# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 17:44:48 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-cyclohexylglycyl-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)CNC3CCCCC3)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
 11U  11U  N-cyclohexylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  peptide  59  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_11U
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
 11U  C14   C  C     0   0.543   2.2637   0.5449   0.3010
 11U  O32   O  O     0  -0.501   1.7754  -0.4928   0.7306
 11U  C15   C  CH2   0  -0.392   3.7472   0.6827   0.0192
 11U  N5    N  NH1   0  -0.604   4.3836  -0.6095  -0.0132
 11U  C16   C  CH1   0  -0.058   5.8207  -0.5743  -0.2403
 11U  C21   C  CH2   0  -0.442   6.6351   0.0049   0.9218
 11U  C20   C  CH2   0  -0.431   8.1340  -0.0248   0.6361
 11U  C19   C  CH2   0  -0.429   8.6094  -1.4308   0.2897
 11U  C18   C  CH2   0  -0.435   7.8059  -2.0130  -0.8681
 11U  C17   C  CH2   0  -0.429   6.3087  -1.9795  -0.5811
 11U  N1    N  NT    0  -0.480   1.5112   1.6340   0.0817
 11U  C2    C  CH1   0  -0.167   0.0807   1.5959   0.3149
 11U  C7    C  C     0   0.563  -0.5770   0.4791  -0.4876
 11U  O22   O  O     0  -0.492  -0.2461   0.2453  -1.6387
 11U  C3    C  CH2   0  -0.480  -0.3963   2.9755  -0.1620
 11U  C4    C  CH2   0  -0.472   0.8358   3.8589   0.0040
 11U  C5    C  CH2   0  -0.277   1.9780   2.9321  -0.3871
 11U  N23   N  NH1   0  -0.633  -1.5759  -0.1483   0.1517
 11U  C24   C  CH2   0  -0.341  -2.3544  -1.2223  -0.4169
 11U  C25   C  CR6   0   0.091  -3.8339  -1.0166  -0.2253
 11U  C26   C  CR16  0  -0.297  -4.6278  -2.0405   0.2733
 11U  C27   C  CR16  0  -0.277  -5.9973  -1.8708   0.4279
 11U  C28   C  CR6   0   0.035  -6.6038  -0.6654   0.0876
 11U  C31   C  C     0   0.335  -8.0697  -0.4499   0.2366
 11U  N49   N  N     0  -0.651  -8.6343   0.4382  -0.4884
 11U  N48   N  NH2   0  -0.824  -8.6963  -1.2791   1.1226
 11U  C29   C  CR16  0  -0.260  -5.8066   0.3610  -0.4196
 11U  C30   C  CR16  0  -0.275  -4.4422   0.1901  -0.5681
 11U  H15   H  HCH2  0   0.257   3.8916   1.1699  -0.9506
 11U  H15A  H  HCH2  0   0.237   4.1593   1.3838   0.7644
 11U  H20   H  HNH1  0   0.336   4.1853  -1.1115   0.8441
 11U  H21   H  HCH1  0   0.210   5.9876   0.0606  -1.1206
 11U  H301  H  HCH2  0   0.230   6.3222   1.0306   1.1359
 11U  H31   H  HCH2  0   0.205   6.4199  -0.5814   1.8239
 11U  H28   H  HCH2  0   0.227   8.6871   0.3618   1.4956
 11U  H291  H  HCH2  0   0.210   8.3552   0.6487  -0.1996
 11U  H261  H  HCH2  0   0.208   8.4995  -2.0776   1.1670
 11U  H271  H  HCH2  0   0.226   9.6741  -1.4207   0.0435
 11U  H241  H  HCH2  0   0.227   8.1223  -3.0389  -1.0717
 11U  H25   H  HCH2  0   0.209   8.0163  -1.4407  -1.7785
 11U  H22   H  HCH2  0   0.206   6.0872  -2.6477   0.2607
 11U  H23   H  HCH2  0   0.227   5.7443  -2.3579  -1.4371
 11U  H2    H  HCH1  0   0.273  -0.1262   1.4694   1.3829
 11U  H3    H  HCH2  0   0.266  -1.2579   3.3216   0.4063
 11U  H3A   H  HCH2  0   0.252  -0.6837   2.9337  -1.2147
 11U  H4    H  HCH2  0   0.245   0.9465   4.1728   1.0437
 11U  H4A   H  HCH2  0   0.258   0.8006   4.7534  -0.6163
 11U  H5    H  HCH2  0   0.260   2.9198   3.2101   0.0856
 11U  H5A   H  HCH2  0   0.245   2.1310   2.9258  -1.4707
 11U  HN23  H  HNH1  0   0.403  -1.7275   0.0618   1.1256
 11U  H24   H  HCH2  0   0.271  -2.1224  -1.2781  -1.4809
 11U  H24A  H  HCH2  0   0.263  -2.0553  -2.1778   0.0219
