# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:37:41 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-(2-aminoethyl)-N-(2,2'-bipyridin-5-ylacetyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN(CC(O)=O)C(=O)Cc1ccc(nc1)c2ccccn2
#
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
 KPN  KPN  N-(2-aminoethyl)-N-(2,2'-bipyridin-5-ylacetyl)glycine  peptide  41  23  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KPN
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
 KPN  C'    C  C     0   0.552  -4.3580  -1.8667   0.1211
 KPN  C1    C  CR16  0  -0.115   1.1027   0.0998   1.4242
 KPN  N1    N  N     0  -0.431   2.4072   0.2513   1.2606
 KPN  C2    C  CR6   0   0.089   0.2735  -0.5368   0.5092
 KPN  N2    N  N     0  -0.433   5.0062  -0.5060  -1.0898
 KPN  C3    C  CR16  0  -0.181   0.8758  -1.0416  -0.6364
 KPN  C4    C  CR16  0  -0.295   2.2382  -0.8924  -0.8182
 KPN  C5    C  CR6   0   0.195   2.9777  -0.2299   0.1601
 KPN  C6    C  CR6   0   0.199   4.4403  -0.0326   0.0183
 KPN  C7    C  CR16  0  -0.304   5.1776   0.6207   1.0048
 KPN  C8    C  CR16  0  -0.152   6.5409   0.7799   0.8217
 KPN  C9    C  CR16  0  -0.321   7.1276   0.2868  -0.3339
 KPN  N1'   N  NH2   0  -0.800  -5.2422   3.4403  -0.8045
 KPN  O1'   O  O     0  -0.430  -3.9734  -2.1139  -0.9911
 KPN  C10   C  CR16  0  -0.074   6.3106  -0.3487  -1.2578
 KPN  C2'   C  CH2   0  -0.277  -4.3999   2.5863   0.0157
 KPN  C3'   C  CH2   0  -0.323  -4.1279   1.2809  -0.7223
 KPN  N4'   N  NT    0  -0.446  -3.3257   0.3579   0.0659
 KPN  C5'   C  CH2   0  -0.475  -4.0419  -0.5885   0.8736
 KPN  C7'   C  C     0   0.582  -1.9781   0.3789  -0.0478
 KPN  O7'   O  O     0  -0.479  -1.4026   1.1884  -0.7559
 KPN  C8'   C  CH2   0  -0.717  -1.1971  -0.6578   0.7511
 KPN  O3    O  OH1   0  -0.587  -5.1073  -2.6751   0.8543
 KPN  H1    H  HCR6  0   0.257   0.6837   0.5070   2.3396
 KPN  H3    H  HCR6  0   0.264   0.2849  -1.5561  -1.3846
 KPN  H4    H  HCR6  0   0.269   2.7258  -1.2799  -1.7006
 KPN  H7    H  HCR6  0   0.270   4.6878   0.9942   1.8920
 KPN  H8    H  HCR6  0   0.275   7.1360   1.2827   1.5726
 KPN  H9    H  HCR6  0   0.273   8.1879   0.3894  -0.5195
 KPN  HN1'  H  HNH2  0   0.352  -5.5254   4.2506  -0.2696
 KPN  HN1A  H  HNH2  0   0.343  -4.7008   3.8008  -1.5804
 KPN  H10   H  HCR6  0   0.263   6.7300  -0.7486  -2.1742
 KPN  H2'   H  HCH2  0   0.206  -3.4422   3.0404   0.3013
 KPN  H2'A  H  HCH2  0   0.221  -4.9303   2.3673   0.9459
 KPN  H3'   H  HCH2  0   0.251  -5.0748   0.7949  -0.9641
 KPN  H3'A  H  HCH2  0   0.254  -3.6234   1.4817  -1.6675
 KPN  H5'   H  HCH2  0   0.322  -4.9794  -0.1392   1.2094
