# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 01:13:10 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: N-[(1R)-2-[(1-{[(6-carbamimidoylpyridin-3-yl)methyl]carbamoyl}cyclopentyl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)C2(CCCC2)NC(=O)[C@@H](CC3CCCCC3)NCC(O)=O)cn1
#
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
 N12  N12  N-[(1R)-2-[(1-{[(6-carbamimidoylpyridin-3-yl)methyl]carbamoyl}cyclopentyl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]glycine  ligand  70  34  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N12
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
 N12  C1    C  C     0   0.524   0.0195  -6.9686   -0.5147
 N12  C2    C  CH2   0  -0.393   1.3106  -6.5790   -1.1890
 N12  N3    N  NH1   0  -0.573   1.0804  -6.1134   -2.5319
 N12  C4    C  CH1   0  -0.219   2.2673  -5.6065   -3.1821
 N12  C5    C  C     0   0.554   3.3388  -6.6841   -3.3517
 N12  C6    C  CH2   0  -0.423   1.9241  -5.0765   -4.5769
 N12  C7    C  CH1   0  -0.214   0.8992  -3.9470   -4.6091
 N12  C8    C  CH2   0  -0.427   1.4159  -2.6732   -3.9407
 N12  C9    C  CH2   0  -0.427   0.4003  -1.5368   -4.0227
 N12  C10   C  CH2   0  -0.430  -0.0057  -1.2519   -5.4652
 N12  C11   C  CH2   0  -0.430  -0.5198  -2.5167   -6.1461
 N12  C12   C  CH2   0  -0.412   0.4995  -3.6463   -6.0539
 N12  O13   O  O     0  -0.485   3.0681  -7.7782   -3.8262
 N12  N14   N  NH1   0  -0.681   4.5879  -6.3457   -2.9905
 N12  C15   C  CR5   0   0.058   5.7108  -7.2511   -3.1583
 N12  C16   C  C     0   0.562   5.8833  -7.6088   -4.6423
 N12  O17   O  O     0  -0.481   6.2747  -8.7082   -4.9981
 N12  N18   N  NH1   0  -0.620   5.6677  -6.5868   -5.4881
 N12  C19   C  CH2   0  -0.367   5.7710  -6.6723   -6.9256
 N12  C20   C  CR6   0   0.017   4.4683  -6.2992   -7.5775
 N12  C21   C  CR16  0  -0.159   3.3171  -7.0541   -7.3957
 N12  C22   C  CR16  0  -0.300   2.1364  -6.6502   -7.9941
 N12  C23   C  CR6   0   0.163   2.1351  -5.4815   -8.7489
 N12  N24   N  N     0  -0.427   3.2288  -4.7480   -8.9144
 N12  C25   C  CR16  0  -0.107   4.3566  -5.1491   -8.3502
 N12  O26   O  O     0  -0.437  -1.0590  -6.9985   -1.0481
 N12  O27   O  OH1   0  -0.595   0.2233  -7.2981    0.7556
 N12  C28   C  C     0   0.354   0.8924  -4.9407   -9.3873
 N12  N29   N  N     0  -0.630   0.7478  -3.7145   -9.7022
 N12  N30   N  NH2   0  -0.818  -0.1168  -5.8419   -9.5596
 N12  C31   C  CH2   0  -0.439   5.5943  -8.5132   -2.2684
 N12  C32   C  CH2   0  -0.486   7.0194  -6.5526   -2.6837
 N12  C33   C  CH2   0  -0.444   6.9510  -8.6607   -1.5847
 N12  C34   C  CH2   0  -0.441   7.3775  -7.2162   -1.3574
 N12  H21A  H  HCH2  0   0.278   1.7722  -5.7781   -0.6032
 N12  H22A  H  HCH2  0   0.250   1.9946  -7.4389   -1.1056
 N12  HN3   H  HNH1  0   0.349   0.6745  -6.8499   -3.0976
 N12  H4    H  HCH1  0   0.255   2.6662  -4.7907   -2.5682
 N12  H61   H  HCH2  0   0.223   2.8453  -4.7376   -5.0637
 N12  H62   H  HCH2  0   0.239   1.5589  -5.9154   -5.1771
 N12  H7    H  HCH1  0   0.214   0.0056  -4.2804   -4.0685
 N12  H81   H  HCH2  0   0.203   2.3474  -2.3714   -4.4359
 N12  H82   H  HCH2  0   0.227   1.6689  -2.8626   -2.8941
 N12  H91   H  HCH2  0   0.224   0.8064  -0.6357   -3.5562
