# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:30:24 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: N~6~-{[(6-aminopyridin-3-yl)methoxy]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccc(N)nc1)C(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
 9UF  9UF  N~6~-{[(6-aminopyridin-3-yl)methoxy]carbonyl}-L-lysine  peptide  40  21  .  2019-07-05  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_9UF
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
 9UF  C15  C  CR6    0  -0.040  263.5096  38.9060  140.4412
 9UF  C20  C  CR16   0  -0.379  263.4554  38.7727  138.0424
 9UF  C21  C  CR16   0  -0.167  263.3448  38.1630  139.2703
 9UF  C    C  C      0   0.387  256.2766  41.2043  147.0204
 9UF  CA   C  CH1    0  -0.217  257.1661  40.6022  145.9017
 9UF  CB   C  CH2    0  -0.433  256.9731  39.0809  145.8634
 9UF  CG   C  CH2    0  -0.406  257.8594  38.3503  144.8598
 9UF  CD   C  CH2    0  -0.483  257.6670  38.8080  143.4193
 9UF  CE   C  CH2    0  -0.253  258.6331  38.1622  142.4392
 9UF  C11  C  C      0   0.756  261.0484  38.0932  142.0676
 9UF  C14  C  CH2    0  -0.270  263.3939  38.3026  141.8060
 9UF  C16  C  CR16   0  -0.083  263.7858  40.2542  140.2802
 9UF  C18  C  CR6    0   0.450  263.7264  40.1524  137.9986
 9UF  N    N  NH2    0  -0.785  258.5834  40.9241  145.9781
 9UF  NZ   N  NH1    0  -0.659  259.9868  38.6055  142.7070
 9UF  N17  N  N      0  -0.456  263.8917  40.8698  139.1095
 9UF  N19  N  NH2    0  -0.831  263.7927  40.8184  136.8132
 9UF  O12  O  O      0  -0.516  260.9987  37.2033  141.2415
 9UF  O13  O  O2     0  -0.484  262.1841  38.6799  142.4719
 9UF  H20  H  HCR6   0   0.264  263.3349  38.2092  137.1260
 9UF  H21  H  HCR6   0   0.259  263.1361  37.1021  139.3275
 9UF  HA   H  HCH1   0   0.208  256.7972  41.0101  144.9529
 9UF  HB2  H  HCH2   0   0.214  255.9223  38.8698  145.6545
 9UF  HB3  H  HCH2   0   0.211  257.1740  38.6714  146.8606
 9UF  HG2  H  HCH2   0   0.214  257.6503  37.2771  144.9181
 9UF  HG3  H  HCH2   0   0.212  258.9037  38.4704  145.1558
 9UF  HD2  H  HCH2   0   0.231  257.7694  39.8944  143.3457
 9UF  HD3  H  HCH2   0   0.234  256.6494  38.5780  143.0929
 9UF  HE2  H  HCH2   0   0.235  258.3448  38.4171  141.4151
 9UF  HE3  H  HCH2   0   0.228  258.5782  37.0739  142.5253
 9UF  H14  H  HCH2   0   0.249  263.4875  37.2161  141.7603
 9UF  H13  H  HCH2   0   0.256  264.1814  38.6762  142.4599
 9UF  H16  H  HCR6   0   0.253  263.9374  40.8806  141.1555
 9UF  H    H  HNH2   0   0.331  258.6850  41.9316  145.9983
 9UF  H2   H  HNH2   0   0.321  258.9332  40.6195  146.8801
 9UF  HZ   H  HNH1   0   0.394  260.1195  39.3912  143.3251
 9UF  H19  H  HNH2   0   0.382  264.2339  41.7231  136.8271
 9UF  H18  H  HNH2   0   0.391  263.9596  40.2830  135.9779
 9UF  OXT  O  OC    -1  -0.602  256.8489  41.7724  147.9715
 9UF  O    O  O      0  -0.618  255.0449  41.0575  146.8703

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
 9UF  N19  C18  single    1.361  0.020  1.361
