# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 12:05:34 2022
#   Inital geometry file: a 174 line input string
#   Ligand name: N~6~-[(2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-yl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(\C=C\C(C)=C\C=C/C(C)=C/CNCCCC[C@H](N)C(O)=O)C(C)(C)CCC1
#
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
 LYR  LYR  N~6~-[(2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-yl]-L-lysine  L-peptide  71  30  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LYR
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
 LYR  N     N  NH2    0  -0.821   -6.0383  -4.7683   1.3863
 LYR  CA    C  CH1    0  -0.192   -5.4824  -3.5232   1.9086
 LYR  C     C  C      0  -0.040   -4.0481  -3.4182   1.4161
 LYR  O     O  O      0  -0.170   -3.7476  -2.1899   1.3521
 LYR  OXT   O  OC    -1  -0.595   -2.4241  -1.8717   1.0017
 LYR  CB    C  CH2    0  -0.404   -5.4405  -3.5600   3.4416
 LYR  CG    C  CH2    0  -0.441   -6.8094  -3.7339   4.0895
 LYR  CD    C  CH2    0  -0.392   -6.7571  -3.6747   5.6107
 LYR  CE    C  CH2    0  -0.297   -8.1010  -3.9004   6.2996
 LYR  NZ    N  NH1    0  -0.601   -9.1093  -2.9270   5.9044
 LYR  C1    C  CH2    0  -0.349  -10.0261  -3.3519   4.8480
 LYR  C2    C  C1     0  -0.239  -10.4131  -2.1727   4.0086
 LYR  C3    C  C      0   0.054  -10.2289  -2.0193   2.6891
 LYR  C4    C  CH3    0  -0.766   -9.7145  -3.1223   1.7978
 LYR  C5    C  C1     0  -0.265  -10.5843  -0.7242   2.0898
 LYR  C6    C  C1     0  -0.254   -9.9592  -0.0660   1.0938
 LYR  C7    C  C1     0  -0.331   -8.7036  -0.4345   0.4834
 LYR  C80   C  C      0   0.130   -8.0840   0.1729  -0.5563
 LYR  C8    C  CH3    0  -0.758   -8.6590   1.3204  -1.3293
 LYR  C9    C  C1     0  -0.268   -6.7759  -0.3317  -0.9433
 LYR  C10   C  C1     0  -0.319   -6.0162   0.1259  -1.9506
 LYR  C11   C  C      0   0.118   -4.6979  -0.4172  -2.3081
 LYR  C12   C  C      0   0.023   -4.4904  -1.7374  -2.4740
 LYR  C13   C  CH3    0  -0.739   -5.5646  -2.7860  -2.4397
 LYR  C14   C  CH2    0  -0.476   -3.1319  -2.3219  -2.7520
 LYR  C15   C  CH2    0  -0.458   -1.9864  -1.3568  -2.5114
 LYR  C16   C  CH2    0  -0.409   -2.3382  -0.0017  -3.0947
 LYR  C17   C  CT     0  -0.141   -3.5789   0.6171  -2.4429
 LYR  C18   C  CH3    0  -0.647   -3.2356   1.1560  -1.0461
 LYR  C19   C  CH3    0  -0.658   -4.0186   1.7947  -3.3235
 LYR  H     H  HNH2   0   0.341   -5.8809  -4.8109   0.3868
 LYR  H2    H  HNH2   0   0.342   -7.0434  -4.7761   1.5044
 LYR  HA    H  HCH1   0   0.198   -6.0804  -2.6390   1.6148
 LYR  HB2   H  HCH2   0   0.211   -4.9961  -2.6259   3.7990
 LYR  HB3   H  HCH2   0   0.206   -4.7728  -4.3671   3.7621
 LYR  HG2   H  HCH2   0   0.207   -7.2513  -4.6879   3.7830
 LYR  HG3   H  HCH2   0   0.218   -7.4756  -2.9484   3.7200
 LYR  HD2   H  HCH2   0   0.205   -6.3598  -2.7022   5.9188
 LYR  HD3   H  HCH2   0   0.204   -6.0526  -4.4276   5.9801
 LYR  HE2   H  HCH2   0   0.229   -7.9490  -3.8161   7.3780
 LYR  HE3   H  HCH2   0   0.196   -8.4339  -4.9333   6.1225
