# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:06:03 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: N~6~-(tert-butoxycarbonyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)NCCCC[C@H](N)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
 LBY  LBY  N~6~-(tert-butoxycarbonyl)-L-lysine  L-peptide  38  17  .  2012-08-28  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_LBY
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
 LBY  C1   C  CH3    0  -0.669  -8.8879  50.0528  -1.7727
 LBY  CT   C  CT     0   0.201  -7.5720  50.0704  -2.5412
 LBY  C2   C  CH3    0  -0.669  -6.6546  51.1955  -2.0770
 LBY  C3   C  CH3    0  -0.657  -7.8485  50.2189  -4.0325
 LBY  O2   O  O2     0  -0.494  -6.9104  48.7833  -2.4602
 LBY  CZ   C  C      0   0.732  -6.4732  48.2571  -1.3175
 LBY  O1   O  O      0  -0.524  -6.5598  48.7762  -0.2203
 LBY  NZ   N  NH1    0  -0.655  -5.8877  47.0592  -1.5274
 LBY  CE   C  CH2    0  -0.276  -5.8838  46.3095  -2.7677
 LBY  CD   C  CH2    0  -0.424  -7.1854  45.5686  -3.0517
 LBY  CG   C  CH2    0  -0.417  -7.1189  44.7720  -4.3491
 LBY  CB   C  CH2    0  -0.395  -8.4108  44.0191  -4.6383
 LBY  CA   C  CH1    0  -0.218  -8.3606  43.1087  -5.8662
 LBY  C    C  C      0   0.405  -8.0707  43.8913  -7.1717
 LBY  OXT  O  OC    -1  -0.611  -8.7190  44.9447  -7.3354
 LBY  O    O  O      0  -0.602  -7.2525  43.3921  -7.9702
 LBY  N    N  NH2    0  -0.807  -7.3945  42.0386  -5.6606
 LBY  H11  H  HCH3   0   0.243  -8.7399  49.9917  -0.6971
 LBY  H12  H  HCH3   0   0.233  -9.4391  50.9704  -1.9823
 LBY  H13  H  HCH3   0   0.233  -9.5110  49.2145  -2.0888
 LBY  H21  H  HCH3   0   0.243  -6.4702  51.1690  -1.0059
 LBY  H22  H  HCH3   0   0.233  -5.6968  51.1562  -2.5982
 LBY  H23  H  HCH3   0   0.232  -7.1190  52.1538  -2.3132
 LBY  H31  H  HCH3   0   0.229  -8.3512  51.1667  -4.2234
 LBY  H32  H  HCH3   0   0.236  -6.9232  50.2085  -4.6107
 LBY  H33  H  HCH3   0   0.236  -8.4923  49.4177  -4.3987
 LBY  HZ1  H  HNH1   0   0.393  -5.6093  46.5718  -0.6912
 LBY  HE2  H  HCH2   0   0.240  -5.0646  45.5918  -2.6978
 LBY  HE3  H  HCH2   0   0.236  -5.6387  46.9737  -3.5974
 LBY  HD2  H  HCH2   0   0.215  -8.0118  46.2839  -3.1008
 LBY  HD3  H  HCH2   0   0.212  -7.4032  44.8957  -2.2161
 LBY  HG2  H  HCH2   0   0.205  -6.2854  44.0661  -4.3013
 LBY  HG3  H  HCH2   0   0.207  -6.9008  45.4547  -5.1766
 LBY  HB2  H  HCH2   0   0.202  -9.2277  44.7333  -4.7634
 LBY  HB3  H  HCH2   0   0.199  -8.6736  43.4118  -3.7641
 LBY  HA   H  HCH1   0   0.198  -9.3826  42.7101  -5.9963
 LBY  H    H  HNH2   0   0.326  -7.8076  41.3092  -5.0943
 LBY  H2   H  HNH2   0   0.330  -7.1732  41.6297  -6.5583

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
 LBY  O   C    deloc   1.231  0.020  1.231
 LBY  C   OXT  deloc   1.248  0.020  1.248
 LBY  C   CA   single  1.525  0.021  1.525
 LBY  N   CA   single  1.458  0.019  1.458
 LBY  CA  CB   single  1.530  0.020  1.530
 LBY  CB  CG   single  1.523  0.020  1.523
 LBY  CG  CD   single  1.524  0.020  1.524
 LBY  C3  CT   single  1.524  0.020  1.524
 LBY  O2  CT   single  1.449  0.020  1.449
 LBY  O2  CZ   single  1.332  0.020  1.332
 LBY  CT  C1   single  1.524  0.020  1.524
 LBY  CT  C2   single  1.524  0.020  1.524
 LBY  CD  CE   single  1.524  0.020  1.524
 LBY  CE  NZ   single  1.449  0.020  1.449
 LBY  CZ  NZ   single  1.350  0.020  1.350
 LBY  CZ  O1   double  1.217  0.020  1.217
 LBY  C1  H11  single  0.970  0.020  1.090
 LBY  C1  H12  single  0.970  0.020  1.090
 LBY  C1  H13  single  0.970  0.020  1.090
 LBY  C2  H21  single  0.970  0.020  1.090
 LBY  C2  H22  single  0.970  0.020  1.090
 LBY  C2  H23  single  0.970  0.020  1.090
 LBY  C3  H31  single  0.970  0.020  1.090
