# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:14:34 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: (3R)-pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCNC1
#
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
 04S  04S  '(3R)-pyrrolidin-3-amine  '  ligand  16  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 GRAND
;

data_comp_04S
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
 04S  N29   N  NH2   0  -0.803   2.0313  -0.0123   0.3310
 04S  C30   C  CH1   0  -0.101   0.7899   0.0629  -0.4285
 04S  C31   C  CH2   0  -0.273  -0.0950  -1.1853  -0.2139
 04S  N32   N  NH1   0  -0.613  -1.3183  -0.6907   0.4115
 04S  C33   C  CH2   0  -0.287  -1.4998   0.6707  -0.0679
 04S  C34   C  CH2   0  -0.452  -0.0902   1.2285   0.0413
 04S  HN29  H  HNH2  0   0.341   2.6211  -0.7369  -0.0612
 04S  H30   H  HCH1  0   0.211   0.9700   0.1761  -1.5061
 04S  H31   H  HCH2  0   0.202  -0.2809  -1.6761  -1.1772
 04S  H31A  H  HCH2  0   0.213   0.4053  -1.9136   0.4307
 04S  HN32  H  HNH1  0   0.346  -2.1106  -1.2766   0.1858
 04S  H33   H  HCH2  0   0.193  -1.8476   0.7252  -1.1111
 04S  H33A  H  HCH2  0   0.226  -2.2219   1.2129   0.5459
 04S  H34   H  HCH2  0   0.223   0.1407   1.4530   1.0857
 04S  H34A  H  HCH2  0   0.233   0.0595   2.1354  -0.5450
 04S  H2    H  HNH2  0   0.341   2.5504   0.8484   0.1995

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
 04S  C30  N29   single  1.457  0.020  1.457
 04S  N29  HN29  single  0.890  0.020  1.040
 04S  C34  C30   single  1.534  0.020  1.534
 04S  C30  C31   single  1.545  0.020  1.545
 04S  C30  H30   single  0.970  0.020  1.090
 04S  N32  C31   single  1.460  0.020  1.460
 04S  C31  H31   single  0.970  0.020  1.090
 04S  C31  H31A  single  0.970  0.020  1.090
 04S  C33  N32   single  1.455  0.020  1.455
 04S  N32  HN32  single  0.890  0.020  1.040
 04S  C33  C34   single  1.520  0.020  1.520
 04S  C33  H33   single  0.970  0.020  1.090
 04S  C33  H33A  single  0.970  0.020  1.090
 04S  C34  H34   single  0.970  0.020  1.090
 04S  C34  H34A  single  0.970  0.020  1.090
 04S  N29  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
 04S  H2    N29  HN29  105.01  3.000
 04S  H2    N29  C30   108.95  3.000
 04S  HN29  N29  C30   109.32  3.000
 04S  H30   C30  C34   108.43  3.000
 04S  H30   C30  C31   108.27  3.000
 04S  C34   C30  C31   104.04  3.000
 04S  H30   C30  N29   112.15  3.000
 04S  C31   C30  N29   111.95  3.000
 04S  C34   C30  N29   111.61  3.000
 04S  H31A  C31  H31   107.28  3.000
 04S  H31A  C31  N32   110.88  3.000
 04S  H31   C31  N32   112.69  3.000
 04S  H31A  C31  C30   110.97  3.000
 04S  H31   C31  C30   109.66  3.000
 04S  N32   C31  C30   105.41  3.000
 04S  HN32  N32  C33   111.78  3.000
 04S  HN32  N32  C31   111.39  3.000
 04S  C33   N32  C31   106.28  3.000
 04S  H33A  C33  H33   107.41  3.000
 04S  H33A  C33  C34   113.00  3.000
 04S  H33   C33  C34   110.05  3.000
 04S  H33A  C33  N32   111.22  3.000
 04S  H33   C33  N32   113.45  3.000
 04S  C34   C33  N32   101.77  3.000
 04S  H34A  C34  H34   108.29  3.000
 04S  H34A  C34  C33   113.21  3.000
 04S  H34   C34  C33   109.88  3.000
 04S  H34A  C34  C30   112.86  3.000
 04S  H34   C34  C30   109.12  3.000
 04S  C33   C34  C30   103.37  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
 04S  Var_01  N32  C33  C34  C30   40.07  30.0  1
 04S  Var_02  C33  N32  C31  C30   29.57  30.0  1
 04S  Var_03  C34  C33  N32  C31  -43.72  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
 04S  chir_01  C30  N29  C34  C31  positiv

