# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:38:12 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-(4-carbamimidoylbenzyl)-1-(3-cyclohexylpropanoyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CCC3CCCCC3)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
 50U  50U  N-(4-carbamimidoylbenzyl)-1-(3-cyclohexylpropanoyl)-L-prolinamide  peptide  60  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_50U
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
 50U  C44   C  CH1   0  -0.227  -5.7833  -0.7580  -0.5091
 50U  C45   C  CH2   0  -0.423  -6.3063  -0.3713   0.8759
 50U  C46   C  CH2   0  -0.427  -7.8275  -0.4494   0.9619
 50U  C47   C  CH2   0  -0.429  -8.3433  -1.8251   0.5562
 50U  C48   C  CH2   0  -0.431  -7.8475  -2.2044  -0.8346
 50U  C49   C  CH2   0  -0.412  -6.3274  -2.1288  -0.9173
 50U  C43   C  CH2   0  -0.393  -4.2566  -0.7614  -0.5822
 50U  C5    C  CH2   0  -0.610  -3.6257   0.5989  -0.3296
 50U  C14   C  C     0   0.584  -2.1205   0.6012  -0.4745
 50U  O32   O  O     0  -0.507  -1.4715  -0.4194  -0.6733
 50U  N1    N  NT    0  -0.468  -1.5123   1.7975  -0.3691
 50U  C1    C  CH1   0  -0.214  -0.0711   1.8889  -0.4408
 50U  C7    C  C     0   0.579   0.5734   1.1948   0.7555
 50U  O22   O  O     0  -0.495   0.0312   1.1395   1.8486
 50U  C2    C  CH2   0  -0.471   0.1872   3.4025  -0.4084
 50U  C3    C  CH2   0  -0.473  -0.9906   3.9522   0.3889
 50U  C4    C  CH2   0  -0.267  -2.1527   3.0675  -0.0460
 50U  N23   N  NH1   0  -0.638   1.8010   0.7110   0.5252
 50U  C24   C  CH2   0  -0.315   2.5922   0.0744   1.5635
 50U  C25   C  CR6   0   0.044   3.9307  -0.3242   1.0099
 50U  C26   C  CR16  0  -0.279   5.0509   0.4807   1.1963
 50U  C27   C  CR16  0  -0.259   6.2753   0.1272   0.6538
 50U  C28   C  CR6   0   0.039   6.4070  -1.0340  -0.1041
 50U  C21   C  C     0   0.335   7.7355  -1.3841  -0.6800
 50U  N46   N  N     0  -0.651   8.7860  -0.9324  -0.1098
 50U  N47   N  NH2   0  -0.823   7.7020  -2.2126  -1.7643
 50U  C29   C  CR16  0  -0.279   5.2875  -1.8435  -0.2876
 50U  C30   C  CR16  0  -0.266   4.0655  -1.4914   0.2656
 50U  H44   H  HCH1  0   0.203  -6.1626  -0.0189  -1.2295
 50U  H45   H  HCH2  0   0.203  -5.8625  -1.0420   1.6224
 50U  H45A  H  HCH2  0   0.228  -5.9825   0.6388   1.1388
 50U  H46   H  HCH2  0   0.207  -8.2650   0.3098   0.3040
 50U  H46A  H  HCH2  0   0.224  -8.1559  -0.2039   1.9750
 50U  H47   H  HCH2  0   0.224  -9.4355  -1.8469   0.5909
 50U  H47A  H  HCH2  0   0.206  -7.9942  -2.5704   1.2798
 50U  H48   H  HCH2  0   0.206  -8.2857  -1.5251  -1.5743
 50U  H48A  H  HCH2  0   0.224  -8.1876  -3.2087  -1.0994
 50U  H49   H  HCH2  0   0.222  -5.9942  -2.3683  -1.9314
 50U  H49A  H  HCH2  0   0.203  -5.8905  -2.8923  -0.2616
 50U  H43   H  HCH2  0   0.224  -3.9562  -1.1203  -1.5708