 KPN  H5'A  H  HCH2  0   0.315  -3.5050  -0.8398   1.7895
 KPN  H8'   H  HCH2  0   0.298  -1.5374  -1.6619   0.4850
 KPN  H8'A  H  HCH2  0   0.302  -1.4081  -0.5387   1.8175
 KPN  H18   H  HOH1  0   0.487  -5.2934  -3.4946   0.3713

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
 KPN  C'   O1'   double    1.202  0.020  1.202
 KPN  C'   C5'   single    1.517  0.020  1.517
 KPN  C'   O3    single    1.324  0.020  1.324
 KPN  C1   N1    aromatic  1.323  0.020  1.323
 KPN  C1   C2    aromatic  1.389  0.020  1.389
 KPN  C1   H1    single    0.930  0.020  1.080
 KPN  N1   C5    aromatic  1.330  0.020  1.330
 KPN  C2   C3    aromatic  1.389  0.020  1.389
 KPN  C2   C8'   single    1.495  0.020  1.495
 KPN  N2   C6    aromatic  1.331  0.020  1.331
 KPN  N2   C10   aromatic  1.325  0.020  1.325
 KPN  C3   C4    aromatic  1.383  0.020  1.383
 KPN  C3   H3    single    0.930  0.020  1.080
 KPN  C4   C5    aromatic  1.394  0.020  1.394
 KPN  C4   H4    single    0.930  0.020  1.080
 KPN  C5   C6    single    1.483  0.020  1.483
 KPN  C6   C7    aromatic  1.394  0.020  1.394
 KPN  C7   C8    aromatic  1.385  0.020  1.385
 KPN  C7   H7    single    0.930  0.020  1.080
 KPN  C8   C9    aromatic  1.387  0.020  1.387
 KPN  C8   H8    single    0.930  0.020  1.080
 KPN  C9   C10   aromatic  1.387  0.020  1.387
 KPN  C9   H9    single    0.930  0.020  1.080
 KPN  N1'  C2'   single    1.453  0.020  1.453
 KPN  N1'  HN1'  single    0.890  0.020  1.040
 KPN  N1'  HN1A  single    0.890  0.020  1.040
 KPN  C10  H10   single    0.930  0.020  1.080
 KPN  C2'  C3'   single    1.524  0.020  1.524
 KPN  C2'  H2'   single    0.970  0.020  1.090
 KPN  C2'  H2'A  single    0.970  0.020  1.090
 KPN  C3'  N4'   single    1.455  0.020  1.455
 KPN  C3'  H3'   single    0.970  0.020  1.090
 KPN  C3'  H3'A  single    0.970  0.020  1.090
 KPN  N4'  C5'   single    1.436  0.020  1.436
 KPN  N4'  C7'   single    1.353  0.020  1.353
 KPN  C5'  H5'   single    0.970  0.020  1.090
 KPN  C5'  H5'A  single    0.970  0.020  1.090
 KPN  C7'  O7'   double    1.220  0.020  1.220
 KPN  C7'  C8'   single    1.524  0.020  1.524
 KPN  C8'  H8'   single    0.970  0.020  1.090
 KPN  C8'  H8'A  single    0.970  0.020  1.090
 KPN  O3   H18   single    0.850  0.020  0.980

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
 KPN  O3    C'   C5'   110.97  3.000
 KPN  O3    C'   O1'   124.59  3.000
 KPN  C5'   C'   O1'   124.44  3.000
 KPN  H1    C1   C2    119.78  3.000
 KPN  H1    C1   N1    116.21  3.000
 KPN  C2    C1   N1    124.01  3.000
 KPN  C5    N1   C1    118.94  3.000
 KPN  C8'   C2   C3    122.03  3.000
 KPN  C8'   C2   C1    121.17  3.000
 KPN  C3    C2   C1    116.80  3.000