 LYR  HZ    H  HNH1   0   0.347   -9.6448  -2.6410   6.7105
 LYR  H1    H  HCH2   0   0.240   -9.5377  -4.1113   4.2391
 LYR  H11   H  HCH2   0   0.225  -10.9264  -3.8306   5.2592
 LYR  HC2   H  H      0   0.233  -10.8377  -1.3380   4.5620
 LYR  H41   H  HCH3   0   0.248  -10.1074  -3.0165   0.7870
 LYR  H42   H  HCH3   0   0.251  -10.0089  -4.1047   2.1632
 LYR  H43   H  HCH3   0   0.245   -8.6267  -3.1249   1.7160
 LYR  H5    H  H      0   0.246  -11.4461  -0.2314   2.5294
 LYR  H6    H  H      0   0.241  -10.4138   0.8669   0.7794
 LYR  H7    H  H      0   0.244   -8.1654  -1.2569   0.9410
 LYR  H81   H  HCH3   0   0.243   -7.9984   2.1891  -1.2878
 LYR  H82   H  HCH3   0   0.254   -9.6364   1.6285  -0.9672
 LYR  H83   H  HCH3   0   0.245   -8.7681   1.0602  -2.3842
 LYR  H9    H  H      0   0.245   -6.3897  -1.1494  -0.3405
 LYR  H10   H  H      0   0.249   -6.3689   0.9796  -2.5210
 LYR  H131  H  HCH3   0   0.233   -5.4069  -3.4982  -3.2540
 LYR  H132  H  HCH3   0   0.242   -6.5715  -2.3853  -2.5260
 LYR  H133  H  HCH3   0   0.238   -5.5166  -3.3676  -1.5140
 LYR  H141  H  HCH2   0   0.228   -3.1172  -2.6870  -3.7868
 LYR  H142  H  HCH2   0   0.231   -3.0095  -3.2171  -2.1319
 LYR  H151  H  HCH2   0   0.222   -1.0686  -1.7413  -2.9620
 LYR  H152  H  HCH2   0   0.227   -1.8065  -1.2819  -1.4375
 LYR  H161  H  HCH2   0   0.214   -2.5190  -0.1160  -4.1700
 LYR  H162  H  HCH2   0   0.220   -1.5027   0.6976  -2.9961
 LYR  H181  H  HCH3   0   0.225   -2.9304   0.3604  -0.3648
 LYR  H182  H  HCH3   0   0.220   -4.0971   1.6574  -0.6004
 LYR  H183  H  HCH3   0   0.215   -2.4247   1.8859  -1.1068
 LYR  H191  H  HCH3   0   0.229   -3.1680   2.4551  -3.5065
 LYR  H192  H  HCH3   0   0.225   -4.7976   2.4010  -2.8599
 LYR  H193  H  HCH3   0   0.224   -4.3867   1.4545  -4.2937

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
 LYR  N    CA    single  1.458  0.019  1.458
 LYR  N    H     single  0.860  0.020  0.860
 LYR  N    H2    single  0.890  0.020  1.040
 LYR  CA   C     single  1.525  0.021  1.525
 LYR  CA   CB    single  1.530  0.020  1.530
 LYR  CA   HA    single  0.970  0.020  0.970
 LYR  C    O     deloc   1.231  0.020  1.231
 LYR  C    OXT   deloc   2.281  0.020  2.281
 LYR  CB   CG    single  1.524  0.020  1.524
 LYR  CB   HB2   single  0.970  0.020  1.090
 LYR  CB   HB3   single  0.970  0.020  1.090
 LYR  CG   CD    single  1.523  0.020  1.523
 LYR  CG   HG2   single  0.970  0.020  1.090
 LYR  CG   HG3   single  0.970  0.020  1.090
 LYR  CD   CE    single  1.527  0.020  1.527
 LYR  CD   HD2   single  0.970  0.020  1.090
 LYR  CD   HD3   single  0.970  0.020  1.090
 LYR  CE   NZ    single  1.456  0.020  1.456
 LYR  CE   HE2   single  0.970  0.020  1.090
 LYR  CE   HE3   single  0.970  0.020  1.090
 LYR  NZ   C1    single  1.462  0.020  1.462
 LYR  NZ   HZ    single  0.890  0.020  1.040
 LYR  C1   C2    single  1.498  0.020  1.498
 LYR  C1   H1    single  0.970  0.020  1.090
 LYR  C1   H11   single  0.970  0.020  1.090
