# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 07:51:20 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)N1CCC[C@H]1C(=O)NCc2ccc(cc2)C(N)=N
#
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
 24U  24U  1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  ligand  47  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_24U
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
 24U  C17   C  CH3   0  -0.666  -7.6803  -0.6986   0.9666
 24U  C33   C  CH2   0  -0.415  -6.3536  -1.1502   0.3712
 24U  C15   C  CH2   0  -0.582  -5.3320  -0.0233   0.3650
 24U  C14   C  C     0   0.569  -4.0070  -0.4016  -0.2569
 24U  O32   O  O     0  -0.506  -3.7288  -1.5515  -0.5772
 24U  N1    N  NT    0  -0.464  -3.1370   0.6049  -0.4588
 24U  C1    C  CH1   0  -0.222  -1.8446   0.3458  -1.0483
 24U  C7    C  C     0   0.572  -0.9577  -0.4464  -0.0924
 24U  O22   O  O     0  -0.486  -1.0962  -0.3876   1.1183
 24U  C2    C  CH2   0  -0.471  -1.2804   1.7544  -1.2831
 24U  C3    C  CH2   0  -0.475  -1.9109   2.5837  -0.1700
 24U  C4    C  CH2   0  -0.265  -3.3084   1.9895  -0.0323
 24U  N23   N  NH1   0  -0.629   0.0099  -1.1512  -0.7027
 24U  C24   C  CH2   0  -0.363   1.0423  -1.8810  -0.0089
 24U  C25   C  CR6   0   0.110   2.3741  -1.1711   0.0125
 24U  C26   C  CR16  0  -0.296   3.5488  -1.8822  -0.2137
 24U  C27   C  CR16  0  -0.259   4.7831  -1.2548  -0.1640
 24U  C28   C  CR6   0   0.033   4.8760   0.1053   0.1188
 24U  C21   C  C     0   0.334   6.2147   0.7562   0.1635
 24U  N47   N  N     0  -0.652   7.1792   0.2189  -0.4805
 24U  N46   N  NH2   0  -0.823   6.2723   1.9240   0.8697
 24U  C29   C  CR16  0  -0.275   3.6994   0.8210   0.3369
 24U  C30   C  CR16  0  -0.280   2.4664   0.1901   0.2845
 24U  H17   H  HCH3  0   0.219  -7.5639  -0.3734   2.0020
 24U  H17A  H  HCH3  0   0.219  -8.1013   0.1373   0.4049
 24U  H17B  H  HCH3  0   0.231  -8.4124  -1.5061   0.9551
 24U  H33   H  HCH2  0   0.223  -6.5154  -1.5058  -0.6488
 24U  H33A  H  HCH2  0   0.224  -5.9676  -2.0008   0.9364
 24U  H15   H  HCH2  0   0.265  -5.1497   0.3224   1.3892
 24U  H15A  H  HCH2  0   0.258  -5.7390   0.8453  -0.1632
 24U  H1    H  HCH1  0   0.285  -1.9462  -0.1969  -1.9914
 24U  H2    H  HCH2  0   0.259  -0.1907   1.7799  -1.2822
 24U  H2A   H  HCH2  0   0.261  -1.6128   2.1107  -2.2599
 24U  H3    H  HCH2  0   0.245  -1.3538   2.4669   0.7603
 24U  H3A   H  HCH2  0   0.257  -1.9419   3.6466  -0.4044
 24U  H4    H  HCH2  0   0.242  -4.0243   2.5062  -0.6781
 24U  H4A   H  HCH2  0   0.254  -3.6790   2.0494   0.9916
 24U  HN23  H  HNH1  0   0.404   0.0546  -1.1373  -1.7094
 24U  H24   H  HCH2  0   0.271   0.7030  -2.0609   1.0119
 24U  H24A  H  HCH2  0   0.271   1.1573  -2.8600  -0.4766
 24U  H26   H  HCR6  0   0.255   3.4991  -2.9426  -0.4314
 24U  H27   H  HCR6  0   0.255   5.6859  -1.8226  -0.3430
 24U  HN47  H  H     0   0.323   8.0437   0.7358  -0.3437
 24U  HN46  H  HNH2  0   0.395   5.6328   2.0511   1.6367
 24U  HN4A  H  HNH2  0   0.391   7.1845   2.3177   1.0385
 24U  H29   H  HCR6  0   0.258   3.7304   1.8854   0.5319
 24U  H30   H  HCR6  0   0.249   1.5721   0.7746   0.4609

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
 24U  C1   N1    single    1.444  0.020  1.444
 24U  C4   N1    single    1.459  0.020  1.459
 24U  N1   C14   single    1.346  0.020  1.346
 24U  C2   C1    single    1.536  0.020  1.536
 24U  C7   C1    single    1.526  0.020  1.526
 24U  C1   H1    single    0.970  0.020  1.090
 24U  O22  C7    double    1.220  0.020  1.220
 24U  C7   N23   single    1.344  0.020  1.344
 24U  C24  N23   single    1.442  0.020  1.442
 24U  N23  HN23  single    0.860  0.020  1.020
 24U  C24  C25   single    1.509  0.020  1.509
 24U  C24  H24   single    0.970  0.020  1.090
 24U  C24  H24A  single    0.970  0.020  1.090
