# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:32:51 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-[(2S,3S)-3-amino-2-hydroxy-4-phenylbutyl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)CN2CCC[C@H]2C(O)=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
 JG3  JG3  1-[(2S,3S)-3-amino-2-hydroxy-4-phenylbutyl]-L-proline  peptide  42  20  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_JG3
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
 JG3  C1   C  CH1   0   0.055  -0.1717  -0.8746  -0.2409
 JG3  N    N  NH2   0  -0.803   1.4470  -0.4229   1.5353
 JG3  O1   O  OH1   0  -0.671  -0.2744  -2.2252   0.1665
 JG3  C    C  C     0   0.525  -3.7682   1.7101   0.2949
 JG3  N2   N  NT    0  -0.430  -2.6080  -0.4658  -0.0860
 JG3  C3   C  CH2   0  -0.270  -3.3338  -1.3654   0.7873
 JG3  C4   C  CH2   0  -0.295  -1.2960  -0.0108   0.3243
 JG3  C5   C  CR16  0  -0.275   6.1491   0.8069   0.0813
 JG3  C6   C  CR16  0  -0.326   4.5463  -0.9644   0.3789
 JG3  C7   C  CR16  0  -0.307   4.0415   0.8633  -1.0797
 JG3  C8   C  CH1   0  -0.106   1.2065  -0.2946   0.1048
 JG3  CA   C  CH1   0  -0.198  -3.5387   0.5033  -0.6021
 JG3  C10  C  CH2   0  -0.533   2.3020  -0.9265  -0.7732
 JG3  C11  C  CH2   0  -0.475  -4.8689  -0.2833  -0.7412
 JG3  C12  C  CR16  0  -0.240   5.7810  -0.3964   0.6674
 JG3  C13  C  CR16  0  -0.240   5.2736   1.4356  -0.7960
 JG3  C14  C  CR6   0   0.146   3.6584  -0.3449  -0.4981
 JG3  C15  C  CH2   0  -0.458  -4.6309  -1.5983   0.0218
 JG3  H1   H  HCH1  0   0.219  -0.2778  -0.8862  -1.3310
 JG3  H2   H  HNH2  0   0.340   1.8116  -1.3439   1.7500
 JG3  H3   H  HOH1  0   0.440  -0.2808  -2.2423   1.1302
 JG3  H4   H  HCH2  0   0.230  -2.7800  -2.2902   0.9444
 JG3  H5   H  HCH2  0   0.200  -3.5336  -0.9305   1.7777
 JG3  H6   H  HCH2  0   0.219  -1.2030   0.0442   1.4164
 JG3  H7   H  HCH2  0   0.229  -1.1347   1.0062  -0.0437
 JG3  H9   H  HCR6  0   0.245   4.2742  -1.9095   0.8344
 JG3  H10  H  HCR6  0   0.244   3.3665   1.3609  -1.7668
 JG3  H11  H  HCH1  0   0.235   1.1703   0.7765  -0.1228
 JG3  H12  H  HCH1  0   0.278  -3.2033   0.8764  -1.5753
 JG3  H13  H  HCH2  0   0.243   2.3143  -2.0061  -0.5970
 JG3  H14  H  HCH2  0   0.241   2.0437  -0.7785  -1.8256
 JG3  H15  H  HCH2  0   0.251  -5.7143   0.2709  -0.3325
 JG3  H16  H  HCH2  0   0.258  -5.0934  -0.4622  -1.7913
 JG3  H17  H  HCR6  0   0.252   6.4556  -0.8958   1.3511
 JG3  H18  H  HCR6  0   0.252   5.5516   2.3729  -1.2609
 JG3  H19  H  HCH2  0   0.236  -4.5074  -2.4234  -0.6801
 JG3  H20  H  HCH2  0   0.236  -5.4594  -1.8498   0.6829
 JG3  H21  H  HNH2  0   0.356   2.1658   0.2259   1.8268
 JG3  OXT  O  OH1   0  -0.596  -4.3597   2.6991  -0.3706
 JG3  HXT  H  HOH1  0   0.477  -4.5392   3.4406   0.2270
 JG3  O    O  O     0  -0.438  -3.4829   1.7823   1.4640
 JG3  H8   H  HCR6  0   0.252   7.1117   1.2497   0.3029

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
 JG3  C1   O1   single    1.414  0.020  1.414
 JG3  C1   H1   single    0.970  0.020  1.090
 JG3  N    C8   single    1.456  0.020  1.456
 JG3  N    H2   single    0.890  0.020  1.040
