# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:04:59 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-(4-carbamimidoylbenzyl)-1-[(cyclohexyloxy)acetyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)COC3CCCCC3)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
 46U  46U  N-(4-carbamimidoylbenzyl)-1-[(cyclohexyloxy)acetyl]-L-prolinamide  peptide  58  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 PERFECT
;

data_comp_46U
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
 46U  O32   O  O     0  -0.491   1.6814  -0.5423   0.4755
 46U  C14   C  C     0   0.514   2.2262   0.5240   0.2350
 46U  C5    C  CH2   0  -0.266   3.7221   0.6402   0.0074
 46U  O21   O  O2    0  -0.492   4.3068  -0.5919   0.2832
 46U  C44   C  CH1   0   0.087   5.6715  -0.6966  -0.0832
 46U  C49   C  CH2   0  -0.460   6.0383  -2.1720  -0.0179
 46U  C48   C  CH2   0  -0.442   7.5040  -2.3965  -0.3781
 46U  C47   C  CH2   0  -0.430   8.4259  -1.5677   0.5093
 46U  C46   C  CH2   0  -0.438   8.0555  -0.0905   0.4467
 46U  C45   C  CH2   0  -0.471   6.5891   0.1330   0.8116
 46U  N1    N  NT    0  -0.463   1.5381   1.6739   0.1579
 46U  C1    C  CH1   0  -0.212   0.1028   1.6723   0.3374
 46U  C7    C  C     0   0.579  -0.5808   0.9178  -0.7984
 46U  O22   O  O     0  -0.492  -0.1444   0.9306  -1.9386
 46U  C2    C  CH2   0  -0.472  -0.2558   3.1655   0.3076
 46U  C3    C  CH2   0  -0.470   0.8289   3.7838  -0.5677
 46U  C4    C  CH2   0  -0.278   2.0734   2.9812  -0.2075
 46U  N23   N  NH1   0  -0.635  -1.7235   0.3092  -0.4513
 46U  C24   C  CH2   0  -0.320  -2.5455  -0.4219  -1.3946
 46U  C25   C  CR6   0   0.060  -3.9431  -0.5732  -0.8621
 46U  C30   C  CR16  0  -0.287  -4.4387  -1.8185  -0.5010
 46U  C29   C  CR16  0  -0.275  -5.7254  -1.9527   0.0043
 46U  C28   C  CR6   0   0.037  -6.5450  -0.8383   0.1551
 46U  C21   C  C     0   0.330  -7.9333  -0.9512   0.6811
 46U  N46   N  N     0  -0.650  -8.7976  -0.0848   0.3149
 46U  N47   N  NH2   0  -0.821  -8.1637  -2.0305   1.4867
 46U  C27   C  CR16  0  -0.259  -6.0508   0.4120  -0.2170
 46U  C26   C  CR16  0  -0.269  -4.7660   0.5428  -0.7115
 46U  H5    H  HCH2  0   0.237   3.8982   0.9500  -1.0352
 46U  H5A   H  HCH2  0   0.238   4.1224   1.4484   0.6350
 46U  H44   H  HCH1  0   0.194   5.7953  -0.3493  -1.1231
 46U  H49   H  HCH2  0   0.217   5.8512  -2.5406   0.9969
 46U  H49A  H  HCH2  0   0.235   5.3913  -2.7414  -0.6900
 46U  H48   H  HCH2  0   0.233   7.7452  -3.4588  -0.2984
 46U  H48A  H  HCH2  0   0.214   7.6668  -2.1203  -1.4255
 46U  H47   H  HCH2  0   0.211   8.3469  -1.9174   1.5445
 46U  H47A  H  HCH2  0   0.229   9.4674  -1.7104   0.2114
 46U  H46   H  HCH2  0   0.233   8.6928   0.4927   1.1147
 46U  H46A  H  HCH2  0   0.214   8.2413   0.2878  -0.5645
 46U  H45   H  HCH2  0   0.237   6.3524   1.1976   0.7351
 46U  H45A  H  HCH2  0   0.217   6.4217  -0.1577   1.8548
 46U  H1    H  HCH1  0   0.283  -0.1682   1.2253   1.2974
 46U  H2    H  HCH2  0   0.264  -1.2657   3.3454  -0.0601
 46U  H2A   H  HCH2  0   0.260  -0.2003   3.5626   1.3223
 46U  H3    H  HCH2  0   0.247   0.5916   3.6574  -1.6241
 46U  H3A   H  HCH2  0   0.257   0.9639   4.8479  -0.3798
 46U  H4    H  HCH2  0   0.247   2.6046   3.4312   0.6363
 46U  H4A   H  HCH2  0   0.258   2.7701   2.9105  -1.0435
 46U  HN23  H  HNH1  0   0.404  -1.9621   0.2449   0.5255
 46U  H24   H  HCH2  0   0.262  -2.5638   0.1267  -2.3377
 46U  H24A  H  HCH2  0   0.256  -2.1152  -1.4054  -1.6039