 LYR  C2   C3    double  1.341  0.020  1.341
 LYR  C2   HC2   single  0.930  0.020  1.080
 LYR  C3   C4    single  1.509  0.020  1.509
 LYR  C3   C5    single  1.471  0.020  1.471
 LYR  C4   H41   single  0.970  0.020  1.090
 LYR  C4   H42   single  0.970  0.020  1.090
 LYR  C4   H43   single  0.970  0.020  1.090
 LYR  C5   C6    double  1.348  0.020  1.348
 LYR  C5   H5    single  0.930  0.020  1.080
 LYR  C6   C7    single  1.444  0.020  1.444
 LYR  C6   H6    single  0.930  0.020  1.080
 LYR  C7   C80   double  1.354  0.020  1.354
 LYR  C7   H7    single  0.930  0.020  1.080
 LYR  C80  C8    single  1.498  0.020  1.498
 LYR  C80  C9    single  1.454  0.020  1.454
 LYR  C8   H81   single  0.970  0.020  1.090
 LYR  C8   H82   single  0.970  0.020  1.090
 LYR  C8   H83   single  0.970  0.020  1.090
 LYR  C9   C10   double  1.342  0.020  1.342
 LYR  C9   H9    single  0.930  0.020  1.080
 LYR  C10  C11   single  1.470  0.020  1.470
 LYR  C10  H10   single  0.930  0.020  1.080
 LYR  C11  C12   double  1.347  0.020  1.347
 LYR  C11  C17   single  1.530  0.020  1.530
 LYR  C12  C13   single  1.501  0.020  1.501
 LYR  C12  C14   single  1.505  0.020  1.505
 LYR  C13  H131  single  0.970  0.020  1.090
 LYR  C13  H132  single  0.970  0.020  1.090
 LYR  C13  H133  single  0.970  0.020  1.090
 LYR  C14  C15   single  1.517  0.020  1.517
 LYR  C14  H141  single  0.970  0.020  1.090
 LYR  C14  H142  single  0.970  0.020  1.090
 LYR  C15  C16   single  1.517  0.020  1.517
 LYR  C15  H151  single  0.970  0.020  1.090
 LYR  C15  H152  single  0.970  0.020  1.090
 LYR  C16  C17   single  1.532  0.020  1.532
 LYR  C16  H161  single  0.970  0.020  1.090
 LYR  C16  H162  single  0.970  0.020  1.090
 LYR  C17  C18   single  1.536  0.020  1.536
 LYR  C17  C19   single  1.535  0.020  1.535
 LYR  C18  H181  single  0.970  0.020  1.090
 LYR  C18  H182  single  0.970  0.020  1.090
 LYR  C18  H183  single  0.970  0.020  1.090
 LYR  C19  H191  single  0.970  0.020  1.090
 LYR  C19  H192  single  0.970  0.020  1.090
 LYR  C19  H193  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
 LYR  H2    N    H     105.62  3.000
 LYR  H2    N    CA    110.05  3.000
 LYR  H     N    CA    114.00  3.000
 LYR  HA    CA   CB    109.00  3.000
 LYR  HA    CA   C     109.00  3.000
 LYR  CB    CA   C     110.10  1.900
 LYR  HA    CA   N     110.00  3.000
 LYR  CB    CA   N     110.50  1.700
 LYR  C     CA   N     111.00  2.800
 LYR  OXT   C    O      33.28  3.000
 LYR  OXT   C    CA    141.04  3.000
 LYR  O     C    CA    120.80  1.700
 LYR  HB3   CB   HB2   106.60  3.000
 LYR  HB3   CB   CG    109.81  3.000
 LYR  HB2   CB   CG    108.85  3.000
 LYR  HB3   CB   CA    109.07  3.000
 LYR  HB2   CB   CA    108.48  3.000
 LYR  CG    CB   CA    113.76  3.000
 LYR  HG3   CG   HG2   106.57  3.000
 LYR  HG3   CG   CD    109.28  3.000
 LYR  HG2   CG   CD    109.09  3.000
 LYR  HG3   CG   CB    108.74  3.000
 LYR  HG2   CG   CB    110.04  3.000
 LYR  CD    CG   CB    112.91  3.000
 LYR  HD3   CD   HD2   106.39  3.000
