# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:27:37 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N~2~-[3-(pyridin-3-yl)benzyl]-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NCc1cccc(c1)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
 3D2  3D2  N~2~-[3-(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_3D2
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
 3D2  C19  C  CR16  0  -0.072   6.8535   0.4113   0.6149
 3D2  C14  C  CR16  0  -0.326   2.6297  -2.1906  -0.5130
 3D2  C15  C  CR6   0   0.107   2.9556  -0.8470  -0.3425
 3D2  C16  C  CR6   0  -0.008   4.3274  -0.4431   0.0152
 3D2  C17  C  CR16  0  -0.196   5.1066  -1.1835   0.9019
 3D2  C18  C  CR16  0  -0.315   6.3870  -0.7531   1.2057
 3D2  C13  C  CR16  0  -0.227   1.3311  -2.5605  -0.8368
 3D2  C12  C  CR16  0  -0.296   0.3465  -1.5984  -0.9947
 3D2  C11  C  CR6   0   0.120   0.6525  -0.2479  -0.8360
 3D2  C22  C  CR16  0  -0.381   1.9523   0.1114  -0.5063
 3D2  C10  C  CH2   0  -0.333  -0.4177   0.7979  -0.9986
 3D2  N20  N  N     0  -0.398   6.1296   1.1285  -0.2365
 3D2  C21  C  CR16  0  -0.102   4.9060   0.7070  -0.5244
 3D2  N09  N  NH1   0  -0.569  -1.5517   0.5032  -0.1437
 3D2  C03  C  CH1   0  -0.207  -2.6862   1.3747  -0.3315
 3D2  C02  C  C     0   0.501  -2.4046   2.8211   0.0883
 3D2  O23  O  O     0  -0.494  -1.7181   3.0731   1.0697
 3D2  N01  N  NH2   0  -0.796  -2.9902   3.7635  -0.6619
 3D2  C04  C  CH2   0  -0.423  -3.8887   0.8675   0.4723
 3D2  C05  C  CH2   0  -0.415  -4.3728  -0.5072   0.0326
 3D2  C06  C  CH2   0  -0.426  -5.5541  -0.9957   0.8612
 3D2  C07  C  CH2   0  -0.272  -6.0462  -2.3696   0.4347
 3D2  N08  N  NH2   0  -0.801  -7.1703  -2.8003   1.2548
 3D2  H1   H  HCR6  0   0.266   7.8495   0.7779   0.8367
 3D2  H3   H  HCR6  0   0.270   4.7118  -2.0786   1.3661
 3D2  H4   H  HCR6  0   0.274   7.0104  -1.3027   1.8972
 3D2  H5   H  HCR6  0   0.257   1.0905  -3.6073  -0.9705
 3D2  H6   H  HCR6  0   0.251  -0.6669  -1.8919  -1.2381
 3D2  H7   H  HCR6  0   0.251   2.1805   1.1592  -0.3463
 3D2  H8   H  HCH2  0   0.218   0.0212   1.7913  -0.8280
 3D2  H9   H  HCH2  0   0.242  -0.7726   0.7939  -2.0343
 3D2  H10  H  HCR6  0   0.261   4.3501   1.3061  -1.2389
 3D2  H11  H  HNH1  0   0.341  -1.2604   0.5345   0.8270
 3D2  H13  H  HCH1  0   0.248  -2.9494   1.3542  -1.3956
 3D2  H14  H  HNH2  0   0.407  -3.5405   3.5309  -1.4704
 3D2  H15  H  HNH2  0   0.399  -2.9209   4.7377  -0.4149
 3D2  H16  H  HCH2  0   0.225  -3.6211   0.8454   1.5342
 3D2  H17  H  HCH2  0   0.233  -4.7071   1.5880   0.3791
 3D2  H18  H  HCH2  0   0.210  -4.6576  -0.4678  -1.0245
 3D2  H19  H  HCH2  0   0.224  -3.5496  -1.2225   0.1014
 3D2  H20  H  HCH2  0   0.212  -5.2752  -1.0307   1.9190