 N12  H92   H  HCH2  0   0.207  -0.4895  -1.8108   -3.4451
 N12  H101  H  HCH2  0   0.223  -0.7648  -0.4662   -5.4980
 N12  H102  H  HCH2  0   0.206   0.8601  -0.8707   -6.0180
 N12  H111  H  HCH2  0   0.205  -1.4548  -2.8292   -5.6682
 N12  H112  H  HCH2  0   0.223  -0.7551  -2.3190   -7.1951
 N12  H121  H  HCH2  0   0.221   0.1047  -4.5485   -6.5286
 N12  H122  H  HCH2  0   0.200   1.3943  -3.3670   -6.6235
 N12  HN14  H  HNH1  0   0.405   4.7457  -5.4520   -2.5513
 N12  HN18  H  HNH1  0   0.399   5.3523  -5.7087   -5.1073
 N12  H191  H  HCH2  0   0.275   6.0532  -7.6909   -7.1883
 N12  H192  H  HCH2  0   0.268   6.5666  -6.0156   -7.2852
 N12  H21   H  HCR6  0   0.272   3.3334  -7.9416   -6.7754
 N12  H22   H  HCR6  0   0.276   1.2310  -7.2207   -7.8421
 N12  H25   H  HCR6  0   0.266   5.2273  -4.5209   -8.5125
 N12  HO27  H  HOH1  0   0.483  -0.6119  -7.5626    1.1690
 N12  HN29  H  H     0   0.330   1.5766  -3.1972   -9.4292
 N12  H301  H  HNH2  0   0.385  -0.9026  -5.5162  -10.1002
 N12  H302  H  HNH2  0   0.392   0.1282  -6.8003   -9.7461
 N12  H311  H  HCH2  0   0.248   5.2930  -9.3969   -2.8258
 N12  H312  H  HCH2  0   0.237   4.8291  -8.3293   -1.5119
 N12  H321  H  HCH2  0   0.258   6.9048  -5.4688   -2.6224
 N12  H322  H  HCH2  0   0.259   7.8205  -6.7346   -3.4031
 N12  H331  H  HCH2  0   0.225   7.6608  -9.1602   -2.2496
 N12  H332  H  HCH2  0   0.236   6.8920  -9.2476   -0.6671
 N12  H341  H  HCH2  0   0.227   6.7996  -6.7785   -0.5390
 N12  H342  H  HCH2  0   0.242   8.4339  -7.1030   -1.1120

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
 N12  C1   O26   double    1.204  0.020  1.204
 N12  C1   C2    single    1.508  0.020  1.508
 N12  C1   O27   single    1.328  0.020  1.328
 N12  C2   N3    single    1.440  0.020  1.440
 N12  C2   H21A  single    0.970  0.020  1.090
 N12  C2   H22A  single    0.970  0.020  1.090
 N12  N3   C4    single    1.445  0.020  1.445
 N12  N3   HN3   single    0.890  0.020  1.040
 N12  C4   C5    single    1.529  0.020  1.529
 N12  C4   C6    single    1.531  0.020  1.531
 N12  C4   H4    single    0.970  0.020  1.090
 N12  C5   N14   single    1.344  0.020  1.344
 N12  C5   O13   double    1.223  0.020  1.223
 N12  C6   C7    single    1.525  0.020  1.525
 N12  C6   H61   single    0.970  0.020  1.090
 N12  C6   H62   single    0.970  0.020  1.090
 N12  C7   C12   single    1.529  0.020  1.529
 N12  C7   C8    single    1.528  0.020  1.528
 N12  C7   H7    single    0.970  0.020  1.090
 N12  C8   C9    single    1.526  0.020  1.526
 N12  C8   H81   single    0.970  0.020  1.090
 N12  C8   H82   single    0.970  0.020  1.090
 N12  C9   C10   single    1.525  0.020  1.525
 N12  C9   H91   single    0.970  0.020  1.090
 N12  C9   H92   single    0.970  0.020  1.090
 N12  C10  C11   single    1.526  0.020  1.526
 N12  C10  H101  single    0.970  0.020  1.090
 N12  C10  H102  single    0.970  0.020  1.090
 N12  C11  C12   single    1.524  0.020  1.524
 N12  C11  H111  single    0.970  0.020  1.090
 N12  C11  H112  single    0.970  0.020  1.090
 N12  C12  H121  single    0.970  0.020  1.090
 N12  C12  H122  single    0.970  0.020  1.090
 N12  N14  C15   single    1.452  0.020  1.452
 N12  N14  HN14  single    0.860  0.020  1.020
