# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:53:24 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(cyclopentylmethyl)pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CCCC1)N2CCCC2
#
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
 6C5  6C5  N-(cyclopentylmethyl)pyrrolidine-1-carboxamide  ligand  34  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_6C5
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
 6C5  C1   C  CH2   0  -0.249  -3.5857   0.7086  -0.2876
 6C5  C2   C  CH2   0  -0.288  -2.3212  -1.2441   0.3984
 6C5  C3   C  CH2   0  -0.476  -3.7347  -1.6592   0.0021
 6C5  C5   C  CH2   0  -0.226   1.2655   1.0277   0.2641
 6C5  C6   C  CH1   0  -0.289   2.4329   0.0777   0.4551
 6C5  C7   C  CH2   0  -0.417   2.6011  -0.9797  -0.6355
 6C5  N1   N  NH1   0  -0.695   0.0109   0.3062   0.2771
 6C5  C8   C  CH2   0  -0.448   4.0208  -1.4849  -0.3974
 6C5  C9   C  CH2   0  -0.445   4.8206  -0.2132  -0.0717
 6C5  C10  C  CH2   0  -0.435   3.7882   0.8032   0.4682
 6C5  O    O  O     0  -0.563  -1.1844   2.0634  -0.5200
 6C5  N    N  NT    0  -0.512  -2.2771   0.1683   0.0484
 6C5  C    C  CH2   0  -0.481  -4.5403  -0.3780   0.1943
 6C5  H1   H  HCH2  0   0.239  -3.7632   1.6662   0.2031
 6C5  H2   H  HCH2  0   0.224  -3.6841   0.8672  -1.3665
 6C5  H3   H  HCH2  0   0.235  -2.1550  -1.3950   1.4709
 6C5  H4   H  HCH2  0   0.244  -1.5606  -1.8141  -0.1403
 6C5  H5   H  HCH2  0   0.239  -3.7541  -1.9620  -1.0472
 6C5  H6   H  HCH2  0   0.251  -4.1005  -2.4959   0.5958
 6C5  H7   H  HCH2  0   0.224   1.2895   1.8025   1.0403
 6C5  H8   H  HCH2  0   0.224   1.3733   1.5393  -0.6949
 6C5  H9   H  HCH1  0   0.228   2.3103  -0.4426   1.4142
 6C5  H10  H  HCH2  0   0.230   1.8496  -1.7699  -0.5955
 6C5  H11  H  HCH2  0   0.211   2.5282  -0.5061  -1.6209
 6C5  H12  H  HNH1  0   0.397  -0.0267  -0.5057   0.8728
 6C5  H13  H  HCH2  0   0.218   4.0236  -2.1632   0.4598
 6C5  H14  H  HCH2  0   0.229   4.4311  -2.0373  -1.2441
 6C5  H15  H  HCH2  0   0.228   5.6217  -0.4072   0.6423
 6C5  H16  H  HCH2  0   0.225   5.2957   0.1751  -0.9743
 6C5  H17  H  HCH2  0   0.222   3.7454   1.6813  -0.1826
 6C5  H18  H  HCH2  0   0.233   4.0401   1.1650   1.4657
 6C5  H19  H  HCH2  0   0.236  -4.7734  -0.2324   1.2514
 6C5  H20  H  HCH2  0   0.249  -5.4793  -0.3747  -0.3580
 6C5  C4   C  C     0   0.737  -1.1541   0.9135  -0.0820

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
 6C5  O    C4   double  1.231  0.020  1.231
 6C5  C1   C    single  1.525  0.020  1.525
 6C5  C1   N    single  1.455  0.020  1.455
 6C5  C    C3   single  1.526  0.020  1.526
 6C5  C4   N    single  1.354  0.020  1.354
 6C5  C4   N1   single  1.362  0.020  1.362
 6C5  N    C2   single  1.456  0.020  1.456
 6C5  C5   N1   single  1.447  0.020  1.447
 6C5  C5   C6   single  1.517  0.020  1.517
 6C5  C3   C2   single  1.526  0.020  1.526
 6C5  C7   C6   single  1.528  0.020  1.528
 6C5  C7   C8   single  1.526  0.020  1.526
 6C5  C6   C10  single  1.537  0.020  1.537
 6C5  C8   C9   single  1.537  0.020  1.537
 6C5  C10  C9   single  1.546  0.020  1.546
 6C5  C1   H1   single  0.970  0.020  1.090
 6C5  C1   H2   single  0.970  0.020  1.090
 6C5  C2   H3   single  0.970  0.020  1.090
 6C5  C2   H4   single  0.970  0.020  1.090
 6C5  C3   H5   single  0.970  0.020  1.090
 6C5  C3   H6   single  0.970  0.020  1.090
 6C5  C5   H7   single  0.970  0.020  1.090
 6C5  C5   H8   single  0.970  0.020  1.090
 6C5  C6   H9   single  0.970  0.020  1.090
 6C5  C7   H10  single  0.970  0.020  1.090
 6C5  C7   H11  single  0.970  0.020  1.090
 6C5  N1   H12  single  0.890  0.020  1.040
 6C5  C8   H13  single  0.970  0.020  1.090
 6C5  C8   H14  single  0.970  0.020  1.090
 6C5  C9   H15  single  0.970  0.020  1.090