 46U  H30   H  HCR6  0   0.258  -3.8186  -2.6989  -0.6175
 46U  H29   H  HCR6  0   0.260  -6.0855  -2.9407   0.2609
 46U  HN46  H  H     0   0.324  -9.6953  -0.2511   0.7622
 46U  HN47  H  HNH2  0   0.395  -7.3953  -2.3889   2.0301
 46U  HN4A  H  HNH2  0   0.391  -9.0450  -2.0584   1.9755
 46U  H27   H  HCR6  0   0.256  -6.6807   1.2848  -0.1101
 46U  H26   H  HCR6  0   0.257  -4.3983   1.5241  -0.9867

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
 46U  O32  C14   double    1.221  0.020  1.221
 46U  C14  C5    single    1.518  0.020  1.518
 46U  C14  N1    single    1.342  0.020  1.342
 46U  C5   O21   single    1.391  0.020  1.391
 46U  O21  C44   single    1.417  0.020  1.417
 46U  C44  C49   single    1.522  0.020  1.522
 46U  C44  C45   single    1.527  0.020  1.527
 46U  C49  C48   single    1.526  0.020  1.526
 46U  C48  C47   single    1.525  0.020  1.525
 46U  C47  C46   single    1.524  0.020  1.524
 46U  C46  C45   single    1.528  0.020  1.528
 46U  N1   C1    single    1.446  0.020  1.446
 46U  N1   C4    single    1.459  0.020  1.459
 46U  C1   C2    single    1.536  0.020  1.536
 46U  C1   C7    single    1.525  0.020  1.525
 46U  C2   C3    single    1.525  0.020  1.525
 46U  C3   C4    single    1.524  0.020  1.524
 46U  C7   O22   double    1.221  0.020  1.221
 46U  C7   N23   single    1.340  0.020  1.340
 46U  N23  C24   single    1.449  0.020  1.449
 46U  C24  C25   single    1.503  0.020  1.503
 46U  C25  C26   aromatic  1.395  0.020  1.395
 46U  C25  C30   aromatic  1.388  0.020  1.388
 46U  C26  C27   aromatic  1.383  0.020  1.383
 46U  C27  C28   aromatic  1.395  0.020  1.395
 46U  C28  C21   single    1.489  0.020  1.489
 46U  C28  C29   aromatic  1.392  0.020  1.392
 46U  C21  N46   double    1.277  0.020  1.277
 46U  C21  N47   single    1.366  0.020  1.366
 46U  C29  C30   aromatic  1.389  0.020  1.389
 46U  C5   H5    single    0.970  0.020  1.090
 46U  C5   H5A   single    0.970  0.020  1.090
 46U  C44  H44   single    0.970  0.020  1.090
 46U  C49  H49   single    0.970  0.020  1.090
 46U  C49  H49A  single    0.970  0.020  1.090
 46U  C48  H48   single    0.970  0.020  1.090
 46U  C48  H48A  single    0.970  0.020  1.090
 46U  C47  H47   single    0.970  0.020  1.090
 46U  C47  H47A  single    0.970  0.020  1.090
 46U  C46  H46   single    0.970  0.020  1.090
 46U  C46  H46A  single    0.970  0.020  1.090
 46U  C45  H45   single    0.970  0.020  1.090
 46U  C45  H45A  single    0.970  0.020  1.090
 46U  C1   H1    single    0.970  0.020  1.090
 46U  C2   H2    single    0.970  0.020  1.090
 46U  C2   H2A   single    0.970  0.020  1.090
 46U  C3   H3    single    0.970  0.020  1.090
 46U  C3   H3A   single    0.970  0.020  1.090
 46U  C4   H4    single    0.970  0.020  1.090
 46U  C4   H4A   single    0.970  0.020  1.090
 46U  N23  HN23  single    0.860  0.020  1.020
 46U  C24  H24   single    0.970  0.020  1.090
 46U  C24  H24A  single    0.970  0.020  1.090
 46U  C26  H26   single    0.930  0.020  1.080
 46U  C27  H27   single    0.930  0.020  1.080
 46U  N46  HN46  single    0.890  0.020  1.040
 46U  N47  HN47  single    0.890  0.020  1.040
 46U  N47  HN4A  single    0.890  0.020  1.040
 46U  C29  H29   single    0.930  0.020  1.080
 46U  C30  H30   single    0.930  0.020  1.080

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
 46U  N1    C14  C5    115.54  3.000
 46U  N1    C14  O32   122.05  3.000
 46U  C5    C14  O32   122.42  3.000
