# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:17:00 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: N~6~-{[(4-nitrophenyl)methoxy]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccc(cc1)[N+]([O-])=O)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
 9UC  9UC  N~6~-{[(4-nitrophenyl)methoxy]carbonyl}-L-lysine  peptide  41  23  .  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_9UC
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
 9UC  C15  C  CR6    0   0.076  196.5574  31.1626  75.7615
 9UC  C17  C  CR16   0  -0.252  196.7842  33.1455  74.4065
 9UC  C22  C  CR16   0  -0.250  196.1533  31.0449  73.3832
 9UC  C    C  C      0   0.417  188.0003  31.3046  81.0835
 9UC  CA   C  CH1    0  -0.202  189.0858  31.3590  82.1902
 9UC  CB   C  CH2    0  -0.399  190.4833  30.9469  81.7315
 9UC  CG   C  CH2    0  -0.429  191.2379  32.0160  80.9515
 9UC  CD   C  CH2    0  -0.426  192.6348  31.5702  80.5396
 9UC  CE   C  CH2    0  -0.280  193.3678  32.6553  79.7608
 9UC  C11  C  C      0   0.755  194.9596  31.5280  78.2902
 9UC  C14  C  CH2    0  -0.231  196.6687  30.4594  77.0856
 9UC  C16  C  CR16   0  -0.275  196.8473  32.5191  75.6381
 9UC  C18  C  CR6    0   0.236  196.4392  32.3987  73.2888
 9UC  C23  C  CR16   0  -0.293  196.2106  30.4386  74.6253
 9UC  N    N  NH2    0  -0.814  188.6677  30.5093  83.3024
 9UC  NZ   N  NH1    0  -0.659  194.7110  32.2912  79.3634
 9UC  N19  N  N      1   0.327  196.3751  33.0498  71.9902
 9UC  O12  O  O      0  -0.504  194.1337  31.1244  77.4985
 9UC  O13  O  O2     0  -0.486  196.2778  31.2671  78.1816
 9UC  O20  O  O     -1  -0.376  196.6104  34.2343  71.9361
 9UC  O21  O  O      0  -0.376  196.0907  32.3742  71.0290
 9UC  H17  H  HCR6   0   0.296  197.0082  34.1993  74.3275
 9UC  H22  H  HCR6   0   0.296  195.8793  30.4667  72.5129
 9UC  HA   H  HCH1   0   0.185  189.1443  32.4221  82.4934
 9UC  HB2  H  HCH2   0   0.200  190.4257  30.0264  81.1422
 9UC  HB3  H  HCH2   0   0.198  191.0758  30.6975  82.6198
 9UC  HG2  H  HCH2   0   0.199  191.3132  32.9216  81.5647
 9UC  HG3  H  HCH2   0   0.221  190.6652  32.2915  80.0645
 9UC  HD2  H  HCH2   0   0.218  192.5677  30.6676  79.9253
 9UC  HD3  H  HCH2   0   0.213  193.2192  31.3030  81.4258
 9UC  HE2  H  HCH2   0   0.245  193.4468  33.5579  80.3688
 9UC  HE3  H  HCH2   0   0.237  192.7957  32.9306  78.8729
 9UC  H14  H  HCH2   0   0.258  196.1104  29.5210  77.0656
 9UC  H15  H  HCH2   0   0.277  197.7145  30.2136  77.2774
 9UC  H16  H  HCR6   0   0.273  197.1241  33.1036  76.5056
 9UC  H23  H  HCR6   0   0.273  195.9744  29.3852  74.7095
 9UC  H    H  HNH2   0   0.326  189.1762  30.7698  84.1381
 9UC  H2   H  HNH2   0   0.329  187.6905  30.6968  83.4857
 9UC  HZ   H  HNH1   0   0.400  195.4681  32.4990  79.9948
 9UC  O    O  O      0  -0.592  188.3715  31.3389  79.8948
 9UC  OXT  O  OC    -1  -0.613  186.8189  31.2627  81.4875

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
 9UC  O21  N19  double    1.209  0.020  1.209
 9UC  C22  C23  aromatic  1.383  0.020  1.383
 9UC  C22  C18  aromatic  1.387  0.020  1.387
 9UC  N19  C18  single    1.454  0.020  1.454