 11U  H26   H  HCR6  0   0.258  -4.1765  -2.9864   0.5476
 11U  H27   H  HCR6  0   0.257  -6.5826  -2.6997   0.8049
 11U  HN49  H  H     0   0.324  -9.6255   0.5104  -0.2746
 11U  HN48  H  HNH2  0   0.395  -8.1674  -1.6389   1.8998
 11U  HN4A  H  HNH2  0   0.391  -9.6542  -1.0678   1.3532
 11U  H29   H  HCR6  0   0.255  -6.2653   1.3011  -0.6943
 11U  H30   H  HCR6  0   0.251  -3.8455   1.0077  -0.9546

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
 11U  N1   C14   single    1.342  0.020  1.342
 11U  N1   C5    single    1.457  0.020  1.457
 11U  N1   C2    single    1.450  0.020  1.450
 11U  C14  O32   double    1.225  0.020  1.225
 11U  C14  C15   single    1.516  0.020  1.516
 11U  C5   C4    single    1.522  0.020  1.522
 11U  C4   C3    single    1.525  0.020  1.525
 11U  C3   C2    single    1.536  0.020  1.536
 11U  C2   C7    single    1.524  0.020  1.524
 11U  C7   N23   single    1.342  0.020  1.342
 11U  C7   O22   double    1.220  0.020  1.220
 11U  N23  C24   single    1.443  0.020  1.443
 11U  C24  C25   single    1.506  0.020  1.506
 11U  C25  C30   aromatic  1.394  0.020  1.394
 11U  C25  C26   aromatic  1.388  0.020  1.388
 11U  C30  C29   aromatic  1.383  0.020  1.383
 11U  C29  C28   aromatic  1.395  0.020  1.395
 11U  C28  C31   single    1.489  0.020  1.489
 11U  C28  C27   aromatic  1.392  0.020  1.392
 11U  C31  N49   double    1.278  0.020  1.278
 11U  C31  N48   single    1.366  0.020  1.366
 11U  C27  C26   aromatic  1.389  0.020  1.389
 11U  C15  N5    single    1.441  0.020  1.441
 11U  N5   C16   single    1.455  0.020  1.455
 11U  C16  C17   single    1.526  0.020  1.526
 11U  C16  C21   single    1.533  0.020  1.533
 11U  C17  C18   single    1.525  0.020  1.525
 11U  C18  C19   single    1.525  0.020  1.525
 11U  C19  C20   single    1.524  0.020  1.524
 11U  C20  C21   single    1.526  0.020  1.526
 11U  C15  H15   single    0.970  0.020  1.090
 11U  C15  H15A  single    0.970  0.020  1.090
 11U  C5   H5    single    0.970  0.020  1.090
 11U  C5   H5A   single    0.970  0.020  1.090
 11U  C4   H4    single    0.970  0.020  1.090
 11U  C4   H4A   single    0.970  0.020  1.090
 11U  C3   H3    single    0.970  0.020  1.090
 11U  C3   H3A   single    0.970  0.020  1.090
 11U  C2   H2    single    0.970  0.020  1.090
 11U  N23  HN23  single    0.860  0.020  1.020
 11U  C24  H24   single    0.970  0.020  1.090
 11U  C24  H24A  single    0.970  0.020  1.090
 11U  C30  H30   single    0.930  0.020  1.080
 11U  C29  H29   single    0.930  0.020  1.080
 11U  N49  HN49  single    0.890  0.020  1.040
 11U  N48  HN48  single    0.890  0.020  1.040
 11U  N48  HN4A  single    0.890  0.020  1.040
 11U  C27  H27   single    0.930  0.020  1.080
 11U  C26  H26   single    0.930  0.020  1.080
 11U  N5   H20   single    0.890  0.020  1.040
 11U  C16  H21   single    0.970  0.020  1.090
 11U  C17  H22   single    0.970  0.020  1.090
 11U  C17  H23   single    0.970  0.020  1.090
 11U  C18  H241  single    0.970  0.020  1.090
 11U  C18  H25   single    0.970  0.020  1.090
 11U  C19  H261  single    0.970  0.020  1.090
 11U  C19  H271  single    0.970  0.020  1.090
 11U  C20  H28   single    0.970  0.020  1.090
 11U  C20  H291  single    0.970  0.020  1.090
 11U  C21  H301  single    0.970  0.020  1.090
 11U  C21  H31   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
 11U  N1    C14  C15   116.39  3.000
 11U  C15   C14  O32   122.16  3.000
 11U  N1    C14  O32   121.43  3.000