 N12  C15  C31   single    1.549  0.020  1.549
 N12  C15  C16   single    1.536  0.020  1.536
 N12  C15  C32   single    1.557  0.020  1.557
 N12  C16  O17   double    1.220  0.020  1.220
 N12  C16  N18   single    1.344  0.020  1.344
 N12  N18  C19   single    1.444  0.020  1.444
 N12  N18  HN18  single    0.860  0.020  1.020
 N12  C19  C20   single    1.504  0.020  1.504
 N12  C19  H191  single    0.970  0.020  1.090
 N12  C19  H192  single    0.970  0.020  1.090
 N12  C20  C21   aromatic  1.389  0.020  1.389
 N12  C20  C25   aromatic  1.390  0.020  1.390
 N12  C21  C22   aromatic  1.384  0.020  1.384
 N12  C21  H21   single    0.930  0.020  1.080
 N12  C22  C23   aromatic  1.391  0.020  1.391
 N12  C22  H22   single    0.930  0.020  1.080
 N12  C23  N24   aromatic  1.327  0.020  1.327
 N12  C23  C28   single    1.498  0.020  1.498
 N12  N24  C25   aromatic  1.323  0.020  1.323
 N12  C25  H25   single    0.930  0.020  1.080
 N12  O27  HO27  single    0.850  0.020  0.980
 N12  C28  N30   single    1.364  0.020  1.364
 N12  C28  N29   double    1.274  0.020  1.274
 N12  N29  HN29  single    0.890  0.020  1.040
 N12  N30  H301  single    0.890  0.020  1.040
 N12  N30  H302  single    0.890  0.020  1.040
 N12  C31  C33   single    1.526  0.020  1.526
 N12  C31  H311  single    0.970  0.020  1.090
 N12  C31  H312  single    0.970  0.020  1.090
 N12  C32  C34   single    1.526  0.020  1.526
 N12  C32  H321  single    0.970  0.020  1.090
 N12  C32  H322  single    0.970  0.020  1.090
 N12  C33  C34   single    1.523  0.020  1.523
 N12  C33  H331  single    0.970  0.020  1.090
 N12  C33  H332  single    0.970  0.020  1.090
 N12  C34  H341  single    0.970  0.020  1.090
 N12  C34  H342  single    0.970  0.020  1.090

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
 N12  O27   C1   O26   123.73  3.000
 N12  O27   C1   C2    111.13  3.000
 N12  O26   C1   C2    125.14  3.000
 N12  H22A  C2   H21A  105.59  3.000
 N12  H22A  C2   N3    114.97  3.000
 N12  H21A  C2   N3    109.27  3.000
 N12  H22A  C2   C1    107.22  3.000
 N12  H21A  C2   C1    108.11  3.000
 N12  N3    C2   C1    111.33  3.000
 N12  HN3   N3   C4    109.43  3.000
 N12  HN3   N3   C2    110.47  3.000
 N12  C4    N3   C2    113.69  3.000
 N12  H4    C4   C6    109.52  3.000
 N12  H4    C4   C5    109.37  3.000
 N12  C6    C4   C5    107.46  3.000
 N12  H4    C4   N3    107.93  3.000
 N12  C6    C4   N3    110.32  3.000
 N12  C5    C4   N3    112.22  3.000
 N12  N14   C5   O13   122.37  3.000
 N12  O13   C5   C4    121.23  3.000
 N12  N14   C5   C4    116.37  3.000
 N12  H62   C6   H61   105.90  3.000
 N12  H62   C6   C7    109.38  3.000
 N12  H61   C6   C7    109.06  3.000
 N12  H62   C6   C4    108.00  3.000
 N12  H61   C6   C4    108.86  3.000
 N12  C7    C6   C4    115.23  3.000
 N12  H7    C7   C12   108.22  3.000
 N12  H7    C7   C8    108.26  3.000
 N12  C12   C7   C8    109.74  3.000
 N12  H7    C7   C6    108.18  3.000
 N12  C8    C7   C6    112.38  3.000
 N12  C12   C7   C6    109.95  3.000
 N12  H82   C8   H81   106.45  3.000
 N12  H82   C8   C9    109.54  3.000
 N12  H81   C8   C9    109.63  3.000
 N12  H82   C8   C7    110.64  3.000
 N12  H81   C8   C7    108.59  3.000
 N12  C9    C8   C7    111.85  3.000
