# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 18:17:39 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: cyclopentanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCCC1
#
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
 1CB  1CB  'cyclopentanamine         '  ligand  17  6  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1CB
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
 1CB  C2    C  CH2   0  -0.445  -0.0547  -1.2025   0.0652
 1CB  C1    C  CR15  0  -0.080   0.7209   0.0249  -0.4226
 1CB  C4    C  CH2   0  -0.448  -0.0689   1.1851   0.1913
 1CB  C5    C  CH2   0  -0.453  -1.5214   0.7752  -0.0345
 1CB  C3    C  CH2   0  -0.445  -1.5291  -0.7613   0.1382
 1CB  N2    N  NH2   0  -0.797   2.1390  -0.0650  -0.1255
 1CB  H21   H  HCH2  0   0.230   0.0995  -2.0713  -0.5764
 1CB  H22   H  HCH2  0   0.216   0.3111  -1.4727   1.0607
 1CB  H1    H  HCR5  0   0.215   0.6201   0.0918  -1.5126
 1CB  H41   H  HCH2  0   0.208   0.1536   1.2433   1.2630
 1CB  H42   H  HCH2  0   0.226   0.1840   2.1523  -0.2486
 1CB  H51   H  HCH2  0   0.220  -1.8218   1.0380  -1.0517
 1CB  H52   H  HCH2  0   0.229  -2.2176   1.2771   0.6382
 1CB  H31   H  HCH2  0   0.226  -2.1311  -1.2372  -0.6367
 1CB  H32   H  HCH2  0   0.225  -1.9721  -1.0476   1.0931
 1CB  HN21  H  HNH2  0   0.341   2.6129   0.7609  -0.4705
 1CB  HN22  H  HNH2  0   0.332   2.2692  -0.0536   0.8803

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
 1CB  C2  C1    single  1.532  0.020  1.532
 1CB  C2  C3    single  1.541  0.020  1.541
 1CB  C2  H21   single  0.970  0.020  1.090
 1CB  C2  H22   single  0.970  0.020  1.090
 1CB  C1  C4    single  1.532  0.020  1.532
 1CB  C1  N2    single  1.452  0.020  1.452
 1CB  C1  H1    single  0.970  0.020  1.090
 1CB  C4  C5    single  1.526  0.020  1.526
 1CB  C4  H41   single  0.970  0.020  1.090
 1CB  C4  H42   single  0.970  0.020  1.090
 1CB  C5  C3    single  1.546  0.020  1.546
 1CB  C5  H51   single  0.970  0.020  1.090
 1CB  C5  H52   single  0.970  0.020  1.090
 1CB  C3  H31   single  0.970  0.020  1.090
 1CB  C3  H32   single  0.970  0.020  1.090
 1CB  N2  HN21  single  0.890  0.020  1.040
 1CB  N2  HN22  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
 1CB  H22   C2  H21   106.93  3.000
 1CB  H22   C2  C3    110.33  3.000
 1CB  H21   C2  C3    113.02  3.000
 1CB  H22   C2  C1    108.56  3.000
 1CB  H21   C2  C1    112.29  3.000
 1CB  C3    C2  C1    105.68  3.000
 1CB  H1    C1  N2    107.28  3.000
 1CB  H1    C1  C4    107.73  3.000
 1CB  N2    C1  C4    117.94  3.000
 1CB  H1    C1  C2    108.59  3.000
 1CB  N2    C1  C2    112.33  3.000
 1CB  C4    C1  C2    102.60  3.000
 1CB  H42   C4  H41   107.44  3.000
 1CB  H42   C4  C5    113.49  3.000
 1CB  H41   C4  C5    110.62  3.000
 1CB  H42   C4  C1    112.95  3.000
 1CB  H41   C4  C1    109.11  3.000
 1CB  C5    C4  C1    103.18  3.000
 1CB  H52   C5  H51   106.74  3.000
 1CB  H52   C5  C3    112.66  3.000
 1CB  H51   C5  C3    109.97  3.000
 1CB  H52   C5  C4    113.13  3.000
 1CB  H51   C5  C4    109.56  3.000
 1CB  C3    C5  C4    104.78  3.000
 1CB  H32   C3  H31   106.45  3.000
 1CB  H32   C3  C5    111.14  3.000
 1CB  H31   C3  C5    110.92  3.000
 1CB  H32   C3  C2    110.79  3.000
 1CB  H31   C3  C2    111.69  3.000
 1CB  C5    C3  C2    105.93  3.000
 1CB  HN22  N2  HN21  105.58  3.000
 1CB  HN22  N2  C1    109.13  3.000
 1CB  HN21  N2  C1    109.69  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
 1CB  Var_01  C4  C5  C3  C2  -15.26  30.0  1
 1CB  Var_02  C5  C3  C2  C1  -11.07  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
 1CB  chir_01  C1  C2  C4  N2  negativ