 3D2  H21  H  HCH2  0   0.210  -6.3771  -0.2756   0.7836
 3D2  H22  H  HCH2  0   0.186  -6.2729  -2.3492  -0.6416
 3D2  H23  H  HCH2  0   0.211  -5.2351  -3.0923   0.5606
 3D2  H24  H  HNH2  0   0.336  -7.9737  -2.2193   1.0469
 3D2  H25  H  HNH2  0   0.345  -7.4410  -3.7391   0.9906
 3D2  H2   H  HCR6  0   0.255   3.3921  -2.9526  -0.4100

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
 3D2  C07  C06  single    1.520  0.020  1.520
 3D2  C07  N08  single    1.457  0.020  1.457
 3D2  C06  C05  single    1.523  0.020  1.523
 3D2  C05  C04  single    1.522  0.020  1.522
 3D2  C13  C14  aromatic  1.388  0.020  1.388
 3D2  C13  C12  aromatic  1.386  0.020  1.386
 3D2  C14  C15  aromatic  1.393  0.020  1.393
 3D2  C04  C03  single    1.533  0.020  1.533
 3D2  C12  C11  aromatic  1.394  0.020  1.394
 3D2  C21  N20  aromatic  1.326  0.020  1.326
 3D2  C21  C16  aromatic  1.396  0.020  1.396
 3D2  C15  C16  single    1.474  0.020  1.474
 3D2  C15  C22  aromatic  1.397  0.020  1.397
 3D2  N20  C19  aromatic  1.328  0.020  1.328
 3D2  C16  C17  aromatic  1.393  0.020  1.393
 3D2  C11  C22  aromatic  1.388  0.020  1.388
 3D2  C11  C10  single    1.505  0.020  1.505
 3D2  C03  N09  single    1.443  0.020  1.443
 3D2  C03  C02  single    1.532  0.020  1.532
 3D2  O23  C02  double    1.224  0.020  1.224
 3D2  N09  C10  single    1.450  0.020  1.450
 3D2  C19  C18  aromatic  1.387  0.020  1.387
 3D2  C02  N01  single    1.339  0.020  1.339
 3D2  C17  C18  aromatic  1.384  0.020  1.384
 3D2  C19  H1   single    0.930  0.020  1.080
 3D2  C14  H2   single    0.930  0.020  1.080
 3D2  C17  H3   single    0.930  0.020  1.080
 3D2  C18  H4   single    0.930  0.020  1.080
 3D2  C13  H5   single    0.930  0.020  1.080
 3D2  C12  H6   single    0.930  0.020  1.080
 3D2  C22  H7   single    0.930  0.020  1.080
 3D2  C10  H8   single    0.970  0.020  1.090
 3D2  C10  H9   single    0.970  0.020  1.090
 3D2  C21  H10  single    0.930  0.020  1.080
 3D2  N09  H11  single    0.890  0.020  1.040
 3D2  C03  H13  single    0.970  0.020  1.090
 3D2  N01  H14  single    0.860  0.020  1.020
 3D2  N01  H15  single    0.860  0.020  1.020
 3D2  C04  H16  single    0.970  0.020  1.090
 3D2  C04  H17  single    0.970  0.020  1.090
 3D2  C05  H18  single    0.970  0.020  1.090
 3D2  C05  H19  single    0.970  0.020  1.090
 3D2  C06  H20  single    0.970  0.020  1.090
 3D2  C06  H21  single    0.970  0.020  1.090
 3D2  C07  H22  single    0.970  0.020  1.090
 3D2  C07  H23  single    0.970  0.020  1.090
 3D2  N08  H24  single    0.890  0.020  1.040
 3D2  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
 3D2  H1   C19  N20  116.70  3.000
 3D2  H1   C19  C18  120.39  3.000
 3D2  N20  C19  C18  122.91  3.000
