# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:47:01 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: N~6~-{[(3-ethynylphenyl)methoxy]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1cccc(c1)C#C)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
 9TX  9TX  N~6~-{[(3-ethynylphenyl)methoxy]carbonyl}-L-lysine  peptide  41  22  .  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_9TX
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
 9TX  C15   C  C      0   0.079  -21.8894  3.5473  12.1927
 9TX  C17   C  C      0  -0.037  -21.8606  4.4623   9.9537
 9TX  C20   C  C1     0  -0.288  -21.6828  3.1787   9.4303
 9TX  C21   C  C1     0  -0.231  -21.6076  2.0935  10.2861
 9TX  C22   C  C1     0  -0.293  -21.7164  2.2754  11.6583
 9TX  C     C  C      0   0.416  -29.6883  4.5789  18.8184
 9TX  OXT   O  OC    -1  -0.618  -29.5741  4.9773  19.9978
 9TX  CA    C  CH1    0  -0.199  -28.6857  3.4677  18.4076
 9TX  N     N  NH2    0  -0.813  -28.7899  2.3882  19.3928
 9TX  CB    C  CH2    0  -0.411  -28.8970  2.8895  17.0124
 9TX  CG    C  CH2    0  -0.435  -28.4550  3.7807  15.8541
 9TX  CD    C  CH2    0  -0.431  -26.9465  3.9855  15.7614
 9TX  CE    C  CH2    0  -0.276  -26.5633  4.7626  14.5068
 9TX  NZ    N  NH1    0  -0.659  -25.1489  5.0521  14.4003
 9TX  C11   C  C      0   0.752  -24.2554  4.1305  14.0104
 9TX  O12   O  O      0  -0.507  -24.5203  3.0085  13.6313
 9TX  O13   O  O2     0  -0.486  -23.0024  4.6162  14.0835
 9TX  C14   C  CH2    0  -0.244  -21.9547  3.7436  13.6826
 9TX  C16   C  C1     0  -0.315  -21.9582  4.6381  11.3347
 9TX  C18   C  CSP    0   0.305  -21.9363  5.5891   9.0807
 9TX  C19   C  CSP1   0  -0.553  -22.0026  6.5407   8.3467
 9TX  H201  H  H      0   0.262  -21.6053  3.0395   8.3602
 9TX  H211  H  H      0   0.263  -21.4737  1.0987   9.8824
 9TX  H221  H  H      0   0.260  -21.6686  1.4183  12.3192
 9TX  HA    H  HCH1   0   0.189  -27.6868  3.9366  18.4375
 9TX  H2    H  HNH2   0   0.328  -27.9935  1.7697  19.2963
 9TX  H     H  HNH2   0   0.328  -28.7165  2.7977  20.3154
 9TX  HB2   H  HCH2   0   0.208  -29.9514  2.6298  16.8904
 9TX  HB3   H  HCH2   0   0.197  -28.3422  1.9462  16.9404
 9TX  HG2   H  HCH2   0   0.216  -28.9550  4.7489  15.9239
 9TX  HG3   H  HCH2   0   0.210  -28.8002  3.3278  14.9185
 9TX  HD2   H  HCH2   0   0.216  -26.4409  3.0156  15.7512
 9TX  HD3   H  HCH2   0   0.219  -26.5753  4.5233  16.6380
 9TX  HE2   H  HCH2   0   0.245  -27.0859  5.7197  14.4910
 9TX  HE3   H  HCH2   0   0.235  -26.8856  4.2183  13.6169
 9TX  HZ    H  HNH1   0   0.399  -24.8117  5.9264  14.7697
 9TX  H142  H  HCH2   0   0.253  -22.0291  2.7803  14.1914
 9TX  H141  H  HCH2   0   0.266  -21.0445  4.2312  14.0341
 9TX  H161  H  H      0   0.261  -22.0873  5.6380  11.7306
 9TX  H191  H  H      0   0.282  -22.0642  7.3802   7.6923
 9TX  O     O  O      0  -0.592  -30.5071  4.9927  17.9757

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
 9TX  C21  C20   aromatic  1.384  0.020  1.384
 9TX  C21  C22   aromatic  1.389  0.020  1.389
 9TX  C20  C17   aromatic  1.398  0.020  1.398
