# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 05:37:41 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-cyclopentylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CNC3CCCC3)cc1
#
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
 10U  10U  N-cyclopentylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  peptide  56  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_10U
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
 10U  C14   C  C     0   0.537   2.6236   0.4554   1.0059
 10U  O32   O  O     0  -0.500   2.4210  -0.6557   1.4784
 10U  C15   C  CH2   0  -0.392   3.9450   0.8367   0.3672
 10U  N16   N  NH1   0  -0.599   4.8189  -0.3018   0.2532
 10U  C17   C  CH1   0  -0.095   6.1360   0.0357  -0.2709
 10U  C21   C  CH2   0  -0.438   6.0914   0.1754  -1.7997
 10U  C20   C  CH2   0  -0.444   6.3464  -1.2419  -2.3661
 10U  C19   C  CH2   0  -0.434   6.6469  -2.1363  -1.1520
 10U  C18   C  CH2   0  -0.461   7.0764  -1.1494  -0.0688
 10U  N1    N  NR5   0  -0.479   1.6835   1.4134   1.0433
 10U  C2    C  CR15  0  -0.168   0.3908   1.1435   1.6393
 10U  C7    C  C     0   0.567  -0.3140  -0.0174   0.9524
 10U  O22   O  O     0  -0.483  -0.2387  -0.2024  -0.2505
 10U  C3    C  CH2   0  -0.478  -0.3857   2.4514   1.4242
 10U  C4    C  CH2   0  -0.472   0.7118   3.5059   1.3433
 10U  C5    C  CH2   0  -0.275   1.8185   2.7893   0.5824
 10U  N23   N  NH1   0  -0.633  -1.0838  -0.7578   1.7628
 10U  C24   C  CH2   0  -0.371  -1.9441  -1.8045   1.2611
 10U  C25   C  CR6   0   0.119  -3.1330  -1.2721   0.5011
 10U  C30   C  CR16  0  -0.277  -4.0168  -0.3791   1.1044
 10U  C29   C  CR16  0  -0.262  -5.1195   0.0979   0.4187
 10U  C28   C  CR6   0   0.034  -5.3785  -0.3160  -0.8875
 10U  C31   C  C     0   0.329  -6.5723   0.2128  -1.6020
 10U  N49   N  N     0  -0.653  -7.0114   1.3709  -1.2873
 10U  N48   N  NH2   0  -0.820  -7.0657  -0.5965  -2.5849
 10U  C27   C  CR16  0  -0.278  -4.4929  -1.2027  -1.4937
 10U  C26   C  CR16  0  -0.288  -3.3786  -1.6658  -0.8068
 10U  H15   H  HCH2  0   0.258   3.7469   1.2540  -0.6251
 10U  H15A  H  HCH2  0   0.234   4.3840   1.6644   0.9518
 10U  HN16  H  HNH1  0   0.343   4.9258  -0.7212   1.1687
 10U  H17   H  HCH1  0   0.211   6.5337   0.9472   0.2026
 10U  H21   H  HCH2  0   0.232   5.1417   0.5904  -2.1408
 10U  H21A  H  HCH2  0   0.226   6.8673   0.8689  -2.1290
 10U  H20   H  HCH2  0   0.226   5.4982  -1.6131  -2.9420
 10U  H20A  H  HCH2  0   0.223   7.2003  -1.2257  -3.0449
 10U  H19   H  HCH2  0   0.221   5.7490  -2.6669  -0.8322
 10U  H19A  H  HCH2  0   0.225   7.4079  -2.8894  -1.3614
 10U  H18   H  HCH2  0   0.228   8.1039  -0.8185  -0.2436
 10U  H18A  H  HCH2  0   0.231   7.0354  -1.5579   0.9444
 10U  H2    H  HCR5  0   0.274   0.5013   0.9373   2.7096
 10U  H3    H  HCH2  0   0.265  -1.1029   2.6281   2.2239
 10U  H3A   H  HCH2  0   0.250  -0.9380   2.4157   0.4825
 10U  H4    H  HCH2  0   0.245   1.0596   3.7727   2.3430
 10U  H4A   H  HCH2  0   0.258   0.3891   4.4176   0.8429
 10U  H5    H  HCH2  0   0.258   2.8039   3.1936   0.8138
 10U  H5A   H  HCH2  0   0.245   1.6682   2.8581  -0.4993
 10U  HN23  H  HNH1  0   0.406  -1.0837  -0.5694   2.7511
 10U  H24   H  HCH2  0   0.261  -1.3741  -2.4868   0.6284
 10U  H24A  H  HCH2  0   0.277  -2.2832  -2.3780   2.1242
 10U  H30   H  HCR6  0   0.250  -3.8409  -0.0493   2.1214