 JG3  O1   H3   single    0.850  0.020  0.980
 JG3  C    CA   single    1.525  0.021  1.525
 JG3  N2   CA   single    1.439  0.020  1.439
 JG3  O    C    double    1.231  0.020  1.231
 JG3  C3   N2   single    1.449  0.020  1.449
 JG3  C3   C15  single    1.524  0.020  1.524
 JG3  C3   H4   single    0.970  0.020  1.090
 JG3  C3   H5   single    0.970  0.020  1.090
 JG3  C4   C1   single    1.526  0.020  1.526
 JG3  C4   N2   single    1.448  0.020  1.448
 JG3  C4   H6   single    0.970  0.020  1.090
 JG3  C4   H7   single    0.970  0.020  1.090
 JG3  C5   C12  aromatic  1.388  0.020  1.388
 JG3  C5   C13  aromatic  1.390  0.020  1.390
 JG3  C5   H8   single    0.930  0.020  1.080
 JG3  C6   C14  aromatic  1.393  0.020  1.393
 JG3  C6   H9   single    0.930  0.020  1.080
 JG3  C7   C14  aromatic  1.395  0.020  1.395
 JG3  C7   H10  single    0.930  0.020  1.080
 JG3  C8   C1   single    1.535  0.020  1.535
 JG3  C8   C10  single    1.540  0.020  1.540
 JG3  C8   H11  single    0.970  0.020  1.090
 JG3  CA   C11  single    1.552  0.020  1.552
 JG3  CA   H12  single    0.970  0.020  1.090
 JG3  C10  H13  single    0.970  0.020  1.090
 JG3  C10  H14  single    0.970  0.020  1.090
 JG3  C11  H15  single    0.970  0.020  1.090
 JG3  C11  H16  single    0.970  0.020  1.090
 JG3  C12  C6   aromatic  1.389  0.020  1.389
 JG3  C12  H17  single    0.930  0.020  1.080
 JG3  C13  C7   aromatic  1.388  0.020  1.388
 JG3  C13  H18  single    0.930  0.020  1.080
 JG3  C14  C10  single    1.501  0.020  1.501
 JG3  C15  C11  single    1.539  0.020  1.539
 JG3  C15  H19  single    0.970  0.020  1.090
 JG3  C15  H20  single    0.970  0.020  1.090
 JG3  N    H21  single    0.890  0.020  1.040
 JG3  C    OXT  single    1.331  0.020  1.331
 JG3  OXT  HXT  single    0.850  0.020  0.980

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
 JG3  H1   C1   C8   108.37  3.000
 JG3  C8   C1   C4   111.36  3.000
 JG3  H1   C1   C4   107.65  3.000
 JG3  C8   C1   O1   111.18  3.000
 JG3  C4   C1   O1   112.35  3.000
 JG3  H1   C1   O1   105.63  3.000
 JG3  H21  N    H2   105.45  3.000
 JG3  H21  N    C8   110.12  3.000
 JG3  H2   N    C8   110.34  3.000
 JG3  H3   O1   C1   107.78  3.000
 JG3  OXT  C    CA   120.80  1.700
 JG3  OXT  C    O    123.07  3.000
 JG3  CA   C    O    120.80  1.700
 JG3  CA   N2   C4   118.42  3.000
 JG3  C4   N2   C3   118.57  3.000
 JG3  CA   N2   C3   108.08  3.000
 JG3  H5   C3   H4   107.35  3.000
 JG3  H5   C3   C15  110.98  3.000
 JG3  H4   C3   C15  112.05  3.000
 JG3  H5   C3   N2   112.84  3.000
 JG3  H4   C3   N2   111.06  3.000
 JG3  C15  C3   N2   102.62  3.000
 JG3  H7   C4   H6   106.01  3.000
 JG3  H7   C4   N2   109.30  3.000
 JG3  H6   C4   N2   111.99  3.000
 JG3  H7   C4   C1   107.04  3.000
 JG3  H6   C4   C1   109.54  3.000
 JG3  N2   C4   C1   112.63  3.000
 JG3  H8   C5   C13  120.29  3.000
 JG3  H8   C5   C12  120.26  3.000
 JG3  C13  C5   C12  119.44  3.000
 JG3  H9   C6   C14  119.49  3.000
 JG3  H9   C6   C12  119.49  3.000
 JG3  C14  C6   C12  121.02  3.000
 JG3  H10  C7   C14  119.40  3.000
 JG3  H10  C7   C13  119.54  3.000
 JG3  C14  C7   C13  121.05  3.000