 KPN  C10   N2   C6    118.82  3.000
 KPN  H3    C3   C4    119.86  3.000
 KPN  H3    C3   C2    120.37  3.000
 KPN  C4    C3   C2    119.76  3.000
 KPN  H4    C4   C5    120.29  3.000
 KPN  H4    C4   C3    120.90  3.000
 KPN  C5    C4   C3    118.80  3.000
 KPN  C6    C5   C4    121.29  3.000
 KPN  C6    C5   N1    117.02  3.000
 KPN  C4    C5   N1    121.68  3.000
 KPN  C7    C6   C5    121.09  3.000
 KPN  C7    C6   N2    122.06  3.000
 KPN  C5    C6   N2    116.85  3.000
 KPN  H7    C7   C8    121.02  3.000
 KPN  H7    C7   C6    120.23  3.000
 KPN  C8    C7   C6    118.75  3.000
 KPN  H8    C8   C9    120.72  3.000
 KPN  H8    C8   C7    120.21  3.000
 KPN  C9    C8   C7    119.07  3.000
 KPN  H9    C9   C10   120.44  3.000
 KPN  H9    C9   C8    121.62  3.000
 KPN  C10   C9   C8    117.94  3.000
 KPN  HN1A  N1'  HN1'  105.65  3.000
 KPN  HN1A  N1'  C2'   109.38  3.000
 KPN  HN1'  N1'  C2'   109.55  3.000
 KPN  H10   C10  C9    120.26  3.000
 KPN  H10   C10  N2    116.38  3.000
 KPN  C9    C10  N2    123.36  3.000
 KPN  H2'A  C2'  H2'   106.55  3.000
 KPN  H2'A  C2'  C3'   109.10  3.000
 KPN  H2'   C2'  C3'   108.94  3.000
 KPN  H2'A  C2'  N1'   108.47  3.000
 KPN  H2'   C2'  N1'   114.17  3.000
 KPN  C3'   C2'  N1'   109.48  3.000
 KPN  H3'A  C3'  H3'   106.95  3.000
 KPN  H3'A  C3'  N4'   109.36  3.000
 KPN  H3'   C3'  N4'   108.41  3.000
 KPN  H3'A  C3'  C2'   110.17  3.000
 KPN  H3'   C3'  C2'   109.50  3.000
 KPN  N4'   C3'  C2'   112.30  3.000
 KPN  C7'   N4'  C5'   123.68  3.000
 KPN  C7'   N4'  C3'   119.60  3.000
 KPN  C5'   N4'  C3'   116.61  3.000
 KPN  H5'A  C5'  H5'   105.01  3.000
 KPN  H5'A  C5'  N4'   112.25  3.000
 KPN  H5'   C5'  N4'   109.26  3.000
 KPN  H5'A  C5'  C'    108.97  3.000
 KPN  H5'   C5'  C'    108.68  3.000
 KPN  N4'   C5'  C'    112.36  3.000
 KPN  C8'   C7'  O7'   120.93  3.000
 KPN  C8'   C7'  N4'   117.12  3.000
 KPN  O7'   C7'  N4'   121.95  3.000
 KPN  H8'A  C8'  H8'   106.11  3.000
 KPN  H8'A  C8'  C7'   109.77  3.000
 KPN  H8'   C8'  C7'   109.73  3.000
 KPN  H8'A  C8'  C2    109.80  3.000
 KPN  H8'   C8'  C2    109.94  3.000
 KPN  C7'   C8'  C2    111.35  3.000
 KPN  H18   O3   C'    110.43  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
 KPN  CONST_01  C4    C5   N1   C1      0.00   0.0  0
 KPN  CONST_02  C6    C5   N1   C1    180.00   0.0  0
 KPN  CONST_03  C4    C3   C2   C1      0.00   0.0  0
 KPN  CONST_04  C3    C2   C1   N1      0.00   0.0  0
 KPN  CONST_05  C3    C4   C5   N1      0.00   0.0  0
 KPN  CONST_06  N2    C6   C5   N1    180.00   0.0  0
 KPN  CONST_07  C7    C6   C5   N1      0.00   0.0  0
 KPN  CONST_08  C5    N1   C1   C2      0.00   0.0  0
