# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:04:00 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N~2~-[4-(pyridin-3-yl)benzyl]-D-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
 3D5  3D5  N~2~-[4-(pyridin-3-yl)benzyl]-D-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 PERFECT
;

data_comp_3D5
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
 3D5  C18  C  CR16  0  -0.197  -5.3183   0.4065   0.9707
 3D5  C19  C  CR16  0  -0.315  -6.6122  -0.0291   1.2008
 3D5  C20  C  CR16  0  -0.072  -7.0905  -1.1056   0.4691
 3D5  N21  N  N     0  -0.398  -6.3589  -1.7448  -0.4366
 3D5  C22  C  CR16  0  -0.103  -5.1200  -1.3240  -0.6467
 3D5  C17  C  CR6   0  -0.005  -4.5355  -0.2457   0.0199
 3D5  C16  C  CR6   0   0.071  -3.1519   0.1708  -0.2679
 3D5  C15  C  CR16  0  -0.296  -2.3076   0.5992   0.7593
 3D5  C14  C  CR16  0  -0.267  -1.0056   0.9873   0.4949
 3D5  C13  C  CR16  0  -0.291  -2.6480   0.1476  -1.5673
 3D5  C12  C  CR16  0  -0.302  -1.3417   0.5371  -1.8281
 3D5  C11  C  CR6   0   0.074  -0.5039   0.9661  -0.8056
 3D5  C10  C  CH2   0  -0.324   0.9094   1.3974  -1.0860
 3D5  N09  N  NH1   0  -0.601   1.8384   0.7163  -0.2033
 3D5  C03  C  CH1   0  -0.174   3.2224   1.0663  -0.4265
 3D5  C02  C  C     0   0.503   3.4670   2.5137  -0.0010
 3D5  O23  O  O     0  -0.485   2.9827   2.9835   1.0167
 3D5  N01  N  NH2   0  -0.798   4.2920   3.1960  -0.8079
 3D5  C04  C  CH2   0  -0.424   4.1524   0.1737   0.4032
 3D5  C05  C  CH2   0  -0.440   4.0971  -1.3028   0.0262
 3D5  C06  C  CH2   0  -0.423   5.1220  -2.1319   0.7903
 3D5  C07  C  CH2   0  -0.272   5.0457  -3.6123   0.4504
 3D5  N08  N  NH2   0  -0.801   6.0207  -4.3761   1.2161
 3D5  H1   H  HCR6  0   0.271  -4.9269   1.2579   1.5139
 3D5  H2   H  HCR6  0   0.273  -7.2444   0.4608   1.9283
 3D5  H3   H  HCR6  0   0.266  -8.1020  -1.4651   0.6201
 3D5  H4   H  HCR6  0   0.260  -4.5425  -1.8828  -1.3763
 3D5  H5   H  HCR6  0   0.253  -2.6652   0.6094   1.7818
 3D5  H6   H  HCR6  0   0.251  -0.3651   1.3040   1.3086
 3D5  H7   H  HCR6  0   0.253  -3.2805  -0.1625  -2.3901
 3D5  H8   H  HCR6  0   0.253  -0.9746   0.5108  -2.8473
 3D5  H9   H  HCH2  0   0.219   1.1338   1.2400  -2.1517
 3D5  H10  H  HCH2  0   0.246   0.9897   2.4751  -0.9138
 3D5  H11  H  HNH1  0   0.356   1.7270  -0.2809  -0.3364
 3D5  H13  H  HCH1  0   0.222   3.5108   0.9611  -1.4873
 3D5  H14  H  HNH2  0   0.406   4.6514   2.7969  -1.6575
 3D5  H15  H  HNH2  0   0.400   4.5776   4.1342  -0.5790
 3D5  H16  H  HCH2  0   0.233   5.1776   0.5318   0.2711
 3D5  H17  H  HCH2  0   0.231   3.9082   0.2971   1.4620
 3D5  H18  H  HCH2  0   0.217   3.1024  -1.7116   0.2305
 3D5  H19  H  HCH2  0   0.221   4.2630  -1.4121  -1.0506