 46U  H5A   C5   H5    105.99  3.000
 46U  H5A   C5   O21   112.65  3.000
 46U  H5    C5   O21   111.68  3.000
 46U  H5A   C5   C14   109.25  3.000
 46U  H5    C5   C14   108.73  3.000
 46U  O21   C5   C14   108.46  3.000
 46U  C44   O21  C5    114.76  3.000
 46U  H44   C44  C45   108.29  3.000
 46U  H44   C44  C49   108.58  3.000
 46U  C45   C44  C49   110.90  3.000
 46U  H44   C44  O21   109.18  3.000
 46U  C45   C44  O21   112.78  3.000
 46U  C49   C44  O21   107.02  3.000
 46U  H49A  C49  H49   107.05  3.000
 46U  H49A  C49  C48   110.30  3.000
 46U  H49   C49  C48   109.46  3.000
 46U  H49A  C49  C44   109.63  3.000
 46U  H49   C49  C44   108.95  3.000
 46U  C48   C49  C44   111.35  3.000
 46U  H48A  C48  H48   106.39  3.000
 46U  H48A  C48  C47   109.25  3.000
 46U  H48   C48  C47   110.66  3.000
 46U  H48A  C48  C49   109.35  3.000
 46U  H48   C48  C49   109.75  3.000
 46U  C47   C48  C49   111.32  3.000
 46U  H47A  C47  H47   106.54  3.000
 46U  H47A  C47  C46   110.31  3.000
 46U  H47   C47  C46   109.31  3.000
 46U  H47A  C47  C48   110.29  3.000
 46U  H47   C47  C48   109.44  3.000
 46U  C46   C47  C48   110.85  3.000
 46U  H46A  C46  H46   106.33  3.000
 46U  H46A  C46  C45   109.44  3.000
 46U  H46   C46  C45   109.63  3.000
 46U  H46A  C46  C47   109.35  3.000
 46U  H46   C46  C47   110.52  3.000
 46U  C45   C46  C47   111.43  3.000
 46U  H45A  C45  H45   106.97  3.000
 46U  H45A  C45  C46   109.59  3.000
 46U  H45   C45  C46   109.49  3.000
 46U  H45A  C45  C44   108.78  3.000
 46U  H45   C45  C44   110.98  3.000
 46U  C46   C45  C44   110.94  3.000
 46U  C4    N1   C1    113.34  3.000
 46U  C4    N1   C14   126.43  3.000
 46U  C1    N1   C14   120.04  3.000
 46U  H1    C1   C2    110.90  3.000
 46U  H1    C1   C7    109.91  3.000
 46U  C2    C1   C7    111.21  3.000
 46U  H1    C1   N1    110.82  3.000
 46U  C7    C1   N1    110.67  3.000
 46U  C2    C1   N1    103.19  3.000
 46U  N23   C7   O22   123.46  3.000
 46U  N23   C7   C1    114.45  3.000
 46U  O22   C7   C1    122.01  3.000
 46U  H2A   C2   H2    107.51  3.000
 46U  H2A   C2   C3    110.49  3.000
 46U  H2    C2   C3    113.49  3.000
 46U  H2A   C2   C1    108.90  3.000
 46U  H2    C2   C1    112.55  3.000
 46U  C3    C2   C1    103.84  3.000
 46U  H3A   C3   H3    107.91  3.000
 46U  H3A   C3   C4    111.88  3.000
 46U  H3    C3   C4    110.23  3.000
 46U  H3A   C3   C2    112.67  3.000
 46U  H3    C3   C2    110.75  3.000
 46U  C4    C3   C2    103.39  3.000
 46U  H4A   C4   H4    107.93  3.000
 46U  H4A   C4   C3    112.00  3.000
 46U  H4    C4   C3    111.23  3.000
 46U  H4A   C4   N1    111.61  3.000
 46U  H4    C4   N1    110.70  3.000
 46U  C3    C4   N1    103.38  3.000
 46U  HN23  N23  C24   117.68  3.000
 46U  HN23  N23  C7    118.81  3.000
 46U  C24   N23  C7    122.97  3.000
 46U  H24A  C24  H24   107.05  3.000
 46U  H24A  C24  C25   110.07  3.000
 46U  H24   C24  C25   109.95  3.000
 46U  H24A  C24  N23   110.80  3.000
 46U  H24   C24  N23   108.57  3.000
 46U  C25   C24  N23   110.34  3.000
 46U  C26   C25  C30   118.62  3.000
 46U  C30   C25  C24   120.96  3.000
 46U  C26   C25  C24   120.42  3.000
 46U  H30   C30  C29   119.41  3.000
 46U  H30   C30  C25   119.78  3.000
 46U  C29   C30  C25   120.81  3.000
 46U  H29   C29  C28   120.62  3.000
 46U  H29   C29  C30   118.86  3.000
 46U  C28   C29  C30   120.51  3.000
 46U  C27   C28  C21   119.51  3.000
 46U  C21   C28  C29   121.78  3.000
 46U  C27   C28  C29   118.70  3.000