 3D2  H2   C14  C13  119.55  3.000
 3D2  H2   C14  C15  120.16  3.000
 3D2  C13  C14  C15  120.28  3.000
 3D2  C22  C15  C16  120.59  3.000
 3D2  C22  C15  C14  118.64  3.000
 3D2  C16  C15  C14  120.78  3.000
 3D2  C21  C16  C17  116.87  3.000
 3D2  C17  C16  C15  121.96  3.000
 3D2  C21  C16  C15  121.17  3.000
 3D2  H3   C17  C18  120.00  3.000
 3D2  H3   C17  C16  120.54  3.000
 3D2  C18  C17  C16  119.45  3.000
 3D2  H4   C18  C17  121.04  3.000
 3D2  H4   C18  C19  120.36  3.000
 3D2  C17  C18  C19  118.60  3.000
 3D2  H5   C13  C12  119.97  3.000
 3D2  H5   C13  C14  119.63  3.000
 3D2  C12  C13  C14  120.41  3.000
 3D2  H6   C12  C11  119.59  3.000
 3D2  H6   C12  C13  120.16  3.000
 3D2  C11  C12  C13  120.25  3.000
 3D2  C10  C11  C22  120.77  3.000
 3D2  C10  C11  C12  120.32  3.000
 3D2  C22  C11  C12  118.91  3.000
 3D2  H7   C22  C11  118.83  3.000
 3D2  H7   C22  C15  119.63  3.000
 3D2  C11  C22  C15  121.51  3.000
 3D2  H9   C10  H8   106.23  3.000
 3D2  H9   C10  N09  107.66  3.000
 3D2  H8   C10  N09  113.85  3.000
 3D2  H9   C10  C11  109.28  3.000
 3D2  H8   C10  C11  109.10  3.000
 3D2  N09  C10  C11  110.55  3.000
 3D2  C21  N20  C19  118.08  3.000
 3D2  H10  C21  N20  116.11  3.000
 3D2  H10  C21  C16  119.79  3.000
 3D2  N20  C21  C16  124.09  3.000
 3D2  H11  N09  C03  109.38  3.000
 3D2  H11  N09  C10  109.47  3.000
 3D2  C03  N09  C10  114.54  3.000
 3D2  H13  C03  C04  108.33  3.000
 3D2  H13  C03  C02  109.13  3.000
 3D2  C04  C03  C02  108.24  3.000
 3D2  H13  C03  N09  107.68  3.000
 3D2  C02  C03  N09  112.96  3.000
 3D2  C04  C03  N09  110.41  3.000
 3D2  N01  C02  O23  123.33  3.000
 3D2  N01  C02  C03  115.50  3.000
 3D2  O23  C02  C03  121.14  3.000
 3D2  H15  N01  H14  117.29  3.000
 3D2  H15  N01  C02  120.87  3.000
 3D2  H14  N01  C02  121.81  3.000
 3D2  H17  C04  H16  106.17  3.000
 3D2  H17  C04  C05  109.40  3.000
 3D2  H16  C04  C05  109.85  3.000
 3D2  H17  C04  C03  108.92  3.000
 3D2  H16  C04  C03  108.87  3.000
 3D2  C05  C04  C03  113.38  3.000
 3D2  H19  C05  H18  106.27  3.000
 3D2  H19  C05  C06  109.88  3.000
 3D2  H18  C05  C06  109.56  3.000
 3D2  H19  C05  C04  109.47  3.000
 3D2  H18  C05  C04  109.20  3.000
 3D2  C06  C05  C04  112.28  3.000
 3D2  H21  C06  H20  106.30  3.000
 3D2  H21  C06  C07  109.32  3.000
 3D2  H20  C06  C07  108.95  3.000
 3D2  H21  C06  C05  109.45  3.000
 3D2  H20  C06  C05  109.77  3.000
 3D2  C07  C06  C05  112.84  3.000
 3D2  H23  C07  H22  106.13  3.000
 3D2  H23  C07  N08  108.19  3.000
 3D2  H22  C07  N08  113.41  3.000
 3D2  H23  C07  C06  108.96  3.000
 3D2  H22  C07  C06  108.93  3.000
 3D2  N08  C07  C06  111.04  3.000
 3D2  H25  N08  H24  105.45  3.000
 3D2  H25  N08  C07  109.49  3.000