 N12  H92   C9   H91   106.43  3.000
 N12  H92   C9   C10   109.21  3.000
 N12  H91   C9   C10   110.40  3.000
 N12  H92   C9   C8    109.02  3.000
 N12  H91   C9   C8    110.11  3.000
 N12  C10   C9   C8    111.53  3.000
 N12  H102  C10  H101  106.47  3.000
 N12  H102  C10  C11   109.24  3.000
 N12  H101  C10  C11   110.40  3.000
 N12  H102  C10  C9    109.37  3.000
 N12  H101  C10  C9    110.33  3.000
 N12  C11   C10  C9    110.92  3.000
 N12  H112  C11  H111  106.65  3.000
 N12  H112  C11  C12   109.64  3.000
 N12  H111  C11  C12   109.44  3.000
 N12  H112  C11  C10   110.55  3.000
 N12  H111  C11  C10   109.23  3.000
 N12  C12   C11  C10   111.22  3.000
 N12  H122  C12  H121  106.21  3.000
 N12  H122  C12  C11   108.99  3.000
 N12  H121  C12  C11   110.11  3.000
 N12  H122  C12  C7    109.12  3.000
 N12  H121  C12  C7    110.03  3.000
 N12  C11   C12  C7    112.20  3.000
 N12  HN14  N14  C15   118.82  3.000
 N12  HN14  N14  C5    119.07  3.000
 N12  C15   N14  C5    122.05  3.000
 N12  C32   C15  C31   104.69  3.000
 N12  C32   C15  C16   107.72  3.000
 N12  C31   C15  C16   111.95  3.000
 N12  C32   C15  N14   109.56  3.000
 N12  C16   C15  N14   110.10  3.000
 N12  C31   C15  N14   112.55  3.000
 N12  N18   C16  O17   123.58  3.000
 N12  N18   C16  C15   114.38  3.000
 N12  O17   C16  C15   121.84  3.000
 N12  HN18  N18  C19   116.76  3.000
 N12  HN18  N18  C16   118.36  3.000
 N12  C19   N18  C16   124.76  3.000
 N12  H192  C19  H191  107.11  3.000
 N12  H192  C19  C20   109.81  3.000
 N12  H191  C19  C20   110.60  3.000
 N12  H192  C19  N18   110.14  3.000
 N12  H191  C19  N18   108.31  3.000
 N12  C20   C19  N18   110.79  3.000
 N12  C25   C20  C21   117.12  3.000
 N12  C25   C20  C19   121.05  3.000
 N12  C21   C20  C19   121.78  3.000
 N12  H21   C21  C22   119.98  3.000
 N12  H21   C21  C20   120.53  3.000
 N12  C22   C21  C20   119.48  3.000
 N12  H22   C22  C23   121.26  3.000
 N12  H22   C22  C21   119.99  3.000
 N12  C23   C22  C21   118.72  3.000
 N12  C28   C23  N24   115.52  3.000
 N12  C28   C23  C22   122.36  3.000
 N12  N24   C23  C22   122.08  3.000
 N12  C25   N24  C23   118.79  3.000
 N12  H25   C25  N24   116.38  3.000
 N12  H25   C25  C20   119.82  3.000
 N12  N24   C25  C20   123.79  3.000
 N12  HO27  O27  C1    110.10  3.000
 N12  N30   C28  N29   121.38  3.000
 N12  N29   C28  C23   123.15  3.000
 N12  N30   C28  C23   115.40  3.000
 N12  HN29  N29  C28   109.36  3.000
 N12  H302  N30  H301  113.45  3.000
 N12  H302  N30  C28   118.20  3.000
 N12  H301  N30  C28   115.54  3.000
 N12  H312  C31  H311  107.34  3.000
 N12  H312  C31  C33   109.20  3.000
 N12  H311  C31  C33   113.41  3.000
 N12  H312  C31  C15   108.28  3.000
 N12  H311  C31  C15   112.87  3.000
 N12  C33   C31  C15   105.62  3.000
 N12  H322  C32  H321  106.23  3.000
 N12  H322  C32  C34   109.15  3.000
 N12  H321  C32  C34   114.05  3.000
 N12  H322  C32  C15   109.93  3.000
 N12  H321  C32  C15   111.98  3.000
 N12  C34   C32  C15   105.49  3.000
 N12  H332  C33  H331  107.51  3.000
 N12  H332  C33  C34   113.57  3.000
 N12  H331  C33  C34   110.01  3.000
 N12  H332  C33  C31   112.38  3.000
 N12  H331  C33  C31   110.41  3.000
 N12  C34   C33  C31   102.95  3.000
