# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:25:32 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 3-(8-phenyloctyl)-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cncn1CCCCCCCCc2ccccc2)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
 56A  56A  3-(8-phenyloctyl)-L-histidine  L-peptide  53  25  .  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_56A
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
 56A  C     C  C      0   0.415   1.5946  24.5889  14.1775
 56A  N     N  NH2    0  -0.803   2.2371  25.3105  16.4723
 56A  O     O  O      0  -0.597   2.4630  25.3989  13.7995
 56A  CA    C  CH1    0  -0.206   1.4195  24.3880  15.7042
 56A  CB    C  CH2    0  -0.518  -0.0583  24.5180  16.1018
 56A  CG    C  CR5    0   0.303  -0.6531  25.8493  15.7925
 56A  C28   C  CH2    0  -0.426  -1.3598  26.4697  18.9831
 56A  C29   C  CH2    0  -0.417  -0.9113  26.4946  20.4377
 56A  C30   C  CH2    0  -0.417  -2.0227  26.0888  21.3967
 56A  C31   C  CH2    0  -0.417  -1.5887  26.1072  22.8573
 56A  C32   C  CH2    0  -0.419  -2.7146  25.8174  23.8464
 56A  C33   C  CH2    0  -0.429  -3.2971  24.4143  23.7297
 56A  C34   C  CH2    0  -0.506  -4.3847  24.1155  24.7659
 56A  C35   C  CR6    0   0.129  -3.8803  24.1426  26.1831
 56A  C36   C  CR16   0  -0.312  -4.2379  25.1621  27.0614
 56A  C37   C  CR16   0  -0.239  -3.7508  25.1909  28.3628
 56A  C38   C  CR16   0  -0.274  -2.8916  24.1962  28.8078
 56A  C39   C  CR16   0  -0.239  -2.5267  23.1721  27.9415
 56A  C40   C  CR16   0  -0.302  -3.0177  23.1477  26.6442
 56A  ND1   N  NR5    0  -0.441  -0.6788  26.9198  16.6505
 56A  CD2   C  CR15   0  -0.263  -1.2502  26.3106  14.6482
 56A  CE1   C  CR15   0   0.069  -1.2803  27.9416  16.0026
 56A  NE2   N  N      0  -0.455  -1.6350  27.6143  14.7873
 56A  OXT   O  OC    -1  -0.609   0.8582  23.8888  13.4545
 56A  HN    H  HNH2   0   0.333   2.5111  24.8865  17.3485
 56A  HNA   H  HNH2   0   0.336   3.0827  25.5030  15.9522
 56A  HA    H  HCH1   0   0.207   1.6953  23.3385  15.8986
 56A  HB    H  HCH2   0   0.242  -0.6261  23.7541  15.5708
 56A  HBA   H  HCH2   0   0.239  -0.1671  24.2879  17.1658
 56A  H27   H  HCH2   0   0.263   0.6332  26.3414  18.1346
 56A  H27A  H  HCH2   0   0.256   0.0159  27.9739  18.2801
 56A  H28   H  HCH2   0   0.224  -2.2441  27.1023  18.8596
 56A  H28A  H  HCH2   0   0.227  -1.6617  25.4540  18.7097
 56A  H29   H  HCH2   0   0.215  -0.0541  25.8251  20.5658
 56A  H29A  H  HCH2   0   0.213  -0.5549  27.4980  20.6953
 56A  H30   H  HCH2   0   0.208  -2.8758  26.7642  21.2666
 56A  H30A  H  HCH2   0   0.216  -2.3823  25.0923  21.1231
 56A  H31   H  HCH2   0   0.207  -0.7787  25.3846  23.0060
 56A  H31A  H  HCH2   0   0.216  -1.1636  27.0892  23.0875
 56A  H32   H  HCH2   0   0.223  -2.3371  25.9682  24.8618
 56A  H32A  H  HCH2   0   0.206  -3.5142  26.5539  23.7081
 56A  H33   H  HCH2   0   0.229  -3.7275  24.2678  22.7359
 56A  H33A  H  HCH2   0   0.215  -2.4939  23.6756  23.8241
 56A  H34   H  HCH2   0   0.235  -5.1986  24.8369  24.6531
 56A  H34A  H  HCH2   0   0.244  -4.8113  23.1316  24.5527
