# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:14:55 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  69  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   0.392   0.1095  -7.2387   -0.5250
 N12  C2    C  CH2    0  -0.412   1.3303  -6.5245   -1.1330
 N12  N3    N  NH1    0  -0.578   1.0948  -6.0700   -2.4856
 N12  C4    C  CH1    0  -0.202   2.2662  -5.5892   -3.1725
 N12  C5    C  C      0   0.553   3.3322  -6.6726   -3.3426
 N12  C6    C  CH2    0  -0.420   1.9070  -5.0815   -4.5723
 N12  C7    C  CH1    0  -0.212   0.8760  -3.9581   -4.6120
 N12  C8    C  CH2    0  -0.427   1.3826  -2.6776   -3.9489
 N12  C9    C  CH2    0  -0.427   0.3596  -1.5483   -4.0370
 N12  C10   C  CH2    0  -0.429  -0.0474  -1.2728   -5.4810
 N12  C11   C  CH2    0  -0.429  -0.5517  -2.5443   -6.1567
 N12  C12   C  CH2    0  -0.410   0.4757  -3.6660   -6.0582
 N12  O13   O  O      0  -0.489   3.0650  -7.7631   -3.8279
 N12  N14   N  NH1    0  -0.682   4.5827  -6.3429   -2.9721
 N12  C15   C  CR5    0   0.059   5.7017  -7.2522   -3.1383
 N12  C16   C  C      0   0.561   5.8839  -7.5980   -4.6237
 N12  O17   O  O      0  -0.482   6.2780  -8.6941   -4.9872
 N12  N18   N  NH1    0  -0.619   5.6759  -6.5675   -5.4613
 N12  C19   C  CH2    0  -0.367   5.7865  -6.6389   -6.8986
 N12  C20   C  CR6    0   0.018   4.4825  -6.2795   -7.5557
 N12  C21   C  CR16   0  -0.158   3.3375  -7.0446   -7.3769
 N12  C22   C  CR16   0  -0.299   2.1561  -6.6543   -7.9829
 N12  C23   C  CR6    0   0.163   2.1474  -5.4884   -8.7417
 N12  N24   N  N      0  -0.427   3.2346  -4.7444   -8.9035
 N12  C25   C  CR16   0  -0.108   4.3633  -5.1327   -8.3323
 N12  O26   O  O      0  -0.607  -0.7491  -7.6712   -1.3177
 N12  O27   O  OC    -1  -0.623   0.1122  -7.3575    0.7160
 N12  C28   C  C      0   0.354   0.9032  -4.9623   -9.3894
 N12  N29   N  N      0  -0.631   0.7480  -3.7386   -9.7093
 N12  N30   N  NH2    0  -0.818  -0.0955  -5.8746   -9.5654
 N12  C31   C  CH2    0  -0.440   5.5741  -8.5205   -2.2582
 N12  C32   C  CH2    0  -0.485   7.0094  -6.5624   -2.6496
 N12  C33   C  CH2    0  -0.444   6.9205  -8.6708   -1.5543
 N12  C34   C  CH2    0  -0.441   7.3468  -7.2274   -1.3187
 N12  H21A  H  HCH2   0   0.218   1.6006  -5.6683   -0.5077
 N12  H22A  H  HCH2   0   0.197   2.1768  -7.2305   -1.0474
 N12  HN3   H  HNH1   0   0.330   0.6502  -6.8101   -3.0147
 N12  H4    H  HCH1   0   0.240   2.6878  -4.7635   -2.5865
 N12  H61   H  HCH2   0   0.217   2.8209  -4.7447   -5.0750
 N12  H62   H  HCH2   0   0.234   1.5392  -5.9296   -5.1578
 N12  H7    H  HCH1   0   0.209  -0.0159  -4.2948   -4.0706
 N12  H81   H  HCH2   0   0.201   2.3128  -2.3717   -4.4443
 N12  H82   H  HCH2   0   0.227   1.6358  -2.8614   -2.9013
 N12  H91   H  HCH2   0   0.223   0.7587  -0.6422   -3.5742
 N12  H92   H  HCH2   0   0.207  -0.5289  -1.8258   -3.4590
 N12  H101  H  HCH2   0   0.223  -0.8121  -0.4926   -5.5180
 N12  H102  H  HCH2   0   0.205   0.8161  -0.8878   -6.0350
 N12  H111  H  HCH2   0   0.204  -1.4847  -2.8615   -5.6778
 N12  H112  H  HCH2   0   0.222  -0.7880  -2.3531   -7.2067
 N12  H121  H  HCH2   0   0.220   0.0887  -4.5731   -6.5302
 N12  H122  H  HCH2   0   0.199   1.3693  -3.3826   -6.6279
 N12  HN14  H  HNH1   0   0.402   4.7410  -5.4562   -2.5198
 N12  HN18  H  HNH1   0   0.399   5.3494  -5.6963   -5.0737
 N12  H191  H  HCH2   0   0.274   6.0857  -7.6508   -7.1687
 N12  H192  H  HCH2   0   0.268   6.5741  -5.9673   -7.2483
 N12  H21   H  HCR6   0   0.272   3.3586  -7.9292   -6.7528
 N12  H22   H  HCR6   0   0.276   1.2555  -7.2333   -7.8339
 N12  H25   H  HCR6   0   0.265   5.2285  -4.4963   -8.4922