 46U  N47   C21  N46   126.21  3.000
 46U  N47   C21  C28   115.18  3.000
 46U  N46   C21  C28   118.56  3.000
 46U  HN46  N46  C21   111.12  3.000
 46U  HN4A  N47  HN47  113.30  3.000
 46U  HN4A  N47  C21   117.07  3.000
 46U  HN47  N47  C21   118.07  3.000
 46U  H27   C27  C26   120.01  3.000
 46U  H27   C27  C28   119.37  3.000
 46U  C26   C27  C28   120.62  3.000
 46U  H26   C26  C27   119.46  3.000
 46U  H26   C26  C25   119.80  3.000
 46U  C27   C26  C25   120.74  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
 46U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 46U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 46U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 46U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 46U  CONST_05  C26   C27  C28  C29     0.00   0.0  0
 46U  CONST_06  C26   C25  C30  C29     0.00   0.0  0
 46U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 46U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 46U  CONST_09  C21   C28  C29  C30   180.00   0.0  0
 46U  CONST_10  C26   C27  C28  C21   180.00   0.0  0
 46U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 46U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 46U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 46U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 46U  CONST_15  C1    N1   C14  O32     0.00   0.0  0
 46U  CONST_16  C4    N1   C14  O32   180.00   0.0  0
 46U  CONST_17  C1    N1   C14  C5    180.00   0.0  0
 46U  CONST_18  C4    N1   C14  C5      0.00   0.0  0
 46U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 46U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 46U  CONST_21  HN46  N46  C21  C28   180.00   0.0  0
 46U  CONST_23  HN4A  N47  C21  C28   180.00   0.0  0
 46U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 46U  Var_01    C47   C48  C49  C44    55.73  30.0  1
 46U  Var_02    C47   C46  C45  C44   -55.93  30.0  1
 46U  Var_03    C46   C47  C48  C49   -55.30  30.0  1
 46U  Var_04    C45   C46  C47  C48    55.56  30.0  1
 46U  Var_05    C2    C3   C4   N1     29.75  30.0  1
 46U  Var_06    C3    C4   N1   C1    -12.52  30.0  1
 46U  Var_07    C4    C3   C2   C1    -36.15  30.0  1
 46U  Var_08    C26   C25  C24  N23    67.05  30.0  2
 46U  Var_09    N46   C21  C28  C29  -151.93  30.0  2
 46U  Var_10    N1    C14  C5   O21   172.68  30.0  1
 46U  Var_11    C25   C24  N23  C7   -160.36  30.0  3
 46U  Var_12    H5    C5   O21  C44    50.86  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
 46U  chir_01  C44  O21  C49  C45  positiv
 46U  chir_02  C1   N1   C7   C2   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
 46U  plan-1  O32   0.020
 46U  plan-1  C14   0.020
 46U  plan-1  C5    0.020
 46U  plan-1  N1    0.020
 46U  plan-1  C1    0.020
 46U  plan-1  C4    0.020
 46U  plan-2  C24   0.020
 46U  plan-2  C25   0.020
 46U  plan-2  C30   0.020
 46U  plan-2  C29   0.020
 46U  plan-2  C28   0.020
 46U  plan-2  C21   0.020
 46U  plan-2  C27   0.020
 46U  plan-2  C26   0.020
 46U  plan-2  H30   0.020
 46U  plan-2  H29   0.020
 46U  plan-2  H27   0.020
 46U  plan-2  H26   0.020
 46U  plan-3  C1    0.020
 46U  plan-3  C7    0.020
 46U  plan-3  O22   0.020
 46U  plan-3  N23   0.020
 46U  plan-3  C24   0.020
 46U  plan-3  HN23  0.020
 46U  plan-4  C28   0.020
 46U  plan-4  C21   0.020
 46U  plan-4  N46   0.020
 46U  plan-4  N47   0.020
 46U  plan-4  HN46  0.020
 46U  plan-4  HN47  0.020
 46U  plan-4  HN4A  0.020