 56A  H36   H  HCR6   0   0.244  -4.9063  25.9454  26.7230
 56A  H37   H  HCR6   0   0.249  -4.0430  25.9934  29.0284
 56A  H38   H  HCR6   0   0.249  -2.5102  24.2158  29.8206
 56A  H39   H  HCR6   0   0.249  -1.8602  22.3883  28.2790
 56A  H40   H  HCR6   0   0.244  -2.7281  22.3418  25.9789
 56A  HD2   H  HCR5   0   0.234  -1.4042  25.7616  13.7316
 56A  HE1   H  HCR5   0   0.264  -1.4272  28.9040  16.4718
 56A  C27   C  CH2    0  -0.313  -0.2662  26.9476  18.0393

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
 56A  O    C     deloc     1.231  0.020  1.231
 56A  OXT  C     deloc     1.247  0.020  1.247
 56A  C    CA    single    1.525  0.021  1.525
 56A  CA   N     single    1.458  0.019  1.458
 56A  N    HN    single    0.890  0.020  1.040
 56A  N    HNA   single    0.890  0.020  1.040
 56A  CA   CB    single    1.530  0.020  1.530
 56A  CA   HA    single    0.970  0.020  0.970
 56A  CG   CB    single    1.491  0.020  1.491
 56A  CB   HB    single    0.970  0.020  1.090
 56A  CB   HBA   single    0.970  0.020  1.090
 56A  CD2  CG    aromatic  1.371  0.020  1.371
 56A  CG   ND1   aromatic  1.372  0.020  1.372
 56A  ND1  C27   single    1.449  0.020  1.449
 56A  C27  C28   single    1.522  0.020  1.522
 56A  C27  H27   single    0.970  0.020  1.090
 56A  C27  H27A  single    0.970  0.020  1.090
 56A  C28  C29   single    1.522  0.020  1.522
 56A  C28  H28   single    0.970  0.020  1.090
 56A  C28  H28A  single    0.970  0.020  1.090
 56A  C29  C30   single    1.523  0.020  1.523
 56A  C29  H29   single    0.970  0.020  1.090
 56A  C29  H29A  single    0.970  0.020  1.090
 56A  C30  C31   single    1.524  0.020  1.524
 56A  C30  H30   single    0.970  0.020  1.090
 56A  C30  H30A  single    0.970  0.020  1.090
 56A  C31  C32   single    1.526  0.020  1.526
 56A  C31  H31   single    0.970  0.020  1.090
 56A  C31  H31A  single    0.970  0.020  1.090
 56A  C33  C32   single    1.524  0.020  1.524
 56A  C32  H32   single    0.970  0.020  1.090
 56A  C32  H32A  single    0.970  0.020  1.090
 56A  C33  C34   single    1.532  0.020  1.532
 56A  C33  H33   single    0.970  0.020  1.090
 56A  C33  H33A  single    0.970  0.020  1.090
 56A  C34  C35   single    1.505  0.020  1.505
 56A  C34  H34   single    0.970  0.020  1.090
 56A  C34  H34A  single    0.970  0.020  1.090
 56A  C35  C40   aromatic  1.395  0.020  1.395
 56A  C35  C36   aromatic  1.392  0.020  1.392
 56A  C36  C37   aromatic  1.390  0.020  1.390
 56A  C36  H36   single    0.930  0.020  1.080
 56A  C37  C38   aromatic  1.388  0.020  1.388
 56A  C37  H37   single    0.930  0.020  1.080
 56A  C39  C38   aromatic  1.390  0.020  1.390
 56A  C38  H38   single    0.930  0.020  1.080
 56A  C40  C39   aromatic  1.387  0.020  1.387
 56A  C39  H39   single    0.930  0.020  1.080
 56A  C40  H40   single    0.930  0.020  1.080
 56A  CE1  ND1   aromatic  1.351  0.020  1.351
 56A  NE2  CD2   aromatic  1.366  0.020  1.366
 56A  CD2  HD2   single    0.930  0.020  1.080
 56A  NE2  CE1   aromatic  1.308  0.020  1.308