 3D2  H24  N08  C07  109.08  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
 3D2  CONST_01  C16  C21  N20  C19     0.00   0.0  0
 3D2  CONST_02  C16  C17  C18  C19     0.00   0.0  0
 3D2  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 3D2  CONST_06  C11  C22  C15  C14     0.00   0.0  0
 3D2  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 3D2  CONST_08  N20  C21  C16  C15   180.00   0.0  0
 3D2  CONST_09  C18  C17  C16  C15   180.00   0.0  0
 3D2  CONST_10  C12  C11  C22  C15     0.00   0.0  0
 3D2  CONST_11  C13  C14  C15  C16   180.00   0.0  0
 3D2  CONST_12  C11  C22  C15  C16   180.00   0.0  0
 3D2  CONST_13  N20  C21  C16  C17     0.00   0.0  0
 3D2  CONST_15  N20  C19  C18  C17     0.00   0.0  0
 3D2  CONST_16  C21  N20  C19  C18     0.00   0.0  0
 3D2  CONST_17  C21  C16  C17  C18     0.00   0.0  0
 3D2  CONST_18  C22  C15  C14  C13     0.00   0.0  0
 3D2  CONST_19  C22  C11  C12  C13     0.00   0.0  0
 3D2  CONST_21  C10  C11  C22  C15   180.00   0.0  0
 3D2  CONST_22  C10  C11  C12  C13   180.00   0.0  0
 3D2  CONST_23  H10  C21  N20  C19   180.00   0.0  0
 3D2  CONST_24  H3   C17  C18  C19   180.00   0.0  0
 3D2  CONST_25  H6   C12  C13  C14   180.00   0.0  0
 3D2  CONST_26  H7   C22  C15  C14   180.00   0.0  0
 3D2  CONST_27  H5   C13  C14  C15   180.00   0.0  0
 3D2  CONST_28  H2   C14  C15  C16     0.00   0.0  0
 3D2  CONST_29  H4   C18  C17  C16   180.00   0.0  0
 3D2  CONST_30  H1   C19  C18  C17   180.00   0.0  0
 3D2  CONST_31  H14  N01  C02  C03     0.00   0.0  0
 3D2  CONST_32  H15  N01  C02  C03   180.00   0.0  0
 3D2  Var_01    N09  C10  C11  C12    53.69  30.0  2
 3D2  Var_02    C03  N09  C10  C11  -173.93  30.0  1
 3D2  Var_03    C06  C05  C04  C03   179.13  30.0  2
 3D2  Var_04    C07  C06  C05  C04  -179.87  30.0  1
 3D2  Var_05    N08  C07  C06  C05   179.75  30.0  1
 3D2  Var_06    H24  N08  C07  C06    68.63  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
 3D2  chir_01  C03  C04  N09  C02  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
 3D2  plan-1  C14  0.020
 3D2  plan-1  C15  0.020
 3D2  plan-1  C16  0.020
 3D2  plan-1  C13  0.020
 3D2  plan-1  C12  0.020
 3D2  plan-1  C11  0.020
 3D2  plan-1  C22  0.020
 3D2  plan-1  C10  0.020
 3D2  plan-1  H5   0.020
 3D2  plan-1  H6   0.020
 3D2  plan-1  H7   0.020
 3D2  plan-1  H2   0.020
 3D2  plan-2  C19  0.020
 3D2  plan-2  C15  0.020
 3D2  plan-2  C16  0.020
 3D2  plan-2  C17  0.020
 3D2  plan-2  C18  0.020
 3D2  plan-2  N20  0.020
 3D2  plan-2  C21  0.020
 3D2  plan-2  H1   0.020
 3D2  plan-2  H3   0.020
 3D2  plan-2  H4   0.020
 3D2  plan-2  H10  0.020
 3D2  plan-3  C03  0.020
 3D2  plan-3  C02  0.020
 3D2  plan-3  O23  0.020
 3D2  plan-3  N01  0.020
 3D2  plan-3  H14  0.020
 3D2  plan-3  H15  0.020