 3D5  H20  H  HCH2  0   0.214   6.1285  -1.7602   0.5681
 3D5  H21  H  HCH2  0   0.215   4.9732  -2.0035   1.8669
 3D5  H22  H  HCH2  0   0.211   4.0485  -3.9844   0.7026
 3D5  H23  H  HCH2  0   0.187   5.1510  -3.7323  -0.6379
 3D5  H24  H  HNH2  0   0.345   5.9264  -5.3595   0.9966
 3D5  H25  H  HNH2  0   0.337   6.9541  -4.1214   0.9163

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
 3D5  N08  C07  single    1.456  0.020  1.456
 3D5  C07  C06  single    1.521  0.020  1.521
 3D5  C06  C05  single    1.524  0.020  1.524
 3D5  C05  C04  single    1.525  0.020  1.525
 3D5  C04  C03  single    1.533  0.020  1.533
 3D5  C03  N09  single    1.445  0.020  1.445
 3D5  C03  C02  single    1.528  0.020  1.528
 3D5  N09  C10  single    1.451  0.020  1.451
 3D5  C14  C15  aromatic  1.384  0.020  1.384
 3D5  C14  C11  aromatic  1.394  0.020  1.394
 3D5  C15  C16  aromatic  1.397  0.020  1.397
 3D5  C10  C11  single    1.504  0.020  1.504
 3D5  C02  N01  single    1.341  0.020  1.341
 3D5  C02  O23  double    1.221  0.020  1.221
 3D5  C11  C12  aromatic  1.390  0.020  1.390
 3D5  C22  N21  aromatic  1.325  0.020  1.325
 3D5  C22  C17  aromatic  1.396  0.020  1.396
 3D5  C16  C17  single    1.473  0.020  1.473
 3D5  C16  C13  aromatic  1.394  0.020  1.394
 3D5  N21  C20  aromatic  1.328  0.020  1.328
 3D5  C17  C18  aromatic  1.394  0.020  1.394
 3D5  C12  C13  aromatic  1.388  0.020  1.388
 3D5  C20  C19  aromatic  1.387  0.020  1.387
 3D5  C18  C19  aromatic  1.385  0.020  1.385
 3D5  C18  H1   single    0.930  0.020  1.080
 3D5  C19  H2   single    0.930  0.020  1.080
 3D5  C20  H3   single    0.930  0.020  1.080
 3D5  C22  H4   single    0.930  0.020  1.080
 3D5  C15  H5   single    0.930  0.020  1.080
 3D5  C14  H6   single    0.930  0.020  1.080
 3D5  C13  H7   single    0.930  0.020  1.080
 3D5  C12  H8   single    0.930  0.020  1.080
 3D5  C10  H9   single    0.970  0.020  1.090
 3D5  C10  H10  single    0.970  0.020  1.090
 3D5  N09  H11  single    0.890  0.020  1.040
 3D5  C03  H13  single    0.970  0.020  1.090
 3D5  N01  H14  single    0.860  0.020  1.020
 3D5  N01  H15  single    0.860  0.020  1.020
 3D5  C04  H16  single    0.970  0.020  1.090
 3D5  C04  H17  single    0.970  0.020  1.090
 3D5  C05  H18  single    0.970  0.020  1.090
 3D5  C05  H19  single    0.970  0.020  1.090
 3D5  C06  H20  single    0.970  0.020  1.090
 3D5  C06  H21  single    0.970  0.020  1.090
 3D5  C07  H22  single    0.970  0.020  1.090
 3D5  C07  H23  single    0.970  0.020  1.090
 3D5  N08  H24  single    0.890  0.020  1.040
 3D5  N08  H25  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
 3D5  H1   C18  C17  120.47  3.000
 3D5  H1   C18  C19  120.11  3.000
 3D5  C17  C18  C19  119.41  3.000
