# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:21:35 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-(cyclopentylmethyl)cyclopentanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CCCC1)C2CCCC2
#
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
 6C4  6C4  N-(cyclopentylmethyl)cyclopentanecarboxamide  ligand  35  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6C4
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
 6C4  C2   C  CR15  0  -0.375   2.1969  -0.5694  -0.1509
 6C4  C4   C  CH2   0  -0.445   4.5135  -0.7387   0.6080
 6C4  C5   C  C     0   0.553   1.0487   0.3461   0.2150
 6C4  C6   C  CH2   0  -0.253  -1.3172   0.4093   0.8973
 6C4  C7   C  CR15  0  -0.270  -2.5612  -0.4061   0.5787
 6C4  C9   C  CH2   0  -0.443  -4.2478  -0.4946  -1.1792
 6C4  C11  C  CH2   0  -0.449  -3.8513   0.3130   1.0447
 6C4  O    O  O     0  -0.505   1.1935   1.5572   0.3345
 6C4  C1   C  CH2   0  -0.440   3.1553   0.0508  -1.1932
 6C4  C3   C  CH2   0  -0.441   3.0722  -0.8401   1.1038
 6C4  C    C  CH2   0  -0.435   4.4405   0.3732  -0.4321
 6C4  N    N  NH1   0  -0.638  -0.1244  -0.2677   0.4360
 6C4  C10  C  CH2   0  -0.439  -4.6305   0.6385  -0.2325
 6C4  C8   C  CH2   0  -0.437  -2.7480  -0.6497  -0.9342
 6C4  H1   H  HCR5  0   0.259   1.8028  -1.5155  -0.5287
 6C4  H2   H  HCH2  0   0.233   5.2208  -0.5381   1.4142
 6C4  H3   H  HCH2  0   0.219   4.8174  -1.6755   0.1322
 6C4  H4   H  HCH2  0   0.233  -1.3837   1.3843   0.4092
 6C4  H5   H  HCH2  0   0.237  -1.2581   0.5948   1.9755
 6C4  H6   H  HCR5  0   0.240  -2.4773  -1.3672   1.0962
 6C4  H7   H  HCH2  0   0.216  -4.7761  -1.4100  -0.8968
 6C4  H8   H  HCH2  0   0.229  -4.4879  -0.2882  -2.2235
 6C4  H9   H  HCH2  0   0.231  -4.4395  -0.3518   1.6800
 6C4  H10  H  HCH2  0   0.232  -3.6359   1.2039   1.6391
 6C4  H11  H  HCH2  0   0.231   3.3643  -0.6914  -1.9663
 6C4  H12  H  HCH2  0   0.237   2.7323   0.9204  -1.6960
 6C4  H13  H  HCH2  0   0.233   2.9001  -0.0710   1.8609
 6C4  H14  H  HCH2  0   0.242   2.8394  -1.8012   1.5624
 6C4  H15  H  HCH2  0   0.220   4.3504   1.3418   0.0674
 6C4  H16  H  HCH2  0   0.229   5.3163   0.4183  -1.0813
 6C4  H17  H  HNH1  0   0.395  -0.1544  -1.2733   0.3784
 6C4  H18  H  HCH2  0   0.217  -4.2961   1.5934  -0.6488
 6C4  H19  H  HCH2  0   0.230  -5.7052   0.7190  -0.0621
 6C4  H20  H  HCH2  0   0.221  -2.2063   0.1127  -1.5030
 6C4  H21  H  HCH2  0   0.233  -2.3615  -1.6179  -1.2552

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
 6C4  C9   C8   single  1.528  0.020  1.528
 6C4  C9   C10  single  1.525  0.020  1.525
 6C4  C8   C7   single  1.544  0.020  1.544
 6C4  C10  C11  single  1.531  0.020  1.531
 6C4  C3   C4   single  1.528  0.020  1.528
 6C4  C3   C2   single  1.554  0.020  1.554
 6C4  C11  C7   single  1.549  0.020  1.549
 6C4  C7   C6   single  1.521  0.020  1.521
 6C4  C4   C    single  1.524  0.020  1.524
 6C4  N    C6   single  1.447  0.020  1.447
 6C4  N    C5   single  1.342  0.020  1.342
 6C4  C2   C5   single  1.513  0.020  1.513
 6C4  C2   C1   single  1.546  0.020  1.546
 6C4  C5   O    double  1.226  0.020  1.226
 6C4  C    C1   single  1.528  0.020  1.528
 6C4  C2   H1   single  0.970  0.020  1.090
 6C4  C4   H2   single  0.970  0.020  1.090
 6C4  C4   H3   single  0.970  0.020  1.090
 6C4  C6   H4   single  0.970  0.020  1.090
 6C4  C6   H5   single  0.970  0.020  1.090
 6C4  C7   H6   single  0.970  0.020  1.090
 6C4  C9   H7   single  0.970  0.020  1.090
 6C4  C9   H8   single  0.970  0.020  1.090
 6C4  C11  H9   single  0.970  0.020  1.090
 6C4  C11  H10  single  0.970  0.020  1.090
 6C4  C1   H11  single  0.970  0.020  1.090
 6C4  C1   H12  single  0.970  0.020  1.090
 6C4  C3   H13  single  0.970  0.020  1.090