 KPN  CONST_09  C5    C4   C3   C2      0.00   0.0  0
 KPN  CONST_10  C4    C5   C6   N2      0.00   0.0  0
 KPN  CONST_11  C8    C7   C6   N2      0.00   0.0  0
 KPN  CONST_12  C8    C9   C10  N2      0.00   0.0  0
 KPN  CONST_13  C6    C5   C4   C3    180.00   0.0  0
 KPN  CONST_14  C7    C6   C5   C4    180.00   0.0  0
 KPN  CONST_15  C10   N2   C6   C5    180.00   0.0  0
 KPN  CONST_16  C8    C7   C6   C5    180.00   0.0  0
 KPN  CONST_17  C9    C10  N2   C6      0.00   0.0  0
 KPN  CONST_18  C9    C8   C7   C6      0.00   0.0  0
 KPN  CONST_19  C10   N2   C6   C7      0.00   0.0  0
 KPN  CONST_20  C10   C9   C8   C7      0.00   0.0  0
 KPN  CONST_21  C8'   C2   C1   N1    180.00   0.0  0
 KPN  CONST_22  C8'   C2   C3   C4    180.00   0.0  0
 KPN  CONST_23  H3    C3   C2   C1    180.00   0.0  0
 KPN  CONST_24  H4    C4   C5   N1    180.00   0.0  0
 KPN  CONST_25  H7    C7   C6   N2    180.00   0.0  0
 KPN  CONST_26  H9    C9   C10  N2    180.00   0.0  0
 KPN  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 KPN  CONST_28  H10   C10  N2   C6    180.00   0.0  0
 KPN  CONST_29  H8    C8   C7   C6    180.00   0.0  0
 KPN  CONST_30  O7'   C7'  N4'  C3'     0.00   0.0  0
 KPN  CONST_31  C8'   C7'  N4'  C3'   180.00   0.0  0
 KPN  CONST_32  O7'   C7'  N4'  C5'   180.00   0.0  0
 KPN  CONST_33  C8'   C7'  N4'  C5'     0.00   0.0  0
 KPN  CONST_34  H18   O3   C'   O1'     0.00   0.0  0
 KPN  Var_01    C7'   C8'  C2   C1    100.92  30.0  2
 KPN  Var_02    N4'   C7'  C8'  C2    178.83  30.0  1
 KPN  Var_03    C3'   N4'  C5'  C'     88.65  30.0  2
 KPN  Var_04    N4'   C3'  C2'  N1'  -177.99  30.0  3
 KPN  Var_05    N4'   C5'  C'   O1'     5.23  30.0  3
 KPN  Var_06    C5'   N4'  C3'  C2'    92.30  30.0  3
 KPN  Var_07    HN1'  N1'  C2'  C3'   172.46  30.0  3

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
 KPN  plan-1  C1   0.020
 KPN  plan-1  N1   0.020
 KPN  plan-1  C2   0.020
 KPN  plan-1  C3   0.020
 KPN  plan-1  C4   0.020
 KPN  plan-1  C5   0.020
 KPN  plan-1  C6   0.020
 KPN  plan-1  C8'  0.020
 KPN  plan-1  H1   0.020
 KPN  plan-1  H3   0.020
 KPN  plan-1  H4   0.020
 KPN  plan-2  N2   0.020
 KPN  plan-2  C5   0.020
 KPN  plan-2  C6   0.020
 KPN  plan-2  C7   0.020
 KPN  plan-2  C8   0.020
 KPN  plan-2  C9   0.020
 KPN  plan-2  C10  0.020
 KPN  plan-2  H7   0.020
 KPN  plan-2  H8   0.020
 KPN  plan-2  H9   0.020
 KPN  plan-2  H10  0.020
 KPN  plan-3  C3'  0.020
 KPN  plan-3  N4'  0.020
 KPN  plan-3  C5'  0.020
 KPN  plan-3  C7'  0.020
 KPN  plan-3  O7'  0.020
 KPN  plan-3  C8'  0.020
 KPN  plan-4  C'   0.020
 KPN  plan-4  O1'  0.020
 KPN  plan-4  C5'  0.020
 KPN  plan-4  O3   0.020
 KPN  plan-4  H18  0.020

