# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:45:16 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: N~6~-[(cyclopentyloxy)carbonyl]-D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCCCNC(=O)OC1CCCC1)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
 CCL  CCL  N~6~-[(cyclopentyloxy)carbonyl]-D-lysine  D-peptide  39  18  .  2016-04-22  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_CCL
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
 CCL  CAK   C  CH2    0  -0.468   8.5282  50.2930  31.0813
 CCL  CAG   C  CH2    0  -0.453   8.8119  51.2886  32.2238
 CCL  CAH   C  CH2    0  -0.444   7.4641  51.4892  32.9164
 CCL  CAL   C  CH2    0  -0.464   6.4828  51.4223  31.7504
 CCL  CAR   C  CH1    0   0.023   6.9973  50.2693  30.8960
 CCL  OAN   O  O2     0  -0.494   6.4123  49.0741  31.4351
 CCL  CAP   C  C      0   0.742   6.5615  47.9384  30.7457
 CCL  OAC   O  O      0  -0.520   7.1449  47.8567  29.6821
 CCL  NAM   N  NH1    0  -0.654   5.9550  46.9125  31.3728
 CCL  CAI   C  CH2    0  -0.305   6.1327  45.5385  30.9517
 CCL  CAE   C  CH2    0  -0.428   7.4507  44.9216  31.4092
 CCL  CAF   C  CH2    0  -0.413   7.5948  44.8536  32.9245
 CCL  CB    C  CH2    0  -0.393   8.9438  44.2978  33.3592
 CCL  CA    C  CH1    0  -0.222   9.1394  44.2001  34.8719
 CCL  C     C  C      0   0.408   8.1362  43.2277  35.5442
 CCL  OXT   O  OC    -1  -0.608   7.8884  42.1741  34.9253
 CCL  O     O  O      0  -0.604   7.6988  43.5505  36.6676
 CCL  N     N  NH2    0  -0.808   9.0804  45.5220  35.4822
 CCL  HAK1  H  HCH2   0   0.245   8.9040  49.2987  31.3240
 CCL  HAK2  H  HCH2   0   0.240   9.0223  50.5898  30.1560
 CCL  HAG1  H  HCH2   0   0.234   9.5899  50.9325  32.8993
 CCL  HAG2  H  HCH2   0   0.226   9.1538  52.2421  31.8155
 CCL  HAH1  H  HCH2   0   0.223   7.2676  50.6811  33.6259
 CCL  HAH2  H  HCH2   0   0.233   7.4060  52.4275  33.4690
 CCL  HAL1  H  HCH2   0   0.244   5.4380  51.2990  32.0391
 CCL  HAL2  H  HCH2   0   0.234   6.5509  52.3420  31.1628
 CCL  HAR   H  HCH1   0   0.247   6.7024  50.3686  29.8499
 CCL  HNAM  H  HNH1   0   0.395   5.5754  47.0779  32.2910
 CCL  HAI1  H  HCH2   0   0.242   5.2961  44.9677  31.3583
 CCL  HAI2  H  HCH2   0   0.246   6.0469  45.4865  29.8659
 CCL  HAE1  H  HCH2   0   0.219   7.5182  43.9131  30.9895
 CCL  HAE2  H  HCH2   0   0.215   8.2826  45.4869  30.9776
 CCL  HAF1  H  HCH2   0   0.204   7.4608  45.8488  33.3541
 CCL  HAF2  H  HCH2   0   0.206   6.7908  44.2303  33.3288
 CCL  HB1   H  HCH2   0   0.201   9.0903  43.3064  32.9243
 CCL  HB2   H  HCH2   0   0.197   9.7377  44.9284  32.9412
 CCL  HA    H  HCH1   0   0.199  10.1280  43.7306  35.0259
 CCL  HN1   H  HNH2   0   0.330   8.9450  45.4048  36.4774
