# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 14:40:25 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N~2~-[4-(pyridin-3-yl)benzyl]-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NCc1ccc(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
 3D6  3D6  N~2~-[4-(pyridin-3-yl)benzyl]-L-lysinamide  ligand  47  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3D6
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
 3D6  C10  C  CH2   0  -0.319   0.9359   1.6792   0.6594
 3D6  C13  C  CR16  0  -0.294  -2.8261   1.5580   0.1380
 3D6  C15  C  CR6   0  -0.004  -4.4677  -0.3160   0.0052
 3D6  C17  C  CR16  0  -0.315  -6.6727  -0.2332  -0.9368
 3D6  C20  C  CR16  0  -0.104  -4.9065  -1.4279   0.7264
 3D6  C21  C  CR16  0  -0.295  -2.0153  -0.6871   0.3045
 3D6  C22  C  CR16  0  -0.278  -0.7231  -0.2105   0.4487
 3D6  C02  C  C     0   0.502   3.7119   2.5840  -0.1810
 3D6  C03  C  CH1   0  -0.208   3.2882   1.1873   0.2858
 3D6  C04  C  CH2   0  -0.422   4.2346   0.1631  -0.3497
 3D6  C05  C  CH2   0  -0.415   4.0089  -1.2582   0.1470
 3D6  C06  C  CH2   0  -0.427   4.9642  -2.2558  -0.4954
 3D6  C07  C  CH2   0  -0.271   4.7422  -3.6791  -0.0081
 3D6  N08  N  NH2   0  -0.801   5.6554  -4.6054  -0.6633
 3D6  N09  N  NH1   0  -0.574   1.9173   0.8793  -0.0432
 3D6  C11  C  CR6   0   0.078  -0.4610   1.1582   0.4475
 3D6  C12  C  CR16  0  -0.296  -1.5302   2.0318   0.2813
 3D6  C14  C  CR6   0   0.072  -3.0916   0.1896   0.1507
 3D6  C16  C  CR16  0  -0.198  -5.3934   0.2881  -0.8435
 3D6  C18  C  CR16  0  -0.073  -6.9928  -1.3487  -0.1776
 3D6  N19  N  N     0  -0.398  -6.1277  -1.9353   0.6419
 3D6  H1   H  HCH2  0   0.244   1.1676   1.6261   1.7288
 3D6  H2   H  HCH2  0   0.219   0.9637   2.7475   0.4004
 3D6  H3   H  HCR6  0   0.253  -3.6380   2.2669   0.0320
 3D6  H4   H  HCR6  0   0.273  -7.4078   0.2103  -1.5939
 3D6  H5   H  HCR6  0   0.260  -4.2327  -1.9185   1.4217
 3D6  H6   H  HCR6  0   0.252  -2.1825  -1.7573   0.2927
 3D6  H7   H  HCR6  0   0.254   0.0970  -0.9094   0.5503
 3D6  H8   H  HNH2  0   0.407   4.8729   2.8294   1.4960
 3D6  H9   H  HNH2  0   0.400   4.9522   4.1201   0.3633
 3D6  H10  H  HCH1  0   0.248   3.3928   1.1244   1.3755
 3D6  H11  H  HCH2  0   0.226   4.1180   0.2015  -1.4385
 3D6  H12  H  HCH2  0   0.233   5.2669   0.4609  -0.1425
 3D6  H13  H  HCH2  0   0.210   4.1312  -1.2842   1.2354
 3D6  H14  H  HCH2  0   0.225   2.9763  -1.5537  -0.0534
 3D6  H15  H  HCH2  0   0.212   4.8517  -2.2282  -1.5839
 3D6  H16  H  HCH2  0   0.210   5.9982  -1.9596  -0.2838
 3D6  H17  H  HCH2  0   0.186   4.8160  -3.6949   1.0896
 3D6  H18  H  HCH2  0   0.210   3.7190  -3.9828  -0.2477
 3D6  H19  H  HNH2  0   0.336   6.6024  -4.4060  -0.3647