 24U  C25  C30   aromatic  1.391  0.020  1.391
 24U  C25  C26   aromatic  1.392  0.020  1.392
 24U  C26  C27   aromatic  1.385  0.020  1.385
 24U  C26  H26   single    0.930  0.020  1.080
 24U  C27  C28   aromatic  1.392  0.020  1.392
 24U  C27  H27   single    0.930  0.020  1.080
 24U  C29  C28   aromatic  1.394  0.020  1.394
 24U  C28  C21   single    1.489  0.020  1.489
 24U  C21  N47   double    1.278  0.020  1.278
 24U  C21  N46   single    1.366  0.020  1.366
 24U  N46  HN46  single    0.890  0.020  1.040
 24U  N46  HN4A  single    0.890  0.020  1.040
 24U  N47  HN47  single    0.890  0.020  1.040
 24U  C30  C29   aromatic  1.386  0.020  1.386
 24U  C29  H29   single    0.930  0.020  1.080
 24U  C30  H30   single    0.930  0.020  1.080
 24U  C2   C3    single    1.525  0.020  1.525
 24U  C2   H2    single    0.970  0.020  1.090
 24U  C2   H2A   single    0.970  0.020  1.090
 24U  C3   C4    single    1.525  0.020  1.525
 24U  C3   H3    single    0.970  0.020  1.090
 24U  C3   H3A   single    0.970  0.020  1.090
 24U  C4   H4    single    0.970  0.020  1.090
 24U  C4   H4A   single    0.970  0.020  1.090
 24U  C14  O32   double    1.226  0.020  1.226
 24U  C14  C15   single    1.512  0.020  1.512
 24U  C15  C33   single    1.521  0.020  1.521
 24U  C15  H15   single    0.970  0.020  1.090
 24U  C15  H15A  single    0.970  0.020  1.090
 24U  C33  C17   single    1.523  0.020  1.523
 24U  C33  H33   single    0.970  0.020  1.090
 24U  C33  H33A  single    0.970  0.020  1.090
 24U  C17  H17   single    0.970  0.020  1.090
 24U  C17  H17A  single    0.970  0.020  1.090
 24U  C17  H17B  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
 24U  H17B  C17  H17A  107.62  3.000
 24U  H17B  C17  H17   107.60  3.000
 24U  H17A  C17  H17   107.52  3.000
 24U  H17B  C17  C33   111.19  3.000
 24U  H17A  C17  C33   111.22  3.000
 24U  H17   C17  C33   111.49  3.000
 24U  H33A  C33  H33   106.39  3.000
 24U  H33A  C33  C15   109.99  3.000
 24U  H33   C33  C15   109.69  3.000
 24U  H33A  C33  C17   109.67  3.000
 24U  H33   C33  C17   109.43  3.000
 24U  C15   C33  C17   111.53  3.000
 24U  H15A  C15  H15   105.21  3.000
 24U  H15A  C15  C14   109.01  3.000
 24U  H15   C15  C14   108.51  3.000
 24U  H15A  C15  C33   109.88  3.000
 24U  H15   C15  C33   109.97  3.000
 24U  C14   C15  C33   113.89  3.000
 24U  N1    C14  O32   121.05  3.000
 24U  O32   C14  C15   122.77  3.000
 24U  N1    C14  C15   116.18  3.000
 24U  C4    N1   C1    113.26  3.000
 24U  C4    N1   C14   126.16  3.000
 24U  C1    N1   C14   120.38  3.000
 24U  H1    C1   C2    110.96  3.000
 24U  H1    C1   C7    109.69  3.000
 24U  C2    C1   C7    111.01  3.000
 24U  H1    C1   N1    110.99  3.000
 24U  C7    C1   N1    110.96  3.000
 24U  C2    C1   N1    103.10  3.000
 24U  N23   C7   O22   123.90  3.000
 24U  N23   C7   C1    113.98  3.000
 24U  O22   C7   C1    122.05  3.000
 24U  H2A   C2   H2    107.31  3.000
 24U  H2A   C2   C3    110.48  3.000
 24U  H2    C2   C3    113.59  3.000
 24U  H2A   C2   C1    108.93  3.000
 24U  H2    C2   C1    112.87  3.000
 24U  C3    C2   C1    103.61  3.000
 24U  H3A   C3   H3    107.62  3.000
 24U  H3A   C3   C4    111.95  3.000
 24U  H3    C3   C4    110.44  3.000
 24U  H3A   C3   C2    112.68  3.000
 24U  H3    C3   C2    110.69  3.000
 24U  C4    C3   C2    103.47  3.000
 24U  H4A   C4   H4    107.81  3.000
 24U  H4A   C4   C3    112.01  3.000
 24U  H4    C4   C3    111.25  3.000
 24U  H4A   C4   N1    111.51  3.000
 24U  H4    C4   N1    110.65  3.000
 24U  C3    C4   N1    103.64  3.000
 24U  HN23  N23  C24   117.12  3.000
 24U  HN23  N23  C7    118.58  3.000
 24U  C24   N23  C7    124.23  3.000
 24U  H24A  C24  H24   106.62  3.000
 24U  H24A  C24  C25   109.58  3.000
 24U  H24   C24  C25   109.80  3.000