 JG3  H11  C8   C10  107.84  3.000
 JG3  H11  C8   N    107.20  3.000
 JG3  C10  C8   N    113.98  3.000
 JG3  H11  C8   C1   107.04  3.000
 JG3  C10  C8   C1   110.82  3.000
 JG3  N    C8   C1   109.65  3.000
 JG3  H12  CA   C11  110.84  3.000
 JG3  H12  CA   N2   110.49  3.000
 JG3  C11  CA   N2   104.19  3.000
 JG3  H12  CA   C    107.46  3.000
 JG3  C11  CA   C    109.01  3.000
 JG3  N2   CA   C    114.85  3.000
 JG3  H14  C10  H13  106.93  3.000
 JG3  H14  C10  C14  109.71  3.000
 JG3  H13  C10  C14  110.04  3.000
 JG3  C14  C10  C8   112.30  3.000
 JG3  H14  C10  C8   108.98  3.000
 JG3  H13  C10  C8   108.74  3.000
 JG3  H16  C11  H15  106.57  3.000
 JG3  H16  C11  C15  111.70  3.000
 JG3  H15  C11  C15  111.62  3.000
 JG3  C15  C11  CA   104.85  3.000
 JG3  H16  C11  CA   110.28  3.000
 JG3  H15  C11  CA   111.92  3.000
 JG3  H17  C12  C6   119.76  3.000
 JG3  H17  C12  C5   120.09  3.000
 JG3  C6   C12  C5   120.16  3.000
 JG3  H18  C13  C7   119.82  3.000
 JG3  H18  C13  C5   120.06  3.000
 JG3  C7   C13  C5   120.12  3.000
 JG3  C10  C14  C7   120.49  3.000
 JG3  C10  C14  C6   121.26  3.000
 JG3  C7   C14  C6   118.21  3.000
 JG3  H20  C15  H19  107.59  3.000
 JG3  H20  C15  C11  112.37  3.000
 JG3  H19  C15  C11  110.18  3.000
 JG3  H20  C15  C3   112.19  3.000
 JG3  H19  C15  C3   110.03  3.000
 JG3  C11  C15  C3   104.48  3.000
 JG3  HXT  OXT  C    110.04  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
 JG3  CONST_01  C14  C6   C12  C5      0.00   0.0  0
 JG3  CONST_02  C14  C7   C13  C5      0.00   0.0  0
 JG3  CONST_03  C13  C7   C14  C6      0.00   0.0  0
 JG3  CONST_04  C13  C5   C12  C6      0.00   0.0  0
 JG3  CONST_05  C12  C6   C14  C7      0.00   0.0  0
 JG3  CONST_06  C12  C5   C13  C7      0.00   0.0  0
 JG3  CONST_07  C12  C6   C14  C10   180.00   0.0  0
 JG3  CONST_08  C13  C7   C14  C10   180.00   0.0  0
 JG3  CONST_09  H9   C6   C12  C5    180.00   0.0  0
 JG3  CONST_10  H10  C7   C13  C5    180.00   0.0  0
 JG3  CONST_11  H8   C5   C12  C6    180.00   0.0  0
 JG3  CONST_12  H18  C13  C5   C12   180.00   0.0  0
 JG3  CONST_13  H17  C12  C5   C13   180.00   0.0  0
 JG3  CONST_14  HXT  OXT  C    CA    180.00   0.0  0
 JG3  Var_01    C11  C15  C3   N2    -31.37  30.0  1
 JG3  Var_02    CA   C11  C15  C3     11.78  30.0  1
 JG3  Var_03    C15  C3   N2   CA     41.45  30.0  1
 JG3  Var_04    CA   N2   C4   C1   -131.84  30.0  3
 JG3  Var_05    C8   C10  C14  C6     95.82  30.0  2

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
 JG3  chir_01  C1  O1  C4   C8   negativ
 JG3  chir_02  C8  N   C10  C1   negativ
 JG3  chir_03  CA  N2  C    C11  positiv

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
 JG3  plan-1  C5   0.020
 JG3  plan-1  C6   0.020
 JG3  plan-1  C7   0.020
 JG3  plan-1  C10  0.020
 JG3  plan-1  C12  0.020
 JG3  plan-1  C13  0.020
 JG3  plan-1  C14  0.020
 JG3  plan-1  H9   0.020
 JG3  plan-1  H10  0.020
 JG3  plan-1  H17  0.020
 JG3  plan-1  H18  0.020
 JG3  plan-1  H8   0.020
 JG3  plan-2  C    0.020
 JG3  plan-2  CA   0.020
 JG3  plan-2  OXT  0.020
 JG3  plan-2  HXT  0.020
 JG3  plan-2  O    0.020