 3D6  H20  H  HNH2  0   0.345   5.4657  -5.5475  -0.3468
 3D6  H22  H  HNH1  0   0.342   1.7833   0.9741  -1.0439
 3D6  H24  H  HCR6  0   0.251  -1.3540   3.1010   0.2692
 3D6  H25  H  HCR6  0   0.270  -5.1137   1.1484  -1.4387
 3D6  H26  H  HCR6  0   0.266  -7.9843  -1.7838  -0.2318
 3D6  O23  O  O     0  -0.494   3.3079   3.0461  -1.2396
 3D6  N01  N  NH2   0  -0.796   4.5708   3.2244   0.6224

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
 3D6  N08  C07  single    1.456  0.020  1.456
 3D6  C07  C06  single    1.521  0.020  1.521
 3D6  C06  C05  single    1.523  0.020  1.523
 3D6  C05  C04  single    1.522  0.020  1.522
 3D6  N01  C02  single    1.339  0.020  1.339
 3D6  C04  C03  single    1.533  0.020  1.533
 3D6  C02  C03  single    1.532  0.020  1.532
 3D6  C02  O23  double    1.224  0.020  1.224
 3D6  C03  N09  single    1.443  0.020  1.443
 3D6  C22  C21  aromatic  1.385  0.020  1.385
 3D6  C22  C11  aromatic  1.394  0.020  1.394
 3D6  N09  C10  single    1.448  0.020  1.448
 3D6  C21  C14  aromatic  1.397  0.020  1.397
 3D6  C10  C11  single    1.506  0.020  1.506
 3D6  C11  C12  aromatic  1.391  0.020  1.391
 3D6  C20  N19  aromatic  1.325  0.020  1.325
 3D6  C20  C15  aromatic  1.396  0.020  1.396
 3D6  N19  C18  aromatic  1.328  0.020  1.328
 3D6  C14  C15  single    1.473  0.020  1.473
 3D6  C14  C13  aromatic  1.394  0.020  1.394
 3D6  C15  C16  aromatic  1.394  0.020  1.394
 3D6  C18  C17  aromatic  1.387  0.020  1.387
 3D6  C12  C13  aromatic  1.387  0.020  1.387
 3D6  C16  C17  aromatic  1.385  0.020  1.385
 3D6  C10  H1   single    0.970  0.020  1.090
 3D6  C10  H2   single    0.970  0.020  1.090
 3D6  C13  H3   single    0.930  0.020  1.080
 3D6  C17  H4   single    0.930  0.020  1.080
 3D6  C20  H5   single    0.930  0.020  1.080
 3D6  C21  H6   single    0.930  0.020  1.080
 3D6  C22  H7   single    0.930  0.020  1.080
 3D6  N01  H8   single    0.860  0.020  1.020
 3D6  N01  H9   single    0.860  0.020  1.020
 3D6  C03  H10  single    0.970  0.020  1.090
 3D6  C04  H11  single    0.970  0.020  1.090
 3D6  C04  H12  single    0.970  0.020  1.090
 3D6  C05  H13  single    0.970  0.020  1.090
 3D6  C05  H14  single    0.970  0.020  1.090
 3D6  C06  H15  single    0.970  0.020  1.090
 3D6  C06  H16  single    0.970  0.020  1.090
 3D6  C07  H17  single    0.970  0.020  1.090
 3D6  C07  H18  single    0.970  0.020  1.090
 3D6  N08  H19  single    0.890  0.020  1.040
 3D6  N08  H20  single    0.890  0.020  1.040
 3D6  N09  H22  single    0.890  0.020  1.040
 3D6  C12  H24  single    0.930  0.020  1.080
 3D6  C16  H25  single    0.930  0.020  1.080
 3D6  C18  H26  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
 3D6  H2   C10  H1   105.77  3.000
 3D6  H2   C10  C11  109.05  3.000
 3D6  H1   C10  C11  108.46  3.000