 9UF  C20  C18  aromatic  1.407  0.020  1.407
 9UF  C20  C21  aromatic  1.375  0.020  1.375
 9UF  C18  N17  aromatic  1.333  0.020  1.333
 9UF  C21  C15  aromatic  1.396  0.020  1.396
 9UF  N17  C16  aromatic  1.327  0.020  1.327
 9UF  C15  C16  aromatic  1.386  0.020  1.386
 9UF  C15  C14  single    1.497  0.020  1.497
 9UF  C14  O13  single    1.432  0.020  1.432
 9UF  O12  C11  double    1.215  0.020  1.215
 9UF  C11  O13  single    1.341  0.020  1.341
 9UF  C11  NZ   single    1.341  0.020  1.341
 9UF  NZ   CE   single    1.449  0.020  1.449
 9UF  CE   CD   single    1.520  0.020  1.520
 9UF  CD   CG   single    1.524  0.020  1.524
 9UF  CG   CB   single    1.525  0.020  1.525
 9UF  O    C    deloc     1.231  0.020  1.231
 9UF  CB   CA   single    1.521  0.033  1.521
 9UF  C    CA   single    1.525  0.021  1.525
 9UF  C    OXT  deloc     1.247  0.020  1.247
 9UF  CA   N    single    1.458  0.019  1.458
 9UF  C20  H20  single    0.930  0.020  1.080
 9UF  C21  H21  single    0.930  0.020  1.080
 9UF  CA   HA   single    0.970  0.020  0.970
 9UF  CB   HB2  single    0.970  0.020  1.090
 9UF  CB   HB3  single    0.970  0.020  1.090
 9UF  CG   HG2  single    0.970  0.020  1.090
 9UF  CG   HG3  single    0.970  0.020  1.090
 9UF  CD   HD2  single    0.970  0.020  1.090
 9UF  CD   HD3  single    0.970  0.020  1.090
 9UF  CE   HE2  single    0.970  0.020  1.090
 9UF  CE   HE3  single    0.970  0.020  1.090
 9UF  C14  H14  single    0.970  0.020  1.090
 9UF  C14  H13  single    0.970  0.020  1.090
 9UF  C16  H16  single    0.930  0.020  1.080
 9UF  N    H    single    0.860  0.020  0.860
 9UF  N    H2   single    0.890  0.020  1.040
 9UF  NZ   HZ   single    0.860  0.020  1.020
 9UF  N19  H19  single    0.890  0.020  1.040
 9UF  N19  H18  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
 9UF  C16  C15  C14  120.91  3.000
 9UF  C14  C15  C21  122.74  3.000
 9UF  C16  C15  C21  116.35  3.000
 9UF  H20  C20  C18  120.37  3.000
 9UF  H20  C20  C21  121.07  3.000
 9UF  C18  C20  C21  118.56  3.000
 9UF  H21  C21  C20  119.80  3.000
 9UF  H21  C21  C15  119.99  3.000
 9UF  C20  C21  C15  120.21  3.000
 9UF  O    C    OXT  126.70  3.000
 9UF  OXT  C    CA   120.80  1.700
 9UF  O    C    CA   120.80  1.700
 9UF  HA   CA   N    110.00  3.000
 9UF  HA   CA   CB   109.00  3.000
 9UF  N    CA   CB   110.40  1.500
 9UF  HA   CA   C    110.00  3.000
 9UF  N    CA   C    111.00  2.800
 9UF  CB   CA   C    110.50  1.500
 9UF  HB3  CB   HB2  106.15  3.000
 9UF  HB3  CB   CG   108.24  3.000
 9UF  HB2  CB   CG   109.92  3.000
 9UF  HB3  CB   CA   108.94  3.000
 9UF  HB2  CB   CA   108.52  3.000
 9UF  CG   CB   CA   114.73  3.000
 9UF  HG3  CG   HG2  106.02  3.000
 9UF  HG3  CG   CD   110.12  3.000
 9UF  HG2  CG   CD   108.70  3.000
 9UF  HG3  CG   CB   108.94  3.000
 9UF  HG2  CG   CB   108.87  3.000
 9UF  CD   CG   CB   113.88  3.000
 9UF  HD3  CD   HD2  106.03  3.000
 9UF  HD3  CD   CE   108.04  3.000
 9UF  HD2  CD   CE   108.61  3.000