 24U  H24A  C24  N23   108.87  3.000
 24U  H24   C24  N23   108.13  3.000
 24U  C25   C24  N23   113.61  3.000
 24U  C30   C25  C26   118.41  3.000
 24U  C26   C25  C24   120.15  3.000
 24U  C30   C25  C24   121.44  3.000
 24U  H26   C26  C27   119.42  3.000
 24U  H26   C26  C25   119.60  3.000
 24U  C27   C26  C25   120.98  3.000
 24U  H27   C27  C28   119.39  3.000
 24U  H27   C27  C26   120.00  3.000
 24U  C28   C27  C26   120.61  3.000
 24U  C29   C28  C21   121.97  3.000
 24U  C21   C28  C27   119.54  3.000
 24U  C29   C28  C27   118.48  3.000
 24U  N46   C21  N47   126.02  3.000
 24U  N46   C21  C28   115.28  3.000
 24U  N47   C21  C28   118.65  3.000
 24U  HN47  N47  C21   111.12  3.000
 24U  HN4A  N46  HN46  113.46  3.000
 24U  HN4A  N46  C21   117.30  3.000
 24U  HN46  N46  C21   118.36  3.000
 24U  H29   C29  C30   118.67  3.000
 24U  H29   C29  C28   120.58  3.000
 24U  C30   C29  C28   120.73  3.000
 24U  H30   C30  C29   118.87  3.000
 24U  H30   C30  C25   120.35  3.000
 24U  C29   C30  C25   120.78  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
 24U  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 24U  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 24U  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 24U  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 24U  CONST_05  C30   C25  C26  C27     0.00   0.0  0
 24U  CONST_06  C30   C29  C28  C27     0.00   0.0  0
 24U  CONST_07  C29   C30  C25  C24   180.00   0.0  0
 24U  CONST_08  C27   C26  C25  C24   180.00   0.0  0
 24U  CONST_09  C21   C28  C27  C26   180.00   0.0  0
 24U  CONST_10  C30   C29  C28  C21   180.00   0.0  0
 24U  CONST_11  H29   C29  C30  C25   180.00   0.0  0
 24U  CONST_12  H27   C27  C26  C25   180.00   0.0  0
 24U  CONST_13  H30   C30  C25  C26   180.00   0.0  0
 24U  CONST_14  H26   C26  C27  C28   180.00   0.0  0
 24U  CONST_15  C1    N1   C14  C15   180.00   0.0  0
 24U  CONST_16  C4    N1   C14  C15     0.00   0.0  0
 24U  CONST_17  C1    N1   C14  O32     0.00   0.0  0
 24U  CONST_18  C4    N1   C14  O32   180.00   0.0  0
 24U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 24U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 24U  CONST_21  HN47  N47  C21  C28   180.00   0.0  0
 24U  CONST_23  HN4A  N46  C21  C28   180.00   0.0  0
 24U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 24U  Var_01    C2    C3   C4   N1     28.15  30.0  1
 24U  Var_02    C3    C4   N1   C1     -9.60  30.0  1
 24U  Var_03    C4    C3   C2   C1    -36.18  30.0  1
 24U  Var_04    C30   C25  C24  N23    43.99  30.0  2
 24U  Var_05    N47   C21  C28  C27    23.70  30.0  2
 24U  Var_06    N1    C14  C15  C33   170.96  30.0  1
 24U  Var_07    C25   C24  N23  C7   -101.96  30.0  1
 24U  Var_08    C14   C15  C33  C17  -178.13  30.0  1
 24U  Var_09    H17   C17  C33  C15   -60.74  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
 24U  chir_01  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
 24U  plan-1  C24   0.020
 24U  plan-1  C25   0.020
 24U  plan-1  C26   0.020
 24U  plan-1  C27   0.020
 24U  plan-1  C28   0.020
 24U  plan-1  C21   0.020
 24U  plan-1  C29   0.020
 24U  plan-1  C30   0.020
 24U  plan-1  H26   0.020
 24U  plan-1  H27   0.020
 24U  plan-1  H29   0.020
 24U  plan-1  H30   0.020
 24U  plan-2  C1    0.020
 24U  plan-2  C7    0.020
 24U  plan-2  O22   0.020
 24U  plan-2  N23   0.020
 24U  plan-2  C24   0.020
 24U  plan-2  HN23  0.020
 24U  plan-3  C15   0.020
 24U  plan-3  C14   0.020
 24U  plan-3  O32   0.020
 24U  plan-3  N1    0.020
 24U  plan-3  C1    0.020
 24U  plan-3  C4    0.020
 24U  plan-4  C28   0.020
 24U  plan-4  C21   0.020
 24U  plan-4  N47   0.020
 24U  plan-4  N46   0.020
 24U  plan-4  HN47  0.020
 24U  plan-4  HN46  0.020
 24U  plan-4  HN4A  0.020