 6C4  C3   H14  single  0.970  0.020  1.090
 6C4  C    H15  single  0.970  0.020  1.090
 6C4  C    H16  single  0.970  0.020  1.090
 6C4  N    H17  single  0.860  0.020  1.020
 6C4  C10  H18  single  0.970  0.020  1.090
 6C4  C10  H19  single  0.970  0.020  1.090
 6C4  C8   H20  single  0.970  0.020  1.090
 6C4  C8   H21  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
 6C4  H1   C2   C3   109.37  3.000
 6C4  H1   C2   C1   109.75  3.000
 6C4  C3   C2   C1   105.38  3.000
 6C4  H1   C2   C5   109.50  3.000
 6C4  C1   C2   C5   113.00  3.000
 6C4  C3   C2   C5   109.73  3.000
 6C4  H3   C4   H2   107.38  3.000
 6C4  H3   C4   C    109.95  3.000
 6C4  H2   C4   C    113.65  3.000
 6C4  H3   C4   C3   110.28  3.000
 6C4  H2   C4   C3   112.59  3.000
 6C4  C    C4   C3   102.99  3.000
 6C4  N    C5   O    122.62  3.000
 6C4  O    C5   C2   122.12  3.000
 6C4  N    C5   C2   115.23  3.000
 6C4  H5   C6   H4   106.97  3.000
 6C4  H5   C6   N    110.40  3.000
 6C4  H4   C6   N    108.98  3.000
 6C4  H5   C6   C7   109.94  3.000
 6C4  H4   C6   C7   109.58  3.000
 6C4  N    C6   C7   110.89  3.000
 6C4  H6   C7   C8   109.51  3.000
 6C4  H6   C7   C11  109.22  3.000
 6C4  C8   C7   C11  105.51  3.000
 6C4  H6   C7   C6   107.99  3.000
 6C4  C11  C7   C6   111.67  3.000
 6C4  C8   C7   C6   112.88  3.000
 6C4  H8   C9   H7   107.40  3.000
 6C4  H8   C9   C8   112.88  3.000
 6C4  H7   C9   C8   110.35  3.000
 6C4  H8   C9   C10  113.46  3.000
 6C4  H7   C9   C10  109.89  3.000
 6C4  C8   C9   C10  102.84  3.000
 6C4  H10  C11  H9   106.64  3.000
 6C4  H10  C11  C10  112.39  3.000
 6C4  H9   C11  C10  109.92  3.000
 6C4  H10  C11  C7   112.22  3.000
 6C4  H9   C11  C7   109.95  3.000
 6C4  C10  C11  C7   105.76  3.000
 6C4  H12  C1   H11  106.86  3.000
 6C4  H12  C1   C    112.82  3.000
 6C4  H11  C1   C    109.58  3.000
 6C4  H12  C1   C2   112.98  3.000
 6C4  H11  C1   C2   108.87  3.000
 6C4  C    C1   C2   105.68  3.000
 6C4  H14  C3   H13  107.18  3.000
 6C4  H14  C3   C4   113.37  3.000
 6C4  H13  C3   C4   109.07  3.000
 6C4  H14  C3   C2   111.91  3.000
 6C4  H13  C3   C2   110.37  3.000
 6C4  C4   C3   C2   104.95  3.000
 6C4  H16  C    H15  107.54  3.000
 6C4  H16  C    C1   112.79  3.000
 6C4  H15  C    C1   110.19  3.000
 6C4  H16  C    C4   113.44  3.000
 6C4  H15  C    C4   109.78  3.000
 6C4  C1   C    C4   103.07  3.000
 6C4  H17  N    C6   117.42  3.000
 6C4  H17  N    C5   118.23  3.000
 6C4  C6   N    C5   123.98  3.000
 6C4  H19  C10  H18  107.22  3.000
 6C4  H19  C10  C11  112.75  3.000
 6C4  H18  C10  C11  110.33  3.000
 6C4  H19  C10  C9   113.51  3.000
 6C4  H18  C10  C9   109.60  3.000
 6C4  C11  C10  C9   103.42  3.000
 6C4  H21  C8   H20  106.85  3.000
 6C4  H21  C8   C9   113.00  3.000
 6C4  H20  C8   C9   109.38  3.000
 6C4  H21  C8   C7   112.68  3.000
 6C4  H20  C8   C7   109.84  3.000
 6C4  C9   C8   C7   105.07  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
 6C4  CONST_01  C6   N    C5   C2   180.00   0.0  0
 6C4  CONST_02  H17  N    C5   C2     0.00   0.0  0
 6C4  CONST_03  O    C5   N    C6     0.00   0.0  0
 6C4  Var_01    C    C4   C3   C2    35.85  30.0  1
 6C4  Var_02    C10  C9   C8   C7    36.90  30.0  1
 6C4  Var_03    C9   C10  C11  C7    30.84  30.0  1
 6C4  Var_04    C8   C9   C10  C11  -41.83  30.0  1
 6C4  Var_05    C3   C4   C    C1   -42.77  30.0  1
 6C4  Var_06    C7   C6   N    C5   159.59  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
 6C4  chir_01  C2  C3  C5   C1  negativ
 6C4  chir_02  C7  C8  C11  C6  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
 6C4  plan-1  C2   0.020
 6C4  plan-1  C5   0.020
 6C4  plan-1  C6   0.020
 6C4  plan-1  O    0.020
 6C4  plan-1  N    0.020
 6C4  plan-1  H17  0.020