 50U  H43A  H  HCH2  0   0.215  -3.8696  -1.4900   0.1371
 50U  H5    H  HCH2  0   0.268  -3.8617   0.9540   0.6787
 50U  H5A   H  HCH2  0   0.261  -4.0571   1.3447  -1.0061
 50U  H1    H  HCH1  0   0.281   0.3045   1.4488  -1.3683
 50U  H2    H  HCH2  0   0.263   1.1575   3.6524   0.0198
 50U  H2A   H  HCH2  0   0.258   0.1697   3.7861  -1.4300
 50U  H3    H  HCH2  0   0.245  -0.8139   3.8433   1.4593
 50U  H3A   H  HCH2  0   0.255  -1.1816   5.0051   0.1870
 50U  H4    H  HCH2  0   0.241  -2.6578   3.4804  -0.9242
 50U  H4A   H  HCH2  0   0.254  -2.8975   2.9495   0.7408
 50U  HN23  H  HNH1  0   0.405   2.1762   0.7455  -0.4091
 50U  H24   H  HCH2  0   0.257   2.7198   0.7604   2.4031
 50U  H24A  H  HCH2  0   0.256   2.0659  -0.8051   1.9438
 50U  H26   H  HCR6  0   0.257   4.9679   1.3935   1.7739
 50U  H27   H  HCR6  0   0.257   7.1390   0.7592   0.8100
 50U  HN46  H  H     0   0.324   9.6248  -1.2097  -0.6126
 50U  HN47  H  HNH2  0   0.396   6.8855  -2.2024  -2.3528
 50U  HN4A  H  HNH2  0   0.392   8.5629  -2.3451  -2.2713
 50U  H29   H  HCR6  0   0.260   5.3585  -2.7688  -0.8450
 50U  H30   H  HCR6  0   0.260   3.2099  -2.1401   0.1207

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
 50U  C2   C3    single    1.525  0.020  1.525
 50U  C2   C1    single    1.536  0.020  1.536
 50U  C24  N23   single    1.452  0.020  1.452
 50U  C24  C25   single    1.502  0.020  1.502
 50U  N23  C7    single    1.339  0.020  1.339
 50U  C3   C4    single    1.524  0.020  1.524
 50U  C30  C25   aromatic  1.391  0.020  1.391
 50U  C30  C29   aromatic  1.387  0.020  1.387
 50U  C7   O22   double    1.221  0.020  1.221
 50U  C7   C1    single    1.526  0.020  1.526
 50U  C1   N1    single    1.446  0.020  1.446
 50U  C25  C26   aromatic  1.392  0.020  1.392
 50U  C29  C28   aromatic  1.394  0.020  1.394
 50U  C4   N1    single    1.459  0.020  1.459
 50U  N1   C14   single    1.346  0.020  1.346
 50U  C26  C27   aromatic  1.385  0.020  1.385
 50U  C28  C27   aromatic  1.393  0.020  1.393
 50U  C28  C21   single    1.490  0.020  1.490
 50U  C14  O32   double    1.226  0.020  1.226
 50U  C14  C5    single    1.512  0.020  1.512
 50U  N47  C21   single    1.365  0.020  1.365
 50U  C21  N46   double    1.278  0.020  1.278
 50U  C5   C43   single    1.521  0.020  1.521
 50U  C46  C45   single    1.526  0.020  1.526
 50U  C46  C47   single    1.524  0.020  1.524
 50U  C45  C44   single    1.530  0.020  1.530
 50U  C44  C43   single    1.528  0.020  1.528
 50U  C44  C49   single    1.530  0.020  1.530
 50U  C47  C48   single    1.525  0.020  1.525
 50U  C48  C49   single    1.524  0.020  1.524
 50U  C1   H1    single    0.970  0.020  1.090
 50U  N23  HN23  single    0.860  0.020  1.020
 50U  C24  H24   single    0.970  0.020  1.090
 50U  C24  H24A  single    0.970  0.020  1.090
 50U  C26  H26   single    0.930  0.020  1.080