 10U  H29   H  HCR6  0   0.252  -5.7992   0.7877   0.9006
 10U  HN49  H  H     0   0.322  -7.8438   1.6060  -1.8216
 10U  HN48  H  HNH2  0   0.394  -6.9239  -1.5898  -2.5030
 10U  HN4A  H  HNH2  0   0.391  -7.9547  -0.3483  -2.9892
 10U  H27   H  HCR6  0   0.257  -4.6469  -1.5234  -2.5162
 10U  H26   H  HCR6  0   0.253  -2.6900  -2.3386  -1.3030

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
 10U  C4   C3    single    1.524  0.020  1.524
 10U  C4   C5    single    1.522  0.020  1.522
 10U  C3   C2    single    1.536  0.020  1.536
 10U  C24  N23   single    1.445  0.020  1.445
 10U  C24  C25   single    1.508  0.020  1.508
 10U  O22  C7    double    1.219  0.020  1.219
 10U  C7   N23   single    1.341  0.020  1.341
 10U  C7   C2    single    1.522  0.020  1.522
 10U  C2   N1    single    1.449  0.020  1.449
 10U  C25  C26   aromatic  1.388  0.020  1.388
 10U  C25  C30   aromatic  1.394  0.020  1.394
 10U  C5   N1    single    1.457  0.020  1.457
 10U  N1   C14   single    1.343  0.020  1.343
 10U  C26  C27   aromatic  1.389  0.020  1.389
 10U  C30  C29   aromatic  1.383  0.020  1.383
 10U  C14  C15   single    1.516  0.020  1.516
 10U  C14  O32   double    1.224  0.020  1.224
 10U  C27  C28   aromatic  1.392  0.020  1.392
 10U  C29  C28   aromatic  1.394  0.020  1.394
 10U  C15  N16   single    1.440  0.020  1.440
 10U  C28  C31   single    1.488  0.020  1.488
 10U  C31  N48   single    1.365  0.020  1.365
 10U  C31  N49   double    1.278  0.020  1.278
 10U  N16  C17   single    1.457  0.020  1.457
 10U  C21  C17   single    1.536  0.020  1.536
 10U  C21  C20   single    1.547  0.020  1.547
 10U  C17  C18   single    1.526  0.020  1.526
 10U  C20  C19   single    1.538  0.020  1.538
 10U  C18  C19   single    1.527  0.020  1.527
 10U  C15  H15   single    0.970  0.020  1.090
 10U  C15  H15A  single    0.970  0.020  1.090
 10U  C5   H5    single    0.970  0.020  1.090
 10U  C5   H5A   single    0.970  0.020  1.090
 10U  C4   H4    single    0.970  0.020  1.090
 10U  C4   H4A   single    0.970  0.020  1.090
 10U  C3   H3    single    0.970  0.020  1.090
 10U  C3   H3A   single    0.970  0.020  1.090
 10U  C2   H2    single    0.970  0.020  1.090
 10U  N23  HN23  single    0.860  0.020  1.020
 10U  C24  H24   single    0.970  0.020  1.090
 10U  C24  H24A  single    0.970  0.020  1.090
 10U  C30  H30   single    0.930  0.020  1.080
 10U  C29  H29   single    0.930  0.020  1.080
 10U  N49  HN49  single    0.890  0.020  1.040
 10U  N48  HN48  single    0.890  0.020  1.040
 10U  N48  HN4A  single    0.890  0.020  1.040
 10U  C27  H27   single    0.930  0.020  1.080
 10U  C26  H26   single    0.930  0.020  1.080
 10U  N16  HN16  single    0.890  0.020  1.040
 10U  C17  H17   single    0.970  0.020  1.090
 10U  C21  H21   single    0.970  0.020  1.090
 10U  C21  H21A  single    0.970  0.020  1.090
 10U  C20  H20   single    0.970  0.020  1.090
 10U  C20  H20A  single    0.970  0.020  1.090
 10U  C19  H19   single    0.970  0.020  1.090
 10U  C19  H19A  single    0.970  0.020  1.090
 10U  C18  H18   single    0.970  0.020  1.090
 10U  C18  H18A  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
 10U  N1    C14  C15   116.26  3.000
 10U  C15   C14  O32   122.34  3.000
 10U  N1    C14  O32   121.39  3.000
 10U  H15A  C15  H15   105.43  3.000
