# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 12:41:56 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N~2~-[4-(pyridin-3-yl)benzoyl]-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NC(=O)c1ccc(cc1)c2cccnc2)C(N)=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
 3C6  3C6  N~2~-[4-(pyridin-3-yl)benzoyl]-L-lysinamide  ligand  46  24  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3C6
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
 3C6  CAA  C  CR16  0  -0.193  -5.6303   0.2133   0.7077
 3C6  CAB  C  CR16  0  -0.315  -6.9212  -0.2412   0.5003
 3C6  CAC  C  CR16  0  -0.069  -7.1336  -1.2244  -0.4542
 3C6  NAD  N  N     0  -0.398  -6.1547  -1.7446  -1.1857
 3C6  CAE  C  CR16  0  -0.098  -4.9223  -1.3034  -0.9814
 3C6  CAF  C  CR6   0  -0.006  -4.5879  -0.3261  -0.0427
 3C6  CAG  C  CR6   0   0.089  -3.1926   0.1102   0.1346
 3C6  CAH  C  CR16  0  -0.298  -2.8903   1.4464   0.4035
 3C6  CAI  C  CR16  0  -0.252  -1.5805   1.8565   0.5750
 3C6  CAL  C  CR16  0  -0.295  -2.1415  -0.8028   0.0445
 3C6  CAK  C  CR16  0  -0.273  -0.8291  -0.3904   0.2022
 3C6  CAJ  C  CR6   0  -0.049  -0.5333   0.9456   0.4621
 3C6  CAM  C  C     0   0.546   0.8620   1.4339   0.6612
 3C6  OAX  O  O     0  -0.482   1.1043   2.4235   1.3378
 3C6  N    N  NH1   0  -0.651   1.8330   0.7164   0.0681
 3C6  CA   C  CH1   0  -0.189   3.2150   1.1103   0.1616
 3C6  C    C  C     0   0.520   3.4424   2.4478  -0.5473
 3C6  O    O  O     0  -0.486   2.8233   2.7486  -1.5546
 3C6  NAW  N  NH2   0  -0.800   4.4050   3.2050  -0.0079
 3C6  CB   C  CH2   0  -0.456   4.1046   0.0385  -0.4717
 3C6  CG   C  CH2   0  -0.420   4.0586  -1.2945   0.2661
 3C6  CD   C  CH2   0  -0.427   4.9628  -2.3397  -0.3742
 3C6  CE   C  CH2   0  -0.271   4.9188  -3.6739   0.3542
 3C6  NZ   N  NH2   0  -0.801   5.7847  -4.6503  -0.2920
 3C6  H1   H  HCR6  0   0.273  -5.4355   0.9671   1.4603
 3C6  H2   H  HCR6  0   0.276  -7.7486   0.1504   1.0756
 3C6  H3   H  HCR6  0   0.268  -8.1317  -1.6073  -0.6344
 3C6  H4   H  HCR6  0   0.263  -4.1496  -1.7358  -1.6091
 3C6  H5   H  HCR6  0   0.263  -3.6840   2.1803   0.4626
 3C6  H6   H  HCR6  0   0.263  -1.3707   2.8977   0.7805
 3C6  H7   H  HCR6  0   0.265  -2.3453  -1.8526  -0.1229
 3C6  H8   H  HCR6  0   0.261  -0.0441  -1.1346   0.1558
 3C6  H9   H  HNH1  0   0.407   1.5841   0.0593  -0.6545
 3C6  H10  H  HCH1  0   0.272   3.4848   1.2089   1.2175
 3C6  H11  H  HNH2  0   0.408   4.8605   2.9544   0.8527
 3C6  H12  H  HNH2  0   0.403   4.6776   4.0740  -0.4377
 3C6  H13  H  HCH2  0   0.241   3.8136  -0.0978  -1.5187
 3C6  H14  H  HCH2  0   0.253   5.1325   0.4090  -0.4828
 3C6  H15  H  HCH2  0   0.223   4.3547  -1.1374   1.3083
 3C6  H16  H  HCH2  0   0.220   3.0335  -1.6759   0.2948