 N12  HN29  H  H      0   0.330   1.5700  -3.2124   -9.4330
 N12  H301  H  HNH2   0   0.385  -0.8806  -5.5590  -10.1130
 N12  H302  H  HNH2   0   0.392   0.1612  -6.8308   -9.7466
 N12  H311  H  HCH2   0   0.247   5.2843  -9.4012   -2.8263
 N12  H312  H  HCH2   0   0.238   4.7961  -8.3434   -1.5132
 N12  H321  H  HCH2   0   0.257   6.9018  -5.4777   -2.5913
 N12  H322  H  HCH2   0   0.258   7.8178  -6.7517   -3.3590
 N12  H331  H  HCH2   0   0.224   7.6394  -9.1700   -2.2096
 N12  H332  H  HCH2   0   0.236   6.8472  -9.2589   -0.6385
 N12  H341  H  HCH2   0   0.227   6.7577  -6.7891   -0.5085
 N12  H342  H  HCH2   0   0.241   8.3997  -7.1168   -1.0572

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   deloc     1.246  0.020  1.246
 N12  C1   C2    single    1.540  0.020  1.540
 N12  C1   O27   deloc     1.247  0.020  1.247
 N12  C2   N3    single    1.446  0.020  1.446
 N12  C2   H21A  single    0.970  0.020  1.090
 N12  C2   H22A  single    0.970  0.020  1.090
 N12  N3   C4    single    1.441  0.020  1.441
 N12  N3   HN3   single    0.890  0.020  1.040
 N12  C4   C5    single    1.529  0.020  1.529
 N12  C4   C6    single    1.532  0.020  1.532
 N12  C4   H4    single    0.970  0.020  1.090
 N12  C5   N14   single    1.345  0.020  1.345
 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    1.451  0.020  1.451
 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    1.443  0.020  1.443
 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  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    1.527  0.020  1.527
 N12  C31  H311  single    0.970  0.020  1.090
 N12  C31  H312  single    0.970  0.020  1.090
 N12  C32  C34   single    1.525  0.020  1.525
 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   126.99  3.000
 N12  O27   C1   C2    115.82  3.000
 N12  O26   C1   C2    117.14  3.000
 N12  H22A  C2   H21A  105.45  3.000
 N12  H22A  C2   N3    113.44  3.000
 N12  H21A  C2   N3    109.20  3.000
 N12  H22A  C2   C1    106.28  3.000
 N12  H21A  C2   C1    109.46  3.000
 N12  N3    C2   C1    112.71  3.000
 N12  HN3   N3   C4    110.60  3.000
 N12  HN3   N3   C2    109.30  3.000
 N12  C4    N3   C2    114.74  3.000
 N12  H4    C4   C6    109.20  3.000
 N12  H4    C4   C5    108.96  3.000
 N12  C6    C4   C5    107.25  3.000
 N12  H4    C4   N3    108.00  3.000
 N12  C6    C4   N3    110.84  3.000
 N12  C5    C4   N3    112.54  3.000
 N12  N14   C5   O13   122.06  3.000
 N12  O13   C5   C4    121.56  3.000
 N12  N14   C5   C4    116.34  3.000
 N12  H62   C6   H61   105.84  3.000
 N12  H62   C6   C7    109.25  3.000
 N12  H61   C6   C7    108.98  3.000
 N12  H62   C6   C4    108.12  3.000
 N12  H61   C6   C4    109.00  3.000
 N12  C7    C6   C4    115.24  3.000
 N12  H7    C7   C12   108.22  3.000
 N12  H7    C7   C8    108.22  3.000
 N12  C12   C7   C8    109.71  3.000
 N12  H7    C7   C6    108.11  3.000
 N12  C8    C7   C6    112.44  3.000
 N12  C12   C7   C6    110.02  3.000
 N12  H82   C8   H81   106.45  3.000
 N12  H82   C8   C9    109.57  3.000
 N12  H81   C8   C9    109.62  3.000
 N12  H82   C8   C7    110.59  3.000
 N12  H81   C8   C7    108.58  3.000
 N12  C9    C8   C7    111.88  3.000
 N12  H92   C9   H91   106.42  3.000
 N12  H92   C9   C10   109.19  3.000
 N12  H91   C9   C10   110.40  3.000
 N12  H92   C9   C8    109.01  3.000
 N12  H91   C9   C8    110.14  3.000
 N12  C10   C9   C8    111.54  3.000
 N12  H102  C10  H101  106.47  3.000
 N12  H102  C10  C11   109.23  3.000
 N12  H101  C10  C11   110.40  3.000
 N12  H102  C10  C9    109.37  3.000
 N12  H101  C10  C9    110.34  3.000
 N12  C11   C10  C9    110.91  3.000
 N12  H112  C11  H111  106.64  3.000