 LYR  HD3   CD   CE    108.20  3.000
 LYR  HD2   CD   CE    108.89  3.000
 LYR  HD3   CD   CG    109.40  3.000
 LYR  HD2   CD   CG    109.15  3.000
 LYR  CE    CD   CG    114.50  3.000
 LYR  HE3   CE   HE2   105.87  3.000
 LYR  HE3   CE   NZ    112.00  3.000
 LYR  HE2   CE   NZ    108.23  3.000
 LYR  HE3   CE   CD    109.43  3.000
 LYR  HE2   CE   CD    108.15  3.000
 LYR  NZ    CE   CD    112.84  3.000
 LYR  HZ    NZ   C1    109.08  3.000
 LYR  HZ    NZ   CE    109.88  3.000
 LYR  C1    NZ   CE    115.86  3.000
 LYR  H11   C1   H1    105.83  3.000
 LYR  H11   C1   C2    109.92  3.000
 LYR  H1    C1   C2    110.57  3.000
 LYR  H11   C1   NZ    111.71  3.000
 LYR  H1    C1   NZ    109.00  3.000
 LYR  C2    C1   NZ    109.76  3.000
 LYR  HC2   C2   C3    117.80  3.000
 LYR  HC2   C2   C1    114.82  3.000
 LYR  C3    C2   C1    127.29  3.000
 LYR  C5    C3   C4    119.05  3.000
 LYR  C5    C3   C2    117.94  3.000
 LYR  C4    C3   C2    122.99  3.000
 LYR  H43   C4   H42   107.01  3.000
 LYR  H43   C4   H41   106.88  3.000
 LYR  H42   C4   H41   107.55  3.000
 LYR  H43   C4   C3    112.71  3.000
 LYR  H42   C4   C3    111.67  3.000
 LYR  H41   C4   C3    110.74  3.000
 LYR  H5    C5   C6    116.47  3.000
 LYR  H5    C5   C3    115.25  3.000
 LYR  C6    C5   C3    128.26  3.000
 LYR  H6    C6   C7    117.48  3.000
 LYR  H6    C6   C5    116.11  3.000
 LYR  C7    C6   C5    126.24  3.000
 LYR  H7    C7   C80   115.93  3.000
 LYR  H7    C7   C6    116.54  3.000
 LYR  C80   C7   C6    127.44  3.000
 LYR  C9    C80  C8    118.27  3.000
 LYR  C9    C80  C7    117.40  3.000
 LYR  C8    C80  C7    124.33  3.000
 LYR  H83   C8   H82   107.43  3.000
 LYR  H83   C8   H81   106.66  3.000
 LYR  H82   C8   H81   107.81  3.000
 LYR  H83   C8   C80   110.74  3.000
 LYR  H82   C8   C80   112.98  3.000
 LYR  H81   C8   C80   110.94  3.000
 LYR  H9    C9   C10   118.14  3.000
 LYR  H9    C9   C80   115.66  3.000
 LYR  C10   C9   C80   126.19  3.000
 LYR  H10   C10  C11   117.01  3.000
 LYR  H10   C10  C9    118.59  3.000
 LYR  C11   C10  C9    124.35  3.000
 LYR  C17   C11  C12   122.63  3.000
 LYR  C17   C11  C10   115.32  3.000
 LYR  C12   C11  C10   122.03  3.000
 LYR  C14   C12  C13   112.26  3.000
 LYR  C14   C12  C11   122.86  3.000
 LYR  C13   C12  C11   124.86  3.000
 LYR  H133  C13  H132  107.67  3.000
 LYR  H133  C13  H131  106.11  3.000
 LYR  H132  C13  H131  108.33  3.000
 LYR  H133  C13  C12   111.05  3.000
 LYR  H132  C13  C12   113.79  3.000
 LYR  H131  C13  C12   109.56  3.000
 LYR  H142  C14  H141  105.10  3.000
 LYR  H142  C14  C15   110.22  3.000
 LYR  H141  C14  C15   110.55  3.000
 LYR  H142  C14  C12   108.27  3.000
 LYR  H141  C14  C12   108.39  3.000
 LYR  C15   C14  C12   113.90  3.000
 LYR  H152  C15  H151  106.94  3.000
 LYR  H152  C15  C16   110.81  3.000
 LYR  H151  C15  C16   110.53  3.000
 LYR  H152  C15  C14   108.92  3.000
 LYR  H151  C15  C14   110.19  3.000
 LYR  C16   C15  C14   109.41  3.000
 LYR  H162  C16  H161  106.33  3.000