 50U  C27  H27   single    0.930  0.020  1.080
 50U  N46  HN46  single    0.890  0.020  1.040
 50U  N47  HN47  single    0.890  0.020  1.040
 50U  N47  HN4A  single    0.890  0.020  1.040
 50U  C29  H29   single    0.930  0.020  1.080
 50U  C30  H30   single    0.930  0.020  1.080
 50U  C2   H2    single    0.970  0.020  1.090
 50U  C2   H2A   single    0.970  0.020  1.090
 50U  C3   H3    single    0.970  0.020  1.090
 50U  C3   H3A   single    0.970  0.020  1.090
 50U  C4   H4    single    0.970  0.020  1.090
 50U  C4   H4A   single    0.970  0.020  1.090
 50U  C5   H5    single    0.970  0.020  1.090
 50U  C5   H5A   single    0.970  0.020  1.090
 50U  C43  H43   single    0.970  0.020  1.090
 50U  C43  H43A  single    0.970  0.020  1.090
 50U  C44  H44   single    0.970  0.020  1.090
 50U  C49  H49   single    0.970  0.020  1.090
 50U  C49  H49A  single    0.970  0.020  1.090
 50U  C48  H48   single    0.970  0.020  1.090
 50U  C48  H48A  single    0.970  0.020  1.090
 50U  C47  H47   single    0.970  0.020  1.090
 50U  C47  H47A  single    0.970  0.020  1.090
 50U  C46  H46   single    0.970  0.020  1.090
 50U  C46  H46A  single    0.970  0.020  1.090
 50U  C45  H45   single    0.970  0.020  1.090
 50U  C45  H45A  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
 50U  H44   C44  C43   108.35  3.000
 50U  H44   C44  C49   107.74  3.000
 50U  C43   C44  C49   109.90  3.000
 50U  H44   C44  C45   107.77  3.000
 50U  C49   C44  C45   110.26  3.000
 50U  C43   C44  C45   112.66  3.000
 50U  H45A  C45  H45   106.35  3.000
 50U  H45A  C45  C46   109.22  3.000
 50U  H45   C45  C46   109.49  3.000
 50U  H45A  C45  C44   110.49  3.000
 50U  H45   C45  C44   108.85  3.000
 50U  C46   C45  C44   112.27  3.000
 50U  H46A  C46  H46   106.32  3.000
 50U  H46A  C46  C47   110.35  3.000
 50U  H46   C46  C47   109.29  3.000
 50U  H46A  C46  C45   109.90  3.000
 50U  H46   C46  C45   109.19  3.000
 50U  C47   C46  C45   111.63  3.000
 50U  H47A  C47  H47   106.49  3.000
 50U  H47A  C47  C48   109.24  3.000
 50U  H47   C47  C48   110.42  3.000
 50U  H47A  C47  C46   109.28  3.000
 50U  H47   C47  C46   110.35  3.000
 50U  C48   C47  C46   110.94  3.000
 50U  H48A  C48  H48   106.36  3.000
 50U  H48A  C48  C49   110.05  3.000
 50U  H48   C48  C49   109.36  3.000
 50U  H48A  C48  C47   110.39  3.000
 50U  H48   C48  C47   109.36  3.000
 50U  C49   C48  C47   111.19  3.000
 50U  H49A  C49  H49   106.28  3.000
 50U  H49A  C49  C48   109.28  3.000
 50U  H49   C49  C48   110.07  3.000
 50U  H49A  C49  C44   108.81  3.000
 50U  H49   C49  C44   109.58  3.000
 50U  C48   C49  C44   112.61  3.000
 50U  H43A  C43  H43   106.17  3.000
 50U  H43A  C43  C5    109.85  3.000
 50U  H43   C43  C5    109.25  3.000
 50U  H43A  C43  C44   108.86  3.000
 50U  H43   C43  C44   108.56  3.000
 50U  C5    C43  C44   113.86  3.000