 CCL  HN2   H  HNH2   0   0.326   9.9644  45.9972  35.3554

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
 CCL  CAK  CAR   single  1.542  0.020  1.542
 CCL  CAK  CAG   single  1.542  0.020  1.542
 CCL  CAK  HAK1  single  0.970  0.020  1.090
 CCL  CAK  HAK2  single  0.970  0.020  1.090
 CCL  CAG  CAH   single  1.529  0.020  1.529
 CCL  CAG  HAG1  single  0.970  0.020  1.090
 CCL  CAG  HAG2  single  0.970  0.020  1.090
 CCL  CAH  CAL   single  1.525  0.020  1.525
 CCL  CAH  HAH1  single  0.970  0.020  1.090
 CCL  CAH  HAH2  single  0.970  0.020  1.090
 CCL  CAL  CAR   single  1.525  0.020  1.525
 CCL  CAL  HAL1  single  0.970  0.020  1.090
 CCL  CAL  HAL2  single  0.970  0.020  1.090
 CCL  CAR  OAN   single  1.436  0.020  1.436
 CCL  CAR  HAR   single  0.970  0.020  1.090
 CCL  OAN  CAP   single  1.337  0.020  1.337
 CCL  CAP  OAC   double  1.216  0.020  1.216
 CCL  CAP  NAM   single  1.347  0.020  1.347
 CCL  NAM  CAI   single  1.448  0.020  1.448
 CCL  NAM  HNAM  single  0.860  0.020  1.020
 CCL  CAI  CAE   single  1.525  0.020  1.525
 CCL  CAI  HAI1  single  0.970  0.020  1.090
 CCL  CAI  HAI2  single  0.970  0.020  1.090
 CCL  CAE  CAF   single  1.524  0.020  1.524
 CCL  CAE  HAE1  single  0.970  0.020  1.090
 CCL  CAE  HAE2  single  0.970  0.020  1.090
 CCL  CAF  CB    single  1.522  0.020  1.522
 CCL  CAF  HAF1  single  0.970  0.020  1.090
 CCL  CAF  HAF2  single  0.970  0.020  1.090
 CCL  CB   CA    single  1.521  0.033  1.521
 CCL  CB   HB1   single  0.970  0.020  1.090
 CCL  CB   HB2   single  0.970  0.020  1.090
 CCL  CA   N     single  1.458  0.019  1.458
 CCL  CA   C     single  1.525  0.021  1.525
 CCL  CA   HA    single  0.970  0.020  0.970
 CCL  C    OXT   deloc   1.247  0.020  1.247
 CCL  C    O     deloc   1.231  0.020  1.231
 CCL  N    HN1   single  0.890  0.020  1.040
 CCL  N    HN2   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
 CCL  HAK2  CAK  HAK1  106.32  3.000
 CCL  HAK2  CAK  CAR   110.61  3.000
 CCL  HAK1  CAK  CAR   110.79  3.000
 CCL  HAK2  CAK  CAG   111.70  3.000
 CCL  HAK1  CAK  CAG   111.14  3.000
 CCL  CAR   CAK  CAG   106.36  3.000
 CCL  HAG2  CAG  HAG1  107.06  3.000
 CCL  HAG2  CAG  CAH   109.32  3.000
 CCL  HAG1  CAG  CAH   113.04  3.000
 CCL  HAG2  CAG  CAK   110.14  3.000
 CCL  HAG1  CAG  CAK   112.31  3.000
 CCL  CAH   CAG  CAK   104.97  3.000
 CCL  HAH2  CAH  HAH1  107.31  3.000
 CCL  HAH2  CAH  CAL   113.00  3.000
 CCL  HAH1  CAH  CAL   110.38  3.000
 CCL  HAH2  CAH  CAG   112.92  3.000
 CCL  HAH1  CAH  CAG   110.83  3.000
 CCL  CAL   CAH  CAG   102.42  3.000
 CCL  HAL2  CAL  HAL1  107.27  3.000
 CCL  HAL2  CAL  CAR   108.30  3.000
 CCL  HAL1  CAL  CAR   112.71  3.000
 CCL  HAL2  CAL  CAH   109.50  3.000
 CCL  HAL1  CAL  CAH   114.75  3.000
