# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:33:54 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (2S)-pyrrolidine-2-carboximidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=N)[C@@H]1CCCN1
#
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
 04V  04V  '(2S)-pyrrolidine-2-carboximidic acid'  L-peptide  18  8  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_04V
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
 04V  N7    N  NR15  0  -0.587  -0.7972  -1.1504  -0.2150
 04V  C6    C  CH2   0  -0.308  -2.1809  -0.6788  -0.2008
 04V  C5    C  CH2   0  -0.480  -2.1696   0.8185   0.2007
 04V  C4    C  CH2   0  -0.449  -0.6843   1.1642   0.3509
 04V  C3    C  CR15  0  -0.151   0.0086   0.0339  -0.4376
 04V  C1    C  C     0   0.407   1.4406  -0.1505  -0.0278
 04V  N2    N  N     0  -0.647   1.8077  -1.1269   0.6839
 04V  OXT   O  OH1   0  -0.605   2.1951   0.8616  -0.4818
 04V  H61C  H  HCH2  0   0.221  -2.6160  -0.7927  -1.1967
 04V  H62C  H  HCH2  0   0.235  -2.7737  -1.2931   0.4764
 04V  H3    H  HCR5  0   0.259  -0.0172   0.2847  -1.5051
 04V  H51C  H  HCH2  0   0.235  -2.6349   1.4278  -0.5752
 04V  H52C  H  HCH2  0   0.239  -2.7201   1.0014   1.1235
 04V  H41C  H  HCH2  0   0.242  -0.4356   2.1589  -0.0178
 04V  H42C  H  HCH2  0   0.233  -0.3786   1.1122   1.3992
 04V  H21N  H  H     0   0.340   2.7964  -1.1015   0.9204
 04V  HXT   H  HOH1  0   0.475   3.1089   0.7731  -0.1809
 04V  H2    H  HNR5  0   0.342  -0.5551  -1.5272   0.6941

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
 04V  N7   C6    single  1.462  0.020  1.462
 04V  N7   C3    single  1.450  0.020  1.450
 04V  C6   C5    single  1.550  0.020  1.550
 04V  C5   C4    single  1.532  0.020  1.532
 04V  C4   C3    single  1.543  0.020  1.543
 04V  C3   C1    single  1.501  0.020  1.501
 04V  C1   N2    double  1.263  0.020  1.263
 04V  C1   OXT   single  1.342  0.020  1.342
 04V  C6   H61C  single  0.970  0.020  1.090
 04V  C6   H62C  single  0.970  0.020  1.090
 04V  C3   H3    single  0.970  0.020  1.090
 04V  C5   H51C  single  0.970  0.020  1.090
 04V  C5   H52C  single  0.970  0.020  1.090
 04V  C4   H41C  single  0.970  0.020  1.090
 04V  C4   H42C  single  0.970  0.020  1.090
 04V  N2   H21N  single  0.890  0.020  1.040
 04V  OXT  HXT   single  0.850  0.020  0.980
 04V  N7   H2    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
 04V  H2    N7   C3    107.98  3.000
 04V  H2    N7   C6    109.71  3.000
 04V  C3    N7   C6    105.31  3.000
 04V  H62C  C6   H61C  106.92  3.000
 04V  H62C  C6   C5    112.80  3.000
 04V  H61C  C6   C5    109.85  3.000
 04V  H62C  C6   N7    109.82  3.000
 04V  H61C  C6   N7    109.53  3.000
 04V  C5    C6   N7    107.89  3.000
 04V  H52C  C5   H51C  107.05  3.000
 04V  H52C  C5   C4    111.63  3.000
 04V  H51C  C5   C4    110.93  3.000
 04V  H52C  C5   C6    112.18  3.000
 04V  H51C  C5   C6    110.62  3.000
 04V  C4    C5   C6    104.49  3.000
 04V  H42C  C4   H41C  107.70  3.000
 04V  H42C  C4   C3    109.25  3.000
 04V  H41C  C4   C3    113.17  3.000
 04V  H42C  C4   C5    110.75  3.000
 04V  H41C  C4   C5    113.20  3.000
 04V  C3    C4   C5    102.71  3.000
 04V  H3    C3   C1    108.44  3.000
 04V  H3    C3   C4    108.62  3.000
 04V  C1    C3   C4    112.28  3.000
 04V  H3    C3   N7    108.85  3.000
 04V  C1    C3   N7    112.83  3.000
 04V  C4    C3   N7    105.69  3.000
 04V  OXT   C1   N2    127.63  3.000
 04V  OXT   C1   C3    110.58  3.000
 04V  N2    C1   C3    121.75  3.000
 04V  H21N  N2   C1    113.23  3.000
 04V  HXT   OXT  C1    110.95  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
 04V  Var_01  C4  C5  C6  N7    2.32  30.0  1
 04V  Var_02  C3  C4  C5  C6   19.20  30.0  1
 04V  Var_03  C3  N7  C6  C5  -24.61  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
 04V  chir_01  C3  N7  C4  C1  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
 04V  plan-1  C3    0.020
 04V  plan-1  C1    0.020
 04V  plan-1  N2    0.020
 04V  plan-1  OXT   0.020
 04V  plan-1  H21N  0.020