 50U  H5A   C5   H5    105.25  3.000
 50U  H5A   C5   C14   109.38  3.000
 50U  H5    C5   C14   107.60  3.000
 50U  H5A   C5   C43   110.06  3.000
 50U  H5    C5   C43   110.72  3.000
 50U  C14   C5   C43   113.48  3.000
 50U  N1    C14  O32   120.89  3.000
 50U  O32   C14  C5    122.77  3.000
 50U  N1    C14  C5    116.33  3.000
 50U  C4    N1   C1    113.17  3.000
 50U  C4    N1   C14   126.35  3.000
 50U  C1    N1   C14   120.18  3.000
 50U  H1    C1   C2    110.91  3.000
 50U  H1    C1   C7    109.69  3.000
 50U  C2    C1   C7    111.15  3.000
 50U  H1    C1   N1    111.04  3.000
 50U  C7    C1   N1    110.69  3.000
 50U  C2    C1   N1    103.23  3.000
 50U  N23   C7   O22   122.98  3.000
 50U  O22   C7   C1    122.33  3.000
 50U  N23   C7   C1    114.62  3.000
 50U  H2A   C2   H2    107.55  3.000
 50U  H2A   C2   C3    110.51  3.000
 50U  H2    C2   C3    113.56  3.000
 50U  H2A   C2   C1    108.90  3.000
 50U  H2    C2   C1    112.58  3.000
 50U  C3    C2   C1    103.67  3.000
 50U  H3A   C3   H3    107.87  3.000
 50U  H3A   C3   C4    112.00  3.000
 50U  H3    C3   C4    110.23  3.000
 50U  H3A   C3   C2    112.77  3.000
 50U  H3    C3   C2    110.62  3.000
 50U  C4    C3   C2    103.33  3.000
 50U  H4A   C4   H4    107.75  3.000
 50U  H4A   C4   C3    112.21  3.000
 50U  H4    C4   C3    111.23  3.000
 50U  H4A   C4   N1    111.45  3.000
 50U  H4    C4   N1    110.70  3.000
 50U  C3    C4   N1    103.53  3.000
 50U  HN23  N23  C24   118.37  3.000
 50U  HN23  N23  C7    119.24  3.000
 50U  C24   N23  C7    122.32  3.000
 50U  H24A  C24  H24   107.12  3.000
 50U  H24A  C24  C25   110.10  3.000
 50U  H24   C24  C25   110.24  3.000
 50U  H24A  C24  N23   109.82  3.000
 50U  H24   C24  N23   109.75  3.000
 50U  C25   C24  N23   109.77  3.000
 50U  C30   C25  C26   118.61  3.000
 50U  C26   C25  C24   120.95  3.000
 50U  C30   C25  C24   120.41  3.000
 50U  H26   C26  C27   119.44  3.000
 50U  H26   C26  C25   119.80  3.000
 50U  C27   C26  C25   120.76  3.000
 50U  H27   C27  C28   119.35  3.000
 50U  H27   C27  C26   120.02  3.000
 50U  C28   C27  C26   120.63  3.000
 50U  C29   C28  C21   121.94  3.000
 50U  C21   C28  C27   119.38  3.000
 50U  C29   C28  C27   118.68  3.000
 50U  N47   C21  N46   126.10  3.000
 50U  N46   C21  C28   118.53  3.000
 50U  N47   C21  C28   115.33  3.000
 50U  HN46  N46  C21   111.18  3.000
 50U  HN4A  N47  HN47  113.58  3.000
 50U  HN4A  N47  C21   117.29  3.000
 50U  HN47  N47  C21   118.56  3.000
 50U  H29   C29  C30   118.70  3.000
 50U  H29   C29  C28   120.77  3.000
 50U  C30   C29  C28   120.52  3.000
 50U  H30   C30  C29   119.37  3.000
 50U  H30   C30  C25   119.83  3.000
 50U  C29   C30  C25   120.79  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