 3D6  H2   C10  N09  113.91  3.000
 3D6  H1   C10  N09  107.67  3.000
 3D6  C11  C10  N09  111.67  3.000
 3D6  H3   C13  C14  120.04  3.000
 3D6  H3   C13  C12  119.13  3.000
 3D6  C14  C13  C12  120.82  3.000
 3D6  C16  C15  C14  122.13  3.000
 3D6  C16  C15  C20  116.81  3.000
 3D6  C14  C15  C20  121.06  3.000
 3D6  H4   C17  C18  120.38  3.000
 3D6  H4   C17  C16  120.98  3.000
 3D6  C18  C17  C16  118.63  3.000
 3D6  H5   C20  N19  116.09  3.000
 3D6  H5   C20  C15  119.72  3.000
 3D6  N19  C20  C15  124.17  3.000
 3D6  H6   C21  C14  120.00  3.000
 3D6  H6   C21  C22  119.03  3.000
 3D6  C14  C21  C22  120.96  3.000
 3D6  H7   C22  C11  119.46  3.000
 3D6  H7   C22  C21  119.64  3.000
 3D6  C11  C22  C21  120.89  3.000
 3D6  O23  C02  C03  121.09  3.000
 3D6  O23  C02  N01  123.38  3.000
 3D6  C03  C02  N01  115.50  3.000
 3D6  H10  C03  N09  107.76  3.000
 3D6  H10  C03  C04  108.36  3.000
 3D6  N09  C03  C04  110.45  3.000
 3D6  H10  C03  C02  109.19  3.000
 3D6  N09  C03  C02  112.81  3.000
 3D6  C04  C03  C02  108.18  3.000
 3D6  H12  C04  H11  106.20  3.000
 3D6  H12  C04  C05  109.40  3.000
 3D6  H11  C04  C05  109.95  3.000
 3D6  H12  C04  C03  108.79  3.000
 3D6  H11  C04  C03  108.85  3.000
 3D6  C05  C04  C03  113.40  3.000
 3D6  H14  C05  H13  106.33  3.000
 3D6  H14  C05  C06  109.77  3.000
 3D6  H13  C05  C06  109.48  3.000
 3D6  H14  C05  C04  109.44  3.000
 3D6  H13  C05  C04  109.25  3.000
 3D6  C06  C05  C04  112.39  3.000
 3D6  H16  C06  H15  106.38  3.000
 3D6  H16  C06  C07  109.19  3.000
 3D6  H15  C06  C07  109.10  3.000
 3D6  H16  C06  C05  109.46  3.000
 3D6  H15  C06  C05  109.78  3.000
 3D6  C07  C06  C05  112.73  3.000
 3D6  H18  C07  H17  106.10  3.000
 3D6  H18  C07  N08  108.14  3.000
 3D6  H17  C07  N08  113.44  3.000
 3D6  H18  C07  C06  109.03  3.000
 3D6  H17  C07  C06  108.86  3.000
 3D6  N08  C07  C06  111.07  3.000
 3D6  H20  N08  H19  105.45  3.000
 3D6  H20  N08  C07  109.50  3.000
 3D6  H19  N08  C07  109.17  3.000
 3D6  H22  N09  C03  109.30  3.000
 3D6  H22  N09  C10  109.74  3.000
 3D6  C03  N09  C10  114.54  3.000
 3D6  C12  C11  C22  118.19  3.000
 3D6  C12  C11  C10  120.84  3.000
 3D6  C22  C11  C10  120.94  3.000
 3D6  H24  C12  C11  119.74  3.000
 3D6  H24  C12  C13  119.19  3.000
 3D6  C11  C12  C13  121.06  3.000
 3D6  C21  C14  C15  121.01  3.000
 3D6  C15  C14  C13  120.93  3.000
 3D6  C21  C14  C13  118.06  3.000
 3D6  H25  C16  C17  120.04  3.000
 3D6  H25  C16  C15  120.50  3.000
 3D6  C17  C16  C15  119.45  3.000
 3D6  H26  C18  N19  116.70  3.000
 3D6  H26  C18  C17  120.43  3.000
 3D6  N19  C18  C17  122.87  3.000
 3D6  C18  N19  C20  118.06  3.000
 3D6  H9   N01  H8   117.33  3.000
 3D6  H9   N01  C02  120.92  3.000