 9UC  N19  O20  single    1.209  0.020  1.209
 9UC  C23  C15  aromatic  1.391  0.020  1.391
 9UC  C18  C17  aromatic  1.388  0.020  1.388
 9UC  C15  C14  single    1.503  0.020  1.503
 9UC  C15  C16  aromatic  1.393  0.020  1.393
 9UC  C17  C16  aromatic  1.383  0.020  1.383
 9UC  C14  O13  single    1.416  0.020  1.416
 9UC  NZ   CE   single    1.447  0.020  1.447
 9UC  NZ   C11  single    1.340  0.020  1.340
 9UC  O13  C11  single    1.348  0.020  1.348
 9UC  CE   CD   single    1.524  0.020  1.524
 9UC  C11  O12  double    1.213  0.020  1.213
 9UC  CD   CG   single    1.523  0.020  1.523
 9UC  CG   CB   single    1.523  0.020  1.523
 9UC  O    C    deloc     1.231  0.020  1.231
 9UC  C    CA   single    1.525  0.021  1.525
 9UC  C    OXT  deloc     1.249  0.020  1.249
 9UC  CB   CA   single    1.521  0.033  1.521
 9UC  CA   N    single    1.458  0.019  1.458
 9UC  C17  H17  single    0.930  0.020  1.080
 9UC  C22  H22  single    0.930  0.020  1.080
 9UC  CA   HA   single    0.970  0.020  0.970
 9UC  CB   HB2  single    0.970  0.020  1.090
 9UC  CB   HB3  single    0.970  0.020  1.090
 9UC  CG   HG2  single    0.970  0.020  1.090
 9UC  CG   HG3  single    0.970  0.020  1.090
 9UC  CD   HD2  single    0.970  0.020  1.090
 9UC  CD   HD3  single    0.970  0.020  1.090
 9UC  CE   HE2  single    0.970  0.020  1.090
 9UC  CE   HE3  single    0.970  0.020  1.090
 9UC  C14  H14  single    0.970  0.020  1.090
 9UC  C14  H15  single    0.970  0.020  1.090
 9UC  C16  H16  single    0.930  0.020  1.080
 9UC  C23  H23  single    0.930  0.020  1.080
 9UC  N    H    single    0.860  0.020  0.860
 9UC  N    H2   single    0.890  0.020  1.040
 9UC  NZ   HZ   single    0.860  0.020  1.020

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
 9UC  C23  C15  C16  119.11  3.000
 9UC  C16  C15  C14  121.22  3.000
 9UC  C23  C15  C14  119.62  3.000
 9UC  H17  C17  C18  121.18  3.000
 9UC  H17  C17  C16  119.83  3.000
 9UC  C18  C17  C16  118.99  3.000
 9UC  H22  C22  C23  119.95  3.000
 9UC  H22  C22  C18  121.34  3.000
 9UC  C23  C22  C18  118.71  3.000
 9UC  OXT  C    O    126.25  3.000
 9UC  OXT  C    CA   120.80  1.700
 9UC  O    C    CA   120.80  1.700
 9UC  HA   CA   N    110.00  3.000
 9UC  HA   CA   CB   109.00  3.000
 9UC  N    CA   CB   110.40  1.500
 9UC  HA   CA   C    110.00  3.000
 9UC  N    CA   C    111.00  2.800
 9UC  CB   CA   C    110.50  1.500
 9UC  HB3  CB   HB2  105.87  3.000
 9UC  HB3  CB   CG   107.86  3.000
 9UC  HB2  CB   CG   109.91  3.000
 9UC  HB3  CB   CA   108.20  3.000
 9UC  HB2  CB   CA   109.91  3.000
 9UC  CG   CB   CA   114.68  3.000
 9UC  HG3  CG   HG2  106.38  3.000
 9UC  HG3  CG   CD   109.60  3.000
 9UC  HG2  CG   CD   109.27  3.000
 9UC  HG3  CG   CB   109.48  3.000
 9UC  HG2  CG   CB   109.11  3.000
 9UC  CD   CG   CB   112.79  3.000
 9UC  HD3  CD   HD2  106.62  3.000
 9UC  HD3  CD   CE   109.32  3.000
 9UC  HD2  CD   CE   109.27  3.000
 9UC  HD3  CD   CG   110.01  3.000
 9UC  HD2  CD   CG   109.70  3.000
 9UC  CE   CD   CG   111.78  3.000
 9UC  HE3  CE   HE2  106.42  3.000
 9UC  HE3  CE   NZ   109.06  3.000
 9UC  HE2  CE   NZ   107.09  3.000
 9UC  HE3  CE   CD   110.08  3.000