 3C6  H17  H  HCH2  0   0.216   4.6714  -2.4928  -1.4179
 3C6  H18  H  HCH2  0   0.215   5.9940  -1.9693  -0.3903
 3C6  H19  H  HCH2  0   0.187   5.1602  -3.5079   1.4145
 3C6  H20  H  HCH2  0   0.212   3.8948  -4.0573   0.3310
 3C6  H21  H  HNH2  0   0.337   6.7496  -4.3624  -0.1819
 3C6  H22  H  HNH2  0   0.345   5.7119  -5.5365   0.1914

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
 3C6  OAX  CAM  double    1.223  0.020  1.223
 3C6  CAI  CAH  aromatic  1.383  0.020  1.383
 3C6  CAI  CAJ  aromatic  1.393  0.020  1.393
 3C6  CAH  CAG  aromatic  1.396  0.020  1.396
 3C6  O    C    double    1.220  0.020  1.220
 3C6  CAM  CAJ  single    1.492  0.020  1.492
 3C6  CAM  N    single    1.345  0.020  1.345
 3C6  NZ   CE   single    1.456  0.020  1.456
 3C6  CAJ  CAK  aromatic  1.393  0.020  1.393
 3C6  C    CA   single    1.531  0.020  1.531
 3C6  C    NAW  single    1.338  0.020  1.338
 3C6  CA   N    single    1.440  0.020  1.440
 3C6  CA   CB   single    1.530  0.020  1.530
 3C6  CD   CE   single    1.521  0.020  1.521
 3C6  CD   CG   single    1.523  0.020  1.523
 3C6  CAE  NAD  aromatic  1.325  0.020  1.325
 3C6  CAE  CAF  aromatic  1.396  0.020  1.396
 3C6  CAG  CAF  single    1.473  0.020  1.473
 3C6  CAG  CAL  aromatic  1.395  0.020  1.395
 3C6  NAD  CAC  aromatic  1.328  0.020  1.328
 3C6  CAF  CAA  aromatic  1.393  0.020  1.393
 3C6  CAK  CAL  aromatic  1.385  0.020  1.385
 3C6  CB   CG   single    1.524  0.020  1.524
 3C6  CAC  CAB  aromatic  1.387  0.020  1.387
 3C6  CAA  CAB  aromatic  1.384  0.020  1.384
 3C6  CAA  H1   single    0.930  0.020  1.080
 3C6  CAB  H2   single    0.930  0.020  1.080
 3C6  CAC  H3   single    0.930  0.020  1.080
 3C6  CAE  H4   single    0.930  0.020  1.080
 3C6  CAH  H5   single    0.930  0.020  1.080
 3C6  CAI  H6   single    0.930  0.020  1.080
 3C6  CAL  H7   single    0.930  0.020  1.080
 3C6  CAK  H8   single    0.930  0.020  1.080
 3C6  N    H9   single    0.860  0.020  1.020
 3C6  CA   H10  single    0.970  0.020  1.090
 3C6  NAW  H11  single    0.860  0.020  1.020
 3C6  NAW  H12  single    0.860  0.020  1.020
 3C6  CB   H13  single    0.970  0.020  1.090
 3C6  CB   H14  single    0.970  0.020  1.090
 3C6  CG   H15  single    0.970  0.020  1.090
 3C6  CG   H16  single    0.970  0.020  1.090
 3C6  CD   H17  single    0.970  0.020  1.090
 3C6  CD   H18  single    0.970  0.020  1.090
 3C6  CE   H19  single    0.970  0.020  1.090
 3C6  CE   H20  single    0.970  0.020  1.090
 3C6  NZ   H21  single    0.890  0.020  1.040
 3C6  NZ   H22  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
 3C6  H1   CAA  CAF  120.62  3.000
 3C6  H1   CAA  CAB  120.03  3.000
 3C6  CAF  CAA  CAB  119.34  3.000
 3C6  H2   CAB  CAC  120.39  3.000
 3C6  H2   CAB  CAA  121.00  3.000