 LYR  H162  C16  C17   108.78  3.000
 LYR  H161  C16  C17   109.01  3.000
 LYR  H162  C16  C15   111.06  3.000
 LYR  H161  C16  C15   108.80  3.000
 LYR  C17   C16  C15   112.65  3.000
 LYR  C19   C17  C18   108.45  3.000
 LYR  C19   C17  C16   107.33  3.000
 LYR  C18   C17  C16   110.34  3.000
 LYR  C19   C17  C11   111.09  3.000
 LYR  C18   C17  C11   108.70  3.000
 LYR  C16   C17  C11   110.91  3.000
 LYR  H183  C18  H182  107.54  3.000
 LYR  H183  C18  H181  108.31  3.000
 LYR  H182  C18  H181  107.50  3.000
 LYR  H183  C18  C17   110.47  3.000
 LYR  H182  C18  C17   110.86  3.000
 LYR  H181  C18  C17   112.00  3.000
 LYR  H193  C19  H192  108.07  3.000
 LYR  H193  C19  H191  107.58  3.000
 LYR  H192  C19  H191  106.94  3.000
 LYR  H193  C19  C17   111.55  3.000
 LYR  H192  C19  C17   112.79  3.000
 LYR  H191  C19  C17   109.69  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
 LYR  Var_01  C15   C14  C12  C11    13.47  30.0  1
 LYR  Var_02  C15   C16  C17  C11   -45.36  30.0  1
 LYR  Var_03  C16   C17  C11  C12    13.31  30.0  1
 LYR  Var_04  C16   C15  C14  C12   -44.02  30.0  1
 LYR  Var_05  C17   C11  C12  C14     2.52  30.0  1
 LYR  Var_06  C17   C16  C15  C14    61.52  30.0  1
 LYR  Var_07  C12   C11  C10  C9     49.58  30.0  2
 LYR  Var_08  H131  C13  C12  C11   136.54  30.0  3
 LYR  Var_09  H181  C18  C17  C11    58.15  30.0  3
 LYR  Var_10  H191  C19  C17  C11  -173.01  30.0  3
 LYR  Var_11  C11   C10  C9   C80  -179.90   0.0  2
 LYR  Var_12  C4    C3   C2   C1      6.98   0.0  2
 LYR  Var_13  C7    C6   C5   C3     -6.94   0.0  2
 LYR  Var_14  C8    C80  C7   C6     -4.05   0.0  2
 LYR  Var_15  CD    CG   CB   CA   -176.17  30.0  3
 LYR  Var_16  CE    CD   CG   CB   -177.68  30.0  3
 LYR  Var_17  NZ    CE   CD   CG    -59.16  30.0  3
 LYR  Var_18  C1    NZ   CE   CD     96.90  30.0  3
 LYR  Var_19  C2    C1   NZ   CE   -146.91  30.0  3
 LYR  Var_20  C3    C2   C1   NZ    121.11  30.0  3
 LYR  Var_21  C6    C5   C3   C2    143.37  30.0  2
 LYR  Var_22  C80   C7   C6   C5    176.79  30.0  2
 LYR  Var_23  C10   C9   C80  C7    179.22  30.0  2
 LYR  Var_24  H41   C4   C3   C2    150.32  30.0  3
 LYR  Var_25  H81   C8   C80  C7    121.49  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
 LYR  chir_01  CA  N  C  CB  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
 LYR  plan-1  CA   0.020
 LYR  plan-1  C    0.020
 LYR  plan-1  O    0.020
 LYR  plan-1  OXT  0.020
 LYR  plan-2  C1   0.020
 LYR  plan-2  C2   0.020
 LYR  plan-2  C3   0.020
 LYR  plan-2  C4   0.020
 LYR  plan-2  C5   0.020
 LYR  plan-2  HC2  0.020
 LYR  plan-3  C3   0.020
 LYR  plan-3  C5   0.020
 LYR  plan-3  C6   0.020
 LYR  plan-3  C7   0.020
 LYR  plan-3  H5   0.020
 LYR  plan-3  H6   0.020
 LYR  plan-4  C6   0.020
 LYR  plan-4  C7   0.020
 LYR  plan-4  C80  0.020
 LYR  plan-4  C8   0.020
 LYR  plan-4  C9   0.020
 LYR  plan-4  H7   0.020
 LYR  plan-5  C80  0.020
 LYR  plan-5  C9   0.020
 LYR  plan-5  C10  0.020
 LYR  plan-5  C11  0.020
 LYR  plan-5  H9   0.020
 LYR  plan-5  H10  0.020