 N12  H342  C34  H341  107.58  3.000
 N12  H342  C34  C33   113.78  3.000
 N12  H341  C34  C33   110.08  3.000
 N12  H342  C34  C32   112.21  3.000
 N12  H341  C34  C32   110.64  3.000
 N12  C33   C34  C32   102.54  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
 N12  CONST_01  C23   C22  C21  C20    0.00   0.0  0
 N12  CONST_02  C23   N24  C25  C20    0.00   0.0  0
 N12  CONST_03  N24   C25  C20  C21    0.00   0.0  0
 N12  CONST_04  N24   C23  C22  C21    0.00   0.0  0
 N12  CONST_05  C25   C20  C21  C22    0.00   0.0  0
 N12  CONST_06  C25   N24  C23  C22    0.00   0.0  0
 N12  CONST_07  C22   C21  C20  C19  180.00   0.0  0
 N12  CONST_08  N24   C25  C20  C19  180.00   0.0  0
 N12  CONST_09  C28   C23  C22  C21  180.00   0.0  0
 N12  CONST_10  C28   C23  N24  C25  180.00   0.0  0
 N12  CONST_11  H22   C22  C21  C20  180.00   0.0  0
 N12  CONST_12  H25   C25  C20  C21  180.00   0.0  0
 N12  CONST_13  H21   C21  C22  C23  180.00   0.0  0
 N12  CONST_14  C15   N14  C5   C4   180.00   0.0  0
 N12  CONST_15  C15   N14  C5   O13    0.00   0.0  0
 N12  CONST_16  C19   N18  C16  C15  180.00   0.0  0
 N12  CONST_17  HN18  N18  C16  C15    0.00   0.0  0
 N12  CONST_18  H301  N30  C28  C23  180.00   0.0  0
 N12  CONST_20  HN29  N29  C28  C23    0.00   0.0  0
 N12  CONST_21  C19   N18  C16  O17    0.00   0.0  0
 N12  CONST_22  HN14  N14  C5   C4     0.00   0.0  0
 N12  CONST_23  HO27  O27  C1   C2   180.00   0.0  0
 N12  Var_01    C10   C11  C12  C7    55.92  30.0  1
 N12  Var_02    C10   C9   C8   C7   -55.87  30.0  1
 N12  Var_03    C11   C10  C9   C8    54.87  30.0  1
 N12  Var_04    C12   C11  C10  C9   -54.72  30.0  1
 N12  Var_05    C34   C33  C31  C15   35.03  30.0  1
 N12  Var_06    C33   C34  C32  C15   35.69  30.0  1
 N12  Var_07    C32   C34  C33  C31  -43.62  30.0  1
 N12  Var_08    C21   C20  C19  N18  -64.32  30.0  2
 N12  Var_09    N30   C28  C23  C22  -20.33  30.0  2
 N12  Var_10    C20   C19  N18  C16  121.22  30.0  3
 N12  Var_11    C4    N3   C2   C1   174.42  30.0  3
 N12  Var_12    O26   C1   C2   N3     5.75  30.0  2

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
 N12  chir_01  C4   N3   C5   C6   negativ
 N12  chir_02  C7   C6   C12  C8   positiv
 N12  chir_03  C15  C31  C16  C32  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
 N12  plan-1  C4    0.020
 N12  plan-1  C5    0.020
 N12  plan-1  O13   0.020
 N12  plan-1  N14   0.020
 N12  plan-1  C15   0.020
 N12  plan-1  HN14  0.020
 N12  plan-2  C19   0.020
 N12  plan-2  C20   0.020
 N12  plan-2  C21   0.020
 N12  plan-2  C22   0.020
 N12  plan-2  C23   0.020
 N12  plan-2  N24   0.020
 N12  plan-2  C25   0.020
 N12  plan-2  C28   0.020
 N12  plan-2  H21   0.020
 N12  plan-2  H22   0.020
 N12  plan-2  H25   0.020
 N12  plan-3  C15   0.020
 N12  plan-3  C16   0.020
 N12  plan-3  O17   0.020
 N12  plan-3  N18   0.020
 N12  plan-3  C19   0.020
 N12  plan-3  HN18  0.020
 N12  plan-4  C23   0.020
 N12  plan-4  C28   0.020
 N12  plan-4  N29   0.020
 N12  plan-4  N30   0.020
 N12  plan-4  HN29  0.020
 N12  plan-4  H301  0.020
 N12  plan-4  H302  0.020
 N12  plan-5  C1    0.020
 N12  plan-5  C2    0.020
 N12  plan-5  O26   0.020
 N12  plan-5  O27   0.020
 N12  plan-5  HO27  0.020