 6C5  C9   H16  single  0.970  0.020  1.090
 6C5  C10  H17  single  0.970  0.020  1.090
 6C5  C10  H18  single  0.970  0.020  1.090
 6C5  C    H19  single  0.970  0.020  1.090
 6C5  C    H20  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
 6C5  H2   C1   H1   107.55  3.000
 6C5  H2   C1   C    111.00  3.000
 6C5  H1   C1   C    112.44  3.000
 6C5  H2   C1   N    111.23  3.000
 6C5  H1   C1   N    111.63  3.000
 6C5  C    C1   N    103.03  3.000
 6C5  H4   C2   H3   107.77  3.000
 6C5  H4   C2   N    111.50  3.000
 6C5  H3   C2   N    111.37  3.000
 6C5  H4   C2   C3   112.02  3.000
 6C5  H3   C2   C3   110.93  3.000
 6C5  N    C2   C3   103.27  3.000
 6C5  H6   C3   H5   107.73  3.000
 6C5  H6   C3   C    113.52  3.000
 6C5  H5   C3   C    110.15  3.000
 6C5  H6   C3   C2   112.25  3.000
 6C5  H5   C3   C2   109.97  3.000
 6C5  C    C3   C2   103.18  3.000
 6C5  H8   C5   H7   106.75  3.000
 6C5  H8   C5   N1   109.08  3.000
 6C5  H7   C5   N1   111.39  3.000
 6C5  H8   C5   C6   109.14  3.000
 6C5  H7   C5   C6   109.66  3.000
 6C5  N1   C5   C6   110.72  3.000
 6C5  H9   C6   C10  108.33  3.000
 6C5  H9   C6   C7   107.92  3.000
 6C5  C10  C6   C7   103.63  3.000
 6C5  H9   C6   C5   108.71  3.000
 6C5  C10  C6   C5   112.58  3.000
 6C5  C7   C6   C5   115.35  3.000
 6C5  H11  C7   H10  107.46  3.000
 6C5  H11  C7   C8   110.21  3.000
 6C5  H10  C7   C8   113.29  3.000
 6C5  H11  C7   C6   109.59  3.000
 6C5  H10  C7   C6   113.52  3.000
 6C5  C8   C7   C6   102.72  3.000
 6C5  H12  N1   C5   116.06  3.000
 6C5  H12  N1   C4   118.89  3.000
 6C5  C5   N1   C4   121.12  3.000
 6C5  H14  C8   H13  107.06  3.000
 6C5  H14  C8   C9   112.81  3.000
 6C5  H13  C8   C9   110.23  3.000
 6C5  H14  C8   C7   113.36  3.000
 6C5  H13  C8   C7   109.29  3.000
 6C5  C9   C8   C7   104.08  3.000
 6C5  H16  C9   H15  106.55  3.000
 6C5  H16  C9   C10  110.22  3.000
 6C5  H15  C9   C10  112.27  3.000
 6C5  H16  C9   C8   110.22  3.000
 6C5  H15  C9   C8   111.95  3.000
 6C5  C10  C9   C8   105.69  3.000
 6C5  H18  C10  H17  106.68  3.000
 6C5  H18  C10  C9   112.53  3.000
 6C5  H17  C10  C9   110.25  3.000
 6C5  H18  C10  C6   111.60  3.000
 6C5  H17  C10  C6   109.83  3.000
 6C5  C9   C10  C6   105.99  3.000
 6C5  C4   N    C2   125.61  3.000
 6C5  C2   N    C1   112.86  3.000
 6C5  C4   N    C1   121.28  3.000
 6C5  H20  C    H19  107.84  3.000
 6C5  H20  C    C3   113.19  3.000
 6C5  H19  C    C3   110.28  3.000
 6C5  H20  C    C1   112.17  3.000
 6C5  H19  C    C1   110.15  3.000
 6C5  C3   C    C1   103.18  3.000
 6C5  N    C4   O    121.87  3.000
 6C5  N    C4   N1   116.01  3.000
 6C5  O    C4   N1   122.10  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
 6C5  CONST_01  O    C4  N    C1     0.00   0.0  0
 6C5  CONST_02  O    C4  N    C2   180.00   0.0  0
 6C5  CONST_03  N1   C4  N    C1   180.00   0.0  0
 6C5  CONST_04  N1   C4  N    C2     0.00   0.0  0
 6C5  CONST_05  N    C4  N1   C5   180.00   0.0  0
 6C5  CONST_07  O    C4  N1   C5     0.00   0.0  0
 6C5  Var_01    C2   C3  C    C1    38.30  30.0  1
 6C5  Var_02    C    C1  N    C2    13.18  30.0  1
 6C5  Var_03    N    C1  C    C3   -31.47  30.0  1
 6C5  Var_04    C9   C8  C7   C6   -40.46  30.0  1
 6C5  Var_05    C8   C9  C10  C6     0.80  30.0  1
 6C5  Var_06    C10  C9  C8   C7    24.40  30.0  1
 6C5  Var_07    C    C3  C2   N    -29.98  30.0  1
 6C5  Var_08    C6   C5  N1   C4  -169.67  30.0  2

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
 6C5  chir_01  C6  C5  C7  C10  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
 6C5  plan-1  C1   0.020
 6C5  plan-1  C2   0.020
 6C5  plan-1  C5   0.020
 6C5  plan-1  N1   0.020
 6C5  plan-1  O    0.020
 6C5  plan-1  N    0.020
 6C5  plan-1  H12  0.020
 6C5  plan-1  C4   0.020