 56A  CE1  HE1   single    0.930  0.020  1.080

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
 56A  OXT   C    CA   115.57  3.000
 56A  CA    C    O    120.80  1.700
 56A  OXT   C    O    126.91  3.000
 56A  HNA   N    HN   107.39  3.000
 56A  HNA   N    CA   108.64  3.000
 56A  HN    N    CA   110.15  3.000
 56A  HA    CA   CB   109.00  3.000
 56A  HA    CA   N    110.00  3.000
 56A  CB    CA   N    110.50  1.700
 56A  HA    CA   C    109.00  3.000
 56A  CB    CA   C    110.10  1.900
 56A  N     CA   C    111.00  2.800
 56A  HBA   CB   HB   105.93  3.000
 56A  HBA   CB   CG   110.49  3.000
 56A  HB    CB   CG   108.48  3.000
 56A  HBA   CB   CA   109.25  3.000
 56A  HB    CB   CA   108.41  3.000
 56A  CG    CB   CA   113.95  3.000
 56A  CD2   CG   ND1  104.55  3.000
 56A  ND1   CG   CB   125.06  3.000
 56A  CD2   CG   CB   130.37  3.000
 56A  H28A  C28  H28  106.58  3.000
 56A  H28A  C28  C29  109.58  3.000
 56A  H28   C28  C29  109.66  3.000
 56A  H28A  C28  C27  109.56  3.000
 56A  H28   C28  C27  109.23  3.000
 56A  C29   C28  C27  112.07  3.000
 56A  H29A  C29  H29  106.13  3.000
 56A  H29A  C29  C30  109.47  3.000
 56A  H29   C29  C30  109.55  3.000
 56A  H29A  C29  C28  109.60  3.000
 56A  H29   C29  C28  109.41  3.000
 56A  C30   C29  C28  112.47  3.000
 56A  H30A  C30  H30  106.01  3.000
 56A  H30A  C30  C31  110.13  3.000
 56A  H30   C30  C31  109.15  3.000
 56A  H30A  C30  C29  108.97  3.000
 56A  H30   C30  C29  109.22  3.000
 56A  C31   C30  C29  113.11  3.000
 56A  H31A  C31  H31  106.03  3.000
 56A  H31A  C31  C32  108.70  3.000
 56A  H31   C31  C32  109.40  3.000
 56A  H31A  C31  C30  108.84  3.000
 56A  H31   C31  C30  109.43  3.000
 56A  C32   C31  C30  114.12  3.000
 56A  H32A  C32  H32  106.04  3.000
 56A  H32A  C32  C33  109.28  3.000
 56A  H32   C32  C33  109.27  3.000
 56A  H32A  C32  C31  109.20  3.000
 56A  H32   C32  C31  108.71  3.000
 56A  C33   C32  C31  114.03  3.000
 56A  H33A  C33  H33  106.07  3.000
 56A  H33A  C33  C34  109.32  3.000
 56A  H33   C33  C34  108.02  3.000
 56A  H33A  C33  C32  109.52  3.000
 56A  H33   C33  C32  110.10  3.000
 56A  C34   C33  C32  113.53  3.000
 56A  H34A  C34  H34  106.45  3.000
 56A  H34A  C34  C35  109.31  3.000
 56A  H34   C34  C35  109.57  3.000
 56A  H34A  C34  C33  108.71  3.000
 56A  H34   C34  C33  109.28  3.000
 56A  C35   C34  C33  113.30  3.000
 56A  C40   C35  C36  118.19  3.000
 56A  C36   C35  C34  121.41  3.000
 56A  C40   C35  C34  120.38  3.000
 56A  H36   C36  C37  119.56  3.000
 56A  H36   C36  C35  119.38  3.000
 56A  C37   C36  C35  121.05  3.000
 56A  H37   C37  C38  120.09  3.000
 56A  H37   C37  C36  119.76  3.000
 56A  C38   C37  C36  120.15  3.000
 56A  H38   C38  C39  120.27  3.000
 56A  H38   C38  C37  120.34  3.000
 56A  C39   C38  C37  119.39  3.000
 56A  H39   C39  C40  119.78  3.000
 56A  H39   C39  C38  120.04  3.000
 56A  C40   C39  C38  120.19  3.000
 56A  H40   C40  C39  119.49  3.000
 56A  H40   C40  C35  119.50  3.000
 56A  C39   C40  C35  121.02  3.000
 56A  CE1   ND1  C27  124.88  3.000
 56A  CE1   ND1  CG   107.37  3.000
