONST_07  C1   C2   C3   C4    180.00   0.0  0
 8CI  CONST_08  C1   C2   C13  C12   180.00   0.0  0
 8CI  CONST_09  O2   C5   C12  C13   180.00   0.0  0
 8CI  CONST_10  O2   C5   C4   C3    180.00   0.0  0
 8CI  CONST_11  H13  C12  C5   C4    180.00   0.0  0
 8CI  CONST_12  H14  C13  C12  C5    180.00   0.0  0
 8CI  CONST_13  H17  C3   C4   C5    180.00   0.0  0
 8CI  CONST_14  H1   C4   C5   C12   180.00   0.0  0
 8CI  CONST_15  H17  C3   C2   C13   180.00   0.0  0
 8CI  CONST_16  H14  C13  C2   C3    180.00   0.0  0
 8CI  CONST_17  H13  C12  C13  C2    180.00   0.0  0
 8CI  CONST_18  H1   C4   C3   C2    180.00   0.0  0
 8CI  CONST_19  H15  N1   C1   C2    180.00   0.0  0
 8CI  CONST_20  H16  N1   C1   C2      0.00   0.0  0
 8CI  CONST_21  H15  N1   C1   O1      0.00   0.0  0
 8CI  CONST_22  H16  N1   C1   O1    180.00   0.0  0
 8CI  Var_01    C8   C9   C10  C11    42.33  30.0  1
 8CI  Var_02    C10  C9   C8   C7    -36.03  30.0  1
 8CI  Var_03    C9   C10  C11  C7    -32.50  30.0  1
 8CI  Var_04    H9   C9   C10  C11   -75.10  30.0  1
 8CI  Var_05    H10  C9   C10  C11   164.59  30.0  1
 8CI  Var_06    H9   C9   C8   C7     81.06  30.0  1
 8CI  Var_07    H10  C9   C8   C7   -158.74  30.0  1
 8CI  Var_08    H11  C10  C11  C7   -155.50  30.0  1
 8CI  Var_09    H12  C10  C11  C7     84.58  30.0  1
 8CI  Var_10    H11  C10  C9   C8    164.83  30.0  1
 8CI  Var_11    H12  C10  C9   C8    -75.23  30.0  1
 8CI  Var_12    H4   C11  C10  C9   -155.89  30.0  1
 8CI  Var_13    H5   C11  C10  C9     85.65  30.0  1
 8CI  Var_14    H7   C8   C9   C10  -159.02  30.0  1
 8CI  Var_15    H8   C8   C9   C10    82.12  30.0  1
 8CI  Var_16    C6   O2   C5   C4    177.18  30.0  2
 8CI  Var_17    C7   C6   O2   C5   -178.69  30.0  1
 8CI  Var_18    C12  C5   O2   C6     -3.07  30.0  2
 8CI  Var_19    N1   C1   C2   C13    21.21  30.0  2
 8CI  Var_20    O1   C1   C2   C13  -158.51  30.0  2
 8CI  Var_21    C3   C2   C1   N1   -160.51  30.0  2
 8CI  Var_22    O1   C1   C2   C3     19.78  30.0  2
 8CI  Var_23    H2   C6   O2   C5    -57.90  30.0  1
 8CI  Var_24    H3   C6   O2   C5     60.68  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
 8CI  chir_01  C7  C6  C8  C11  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
 8CI  plan-1  C4   0.020
 8CI  plan-1  C5   0.020
 8CI  plan-1  C12  0.020
 8CI  plan-1  C13  0.020
 8CI  plan-1  C3   0.020
 8CI  plan-1  C2   0.020
 8CI  plan-1  O2   0.020
 8CI  plan-1  H1   0.020
 8CI  plan-1  H13  0.020
 8CI  plan-1  H14  0.020
 8CI  plan-1  H17  0.020
 8CI  plan-1  C1   0.020
 8CI  plan-2  N1   0.020
 8CI  plan-2  O1   0.020
 8CI  plan-2  C2   0.020
 8CI  plan-2  H15  0.020
 8CI  plan-2  H16  0.020
 8CI  plan-2  C1   0.020