 9UF  HD3  CD   CG   109.67  3.000
 9UF  HD2  CD   CG   110.50  3.000
 9UF  CE   CD   CG   113.68  3.000
 9UF  HE3  CE   HE2  107.01  3.000
 9UF  HE3  CE   NZ   109.69  3.000
 9UF  HE2  CE   NZ   110.36  3.000
 9UF  HE3  CE   CD   109.89  3.000
 9UF  HE2  CE   CD   109.69  3.000
 9UF  NZ   CE   CD   110.15  3.000
 9UF  O13  C11  O12  124.06  3.000
 9UF  O13  C11  NZ   111.08  3.000
 9UF  O12  C11  NZ   124.85  3.000
 9UF  H13  C14  H14  107.72  3.000
 9UF  H13  C14  O13  103.96  3.000
 9UF  H14  C14  O13  110.75  3.000
 9UF  H13  C14  C15  110.68  3.000
 9UF  H14  C14  C15  110.89  3.000
 9UF  O13  C14  C15  112.53  3.000
 9UF  H16  C16  N17  115.59  3.000
 9UF  H16  C16  C15  119.67  3.000
 9UF  N17  C16  C15  124.74  3.000
 9UF  N19  C18  N17  117.16  3.000
 9UF  N17  C18  C20  121.73  3.000
 9UF  N19  C18  C20  121.09  3.000
 9UF  H2   N    H    104.26  3.000
 9UF  H2   N    CA   108.42  3.000
 9UF  H    N    CA   114.00  3.000
 9UF  HZ   NZ   C11  119.06  3.000
 9UF  HZ   NZ   CE   118.32  3.000
 9UF  C11  NZ   CE   122.30  3.000
 9UF  C18  N17  C16  118.41  3.000
 9UF  H18  N19  H19  114.65  3.000
 9UF  H18  N19  C18  118.08  3.000
 9UF  H19  N19  C18  116.68  3.000
 9UF  C14  O13  C11  117.40  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
 9UF  CONST_01  C18  C20  C21  C15     0.00   0.0  0
 9UF  CONST_02  C18  N17  C16  C15     0.00   0.0  0
 9UF  CONST_03  C16  N17  C18  C20     0.00   0.0  0
 9UF  CONST_04  C16  C15  C21  C20     0.00   0.0  0
 9UF  CONST_05  N17  C18  C20  C21     0.00   0.0  0
 9UF  CONST_06  N17  C16  C15  C21     0.00   0.0  0
 9UF  CONST_07  C14  C15  C21  C20   180.00   0.0  0
 9UF  CONST_08  N19  C18  C20  C21   180.00   0.0  0
 9UF  CONST_09  N17  C16  C15  C14   180.00   0.0  0
 9UF  CONST_10  N19  C18  N17  C16   180.00   0.0  0
 9UF  CONST_11  H20  C20  C21  C15   180.00   0.0  0
 9UF  CONST_12  H16  C16  C15  C21   180.00   0.0  0
 9UF  CONST_13  H21  C21  C15  C16   180.00   0.0  0
 9UF  Var_01    O13  C14  C15  C21  -106.70  30.0  2
 9UF  Var_02    CD   CG   CB   CA    -59.00  30.0  2
 9UF  Var_03    CE   CD   CG   CB    175.12  30.0  1
 9UF  Var_04    NZ   CE   CD   CG    -66.77  30.0  2
 9UF  Var_05    C11  NZ   CE   CD    173.70  30.0  1
 9UF  Var_06    O12  C11  NZ   CE     -1.90  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
 9UF  chir_01  CA  CB  C  N  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
 9UF  plan-1  C15  0.020
 9UF  plan-1  C20  0.020
 9UF  plan-1  C21  0.020
 9UF  plan-1  C14  0.020
 9UF  plan-1  C16  0.020
 9UF  plan-1  C18  0.020
 9UF  plan-1  N17  0.020
 9UF  plan-1  N19  0.020
 9UF  plan-1  H20  0.020
 9UF  plan-1  H21  0.020
 9UF  plan-1  H16  0.020
 9UF  plan-2  C18  0.020
 9UF  plan-2  N19  0.020
 9UF  plan-2  H19  0.020
 9UF  plan-2  H18  0.020
 9UF  plan-3  C    0.020
 9UF  plan-3  CA   0.020
 9UF  plan-3  OXT  0.020
 9UF  plan-3  O    0.020
 9UF  plan-4  C11  0.020
 9UF  plan-4  NZ   0.020
 9UF  plan-4  O12  0.020
 9UF  plan-4  O13  0.020