 10U  H15A  C15  N16   113.16  3.000
 10U  H15   C15  N16   109.85  3.000
 10U  H15A  C15  C14   108.17  3.000
 10U  H15   C15  C14   108.66  3.000
 10U  N16   C15  C14   111.31  3.000
 10U  HN16  N16  C17   109.00  3.000
 10U  HN16  N16  C15   108.66  3.000
 10U  C17   N16  C15   113.20  3.000
 10U  H17   C17  C18   111.29  3.000
 10U  H17   C17  C21   111.29  3.000
 10U  C18   C17  C21   102.72  3.000
 10U  H17   C17  N16   111.32  3.000
 10U  C18   C17  N16   109.23  3.000
 10U  C21   C17  N16   110.66  3.000
 10U  H21A  C21  H21   106.42  3.000
 10U  H21A  C21  C20   110.75  3.000
 10U  H21   C21  C20   112.17  3.000
 10U  H21A  C21  C17   109.73  3.000
 10U  H21   C21  C17   111.78  3.000
 10U  C20   C21  C17   106.04  3.000
 10U  H20A  C20  H20   106.57  3.000
 10U  H20A  C20  C19   110.30  3.000
 10U  H20   C20  C19   111.78  3.000
 10U  H20A  C20  C21   110.07  3.000
 10U  H20   C20  C21   112.14  3.000
 10U  C19   C20  C21   106.02  3.000
 10U  H19A  C19  H19   107.14  3.000
 10U  H19A  C19  C18   112.71  3.000
 10U  H19   C19  C18   109.75  3.000
 10U  H19A  C19  C20   112.73  3.000
 10U  H19   C19  C20   110.70  3.000
 10U  C18   C19  C20   103.84  3.000
 10U  H18A  C18  H18   107.25  3.000
 10U  H18A  C18  C19   113.91  3.000
 10U  H18   C18  C19   110.27  3.000
 10U  H18A  C18  C17   112.94  3.000
 10U  H18   C18  C17   108.83  3.000
 10U  C19   C18  C17   103.57  3.000
 10U  C5    N1   C2    112.87  3.000
 10U  C5    N1   C14   126.86  3.000
 10U  C2    N1   C14   120.21  3.000
 10U  H2    C2   C3    110.37  3.000
 10U  H2    C2   C7    110.12  3.000
 10U  C3    C2   C7    110.62  3.000
 10U  H2    C2   N1    110.30  3.000
 10U  C7    C2   N1    111.69  3.000
 10U  C3    C2   N1    103.58  3.000
 10U  N23   C7   O22   123.23  3.000
 10U  N23   C7   C2    114.48  3.000
 10U  O22   C7   C2    122.16  3.000
 10U  H3A   C3   H3    107.79  3.000
 10U  H3A   C3   C4    109.94  3.000
 10U  H3    C3   C4    113.65  3.000
 10U  H3A   C3   C2    110.40  3.000
 10U  H3    C3   C2    111.61  3.000
 10U  C4    C3   C2    103.44  3.000
 10U  H4A   C4   H4    108.09  3.000
 10U  H4A   C4   C5    112.33  3.000
 10U  H4    C4   C5    109.95  3.000
 10U  H4A   C4   C3    112.97  3.000
 10U  H4    C4   C3    110.48  3.000
 10U  C5    C4   C3    102.97  3.000
 10U  H5A   C5   H5    108.11  3.000
 10U  H5A   C5   C4    111.38  3.000
 10U  H5    C5   C4    112.12  3.000
 10U  H5A   C5   N1    111.06  3.000
 10U  H5    C5   N1    111.52  3.000
 10U  C4    C5   N1    102.65  3.000
 10U  HN23  N23  C24   118.48  3.000
 10U  HN23  N23  C7    119.36  3.000
 10U  C24   N23  C7    122.15  3.000
 10U  H24A  C24  H24   107.01  3.000
 10U  H24A  C24  C25   109.84  3.000
 10U  H24   C24  C25   109.90  3.000
 10U  H24A  C24  N23   106.94  3.000
 10U  H24   C24  N23   110.08  3.000
 10U  C25   C24  N23   112.87  3.000
 10U  C26   C25  C30   118.52  3.000
 10U  C30   C25  C24   120.53  3.000
 10U  C26   C25  C24   120.95  3.000
 10U  H30   C30  C29   119.32  3.000
 10U  H30   C30  C25   119.89  3.000
 10U  C29   C30  C25   120.79  3.000
 10U  H29   C29  C28   119.33  3.000
 10U  H29   C29  C30   120.00  3.000
 10U  C28   C29  C30   120.66  3.000
 10U  C27   C28  C31   121.83  3.000
 10U  C31   C28  C29   119.55  3.000
 10U  C27   C28  C29   118.61  3.000
 10U  N48   C31  N49   126.18  3.000
 10U  N49   C31  C28   118.64  3.000