 9TX  C22  C15   aromatic  1.390  0.020  1.390
 9TX  C17  C18   single    1.427  0.020  1.427
 9TX  C17  C16   aromatic  1.396  0.020  1.396
 9TX  C18  C19   triple    1.204  0.020  1.204
 9TX  C15  C16   aromatic  1.390  0.020  1.390
 9TX  C15  C14   single    1.504  0.020  1.504
 9TX  C14  O13   single    1.421  0.020  1.421
 9TX  NZ   C11   single    1.342  0.020  1.342
 9TX  NZ   CE    single    1.448  0.020  1.448
 9TX  O13  C11   single    1.346  0.020  1.346
 9TX  C11  O12   double    1.214  0.020  1.214
 9TX  CE   CD    single    1.525  0.020  1.525
 9TX  CD   CG    single    1.525  0.020  1.525
 9TX  CG   CB    single    1.527  0.020  1.527
 9TX  O    C     deloc     1.231  0.020  1.231
 9TX  C    CA    single    1.525  0.021  1.525
 9TX  C    OXT   deloc     1.250  0.020  1.250
 9TX  CB   CA    single    1.530  0.020  1.530
 9TX  CA   N     single    1.458  0.019  1.458
 9TX  C20  H201  single    0.929  0.020  1.085
 9TX  C21  H211  single    0.929  0.020  1.085
 9TX  C22  H221  single    0.929  0.020  1.085
 9TX  CA   HA    single    0.970  0.020  0.970
 9TX  N    H2    single    0.868  0.020  1.013
 9TX  N    H     single    0.860  0.020  0.860
 9TX  CB   HB2   single    0.939  0.020  1.096
 9TX  CB   HB3   single    0.939  0.020  1.096
 9TX  CG   HG2   single    0.939  0.020  1.096
 9TX  CG   HG3   single    0.939  0.020  1.096
 9TX  CD   HD2   single    0.939  0.020  1.096
 9TX  CD   HD3   single    0.939  0.020  1.096
 9TX  CE   HE2   single    0.939  0.020  1.096
 9TX  CE   HE3   single    0.939  0.020  1.096
 9TX  NZ   HZ    single    0.868  0.020  1.013
 9TX  C14  H142  single    0.939  0.020  1.096
 9TX  C14  H141  single    0.939  0.020  1.096
 9TX  C16  H161  single    0.929  0.020  1.085
 9TX  C19  H191  single    0.913  0.020  1.066

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
 9TX  C16   C15  C14   120.46  3.000
 9TX  C14   C15  C22   120.36  3.000
 9TX  C16   C15  C22   119.14  3.000
 9TX  C18   C17  C16   120.13  3.000
 9TX  C16   C17  C20   119.68  3.000
 9TX  C18   C17  C20   120.18  3.000
 9TX  H201  C20  C21   120.45  3.000
 9TX  H201  C20  C17   119.85  3.000
 9TX  C21   C20  C17   119.70  3.000
 9TX  H211  C21  C22   119.93  3.000
 9TX  H211  C21  C20   119.79  3.000
 9TX  C22   C21  C20   120.27  3.000
 9TX  H221  C22  C21   119.72  3.000
 9TX  H221  C22  C15   119.65  3.000
 9TX  C21   C22  C15   120.63  3.000
 9TX  CA    C    OXT   114.76  3.000
 9TX  OXT   C    O     126.33  3.000
 9TX  CA    C    O     120.80  1.700
 9TX  HA    CA   CB    109.00  3.000
 9TX  HA    CA   N     110.00  3.000
 9TX  CB    CA   N     110.50  1.700
 9TX  HA    CA   C     109.00  3.000
 9TX  N     CA   C     111.00  2.800
 9TX  CB    CA   C     110.10  1.900
 9TX  H     N    H2    106.08  3.000
 9TX  H     N    CA    114.00  3.000
 9TX  H2    N    CA    109.27  3.000
 9TX  HB3   CB   HB2   106.04  3.000
 9TX  HB3   CB   CG    107.80  3.000
 9TX  HB2   CB   CG    109.47  3.000
 9TX  HB3   CB   CA    108.43  3.000
 9TX  HB2   CB   CA    109.02  3.000
 9TX  CG    CB   CA    115.64  3.000
 9TX  HG3   CG   HG2   106.08  3.000