 LBY  C3  H32  single  0.970  0.020  1.090
 LBY  C3  H33  single  0.970  0.020  1.090
 LBY  NZ  HZ1  single  0.860  0.020  1.020
 LBY  CE  HE2  single  0.970  0.020  1.090
 LBY  CE  HE3  single  0.970  0.020  1.090
 LBY  CD  HD2  single  0.970  0.020  1.090
 LBY  CD  HD3  single  0.970  0.020  1.090
 LBY  CG  HG2  single  0.970  0.020  1.090
 LBY  CG  HG3  single  0.970  0.020  1.090
 LBY  CB  HB2  single  0.970  0.020  1.090
 LBY  CB  HB3  single  0.970  0.020  1.090
 LBY  CA  HA   single  0.970  0.020  0.970
 LBY  N   H    single  0.860  0.020  0.860
 LBY  N   H2   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
 LBY  H13  C1  H12  107.58  3.000
 LBY  H13  C1  H11  108.72  3.000
 LBY  H12  C1  H11  107.82  3.000
 LBY  H13  C1  CT   110.85  3.000
 LBY  H12  C1  CT   109.25  3.000
 LBY  H11  C1  CT   112.45  3.000
 LBY  O2   CT  C3   102.95  3.000
 LBY  O2   CT  C2   111.33  3.000
 LBY  C3   CT  C2   109.59  3.000
 LBY  C2   CT  C1   112.01  3.000
 LBY  O2   CT  C1   110.84  3.000
 LBY  C3   CT  C1   109.75  3.000
 LBY  H23  C2  H22  107.58  3.000
 LBY  H23  C2  H21  107.88  3.000
 LBY  H22  C2  H21  108.72  3.000
 LBY  H23  C2  CT   109.05  3.000
 LBY  H22  C2  CT   110.87  3.000
 LBY  H21  C2  CT   112.58  3.000
 LBY  H33  C3  H32  108.39  3.000
 LBY  H33  C3  H31  107.92  3.000
 LBY  H32  C3  H31  107.86  3.000
 LBY  H33  C3  CT   111.34  3.000
 LBY  H32  C3  CT   111.33  3.000
 LBY  H31  C3  CT   109.87  3.000
 LBY  CZ   O2  CT   123.27  3.000
 LBY  NZ   CZ  O1   123.34  3.000
 LBY  O1   CZ  O2   125.57  3.000
 LBY  NZ   CZ  O2   111.07  3.000
 LBY  HZ1  NZ  CE   117.35  3.000
 LBY  HZ1  NZ  CZ   114.85  3.000
 LBY  CE   NZ  CZ   126.40  3.000
 LBY  HE3  CE  HE2  106.29  3.000
 LBY  HE3  CE  CD   110.25  3.000
 LBY  HE2  CE  CD   109.47  3.000
 LBY  HE3  CE  NZ   109.67  3.000
 LBY  HE2  CE  NZ   106.70  3.000
 LBY  CD   CE  NZ   114.11  3.000
 LBY  HD3  CD  HD2  106.61  3.000
 LBY  HD3  CD  CG   109.71  3.000
 LBY  HD2  CD  CG   109.67  3.000
 LBY  HD3  CD  CE   109.05  3.000
 LBY  HD2  CD  CE   109.61  3.000
 LBY  CG   CD  CE   112.05  3.000
 LBY  HG3  CG  HG2  106.49  3.000
 LBY  HG3  CG  CB   109.50  3.000
 LBY  HG2  CG  CB   109.62  3.000
 LBY  HG3  CG  CD   109.04  3.000
 LBY  HG2  CG  CD   109.48  3.000
 LBY  CB   CG  CD   112.52  3.000
 LBY  HB3  CB  HB2  105.92  3.000
 LBY  HB3  CB  CA   108.56  3.000
 LBY  HB2  CB  CA   108.77  3.000
 LBY  HB3  CB  CG   109.02  3.000
 LBY  HB2  CB  CG   109.44  3.000
 LBY  CA   CB  CG   114.76  3.000
 LBY  HA   CA  N    110.00  3.000
 LBY  HA   CA  C    109.00  3.000
 LBY  N    CA  C    111.00  2.800
 LBY  HA   CA  CB   109.00  3.000
 LBY  N    CA  CB   110.50  1.700
 LBY  C    CA  CB   110.10  1.900
 LBY  O    C   OXT  126.49  3.000
 LBY  OXT  C   CA   116.09  3.000
 LBY  O    C   CA   120.80  1.700
 LBY  H2   N   H    107.15  3.000
 LBY  H2   N   CA   108.49  3.000
 LBY  H    N   CA   114.00  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
 LBY  Var_01  NZ   CZ  O2  CT  -179.49  30.0  3
 LBY  Var_02  CE   NZ  CZ  O2    -8.74  30.0  2
 LBY  Var_03  CD   CE  NZ  CZ   -78.02  30.0  1
 LBY  Var_04  CG   CD  CE  NZ  -178.71  30.0  2
 LBY  Var_05  CB   CG  CD  CE   179.58  30.0  1
 LBY  Var_06  CA   CB  CG  CD  -175.07  30.0  2
 LBY  Var_07  H31  C3  CT  C1    62.05  30.0  3
 LBY  Var_08  H21  C2  CT  C1    54.71  30.0  3
 LBY  Var_09  H11  C1  CT  C2   -55.55  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
 LBY  chir_01  CA  C  N  CB  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
 LBY  plan-1  CA   0.020
 LBY  plan-1  C    0.020
 LBY  plan-1  OXT  0.020
 LBY  plan-1  O    0.020
 LBY  plan-2  O2   0.020
 LBY  plan-2  CZ   0.020
 LBY  plan-2  O1   0.020
 LBY  plan-2  NZ   0.020