 3D5  H2   C19  C20  120.34  3.000
 3D5  H2   C19  C18  121.05  3.000
 3D5  C20  C19  C18  118.61  3.000
 3D5  H3   C20  N21  116.70  3.000
 3D5  H3   C20  C19  120.38  3.000
 3D5  N21  C20  C19  122.92  3.000
 3D5  C22  N21  C20  118.05  3.000
 3D5  H4   C22  C17  119.73  3.000
 3D5  H4   C22  N21  116.14  3.000
 3D5  C17  C22  N21  124.13  3.000
 3D5  C16  C17  C22  121.22  3.000
 3D5  C16  C17  C18  121.90  3.000
 3D5  C22  C17  C18  116.88  3.000
 3D5  C13  C16  C15  118.17  3.000
 3D5  C13  C16  C17  121.13  3.000
 3D5  C15  C16  C17  120.70  3.000
 3D5  H5   C15  C14  119.22  3.000
 3D5  H5   C15  C16  119.83  3.000
 3D5  C14  C15  C16  120.93  3.000
 3D5  H6   C14  C11  119.51  3.000
 3D5  H6   C14  C15  119.66  3.000
 3D5  C11  C14  C15  120.83  3.000
 3D5  H7   C13  C12  119.15  3.000
 3D5  H7   C13  C16  120.12  3.000
 3D5  C12  C13  C16  120.72  3.000
 3D5  H8   C12  C11  119.69  3.000
 3D5  H8   C12  C13  119.26  3.000
 3D5  C11  C12  C13  121.05  3.000
 3D5  C10  C11  C12  121.19  3.000
 3D5  C12  C11  C14  118.30  3.000
 3D5  C10  C11  C14  120.51  3.000
 3D5  H10  C10  H9   106.16  3.000
 3D5  H10  C10  N09  108.63  3.000
 3D5  H9   C10  N09  113.04  3.000
 3D5  H10  C10  C11  108.79  3.000
 3D5  H9   C10  C11  109.35  3.000
 3D5  N09  C10  C11  110.70  3.000
 3D5  H11  N09  C03  108.89  3.000
 3D5  H11  N09  C10  108.17  3.000
 3D5  C03  N09  C10  113.92  3.000
 3D5  H13  C03  C04  107.82  3.000
 3D5  H13  C03  C02  108.41  3.000
 3D5  C04  C03  C02  107.68  3.000
 3D5  H13  C03  N09  112.06  3.000
 3D5  C02  C03  N09  109.86  3.000
 3D5  C04  C03  N09  110.88  3.000
 3D5  N01  C02  O23  123.36  3.000
 3D5  O23  C02  C03  122.21  3.000
 3D5  N01  C02  C03  114.38  3.000
 3D5  H15  N01  H14  117.44  3.000
 3D5  H15  N01  C02  120.78  3.000
 3D5  H14  N01  C02  121.78  3.000
 3D5  H17  C04  H16  106.81  3.000
 3D5  H17  C04  C05  109.90  3.000
 3D5  H16  C04  C05  108.73  3.000
 3D5  H17  C04  C03  108.84  3.000
 3D5  H16  C04  C03  108.22  3.000
 3D5  C05  C04  C03  114.08  3.000
 3D5  H19  C05  H18  106.49  3.000
 3D5  H19  C05  C06  109.69  3.000
 3D5  H18  C05  C06  108.33  3.000
 3D5  H19  C05  C04  109.53  3.000
 3D5  H18  C05  C04  110.39  3.000
 3D5  C06  C05  C04  112.24  3.000
 3D5  H21  C06  H20  106.53  3.000
 3D5  H21  C06  C07  109.10  3.000
 3D5  H20  C06  C07  109.33  3.000
 3D5  H21  C06  C05  109.76  3.000
 3D5  H20  C06  C05  109.37  3.000
 3D5  C07  C06  C05  112.57  3.000
 3D5  H23  C07  H22  106.16  3.000
 3D5  H23  C07  N08  113.51  3.000
 3D5  H22  C07  N08  108.11  3.000
 3D5  H23  C07  C06  108.81  3.000
 3D5  H22  C07  C06  108.99  3.000
 3D5  N08  C07  C06  111.07  3.000
 3D5  H25  N08  H24  105.43  3.000
 3D5  H25  N08  C07  109.24  3.000