 10U  N48   C31  C28   115.14  3.000
 10U  HN49  N49  C31   111.19  3.000
 10U  HN4A  N48  HN48  113.57  3.000
 10U  HN4A  N48  C31   117.49  3.000
 10U  HN48  N48  C31   118.38  3.000
 10U  H27   C27  C26   118.85  3.000
 10U  H27   C27  C28   120.63  3.000
 10U  C26   C27  C28   120.50  3.000
 10U  H26   C26  C27   119.40  3.000
 10U  H26   C26  C25   119.70  3.000
 10U  C27   C26  C25   120.91  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
 10U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 10U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 10U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 10U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 10U  CONST_05  C26   C25  C30  C29     0.00   0.0  0
 10U  CONST_06  C26   C27  C28  C29     0.00   0.0  0
 10U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 10U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 10U  CONST_09  C31   C28  C29  C30   180.00   0.0  0
 10U  CONST_10  C26   C27  C28  C31   180.00   0.0  0
 10U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 10U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 10U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 10U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 10U  CONST_15  C2    N1   C14  O32     0.00   0.0  0
 10U  CONST_16  C5    N1   C14  O32   180.00   0.0  0
 10U  CONST_17  C2    N1   C14  C15   180.00   0.0  0
 10U  CONST_18  C5    N1   C14  C15     0.00   0.0  0
 10U  CONST_19  C24   N23  C7   C2    180.00   0.0  0
 10U  CONST_20  HN23  N23  C7   C2      0.00   0.0  0
 10U  CONST_22  HN4A  N48  C31  C28   180.00   0.0  0
 10U  CONST_23  HN49  N49  C31  C28   180.00   0.0  0
 10U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 10U  Var_01    C19   C20  C21  C17    -4.59  30.0  1
 10U  Var_02    C20   C19  C18  C17    39.08  30.0  1
 10U  Var_03    C18   C19  C20  C21   -21.01  30.0  1
 10U  Var_04    C3    C4   C5   N1    -34.26  30.0  1
 10U  Var_05    C5    C4   C3   C2     37.65  30.0  1
 10U  Var_06    C4    C5   N1   C2     18.67  30.0  1
 10U  Var_07    C26   C25  C24  N23   123.69  30.0  2
 10U  Var_08    N48   C31  C28  C29  -153.99  30.0  2
 10U  Var_09    C17   N16  C15  C14  -176.01  30.0  3
 10U  Var_10    N1    C14  C15  N16  -173.78  30.0  2
 10U  Var_11    C25   C24  N23  C7    -71.02  30.0  1

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
 10U  chir_01  C17  N16  C21  C18  positiv
 10U  chir_02  C2   N1   C3   C7   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
 10U  plan-1  C14   0.020
 10U  plan-1  O32   0.020
 10U  plan-1  C15   0.020
 10U  plan-1  N1    0.020
 10U  plan-1  C2    0.020
 10U  plan-1  C5    0.020
 10U  plan-2  C24   0.020
 10U  plan-2  C25   0.020
 10U  plan-2  C30   0.020
 10U  plan-2  C29   0.020
 10U  plan-2  C28   0.020
 10U  plan-2  C31   0.020
 10U  plan-2  C27   0.020
 10U  plan-2  C26   0.020
 10U  plan-2  H30   0.020
 10U  plan-2  H29   0.020
 10U  plan-2  H27   0.020
 10U  plan-2  H26   0.020
 10U  plan-3  C2    0.020
 10U  plan-3  C7    0.020
 10U  plan-3  O22   0.020
 10U  plan-3  N23   0.020
 10U  plan-3  C24   0.020
 10U  plan-3  HN23  0.020
 10U  plan-4  C28   0.020
 10U  plan-4  C31   0.020
 10U  plan-4  N49   0.020
 10U  plan-4  N48   0.020
 10U  plan-4  HN49  0.020
 10U  plan-4  HN48  0.020
 10U  plan-4  HN4A  0.020