 3D6  H8   N01  C02  121.75  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
 3D6  CONST_01  C22  C21  C14  C13     0.00   0.0  0
 3D6  CONST_04  C22  C11  C12  C13     0.00   0.0  0
 3D6  CONST_05  C18  N19  C20  C15     0.00   0.0  0
 3D6  CONST_06  C22  C21  C14  C15   180.00   0.0  0
 3D6  CONST_07  C12  C13  C14  C15   180.00   0.0  0
 3D6  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 3D6  CONST_09  C20  N19  C18  C17     0.00   0.0  0
 3D6  CONST_10  C20  C15  C16  C17     0.00   0.0  0
 3D6  CONST_11  C14  C15  C16  C17   180.00   0.0  0
 3D6  CONST_13  C12  C11  C22  C21     0.00   0.0  0
 3D6  CONST_15  C12  C13  C14  C21     0.00   0.0  0
 3D6  CONST_16  C14  C21  C22  C11     0.00   0.0  0
 3D6  CONST_17  C14  C13  C12  C11     0.00   0.0  0
 3D6  CONST_18  N19  C20  C15  C14   180.00   0.0  0
 3D6  CONST_19  N19  C20  C15  C16     0.00   0.0  0
 3D6  CONST_20  N19  C18  C17  C16     0.00   0.0  0
 3D6  CONST_21  C21  C22  C11  C10   180.00   0.0  0
 3D6  CONST_22  C13  C12  C11  C10   180.00   0.0  0
 3D6  CONST_23  H6   C21  C14  C13   180.00   0.0  0
 3D6  CONST_24  H3   C13  C14  C15     0.00   0.0  0
 3D6  CONST_25  H4   C17  C16  C15   180.00   0.0  0
 3D6  CONST_26  H26  C18  N19  C20   180.00   0.0  0
 3D6  CONST_27  H25  C16  C15  C20   180.00   0.0  0
 3D6  CONST_28  H24  C12  C11  C22   180.00   0.0  0
 3D6  CONST_29  H7   C22  C11  C12   180.00   0.0  0
 3D6  CONST_30  H5   C20  C15  C14     0.00   0.0  0
 3D6  CONST_31  H8   N01  C02  C03     0.00   0.0  0
 3D6  CONST_32  H9   N01  C02  C03   180.00   0.0  0
 3D6  Var_01    N09  C10  C11  C22    40.66  30.0  2
 3D6  Var_02    C11  C10  N09  C03  -170.50  30.0  3
 3D6  Var_03    C06  C05  C04  C03  -179.80  30.0  2
 3D6  Var_04    C07  C06  C05  C04  -179.80  30.0  1
 3D6  Var_05    N08  C07  C06  C05   178.89  30.0  2
 3D6  Var_06    H19  N08  C07  C06    67.00  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
 3D6  chir_01  C03  C04  C02  N09  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
 3D6  plan-1  C15  0.020
 3D6  plan-1  C17  0.020
 3D6  plan-1  C20  0.020
 3D6  plan-1  C14  0.020
 3D6  plan-1  C16  0.020
 3D6  plan-1  C18  0.020
 3D6  plan-1  N19  0.020
 3D6  plan-1  H4   0.020
 3D6  plan-1  H5   0.020
 3D6  plan-1  H25  0.020
 3D6  plan-1  H26  0.020
 3D6  plan-2  C10  0.020
 3D6  plan-2  C13  0.020
 3D6  plan-2  C15  0.020
 3D6  plan-2  C21  0.020
 3D6  plan-2  C22  0.020
 3D6  plan-2  C11  0.020
 3D6  plan-2  C12  0.020
 3D6  plan-2  C14  0.020
 3D6  plan-2  H3   0.020
 3D6  plan-2  H6   0.020
 3D6  plan-2  H7   0.020
 3D6  plan-2  H24  0.020
 3D6  plan-3  C02  0.020
 3D6  plan-3  C03  0.020
 3D6  plan-3  H8   0.020
 3D6  plan-3  H9   0.020
 3D6  plan-3  O23  0.020
 3D6  plan-3  N01  0.020