 CCL  CAR   CAL  CAH   104.15  3.000
 CCL  HAR   CAR  OAN   109.00  3.000
 CCL  HAR   CAR  CAL   112.16  3.000
 CCL  OAN   CAR  CAL   106.36  3.000
 CCL  HAR   CAR  CAK   112.46  3.000
 CCL  OAN   CAR  CAK   111.84  3.000
 CCL  CAL   CAR  CAK   104.83  3.000
 CCL  CAP   OAN  CAR   117.91  3.000
 CCL  NAM   CAP  OAC   124.91  3.000
 CCL  NAM   CAP  OAN   110.90  3.000
 CCL  OAC   CAP  OAN   124.17  3.000
 CCL  HNAM  NAM  CAI   117.85  3.000
 CCL  HNAM  NAM  CAP   117.98  3.000
 CCL  CAI   NAM  CAP   122.15  3.000
 CCL  HAI2  CAI  HAI1  106.60  3.000
 CCL  HAI2  CAI  CAE   110.33  3.000
 CCL  HAI1  CAI  CAE   109.82  3.000
 CCL  HAI2  CAI  NAM   108.98  3.000
 CCL  HAI1  CAI  NAM   107.09  3.000
 CCL  CAE   CAI  NAM   113.73  3.000
 CCL  HAE2  CAE  HAE1  106.13  3.000
 CCL  HAE2  CAE  CAF   110.08  3.000
 CCL  HAE1  CAE  CAF   109.54  3.000
 CCL  HAE2  CAE  CAI   109.24  3.000
 CCL  HAE1  CAE  CAI   108.11  3.000
 CCL  CAF   CAE  CAI   113.45  3.000
 CCL  HAF2  CAF  HAF1  106.47  3.000
 CCL  HAF2  CAF  CB    109.73  3.000
 CCL  HAF1  CAF  CB    109.21  3.000
 CCL  HAF2  CAF  CAE   108.86  3.000
 CCL  HAF1  CAF  CAE   109.81  3.000
 CCL  CB    CAF  CAE   112.58  3.000
 CCL  HB2   CB   HB1   105.84  3.000
 CCL  HB2   CB   CA    108.75  3.000
 CCL  HB1   CB   CA    108.59  3.000
 CCL  HB2   CB   CAF   108.83  3.000
 CCL  HB1   CB   CAF   109.65  3.000
 CCL  CA    CB   CAF   114.79  3.000
 CCL  HA    CA   N     110.00  3.000
 CCL  HA    CA   C     110.00  3.000
 CCL  N     CA   C     111.00  2.800
 CCL  HA    CA   CB    109.00  3.000
 CCL  C     CA   CB    110.50  1.500
 CCL  N     CA   CB    110.40  1.500
 CCL  O     C    OXT   126.56  3.000
 CCL  O     C    CA    120.80  1.700
 CCL  OXT   C    CA    120.80  1.700
 CCL  HN2   N    HN1   107.14  3.000
 CCL  HN2   N    CA    109.77  3.000
 CCL  HN1   N    CA    108.21  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
 CCL  Var_01  CAL  CAH  CAG  CAK   -35.44  30.0  1
 CCL  Var_02  CAR  CAL  CAH  CAG    42.04  30.0  1
 CCL  Var_03  CAR  CAK  CAG  CAH    15.90  30.0  1
 CCL  Var_04  OAC  CAP  OAN  CAR    -1.07  30.0  3
 CCL  Var_05  CAI  NAM  CAP  OAN  -170.41  30.0  2
 CCL  Var_06  CAE  CAI  NAM  CAP    78.42  30.0  3
 CCL  Var_07  CAF  CAE  CAI  NAM    61.91  30.0  3
 CCL  Var_08  CB   CAF  CAE  CAI  -177.21  30.0  3
 CCL  Var_09  CA   CB   CAF  CAE  -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
 CCL  chir_01  CAR  CAK  CAL  OAN  positiv
 CCL  chir_02  CA   CB   N    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
 CCL  plan-1  CA   0.020
 CCL  plan-1  C    0.020
 CCL  plan-1  OXT  0.020
 CCL  plan-1  O    0.020
 CCL  plan-2  OAN  0.020
 CCL  plan-2  CAP  0.020
 CCL  plan-2  OAC  0.020
 CCL  plan-2  NAM  0.020