 N12  H112  C11  C12   109.66  3.000
 N12  H111  C11  C12   109.43  3.000
 N12  H112  C11  C10   110.55  3.000
 N12  H111  C11  C10   109.22  3.000
 N12  C12   C11  C10   111.22  3.000
 N12  H122  C12  H121  106.17  3.000
 N12  H122  C12  C11   108.99  3.000
 N12  H121  C12  C11   110.13  3.000
 N12  H122  C12  C7    109.10  3.000
 N12  H121  C12  C7    110.03  3.000
 N12  C11   C12  C7    112.22  3.000
 N12  HN14  N14  C15   118.78  3.000
 N12  HN14  N14  C5    119.03  3.000
 N12  C15   N14  C5    122.11  3.000
 N12  C32   C15  C31   104.68  3.000
 N12  C32   C15  C16   107.67  3.000
 N12  C31   C15  C16   112.02  3.000
 N12  C32   C15  N14   109.51  3.000
 N12  C16   C15  N14   110.07  3.000
 N12  C31   C15  N14   112.61  3.000
 N12  N18   C16  O17   123.58  3.000
 N12  N18   C16  C15   114.31  3.000
 N12  O17   C16  C15   121.91  3.000
 N12  HN18  N18  C19   116.78  3.000
 N12  HN18  N18  C16   118.24  3.000
 N12  C19   N18  C16   124.80  3.000
 N12  H192  C19  H191  107.08  3.000
 N12  H192  C19  C20   109.78  3.000
 N12  H191  C19  C20   110.60  3.000
 N12  H192  C19  N18   110.09  3.000
 N12  H191  C19  N18   108.29  3.000
 N12  C20   C19  N18   110.90  3.000
 N12  C25   C20  C21   117.12  3.000
 N12  C25   C20  C19   121.03  3.000
 N12  C21   C20  C19   121.81  3.000
 N12  H21   C21  C22   119.96  3.000
 N12  H21   C21  C20   120.55  3.000
 N12  C22   C21  C20   119.48  3.000
 N12  H22   C22  C23   121.26  3.000
 N12  H22   C22  C21   119.98  3.000
 N12  C23   C22  C21   118.72  3.000
 N12  C28   C23  N24   115.51  3.000
 N12  C28   C23  C22   122.37  3.000
 N12  N24   C23  C22   122.08  3.000
 N12  C25   N24  C23   118.79  3.000
 N12  H25   C25  N24   116.36  3.000
 N12  H25   C25  C20   119.83  3.000
 N12  N24   C25  C20   123.80  3.000
 N12  N30   C28  N29   121.38  3.000
 N12  N29   C28  C23   123.16  3.000
 N12  N30   C28  C23   115.40  3.000
 N12  HN29  N29  C28   109.33  3.000
 N12  H302  N30  H301  113.47  3.000
 N12  H302  N30  C28   118.16  3.000
 N12  H301  N30  C28   115.53  3.000
 N12  H312  C31  H311  107.34  3.000
 N12  H312  C31  C33   109.26  3.000
 N12  H311  C31  C33   113.34  3.000
 N12  H312  C31  C15   108.28  3.000
 N12  H311  C31  C15   112.84  3.000
 N12  C33   C31  C15   105.66  3.000
 N12  H322  C32  H321  106.25  3.000
 N12  H322  C32  C34   109.12  3.000
 N12  H321  C32  C34   114.10  3.000
 N12  H322  C32  C15   109.93  3.000
 N12  H321  C32  C15   111.97  3.000
 N12  C34   C32  C15   105.45  3.000
 N12  H332  C33  H331  107.53  3.000
 N12  H332  C33  C34   113.57  3.000
 N12  H331  C33  C34   109.96  3.000
 N12  H332  C33  C31   112.39  3.000
 N12  H331  C33  C31   110.39  3.000
 N12  C34   C33  C31   102.99  3.000
 N12  H342  C34  H341  107.56  3.000
 N12  H342  C34  C33   113.79  3.000
 N12  H341  C34  C33   110.10  3.000
 N12  H342  C34  C32   112.25  3.000
 N12  H341  C34  C32   110.65  3.000
 N12  C33   C34  C32   102.49  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  Var_01    C10   C11  C12  C7     55.95  30.0  1
 N12  Var_02    C10   C9   C8   C7    -55.84  30.0  1
 N12  Var_03    C11   C10  C9   C8     54.82  30.0  1
 N12  Var_04    C12   C11  C10  C9    -54.71  30.0  1
 N12  Var_05    C34   C33  C31  C15    34.67  30.0  1
 N12  Var_06    C33   C34  C32  C15    36.04  30.0  1
 N12  Var_07    C32   C34  C33  C31   -43.61  30.0  1
 N12  Var_08    C21   C20  C19  N18   -63.66  30.0  2
 N12  Var_09    N30   C28  C23  C22   -20.38  30.0  2
 N12  Var_10    C20   C19  N18  C16   120.22  30.0  3
 N12  Var_11    C4    N3   C2   C1   -170.54  30.0  3
 N12  Var_12    O26   C1   C2   N3     19.42  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

