# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:02:45 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: 1-(methylamino)cyclopentane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1(CCCC1)C(N)=O
#
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
 UQY  UQY  1-(methylamino)cyclopentane-1-carboxamide  ligand  24  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UQY
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
 UQY  N1   N  NH2   0  -0.792  -1.0852  -6.4138  -34.9439
 UQY  C4   C  CH2   0  -0.435   2.7296  -8.1514  -36.8964
 UQY  C5   C  CH2   0  -0.451   1.7984  -6.9887  -37.2304
 UQY  C6   C  C     0   0.510  -0.3083  -7.0876  -35.7988
 UQY  N    N  NH1   0  -0.618   1.1616  -5.1478  -35.5934
 UQY  C    C  CH3   0  -0.529   0.6815  -4.2759  -36.6483
 UQY  O    O  O     0  -0.492  -0.6797  -8.0817  -36.4093
 UQY  C1   C  CT    0   0.024   1.1323  -6.5734  -35.8906
 UQY  C2   C  CH2   0  -0.469   1.9511  -7.3354  -34.8038
 UQY  C3   C  CH2   0  -0.443   3.2284  -7.7911  -35.5023
 UQY  H12  H  HNH2  0   0.394  -2.0358  -6.6964  -34.7730
 UQY  H13  H  HNH2  0   0.404  -0.7282  -5.5833  -34.4999
 UQY  H8   H  HCH2  0   0.229   3.5303  -8.2727  -37.6277
 UQY  H9   H  HCH2  0   0.221   2.1697  -9.0898  -36.8604
 UQY  H11  H  HCH2  0   0.231   2.3974  -6.1510  -37.5973
 UQY  H10  H  HCH2  0   0.240   1.0786  -7.2239  -38.0135
 UQY  H3   H  HNH1  0   0.355   2.1020  -4.8794  -35.3327
 UQY  H1   H  HCH3  0   0.238   0.7408  -3.2417  -36.3099
 UQY  H2   H  HCH3  0   0.207   1.2346  -4.3465  -37.5925
 UQY  H    H  HCH3  0   0.224  -0.3673  -4.4868  -36.8641
 UQY  H4   H  HCH2  0   0.247   2.1159  -6.7056  -33.9282
 UQY  H5   H  HCH2  0   0.247   1.4052  -8.2166  -34.4591
 UQY  H6   H  HCH2  0   0.221   3.9468  -6.9685  -35.5648
 UQY  H7   H  HCH2  0   0.236   3.7183  -8.6156  -34.9827

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
 UQY  C   N    single  1.450  0.020  1.450
 UQY  N   C1   single  1.456  0.020  1.456
 UQY  C1  C2   single  1.560  0.020  1.560
 UQY  C2  C3   single  1.525  0.020  1.525
 UQY  C3  C4   single  1.524  0.020  1.524
 UQY  C4  C5   single  1.527  0.020  1.527
 UQY  C5  C1   single  1.553  0.020  1.553
 UQY  C1  C6   single  1.532  0.020  1.532
 UQY  C6  O    double  1.224  0.020  1.224
 UQY  N1  C6   single  1.337  0.020  1.337
 UQY  N1  H12  single  0.860  0.020  1.020
 UQY  N1  H13  single  0.860  0.020  1.020
 UQY  C4  H8   single  0.970  0.020  1.090
 UQY  C4  H9   single  0.970  0.020  1.090
 UQY  C5  H11  single  0.970  0.020  1.090
 UQY  C5  H10  single  0.970  0.020  1.090
 UQY  N   H3   single  0.890  0.020  1.040
 UQY  C   H1   single  0.970  0.020  1.090
 UQY  C   H2   single  0.970  0.020  1.090
 UQY  C   H    single  0.970  0.020  1.090
 UQY  C2  H4   single  0.970  0.020  1.090
 UQY  C2  H5   single  0.970  0.020  1.090
 UQY  C3  H6   single  0.970  0.020  1.090
 UQY  C3  H7   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
 UQY  H13  N1  H12  119.44  3.000
 UQY  H13  N1  C6   119.43  3.000
 UQY  H12  N1  C6   121.05  3.000
 UQY  H9   C4  H8   107.60  3.000
 UQY  H9   C4  C3   109.91  3.000
 UQY  H8   C4  C3   113.54  3.000
 UQY  H9   C4  C5   110.40  3.000
 UQY  H8   C4  C5   112.68  3.000
 UQY  C3   C4  C5   102.69  3.000
 UQY  H10  C5  H11  106.63  3.000
 UQY  H10  C5  C1   113.24  3.000
 UQY  H11  C5  C1   108.65  3.000
 UQY  H10  C5  C4   113.32  3.000
 UQY  H11  C5  C4   108.83  3.000
 UQY  C1   C5  C4   106.06  3.000
 UQY  C1   C6  O    121.86  3.000
 UQY  O    C6  N1   123.48  3.000
 UQY  C1   C6  N1   114.54  3.000
 UQY  H3   N   C1   109.32  3.000
 UQY  H3   N   C    109.60  3.000
 UQY  C1   N   C    115.68  3.000
 UQY  H    C   H2   107.58  3.000
 UQY  H    C   H1   107.28  3.000
 UQY  H2   C   H1   107.53  3.000
 UQY  H    C   N    110.23  3.000
 UQY  H2   C   N    114.87  3.000
 UQY  H1   C   N    109.06  3.000
 UQY  C2   C1  N    109.00  3.000
 UQY  C2   C1  C6   106.73  3.000
 UQY  N    C1  C6   109.58  3.000
 UQY  C6   C1  C5   111.42  3.000
 UQY  C2   C1  C5   104.20  3.000
 UQY  N    C1  C5   115.42  3.000
 UQY  H5   C2  H4   106.74  3.000
 UQY  H5   C2  C3   108.78  3.000
 UQY  H4   C2  C3   114.42  3.000
 UQY  H5   C2  C1   110.59  3.000
 UQY  H4   C2  C1   110.88  3.000
 UQY  C3   C2  C1   105.46  3.000
 UQY  H7   C3  H6   107.50  3.000
 UQY  H7   C3  C2   112.57  3.000
 UQY  H6   C3  C2   110.58  3.000
 UQY  H7   C3  C4   113.83  3.000
 UQY  H6   C3  C4   109.90  3.000
 UQY  C2   C3  C4   102.44  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
 UQY  CONST_01  H12  N1  C6  C1  180.00   0.0  0
 UQY  CONST_02  H13  N1  C6  C1    0.00   0.0  0
 UQY  Var_01    C1   C2  C3  C4  -37.05  30.0  1
 UQY  Var_02    C2   C3  C4  C5   43.99  30.0  1
 UQY  Var_03    C3   C4  C5  C1  -34.46  30.0  1
 UQY  Var_04    H1   C   N   C1  179.41  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
 UQY  chir_01  C1  C2  C5  C6  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
 UQY  plan-1  N1   0.020
 UQY  plan-1  C6   0.020
 UQY  plan-1  O    0.020
 UQY  plan-1  C1   0.020
 UQY  plan-1  H12  0.020
 UQY  plan-1  H13  0.020

