# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:09:47 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-[(2~{R})-pyrrolidin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[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
 7RX  7RX  "(R)-homoproline"  D-peptide  19  9  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7RX
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
 7RX  C02  C  C      0   0.415   7.7899  -25.0159  6.4080
 7RX  C03  C  CH2    0  -0.594   8.7432  -26.0144  7.0979
 7RX  C04  C  CR15   0  -0.040   9.0253  -27.3017  6.3523
 7RX  C05  C  CH2    0  -0.435  10.0009  -28.2450  7.0682
 7RX  C06  C  CH2    0  -0.458   9.5723  -29.6599  6.6286
 7RX  C07  C  CH2    0  -0.286   8.3405  -29.4210  5.7449
 7RX  N08  N  NR15   0  -0.611   7.8420  -28.1392  6.2098
 7RX  OXY  O  OC    -1  -0.619   7.5187  -23.9889  7.0624
 7RX  O09  O  O      0  -0.604   7.3748  -25.2972  5.2636
 7RX  H1   H  HCH2   0   0.210   8.3403  -26.2583  8.0877
 7RX  H2   H  HCH2   0   0.219   9.6907  -25.4973  7.2889
 7RX  H3   H  HCR5   0   0.177   9.4545  -27.0541  5.3663
 7RX  H4   H  HCH2   0   0.222  11.0359  -28.0175  6.8117
 7RX  H5   H  HCH2   0   0.216   9.9071  -28.1335  8.1511
 7RX  H6   H  HCH2   0   0.226   9.3168  -30.2732  7.4933
 7RX  H7   H  HCH2   0   0.225  10.3554  -30.1868  6.0837
 7RX  H8   H  HCH2   0   0.216   7.5872  -30.2051  5.8483
 7RX  H9   H  HCH2   0   0.185   8.6457  -29.4003  4.6874
 7RX  H    H  HNR5   0   0.336   7.1992  -27.7163  5.5531

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
 7RX  C07  N08  single  1.452  0.020  1.452
 7RX  C07  C06  single  1.535  0.020  1.535
 7RX  N08  C04  single  1.457  0.020  1.457
 7RX  C04  C03  single  1.514  0.020  1.514
 7RX  C04  C05  single  1.534  0.020  1.534
 7RX  O09  C02  deloc   1.250  0.020  1.250
 7RX  OXY  C02  deloc   1.248  0.020  1.248
 7RX  C02  C03  single  1.543  0.020  1.543
 7RX  C06  C05  single  1.542  0.020  1.542
 7RX  C03  H1   single  0.970  0.020  1.090
 7RX  C03  H2   single  0.970  0.020  1.090
 7RX  C04  H3   single  0.970  0.020  1.090
 7RX  C05  H4   single  0.970  0.020  1.090
 7RX  C05  H5   single  0.970  0.020  1.090
 7RX  C06  H6   single  0.970  0.020  1.090
 7RX  C06  H7   single  0.970  0.020  1.090
 7RX  C07  H8   single  0.970  0.020  1.090
 7RX  C07  H9   single  0.970  0.020  1.090
 7RX  N08  H    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
 7RX  O09  C02  OXY  126.40  3.000
 7RX  OXY  C02  C03  115.62  3.000
 7RX  O09  C02  C03  117.97  3.000
 7RX  H2   C03  H1   105.39  3.000
 7RX  H2   C03  C04  109.01  3.000
 7RX  H1   C03  C04  108.90  3.000
 7RX  H2   C03  C02  107.85  3.000
 7RX  H1   C03  C02  108.70  3.000
 7RX  C04  C03  C02  116.43  3.000
 7RX  H3   C04  N08  110.95  3.000
 7RX  H3   C04  C05  107.91  3.000
 7RX  N08  C04  C05  102.05  3.000
 7RX  H3   C04  C03  108.76  3.000
 7RX  C05  C04  C03  114.29  3.000
 7RX  N08  C04  C03  112.68  3.000
 7RX  H5   C05  H4   107.06  3.000
 7RX  H5   C05  C06  110.62  3.000
 7RX  H4   C05  C06  112.83  3.000
 7RX  H5   C05  C04  110.19  3.000
 7RX  H4   C05  C04  111.44  3.000
 7RX  C06  C05  C04  104.73  3.000
 7RX  H7   C06  H6   107.03  3.000
 7RX  H7   C06  C07  111.35  3.000
 7RX  H6   C06  C07  110.86  3.000
 7RX  H7   C06  C05  112.73  3.000
 7RX  H6   C06  C05  110.79  3.000
 7RX  C07  C06  C05  104.15  3.000
 7RX  H9   C07  H8   107.20  3.000
 7RX  H9   C07  N08  112.72  3.000
 7RX  H8   C07  N08  111.51  3.000
 7RX  H9   C07  C06  109.48  3.000
 7RX  H8   C07  C06  112.79  3.000
 7RX  N08  C07  C06  103.22  3.000
 7RX  H    N08  C07  112.30  3.000
 7RX  H    N08  C04  109.83  3.000
 7RX  C07  N08  C04  105.07  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
 7RX  Var_01  C06  C07  N08  C04    43.82  30.0  1
 7RX  Var_02  C07  C06  C05  C04    -2.57  30.0  1
 7RX  Var_03  N08  C07  C06  C05   -24.10  30.0  1
 7RX  Var_04  H8   C07  N08  C04   165.16  30.0  1
 7RX  Var_05  H9   C07  N08  C04   -74.20  30.0  1
 7RX  Var_06  H6   C06  C05  C04  -121.81  30.0  1
 7RX  Var_07  H7   C06  C05  C04   118.28  30.0  1
 7RX  Var_08  H8   C07  C06  C05  -144.58  30.0  1
 7RX  Var_09  H9   C07  C06  C05    96.15  30.0  1
 7RX  Var_10  H    N08  C07  C06   163.17  30.0  1
 7RX  Var_11  H4   C05  C06  C07  -123.95  30.0  1
 7RX  Var_12  H5   C05  C06  C07   116.14  30.0  1
 7RX  Var_13  H6   C06  C07  N08    95.09  30.0  1
 7RX  Var_14  H7   C06  C07  N08  -145.86  30.0  1
 7RX  Var_15  O09  C02  C03  C04    -3.71  30.0  3
 7RX  Var_16  OXY  C02  C03  C04   176.79  30.0  3
 7RX  Var_17  H1   C03  C02  OXY    53.42  30.0  3
 7RX  Var_18  H2   C03  C02  OXY   -60.37  30.0  3
 7RX  Var_19  H1   C03  C02  O09  -127.09  30.0  3
 7RX  Var_20  H2   C03  C02  O09   119.13  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
 7RX  chir_01  C04  N08  C03  C05  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
 7RX  plan-1  C02  0.020
 7RX  plan-1  C03  0.020
 7RX  plan-1  OXY  0.020
 7RX  plan-1  O09  0.020