 3C6  CAC  CAB  CAA  118.61  3.000
 3C6  H3   CAC  NAD  116.66  3.000
 3C6  H3   CAC  CAB  120.39  3.000
 3C6  NAD  CAC  CAB  122.95  3.000
 3C6  CAE  NAD  CAC  118.05  3.000
 3C6  H4   CAE  CAF  119.83  3.000
 3C6  H4   CAE  NAD  116.12  3.000
 3C6  CAF  CAE  NAD  124.04  3.000
 3C6  CAG  CAF  CAE  121.03  3.000
 3C6  CAG  CAF  CAA  121.96  3.000
 3C6  CAE  CAF  CAA  117.01  3.000
 3C6  CAL  CAG  CAH  118.40  3.000
 3C6  CAL  CAG  CAF  120.81  3.000
 3C6  CAH  CAG  CAF  120.79  3.000
 3C6  H5   CAH  CAI  119.11  3.000
 3C6  H5   CAH  CAG  120.04  3.000
 3C6  CAI  CAH  CAG  120.84  3.000
 3C6  H6   CAI  CAJ  119.95  3.000
 3C6  H6   CAI  CAH  119.51  3.000
 3C6  CAJ  CAI  CAH  120.53  3.000
 3C6  H7   CAL  CAK  119.00  3.000
 3C6  H7   CAL  CAG  120.19  3.000
 3C6  CAK  CAL  CAG  120.79  3.000
 3C6  H8   CAK  CAJ  120.89  3.000
 3C6  H8   CAK  CAL  118.53  3.000
 3C6  CAJ  CAK  CAL  120.54  3.000
 3C6  CAM  CAJ  CAK  122.52  3.000
 3C6  CAK  CAJ  CAI  118.88  3.000
 3C6  CAM  CAJ  CAI  118.58  3.000
 3C6  N    CAM  OAX  122.17  3.000
 3C6  N    CAM  CAJ  116.21  3.000
 3C6  OAX  CAM  CAJ  121.61  3.000
 3C6  H9   N    CA   117.51  3.000
 3C6  H9   N    CAM  119.06  3.000
 3C6  CA   N    CAM  121.21  3.000
 3C6  H10  CA   CB   108.61  3.000
 3C6  H10  CA   C    109.36  3.000
 3C6  CB   CA   C    109.51  3.000
 3C6  H10  CA   N    108.91  3.000
 3C6  CB   CA   N    109.84  3.000
 3C6  C    CA   N    110.58  3.000
 3C6  NAW  C    O    123.94  3.000
 3C6  NAW  C    CA   114.49  3.000
 3C6  O    C    CA   121.50  3.000
 3C6  H12  NAW  H11  117.24  3.000
 3C6  H12  NAW  C    120.73  3.000
 3C6  H11  NAW  C    122.00  3.000
 3C6  H14  CB   H13  106.40  3.000
 3C6  H14  CB   CG   109.26  3.000
 3C6  H13  CB   CG   110.24  3.000
 3C6  H14  CB   CA   108.28  3.000
 3C6  H13  CB   CA   109.17  3.000
 3C6  CG   CB   CA   113.25  3.000
 3C6  H16  CG   H15  106.17  3.000
 3C6  H16  CG   CD   109.15  3.000
 3C6  H15  CG   CD   109.76  3.000
 3C6  H16  CG   CB   110.23  3.000
 3C6  H15  CG   CB   109.10  3.000
 3C6  CD   CG   CB   112.26  3.000
 3C6  H18  CD   H17  106.49  3.000
 3C6  H18  CD   CE   109.32  3.000
 3C6  H17  CD   CE   109.05  3.000
 3C6  H18  CD   CG   109.44  3.000
 3C6  H17  CD   CG   109.81  3.000
 3C6  CE   CD   CG   112.55  3.000
 3C6  H20  CE   H19  106.19  3.000
 3C6  H20  CE   NZ   108.19  3.000
 3C6  H19  CE   NZ   113.48  3.000
 3C6  H20  CE   CD   108.93  3.000
 3C6  H19  CE   CD   108.84  3.000
 3C6  NZ   CE   CD   111.01  3.000
 3C6  H22  NZ   H21  105.39  3.000
 3C6  H22  NZ   CE   109.41  3.000
 3C6  H21  NZ   CE   109.12  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
 3C6  CONST_01  NAD  CAE  CAF  CAA     0.00   0.0  0
 3C6  CONST_04  NAD  CAC  CAB  CAA     0.00   0.0  0