 50U  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 50U  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 50U  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 50U  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 50U  CONST_05  C30   C25  C26  C27     0.00   0.0  0
 50U  CONST_06  C30   C29  C28  C27     0.00   0.0  0
 50U  CONST_07  C29   C30  C25  C24   180.00   0.0  0
 50U  CONST_08  C27   C26  C25  C24   180.00   0.0  0
 50U  CONST_09  C21   C28  C27  C26   180.00   0.0  0
 50U  CONST_10  C30   C29  C28  C21   180.00   0.0  0
 50U  CONST_11  H29   C29  C30  C25   180.00   0.0  0
 50U  CONST_12  H27   C27  C26  C25   180.00   0.0  0
 50U  CONST_13  H30   C30  C25  C26   180.00   0.0  0
 50U  CONST_14  H26   C26  C27  C28   180.00   0.0  0
 50U  CONST_15  C1    N1   C14  C5    180.00   0.0  0
 50U  CONST_16  C4    N1   C14  C5      0.00   0.0  0
 50U  CONST_17  C1    N1   C14  O32     0.00   0.0  0
 50U  CONST_18  C4    N1   C14  O32   180.00   0.0  0
 50U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 50U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 50U  CONST_22  HN4A  N47  C21  C28   180.00   0.0  0
 50U  CONST_23  HN46  N46  C21  C28   180.00   0.0  0
 50U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 50U  Var_01    C47   C46  C45  C44    55.03  30.0  1
 50U  Var_02    C47   C48  C49  C44   -55.33  30.0  1
 50U  Var_03    C48   C47  C46  C45   -55.26  30.0  1
 50U  Var_04    C49   C48  C47  C46    55.20  30.0  1
 50U  Var_05    C2    C3   C4   N1     29.58  30.0  1
 50U  Var_06    C4    C3   C2   C1    -36.42  30.0  1
 50U  Var_07    C3    C4   N1   C1    -11.85  30.0  1
 50U  Var_08    C30   C25  C24  N23   -80.56  30.0  2
 50U  Var_09    N47   C21  C28  C27  -157.19  30.0  2
 50U  Var_10    C14   C5   C43  C44  -177.01  30.0  1
 50U  Var_11    N1    C14  C5   C43   174.85  30.0  2
 50U  Var_12    C25   C24  N23  C7   -178.34  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
 50U  chir_01  C44  C45  C43  C49  negativ
 50U  chir_02  C1   N1   C2   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
 50U  plan-1  C5    0.020
 50U  plan-1  C14   0.020
 50U  plan-1  O32   0.020
 50U  plan-1  N1    0.020
 50U  plan-1  C1    0.020
 50U  plan-1  C4    0.020
 50U  plan-2  C24   0.020
 50U  plan-2  C25   0.020
 50U  plan-2  C26   0.020
 50U  plan-2  C27   0.020
 50U  plan-2  C28   0.020
 50U  plan-2  C21   0.020
 50U  plan-2  C29   0.020
 50U  plan-2  C30   0.020
 50U  plan-2  H26   0.020
 50U  plan-2  H27   0.020
 50U  plan-2  H29   0.020
 50U  plan-2  H30   0.020
 50U  plan-3  C1    0.020
 50U  plan-3  C7    0.020
 50U  plan-3  O22   0.020
 50U  plan-3  N23   0.020
 50U  plan-3  C24   0.020
 50U  plan-3  HN23  0.020
 50U  plan-4  C28   0.020
 50U  plan-4  C21   0.020
 50U  plan-4  N46   0.020
 50U  plan-4  N47   0.020
 50U  plan-4  HN46  0.020
 50U  plan-4  HN47  0.020
 50U  plan-4  HN4A  0.020