 11U  H15A  C15  H15   105.44  3.000
 11U  H15A  C15  N5    114.85  3.000
 11U  H15   C15  N5    108.72  3.000
 11U  H15A  C15  C14   107.32  3.000
 11U  H15   C15  C14   109.52  3.000
 11U  N5    C15  C14   110.79  3.000
 11U  H20   N5   C16   109.72  3.000
 11U  H20   N5   C15   109.81  3.000
 11U  C16   N5   C15   114.71  3.000
 11U  H21   C16  C17   107.75  3.000
 11U  H21   C16  C21   107.97  3.000
 11U  C17   C16  C21   110.33  3.000
 11U  H21   C16  N5    106.81  3.000
 11U  C21   C16  N5    114.55  3.000
 11U  C17   C16  N5    109.17  3.000
 11U  H31   C21  H301  106.51  3.000
 11U  H31   C21  C20   109.64  3.000
 11U  H301  C21  C20   109.63  3.000
 11U  H31   C21  C16   108.50  3.000
 11U  H301  C21  C16   110.54  3.000
 11U  C20   C21  C16   111.88  3.000
 11U  H291  C20  H28   106.27  3.000
 11U  H291  C20  C19   109.31  3.000
 11U  H28   C20  C19   110.32  3.000
 11U  H291  C20  C21   109.21  3.000
 11U  H28   C20  C21   110.06  3.000
 11U  C19   C20  C21   111.52  3.000
 11U  H271  C19  H261  106.48  3.000
 11U  H271  C19  C18   110.23  3.000
 11U  H261  C19  C18   109.26  3.000
 11U  H271  C19  C20   110.28  3.000
 11U  H261  C19  C20   109.35  3.000
 11U  C18   C19  C20   111.13  3.000
 11U  H25   C18  H241  106.26  3.000
 11U  H25   C18  C17   109.48  3.000
 11U  H241  C18  C17   109.87  3.000
 11U  H25   C18  C19   109.29  3.000
 11U  H241  C18  C19   110.33  3.000
 11U  C17   C18  C19   111.48  3.000
 11U  H23   C17  H22   106.61  3.000
 11U  H23   C17  C18   110.62  3.000
 11U  H22   C17  C18   109.22  3.000
 11U  H23   C17  C16   109.18  3.000
 11U  H22   C17  C16   108.95  3.000
 11U  C18   C17  C16   112.10  3.000
 11U  C5    N1   C2    113.03  3.000
 11U  C2    N1   C14   120.38  3.000
 11U  C5    N1   C14   126.59  3.000
 11U  H2    C2   C3    110.36  3.000
 11U  H2    C2   C7    110.32  3.000
 11U  C3    C2   C7    111.14  3.000
 11U  H2    C2   N1    110.26  3.000
 11U  C7    C2   N1    111.11  3.000
 11U  C3    C2   N1    103.47  3.000
 11U  N23   C7   O22   124.18  3.000
 11U  O22   C7   C2    121.33  3.000
 11U  N23   C7   C2    114.39  3.000
 11U  H3A   C3   H3    107.88  3.000
 11U  H3A   C3   C4    109.86  3.000
 11U  H3    C3   C4    113.47  3.000
 11U  H3A   C3   C2    110.29  3.000
 11U  H3    C3   C2    111.67  3.000
 11U  C4    C3   C2    103.63  3.000
 11U  H4A   C4   H4    108.04  3.000
 11U  H4A   C4   C5    112.21  3.000
 11U  H4    C4   C5    110.10  3.000
 11U  H4A   C4   C3    112.81  3.000
 11U  H4    C4   C3    110.62  3.000
 11U  C5    C4   C3    103.03  3.000
 11U  H5A   C5   H5    108.07  3.000
 11U  H5A   C5   C4    111.28  3.000
 11U  H5    C5   C4    112.44  3.000
 11U  H5A   C5   N1    110.99  3.000
 11U  H5    C5   N1    111.38  3.000
 11U  C4    C5   N1    102.68  3.000
 11U  HN23  N23  C24   117.05  3.000
 11U  HN23  N23  C7    118.36  3.000
 11U  C24   N23  C7    124.18  3.000
 11U  H24A  C24  H24   106.78  3.000
 11U  H24A  C24  C25   109.70  3.000
 11U  H24   C24  C25   109.89  3.000
 11U  H24A  C24  N23   110.17  3.000
 11U  H24   C24  N23   107.93  3.000
 11U  C25   C24  N23   112.22  3.000
 11U  C30   C25  C26   118.50  3.000
 11U  C26   C25  C24   120.45  3.000
 11U  C30   C25  C24   121.04  3.000
 11U  H26   C26  C27   119.30  3.000
 11U  H26   C26  C25   119.78  3.000
 11U  C27   C26  C25   120.92  3.000
 11U  H27   C27  C28   120.85  3.000
 11U  H27   C27  C26   118.58  3.000
 11U  C28   C27  C26   120.56  3.000
 11U  C29   C28  C31   119.51  3.000