 3C6  CONST_05  CAE  NAD  CAC  CAB     0.00   0.0  0
 3C6  CONST_06  CAE  CAF  CAA  CAB     0.00   0.0  0
 3C6  CONST_07  CAG  CAF  CAA  CAB   180.00   0.0  0
 3C6  CONST_08  CAF  CAE  NAD  CAC     0.00   0.0  0
 3C6  CONST_09  CAF  CAA  CAB  CAC     0.00   0.0  0
 3C6  CONST_10  CAG  CAF  CAE  NAD   180.00   0.0  0
 3C6  CONST_13  CAI  CAH  CAG  CAF   180.00   0.0  0
 3C6  CONST_14  CAK  CAL  CAG  CAF   180.00   0.0  0
 3C6  CONST_15  CAJ  CAI  CAH  CAG     0.00   0.0  0
 3C6  CONST_16  CAJ  CAK  CAL  CAG     0.00   0.0  0
 3C6  CONST_17  CAK  CAJ  CAI  CAH     0.00   0.0  0
 3C6  CONST_18  CAK  CAL  CAG  CAH     0.00   0.0  0
 3C6  CONST_19  CAL  CAG  CAH  CAI     0.00   0.0  0
 3C6  CONST_20  CAL  CAK  CAJ  CAI     0.00   0.0  0
 3C6  CONST_21  CAM  CAJ  CAI  CAH   180.00   0.0  0
 3C6  CONST_22  CAM  CAJ  CAK  CAL   180.00   0.0  0
 3C6  CONST_23  H4   CAE  CAF  CAA   180.00   0.0  0
 3C6  CONST_24  H3   CAC  CAB  CAA   180.00   0.0  0
 3C6  CONST_25  H1   CAA  CAB  CAC   180.00   0.0  0
 3C6  CONST_26  H2   CAB  CAC  NAD   180.00   0.0  0
 3C6  CONST_27  H5   CAH  CAG  CAF     0.00   0.0  0
 3C6  CONST_28  H7   CAL  CAG  CAF     0.00   0.0  0
 3C6  CONST_29  H6   CAI  CAH  CAG   180.00   0.0  0
 3C6  CONST_30  H8   CAK  CAL  CAG   180.00   0.0  0
 3C6  CONST_31  CA   N    CAM  CAJ   180.00   0.0  0
 3C6  CONST_33  CA   N    CAM  OAX     0.00   0.0  0
 3C6  CONST_34  H11  NAW  C    CA      0.00   0.0  0
 3C6  CONST_35  H12  NAW  C    CA    180.00   0.0  0
 3C6  Var_01    OAX  CAM  CAJ  CAI    25.34  30.0  2
 3C6  Var_02    CD   CG   CB   CA   -179.40  30.0  3
 3C6  Var_03    CE   CD   CG   CB   -179.82  30.0  1
 3C6  Var_04    NZ   CE   CD   CG    179.49  30.0  3
 3C6  Var_05    H21  NZ   CE   CD     67.17  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
 3C6  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
 3C6  plan-1  CAA  0.020
 3C6  plan-1  CAB  0.020
 3C6  plan-1  CAC  0.020
 3C6  plan-1  NAD  0.020
 3C6  plan-1  CAE  0.020
 3C6  plan-1  CAF  0.020
 3C6  plan-1  CAG  0.020
 3C6  plan-1  H1   0.020
 3C6  plan-1  H2   0.020
 3C6  plan-1  H3   0.020
 3C6  plan-1  H4   0.020
 3C6  plan-2  CAF  0.020
 3C6  plan-2  CAG  0.020
 3C6  plan-2  CAH  0.020
 3C6  plan-2  CAI  0.020
 3C6  plan-2  CAL  0.020
 3C6  plan-2  CAK  0.020
 3C6  plan-2  CAJ  0.020
 3C6  plan-2  CAM  0.020
 3C6  plan-2  H5   0.020
 3C6  plan-2  H6   0.020
 3C6  plan-2  H7   0.020
 3C6  plan-2  H8   0.020
 3C6  plan-3  CAJ  0.020
 3C6  plan-3  CAM  0.020
 3C6  plan-3  OAX  0.020
 3C6  plan-3  N    0.020
 3C6  plan-3  CA   0.020
 3C6  plan-3  H9   0.020
 3C6  plan-4  CA   0.020
 3C6  plan-4  C    0.020
 3C6  plan-4  O    0.020
 3C6  plan-4  NAW  0.020
 3C6  plan-4  H11  0.020
 3C6  plan-4  H12  0.020

