# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:19:48 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (R)-amino[(2S)-pyrrolidin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](O)[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
 V8W  V8W  (R)-amino[(2S)-pyrrolidin-2-yl]methanol  ligand  20  8  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V8W
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
 V8W  N7    N  NH1   0  -0.619   0.5892  -1.0096  -0.3574
 V8W  C3    C  CH1   0  -0.080   0.0131  -0.0888   0.6157
 V8W  C1    C  CH1   0   0.161  -1.4243   0.2997   0.2746
 V8W  N2    N  NH2   0  -0.812  -2.3603  -0.8060   0.2289
 V8W  C4    C  CH2   0  -0.464   1.0032   1.0948   0.6553
 V8W  C5    C  CH2   0  -0.447   2.2407   0.6090  -0.1183
 V8W  C6    C  CH2   0  -0.284   2.0316  -0.8968  -0.2172
 V8W  OXT   O  OH1   0  -0.664  -1.4256   0.9642  -0.9601
 V8W  H3    H  HCH1  0   0.209  -0.0255  -0.5435   1.6189
 V8W  H61C  H  HCH2  0   0.191   2.4115  -1.3842   0.6937
 V8W  H62C  H  HCH2  0   0.224   2.5479  -1.3464  -1.0679
 V8W  H41C  H  HCH2  0   0.236   0.5821   1.9892   0.1980
 V8W  H42C  H  HCH2  0   0.229   1.2476   1.3507   1.6863
 V8W  H21N  H  HNH2  0   0.338  -2.0049  -1.5490  -0.3636
 V8W  H22N  H  HNH2  0   0.347  -2.4767  -1.2014   1.1538
 V8W  H51C  H  HCH2  0   0.226   2.2687   1.0504  -1.1159
 V8W  H52C  H  HCH2  0   0.230   3.1784   0.8614   0.3767
 V8W  HOXT  H  HOH1  0   0.445  -2.3372   1.2094  -1.1496
 V8W  H1C   H  HCH1  0   0.192  -1.7746   0.9634   1.0799
 V8W  H2    H  HNH1  0   0.342   0.2859  -1.9593  -0.1864

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
 V8W  N7   C3    single  1.458  0.020  1.458
 V8W  N7   C6    single  1.454  0.020  1.454
 V8W  C3   C1    single  1.528  0.020  1.528
 V8W  C3   C4    single  1.544  0.020  1.544
 V8W  C1   N2    single  1.449  0.020  1.449
 V8W  C1   OXT   single  1.402  0.020  1.402
 V8W  C4   C5    single  1.538  0.020  1.538
 V8W  C5   C6    single  1.523  0.020  1.523
 V8W  C3   H3    single  0.970  0.020  1.090
 V8W  C6   H61C  single  0.970  0.020  1.090
 V8W  C6   H62C  single  0.970  0.020  1.090
 V8W  C4   H41C  single  0.970  0.020  1.090
 V8W  C4   H42C  single  0.970  0.020  1.090
 V8W  N2   H21N  single  0.890  0.020  1.040
 V8W  N2   H22N  single  0.890  0.020  1.040
 V8W  C5   H51C  single  0.970  0.020  1.090
 V8W  C5   H52C  single  0.970  0.020  1.090
 V8W  OXT  HOXT  single  0.850  0.020  0.980
 V8W  C1   H1C   single  0.970  0.020  1.090
 V8W  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
 V8W  H2    N7   C6    110.74  3.000
 V8W  H2    N7   C3    111.20  3.000
 V8W  C6    N7   C3    106.18  3.000
 V8W  H3    C3   C4    108.39  3.000
 V8W  H3    C3   C1    105.98  3.000
 V8W  C4    C3   C1    114.47  3.000
 V8W  H3    C3   N7    111.14  3.000
 V8W  C4    C3   N7    104.35  3.000
 V8W  C1    C3   N7    112.54  3.000
 V8W  H1C   C1   OXT   110.99  3.000
 V8W  H1C   C1   N2    106.11  3.000
 V8W  OXT   C1   N2    109.46  3.000
 V8W  H1C   C1   C3    106.83  3.000
 V8W  OXT   C1   C3    108.55  3.000
 V8W  N2    C1   C3    114.88  3.000
 V8W  H22N  N2   H21N  106.72  3.000
 V8W  H22N  N2   C1    110.08  3.000
 V8W  H21N  N2   C1    110.54  3.000
 V8W  H42C  C4   H41C  106.92  3.000
 V8W  H42C  C4   C5    111.69  3.000
 V8W  H41C  C4   C5    111.06  3.000
 V8W  H42C  C4   C3    110.37  3.000
 V8W  H41C  C4   C3    111.77  3.000
 V8W  C5    C4   C3    105.13  3.000
 V8W  H52C  C5   H51C  107.42  3.000
 V8W  H52C  C5   C6    112.12  3.000
 V8W  H51C  C5   C6    110.12  3.000
 V8W  H52C  C5   C4    112.99  3.000
 V8W  H51C  C5   C4    110.65  3.000
 V8W  C6    C5   C4    103.56  3.000
 V8W  H62C  C6   H61C  107.41  3.000
 V8W  H62C  C6   C5    113.12  3.000
 V8W  H61C  C6   C5    109.67  3.000
 V8W  H62C  C6   N7    111.23  3.000
 V8W  H61C  C6   N7    112.83  3.000
 V8W  C5    C6   N7    102.66  3.000
 V8W  HOXT  OXT  C1    107.15  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
 V8W  Var_01  C4  C5  C6  N7   35.03  30.0  1
 V8W  Var_02  C5  C6  N7  C3  -43.99  30.0  1
 V8W  Var_03  C6  C5  C4  C3  -14.45  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
 V8W  chir_01  C3  N7   C1  C4  positiv
 V8W  chir_02  C1  OXT  N2  C3  negativ