 3D5  H24  N08  C07  109.46  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
 3D5  CONST_01  N21  C22  C17  C18     0.00   0.0  0
 3D5  CONST_04  N21  C20  C19  C18     0.00   0.0  0
 3D5  CONST_05  C22  N21  C20  C19     0.00   0.0  0
 3D5  CONST_06  C22  C17  C18  C19     0.00   0.0  0
 3D5  CONST_07  C16  C17  C18  C19   180.00   0.0  0
 3D5  CONST_08  C17  C22  N21  C20     0.00   0.0  0
 3D5  CONST_09  C17  C18  C19  C20     0.00   0.0  0
 3D5  CONST_10  C16  C17  C22  N21   180.00   0.0  0
 3D5  CONST_13  C14  C15  C16  C17   180.00   0.0  0
 3D5  CONST_14  C12  C13  C16  C17   180.00   0.0  0
 3D5  CONST_15  C11  C14  C15  C16     0.00   0.0  0
 3D5  CONST_16  C11  C12  C13  C16     0.00   0.0  0
 3D5  CONST_17  C12  C11  C14  C15     0.00   0.0  0
 3D5  CONST_18  C12  C13  C16  C15     0.00   0.0  0
 3D5  CONST_19  C13  C16  C15  C14     0.00   0.0  0
 3D5  CONST_20  C13  C12  C11  C14     0.00   0.0  0
 3D5  CONST_21  C10  C11  C14  C15   180.00   0.0  0
 3D5  CONST_22  C10  C11  C12  C13   180.00   0.0  0
 3D5  CONST_23  H4   C22  C17  C18   180.00   0.0  0
 3D5  CONST_24  H3   C20  C19  C18   180.00   0.0  0
 3D5  CONST_25  H1   C18  C19  C20   180.00   0.0  0
 3D5  CONST_26  H2   C19  C20  N21   180.00   0.0  0
 3D5  CONST_27  H5   C15  C16  C17     0.00   0.0  0
 3D5  CONST_28  H7   C13  C16  C17     0.00   0.0  0
 3D5  CONST_29  H6   C14  C15  C16   180.00   0.0  0
 3D5  CONST_30  H8   C12  C13  C16   180.00   0.0  0
 3D5  CONST_31  H14  N01  C02  C03     0.00   0.0  0
 3D5  CONST_32  H15  N01  C02  C03   180.00   0.0  0
 3D5  Var_01    N09  C10  C11  C14    50.80  30.0  2
 3D5  Var_02    C03  N09  C10  C11   179.17  30.0  1
 3D5  Var_03    C06  C05  C04  C03   175.03  30.0  1
 3D5  Var_04    C07  C06  C05  C04   178.30  30.0  2
 3D5  Var_05    N08  C07  C06  C05  -178.94  30.0  1
 3D5  Var_06    H24  N08  C07  C06   177.96  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
 3D5  chir_01  C03  C04  N09  C02  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
 3D5  plan-1  C18  0.020
 3D5  plan-1  C19  0.020
 3D5  plan-1  C20  0.020
 3D5  plan-1  N21  0.020
 3D5  plan-1  C22  0.020
 3D5  plan-1  C17  0.020
 3D5  plan-1  C16  0.020
 3D5  plan-1  H1   0.020
 3D5  plan-1  H2   0.020
 3D5  plan-1  H3   0.020
 3D5  plan-1  H4   0.020
 3D5  plan-2  C17  0.020
 3D5  plan-2  C16  0.020
 3D5  plan-2  C15  0.020
 3D5  plan-2  C14  0.020
 3D5  plan-2  C13  0.020
 3D5  plan-2  C12  0.020
 3D5  plan-2  C11  0.020
 3D5  plan-2  C10  0.020
 3D5  plan-2  H5   0.020
 3D5  plan-2  H6   0.020
 3D5  plan-2  H7   0.020
 3D5  plan-2  H8   0.020
 3D5  plan-3  C03  0.020
 3D5  plan-3  C02  0.020
 3D5  plan-3  O23  0.020
 3D5  plan-3  N01  0.020
 3D5  plan-3  H14  0.020
 3D5  plan-3  H15  0.020