 9TX  HG3   CG   CD    108.38  3.000
 9TX  HG2   CG   CD    109.74  3.000
 9TX  HG3   CG   CB    108.38  3.000
 9TX  HG2   CG   CB    109.66  3.000
 9TX  CD    CG   CB    114.26  3.000
 9TX  HD3   CD   HD2   106.66  3.000
 9TX  HD3   CD   CE    108.89  3.000
 9TX  HD2   CD   CE    109.15  3.000
 9TX  HD3   CD   CG    110.68  3.000
 9TX  HD2   CD   CG    109.80  3.000
 9TX  CE    CD   CG    111.53  3.000
 9TX  HE3   CE   HE2   106.51  3.000
 9TX  HE3   CE   NZ    109.16  3.000
 9TX  HE2   CE   NZ    106.95  3.000
 9TX  HE3   CE   CD    110.03  3.000
 9TX  HE2   CE   CD    109.80  3.000
 9TX  NZ    CE   CD    114.08  3.000
 9TX  HZ    NZ   C11   118.68  3.000
 9TX  HZ    NZ   CE    118.28  3.000
 9TX  C11   NZ   CE    122.32  3.000
 9TX  O13   C11  O12   123.63  3.000
 9TX  O12   C11  NZ    125.49  3.000
 9TX  O13   C11  NZ    110.88  3.000
 9TX  C14   O13  C11   116.71  3.000
 9TX  H141  C14  H142  107.52  3.000
 9TX  H141  C14  O13   104.46  3.000
 9TX  H142  C14  O13   111.10  3.000
 9TX  H141  C14  C15   109.96  3.000
 9TX  H142  C14  C15   110.45  3.000
 9TX  O13   C14  C15   113.05  3.000
 9TX  H161  C16  C17   119.10  3.000
 9TX  H161  C16  C15   120.33  3.000
 9TX  C17   C16  C15   120.57  3.000
 9TX  C19   C18  C17   180.00  3.000
 9TX  H191  C19  C18   180.00  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
 9TX  CONST_01  C20   C21  C22  C15     0.00   0.0  0
 9TX  CONST_02  C20   C17  C16  C15     0.00   0.0  0
 9TX  CONST_03  C22   C21  C20  C17     0.00   0.0  0
 9TX  CONST_04  C22   C15  C16  C17     0.00   0.0  0
 9TX  CONST_05  C16   C17  C20  C21     0.00   0.0  0
 9TX  CONST_06  C16   C15  C22  C21     0.00   0.0  0
 9TX  CONST_07  C18   C17  C16  C15   180.00   0.0  0
 9TX  CONST_08  C14   C15  C16  C17   180.00   0.0  0
 9TX  CONST_09  C18   C17  C20  C21   180.00   0.0  0
 9TX  CONST_10  C14   C15  C22  C21   180.00   0.0  0
 9TX  CONST_11  H211  C21  C22  C15   180.00   0.0  0
 9TX  CONST_12  H221  C22  C21  C20   180.00   0.0  0
 9TX  CONST_13  H161  C16  C17  C20   180.00   0.0  0
 9TX  CONST_14  H201  C20  C21  C22   180.00   0.0  0
 9TX  Var_01    O13   C14  C15  C22  -135.25  30.0  2
 9TX  Var_02    CD    CG   CB   CA     67.84  30.0  1
 9TX  Var_03    CE    CD   CG   CB    174.16  30.0  2
 9TX  Var_04    NZ    CE   CD   CG    176.80  30.0  1
 9TX  Var_05    C11   NZ   CE   CD     77.90  30.0  1
 9TX  Var_06    O13   C11  NZ   CE   -175.64  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
 9TX  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
 9TX  plan-1  C15   0.020
 9TX  plan-1  C17   0.020
 9TX  plan-1  C20   0.020
 9TX  plan-1  C21   0.020
 9TX  plan-1  C22   0.020
 9TX  plan-1  C14   0.020
 9TX  plan-1  C16   0.020
 9TX  plan-1  C18   0.020
 9TX  plan-1  C19   0.020
 9TX  plan-1  H201  0.020
 9TX  plan-1  H211  0.020
 9TX  plan-1  H221  0.020
 9TX  plan-1  H161  0.020
 9TX  plan-2  C     0.020
 9TX  plan-2  OXT   0.020
 9TX  plan-2  CA    0.020
 9TX  plan-2  O     0.020
 9TX  plan-3  NZ    0.020
 9TX  plan-3  C11   0.020
 9TX  plan-3  O12   0.020
 9TX  plan-3  O13   0.020