 9UC  HE2  CE   CD   109.82  3.000
 9UC  NZ   CE   CD   114.06  3.000
 9UC  O13  C11  O12  123.28  3.000
 9UC  O12  C11  NZ   125.86  3.000
 9UC  O13  C11  NZ   110.86  3.000
 9UC  H15  C14  H14  107.44  3.000
 9UC  H15  C14  O13  104.89  3.000
 9UC  H14  C14  O13  111.29  3.000
 9UC  H15  C14  C15  109.34  3.000
 9UC  H14  C14  C15  110.36  3.000
 9UC  O13  C14  C15  113.22  3.000
 9UC  H16  C16  C17  118.74  3.000
 9UC  H16  C16  C15  120.56  3.000
 9UC  C17  C16  C15  120.70  3.000
 9UC  N19  C18  C22  119.26  3.000
 9UC  N19  C18  C17  119.29  3.000
 9UC  C22  C18  C17  121.45  3.000
 9UC  H23  C23  C22  119.15  3.000
 9UC  H23  C23  C15  119.81  3.000
 9UC  C22  C23  C15  121.03  3.000
 9UC  H2   N    H    106.73  3.000
 9UC  H2   N    CA   107.85  3.000
 9UC  H    N    CA   114.00  3.000
 9UC  HZ   NZ   C11  118.68  3.000
 9UC  HZ   NZ   CE   118.26  3.000
 9UC  C11  NZ   CE   122.36  3.000
 9UC  O21  N19  O20  123.91  3.000
 9UC  O20  N19  C18  118.04  3.000
 9UC  O21  N19  C18  118.05  3.000
 9UC  C14  O13  C11  116.27  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
 9UC  CONST_01  C18  C22  C23  C15     0.00   0.0  0
 9UC  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 9UC  CONST_03  C23  C22  C18  C17     0.00   0.0  0
 9UC  CONST_04  C23  C15  C16  C17     0.00   0.0  0
 9UC  CONST_05  C16  C15  C23  C22     0.00   0.0  0
 9UC  CONST_06  C16  C17  C18  C22     0.00   0.0  0
 9UC  CONST_07  C14  C15  C16  C17   180.00   0.0  0
 9UC  CONST_08  C14  C15  C23  C22   180.00   0.0  0
 9UC  CONST_09  N19  C18  C17  C16   180.00   0.0  0
 9UC  CONST_10  N19  C18  C22  C23   180.00   0.0  0
 9UC  CONST_11  H22  C22  C23  C15   180.00   0.0  0
 9UC  CONST_12  H17  C17  C16  C15   180.00   0.0  0
 9UC  CONST_13  H23  C23  C15  C16   180.00   0.0  0
 9UC  CONST_14  H16  C16  C17  C18   180.00   0.0  0
 9UC  CONST_15  O21  N19  C18  C17   180.00   0.0  0
 9UC  CONST_16  O20  N19  C18  C17     0.00   0.0  0
 9UC  CONST_17  O21  N19  C18  C22     0.00   0.0  0
 9UC  CONST_18  O20  N19  C18  C22   180.00   0.0  0
 9UC  Var_01    O13  C14  C15  C16    36.25  30.0  2
 9UC  Var_02    CD   CG   CB   CA    178.86  30.0  1
 9UC  Var_03    CE   CD   CG   CB    179.95  30.0  2
 9UC  Var_04    NZ   CE   CD   CG    179.03  30.0  1
 9UC  Var_05    C11  NZ   CE   CD     80.66  30.0  1
 9UC  Var_06    O13  C11  NZ   CE   -176.30  30.0  2
 9UC  Var_07    NZ   C11  O13  C14   179.67  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
 9UC  chir_01  CA  C  CB  N  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
 9UC  plan-1  C15  0.020
 9UC  plan-1  C17  0.020
 9UC  plan-1  C22  0.020
 9UC  plan-1  C14  0.020
 9UC  plan-1  C16  0.020
 9UC  plan-1  C18  0.020
 9UC  plan-1  C23  0.020
 9UC  plan-1  N19  0.020
 9UC  plan-1  H17  0.020
 9UC  plan-1  H22  0.020
 9UC  plan-1  H16  0.020
 9UC  plan-1  H23  0.020
 9UC  plan-2  C18  0.020
 9UC  plan-2  N19  0.020
 9UC  plan-2  O20  0.020
 9UC  plan-2  O21  0.020
 9UC  plan-3  C    0.020
 9UC  plan-3  CA   0.020
 9UC  plan-3  O    0.020
 9UC  plan-3  OXT  0.020
 9UC  plan-4  C11  0.020
 9UC  plan-4  NZ   0.020
 9UC  plan-4  O12  0.020
 9UC  plan-4  O13  0.020