 11U  C31   C28  C27   122.00  3.000
 11U  C29   C28  C27   118.49  3.000
 11U  N48   C31  N49   125.96  3.000
 11U  N48   C31  C28   115.39  3.000
 11U  N49   C31  C28   118.60  3.000
 11U  HN49  N49  C31   111.16  3.000
 11U  HN4A  N48  HN48  113.43  3.000
 11U  HN4A  N48  C31   117.22  3.000
 11U  HN48  N48  C31   118.48  3.000
 11U  H29   C29  C30   119.91  3.000
 11U  H29   C29  C28   119.30  3.000
 11U  C30   C29  C28   120.79  3.000
 11U  H30   C30  C29   119.23  3.000
 11U  H30   C30  C25   120.04  3.000
 11U  C29   C30  C25   120.73  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
 11U  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 11U  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 11U  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 11U  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 11U  CONST_05  C30   C29  C28  C27     0.00   0.0  0
 11U  CONST_06  C30   C25  C26  C27     0.00   0.0  0
 11U  CONST_07  C29   C30  C25  C24   180.00   0.0  0
 11U  CONST_08  C27   C26  C25  C24   180.00   0.0  0
 11U  CONST_09  C31   C28  C27  C26   180.00   0.0  0
 11U  CONST_10  C30   C29  C28  C31   180.00   0.0  0
 11U  CONST_11  H29   C29  C30  C25   180.00   0.0  0
 11U  CONST_12  H27   C27  C26  C25   180.00   0.0  0
 11U  CONST_13  H30   C30  C25  C26   180.00   0.0  0
 11U  CONST_14  H26   C26  C27  C28   180.00   0.0  0
 11U  CONST_15  C5    N1   C14  O32   180.00   0.0  0
 11U  CONST_16  C2    N1   C14  O32     0.00   0.0  0
 11U  CONST_17  C5    N1   C14  C15     0.00   0.0  0
 11U  CONST_18  C2    N1   C14  C15   180.00   0.0  0
 11U  CONST_19  C24   N23  C7   C2    180.00   0.0  0
 11U  CONST_20  HN23  N23  C7   C2      0.00   0.0  0
 11U  CONST_21  HN49  N49  C31  C28   180.00   0.0  0
 11U  CONST_23  HN4A  N48  C31  C28   180.00   0.0  0
 11U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 11U  Var_01    C19   C18  C17  C16    55.34  30.0  1
 11U  Var_02    C19   C20  C21  C16   -55.27  30.0  1
 11U  Var_03    C18   C19  C20  C21    54.80  30.0  1
 11U  Var_04    C17   C18  C19  C20   -54.73  30.0  1
 11U  Var_05    C3    C4   C5   N1    -33.85  30.0  1
 11U  Var_06    C4    C5   N1   C2     18.47  30.0  1
 11U  Var_07    C5    C4   C3   C2     37.27  30.0  1
 11U  Var_08    C30   C25  C24  N23    50.28  30.0  2
 11U  Var_09    N49   C31  C28  C27  -155.88  30.0  2
 11U  Var_10    C16   N5   C15  C14  -178.32  30.0  3
 11U  Var_11    N1    C14  C15  N5   -166.48  30.0  1
 11U  Var_12    C25   C24  N23  C7   -132.33  30.0  3

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
 11U  chir_01  C16  N5  C17  C21  positiv
 11U  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
 11U  plan-1  C14   0.020
 11U  plan-1  O32   0.020
 11U  plan-1  C15   0.020
 11U  plan-1  N1    0.020
 11U  plan-1  C2    0.020
 11U  plan-1  C5    0.020
 11U  plan-2  C24   0.020
 11U  plan-2  C25   0.020
 11U  plan-2  C26   0.020
 11U  plan-2  C27   0.020
 11U  plan-2  C28   0.020
 11U  plan-2  C31   0.020
 11U  plan-2  C29   0.020
 11U  plan-2  C30   0.020
 11U  plan-2  H26   0.020
 11U  plan-2  H27   0.020
 11U  plan-2  H29   0.020
 11U  plan-2  H30   0.020
 11U  plan-3  C2    0.020
 11U  plan-3  C7    0.020
 11U  plan-3  O22   0.020
 11U  plan-3  N23   0.020
 11U  plan-3  C24   0.020
 11U  plan-3  HN23  0.020
 11U  plan-4  C28   0.020
 11U  plan-4  C31   0.020
 11U  plan-4  N49   0.020
 11U  plan-4  N48   0.020
 11U  plan-4  HN49  0.020
 11U  plan-4  HN48  0.020
 11U  plan-4  HN4A  0.020

