# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:41:42 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: N~2~,N~2~,N~6~,N~6~-tetramethyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCC[C@H](N(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
 DM0  DM0  N~2~,N~2~,N~6~,N~6~-tetramethyl-L-lysine  L-peptide  35  14  .  2012-08-28  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DM0
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
 DM0  OXT   O  OC    -1  -0.607   -8.1465  15.4379  48.4009
 DM0  N     N  NT     0  -0.414   -9.6556  18.2336  49.7040
 DM0  CA    C  CH1    0  -0.103   -8.9375  17.6838  48.5560
 DM0  CB    C  CH2    0  -0.445   -8.1029  18.7478  47.8378
 DM0  CG    C  CH2    0  -0.416   -7.2728  18.1970  46.6836
 DM0  CD    C  CH2    0  -0.442   -6.5560  19.2882  45.8973
 DM0  CE    C  CH2    0  -0.285   -5.7618  18.6950  44.7315
 DM0  NZ    N  NT     0  -0.399   -4.9712  19.6038  43.9239
 DM0  CH1   C  CH3    0  -0.516   -3.8569  20.1911  44.6305
 DM0  CH2   C  CH3    0  -0.518   -5.7567  20.5979  43.2305
 DM0  C     C  C      0   0.376   -7.9989  16.5258  48.9925
 DM0  O     O  O      0  -0.606   -7.1555  16.7934  49.8711
 DM0  HA    H  HCH1   0   0.151   -9.6614  17.2740  47.8259
 DM0  HB    H  HCH2   0   0.216   -8.7509  19.5297  47.4337
 DM0  HBA   H  HCH2   0   0.204   -7.4467  19.2332  48.5672
 DM0  HG    H  HCH2   0   0.215   -6.5281  17.4887  47.0572
 DM0  HGA   H  HCH2   0   0.205   -7.9213  17.6313  46.0054
 DM0  HD    H  HCH2   0   0.213   -7.2898  20.0096  45.5244
 DM0  HDA   H  HCH2   0   0.214   -5.8910  19.8402  46.5690
 DM0  HE    H  HCH2   0   0.217   -5.0862  17.9271  45.1236
 DM0  HEA   H  HCH2   0   0.218   -6.4592  18.1760  44.0646
 DM0  HH1   H  HCH3   0   0.227   -3.2091  20.7169  43.9260
 DM0  HH1A  H  HCH3   0   0.190   -4.1409  20.9134  45.4110
 DM0  HH1B  H  HCH3   0   0.226   -3.2613  19.4095  45.1055
 DM0  HH2   H  HCH3   0   0.191   -6.2026  21.3608  43.8859
 DM0  HH2A  H  HCH3   0   0.227   -5.1321  21.1210  42.5034
 DM0  HH2B  H  HCH3   0   0.226   -6.5692  20.1174  42.6820
 DM0  HM1   H  HCH3   0   0.182  -11.1913  16.7456  49.7156
 DM0  HM1A  H  HCH3   0   0.234   -9.7918  16.4140  50.7498
 DM0  HM1B  H  HCH3   0   0.225  -10.9564  17.6373  51.2248
 DM0  HM2   H  HCH3   0   0.228  -11.0833  19.6574  50.2297
 DM0  HM2A  H  HCH3   0   0.232   -9.9456  20.2030  49.0139
 DM0  HM2B  H  HCH3   0   0.181  -11.2489  19.0935  48.5618
 DM0  CM1   C  CH3    0  -0.525  -10.4332  17.2082  50.3686
 DM0  CM2   C  CH3    0  -0.522  -10.5189  19.3407  49.3511

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
 DM0  OXT  C     deloc   1.247  0.020  1.247
 DM0  N    CA    single  1.458  0.019  1.458
 DM0  N    CM1   single  1.448  0.020  1.448
 DM0  N    CM2   single  1.448  0.020  1.448
 DM0  CA   CB    single  1.530  0.020  1.530
 DM0  CA   C     single  1.525  0.021  1.525
 DM0  CB   CG    single  1.525  0.020  1.525
 DM0  CG   CD    single  1.524  0.020  1.524
 DM0  CD   CE    single  1.530  0.020  1.530
 DM0  CE   NZ    single  1.450  0.020  1.450
 DM0  NZ   CH1   single  1.444  0.020  1.444
 DM0  NZ   CH2   single  1.444  0.020  1.444
 DM0  C    O     deloc   1.231  0.020  1.231
 DM0  CA   HA    single  0.970  0.020  0.970
 DM0  CB   HB    single  0.970  0.020  1.090
 DM0  CB   HBA   single  0.970  0.020  1.090
 DM0  CG   HG    single  0.970  0.020  1.090
 DM0  CG   HGA   single  0.970  0.020  1.090
 DM0  CD   HD    single  0.970  0.020  1.090
 DM0  CD   HDA   single  0.970  0.020  1.090
 DM0  CE   HE    single  0.970  0.020  1.090
 DM0  CE   HEA   single  0.970  0.020  1.090