 56A  C27   ND1  CG   127.51  3.000
 56A  HD2   CD2  NE2  122.11  3.000
 56A  HD2   CD2  CG   126.85  3.000
 56A  NE2   CD2  CG   111.03  3.000
 56A  HE1   CE1  NE2  126.13  3.000
 56A  HE1   CE1  ND1  121.72  3.000
 56A  NE2   CE1  ND1  112.15  3.000
 56A  CE1   NE2  CD2  104.90  3.000
 56A  H27A  C27  H27  106.91  3.000
 56A  H27A  C27  ND1  107.65  3.000
 56A  H27   C27  ND1  107.97  3.000
 56A  H27A  C27  C28  110.13  3.000
 56A  H27   C27  C28  111.38  3.000
 56A  ND1   C27  C28  112.57  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
 56A  CONST_01  CE1  NE2  CD2  CG     0.00   0.0  0
 56A  CONST_02  NE2  CE1  ND1  CG     0.00   0.0  0
 56A  CONST_03  C38  C39  C40  C35    0.00   0.0  0
 56A  CONST_04  C38  C37  C36  C35    0.00   0.0  0
 56A  CONST_05  C39  C40  C35  C36    0.00   0.0  0
 56A  CONST_06  C39  C38  C37  C36    0.00   0.0  0
 56A  CONST_07  C40  C35  C36  C37    0.00   0.0  0
 56A  CONST_08  C40  C39  C38  C37    0.00   0.0  0
 56A  CONST_09  NE2  CD2  CG   ND1    0.00   0.0  0
 56A  CONST_10  CD2  NE2  CE1  ND1    0.00   0.0  0
 56A  CONST_11  CE1  ND1  CG   CD2    0.00   0.0  0
 56A  CONST_12  NE2  CD2  CG   CB   180.00   0.0  0
 56A  CONST_13  CE1  ND1  CG   CB   180.00   0.0  0
 56A  CONST_14  CD2  CG   ND1  C27  180.00   0.0  0
 56A  CONST_15  NE2  CE1  ND1  C27  180.00   0.0  0
 56A  CONST_16  C39  C40  C35  C34  180.00   0.0  0
 56A  CONST_17  C37  C36  C35  C34  180.00   0.0  0
 56A  CONST_18  HE1  CE1  ND1  CG   180.00   0.0  0
 56A  CONST_19  H39  C39  C40  C35  180.00   0.0  0
 56A  CONST_20  H37  C37  C36  C35  180.00   0.0  0
 56A  CONST_21  H40  C40  C35  C36  180.00   0.0  0
 56A  CONST_22  H38  C38  C37  C36  180.00   0.0  0
 56A  CONST_23  H36  C36  C37  C38  180.00   0.0  0
 56A  CONST_24  HD2  CD2  CG   ND1  180.00   0.0  0
 56A  Var_01    CD2  CG   CB   CA    87.42  30.0  2
 56A  Var_02    C28  C27  ND1  CG   -83.94  30.0  2
 56A  Var_03    C40  C35  C34  C33  -69.58  30.0  2
 56A  Var_04    ND1  C27  C28  C29  179.61  30.0  2
 56A  Var_05    C35  C34  C33  C32  -63.57  30.0  3
 56A  Var_06    C30  C29  C28  C27  176.95  30.0  3
 56A  Var_07    C31  C30  C29  C28  179.93  30.0  3
 56A  Var_08    C32  C31  C30  C29  175.17  30.0  3
 56A  Var_09    C33  C32  C31  C30   64.43  30.0  3
 56A  Var_10    C34  C33  C32  C31  177.56  30.0  1

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
 56A  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
 56A  plan-1  CB   0.020
 56A  plan-1  CG   0.020
 56A  plan-1  ND1  0.020
 56A  plan-1  CD2  0.020
 56A  plan-1  CE1  0.020
 56A  plan-1  NE2  0.020
 56A  plan-1  HD2  0.020
 56A  plan-1  HE1  0.020
 56A  plan-1  C27  0.020
 56A  plan-2  C34  0.020
 56A  plan-2  C35  0.020
 56A  plan-2  C36  0.020
 56A  plan-2  C37  0.020
 56A  plan-2  C38  0.020
 56A  plan-2  C39  0.020
 56A  plan-2  C40  0.020
 56A  plan-2  H36  0.020
 56A  plan-2  H37  0.020
 56A  plan-2  H38  0.020
 56A  plan-2  H39  0.020
 56A  plan-2  H40  0.020
 56A  plan-3  C    0.020
 56A  plan-3  O    0.020
 56A  plan-3  CA   0.020
 56A  plan-3  OXT  0.020