 DM0  CH1  HH1   single  0.970  0.020  1.090
 DM0  CH1  HH1A  single  0.970  0.020  1.090
 DM0  CH1  HH1B  single  0.970  0.020  1.090
 DM0  CH2  HH2   single  0.970  0.020  1.090
 DM0  CH2  HH2A  single  0.970  0.020  1.090
 DM0  CH2  HH2B  single  0.970  0.020  1.090
 DM0  CM1  HM1   single  0.970  0.020  1.090
 DM0  CM1  HM1A  single  0.970  0.020  1.090
 DM0  CM1  HM1B  single  0.970  0.020  1.090
 DM0  CM2  HM2   single  0.970  0.020  1.090
 DM0  CM2  HM2A  single  0.970  0.020  1.090
 DM0  CM2  HM2B  single  0.970  0.020  1.090

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
 DM0  CM2   N    CM1   109.46  3.000
 DM0  CM2   N    CA    112.91  3.000
 DM0  CM1   N    CA    110.97  3.000
 DM0  HA    CA   C     109.00  3.000
 DM0  HA    CA   CB    109.00  3.000
 DM0  C     CA   CB    110.10  1.900
 DM0  HA    CA   N     110.00  3.000
 DM0  C     CA   N     111.00  2.800
 DM0  CB    CA   N     110.50  1.700
 DM0  HBA   CB   HB    106.53  3.000
 DM0  HBA   CB   CG    109.77  3.000
 DM0  HB    CB   CG    107.54  3.000
 DM0  HBA   CB   CA    108.80  3.000
 DM0  HB    CB   CA    110.33  3.000
 DM0  CG    CB   CA    113.63  3.000
 DM0  HGA   CG   HG    106.27  3.000
 DM0  HGA   CG   CD    109.18  3.000
 DM0  HG    CG   CD    108.64  3.000
 DM0  HGA   CG   CB    109.44  3.000
 DM0  HG    CG   CB    110.25  3.000
 DM0  CD    CG   CB    112.83  3.000
 DM0  HDA   CD   HD    106.49  3.000
 DM0  HDA   CD   CE    110.35  3.000
 DM0  HD    CD   CE    110.12  3.000
 DM0  HDA   CD   CG    109.28  3.000
 DM0  HD    CD   CG    109.41  3.000
 DM0  CE    CD   CG    111.08  3.000
 DM0  HEA   CE   HE    106.17  3.000
 DM0  HEA   CE   NZ    107.75  3.000
 DM0  HE    CE   NZ    107.60  3.000
 DM0  HEA   CE   CD    108.48  3.000
 DM0  HE    CE   CD    108.61  3.000
 DM0  NZ    CE   CD    117.66  3.000
 DM0  CH2   NZ   CH1   112.00  3.000
 DM0  CH2   NZ   CE    113.72  3.000
 DM0  CH1   NZ   CE    113.76  3.000
 DM0  HH1B  CH1  HH1A  107.58  3.000
 DM0  HH1B  CH1  HH1   107.57  3.000
 DM0  HH1A  CH1  HH1   107.14  3.000
 DM0  HH1B  CH1  NZ    110.04  3.000
 DM0  HH1A  CH1  NZ    114.50  3.000
 DM0  HH1   CH1  NZ    109.75  3.000
 DM0  HH2B  CH2  HH2A  107.57  3.000
 DM0  HH2B  CH2  HH2   107.63  3.000
 DM0  HH2A  CH2  HH2   107.23  3.000
 DM0  HH2B  CH2  NZ    110.06  3.000
 DM0  HH2A  CH2  NZ    109.77  3.000
 DM0  HH2   CH2  NZ    114.31  3.000
 DM0  O     C    CA    120.80  1.700
 DM0  O     C    OXT   126.98  3.000
 DM0  CA    C    OXT   116.46  3.000
 DM0  HM1B  CM1  HM1A  107.12  3.000
 DM0  HM1B  CM1  HM1   107.46  3.000
 DM0  HM1A  CM1  HM1   107.83  3.000
 DM0  HM1B  CM1  N     109.82  3.000
 DM0  HM1A  CM1  N     111.13  3.000
 DM0  HM1   CM1  N     113.23  3.000
 DM0  HM2B  CM2  HM2A  107.71  3.000
 DM0  HM2B  CM2  HM2   107.39  3.000
 DM0  HM2A  CM2  HM2   106.97  3.000
 DM0  HM2B  CM2  N     113.43  3.000
 DM0  HM2A  CM2  N     111.54  3.000
 DM0  HM2   CM2  N     109.52  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
 DM0  Var_01  CD   CG   CB  CA   174.41  30.0  3
 DM0  Var_02  CE   CD   CG  CB  -178.72  30.0  3
 DM0  Var_03  NZ   CE   CD  CG  -177.15  30.0  3
 DM0  Var_04  CH1  NZ   CE  CD    66.98  30.0  3
 DM0  Var_05  HM1  CM1  N   CA   -60.20  30.0  3
 DM0  Var_06  HM2  CM2  N   CA   175.67  30.0  3
 DM0  Var_07  HH1  CH1  NZ  CE   169.98  30.0  3
 DM0  Var_08  HH2  CH2  NZ  CE    70.12  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
 DM0  chir_01  CA  N  CB  C  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
 DM0  plan-1  OXT  0.020
 DM0  plan-1  CA   0.020
 DM0  plan-1  C    0.020
 DM0  plan-1  O    0.020

