# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:32:57 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-(4-carbamimidoylbenzyl)-1-(3-cyclopentylpropanoyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CCC3CCCC3)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
 49U  49U  N-(4-carbamimidoylbenzyl)-1-(3-cyclopentylpropanoyl)-L-prolinamide  ligand  57  27  .  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_49U
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
 49U  C47   C  CH2   0  -0.448   6.4500  -2.5916   0.0269
 49U  C45   C  CH2   0  -0.432   5.2670  -1.6970  -0.3380
 49U  C44   C  CH1   0  -0.232   4.6883  -1.3012   1.0203
 49U  C49   C  CH2   0  -0.432   4.7597  -2.6112   1.8152
 49U  C48   C  CH2   0  -0.444   5.9820  -3.3789   1.2672
 49U  C21   C  CH2   0  -0.404   3.2930  -0.6942   0.9806
 49U  C5    C  CH2   0  -0.605   3.2666   0.6400   0.2511
 49U  C14   C  C     0   0.591   1.9046   1.2942   0.2131
 49U  O32   O  O     0  -0.504   0.9233   0.8139   0.7703
 49U  N1    N  NR5   0  -0.481   1.8194   2.4494  -0.4706
 49U  C1    C  CR15  0  -0.176   0.5526   3.1399  -0.6025
 49U  C7    C  C     0   0.559  -0.5004   2.2651  -1.2686
 49U  O22   O  O     0  -0.485  -0.2218   1.5030  -2.1787
 49U  C2    C  CH2   0  -0.477   0.8863   4.3458  -1.4975
 49U  C3    C  CH2   0  -0.471   2.3778   4.5619  -1.2693
 49U  C4    C  CH2   0  -0.271   2.9146   3.1450  -1.1328
 49U  N23   N  NH1   0  -0.639  -1.7517   2.4814  -0.8317
 49U  C24   C  CH2   0  -0.332  -2.9157   1.8695  -1.4132
 49U  C25   C  CR6   0   0.076  -3.3645   0.5904  -0.7459
 49U  C30   C  CR16  0  -0.276  -4.6329   0.0927  -1.0345
 49U  C29   C  CR16  0  -0.272  -5.0865  -1.0819  -0.4585
 49U  C28   C  CR6   0  -0.005  -4.2722  -1.7998   0.4173
 49U  C9    C  C     0   0.327  -4.7297  -3.0773   1.0310
 49U  N46   N  N     0  -0.642  -3.9717  -4.0754   1.2823
 49U  N47   N  NH2   0  -0.804  -6.0682  -3.1471   1.2839
 49U  C27   C  CR16  0  -0.279  -3.0040  -1.3033   0.7030
 49U  C26   C  CR16  0  -0.303  -2.5557  -0.1205   0.1329
 49U  H47   H  HCH2  0   0.219   7.3125  -1.9690   0.2774
 49U  H47A  H  HCH2  0   0.227   6.7579  -3.2423  -0.7929
 49U  H45   H  HCH2  0   0.209   4.5170  -2.2662  -0.8997
 49U  H45A  H  HCH2  0   0.230   5.5578  -0.8442  -0.9549
 49U  H44   H  HCH1  0   0.214   5.3737  -0.5778   1.4822
 49U  H49   H  HCH2  0   0.228   4.8196  -2.4330   2.8903
 49U  H49A  H  HCH2  0   0.215   3.8456  -3.1875   1.6444
 49U  H48   H  HCH2  0   0.225   6.7782  -3.4606   2.0084
 49U  H48A  H  HCH2  0   0.224   5.7033  -4.3983   0.9971
 49U  H21   H  HCH2  0   0.227   2.9260  -0.5605   2.0016
 49U  H21A  H  HCH2  0   0.216   2.6113  -1.4010   0.4969
 49U  H5    H  HCH2  0   0.269   3.6213   0.5203  -0.7777
 49U  H5A   H  HCH2  0   0.265   3.9749   1.3301   0.7231
 49U  H1    H  HCR5  0   0.274   0.2014   3.4801   0.3777
 49U  H2    H  HCH2  0   0.251   0.7046   4.1025  -2.5465
 49U  H2A   H  HCH2  0   0.265   0.2787   5.2128  -1.2445
 49U  H3    H  HCH2  0   0.257   2.8554   5.1098  -2.0804
 49U  H3A   H  HCH2  0   0.244   2.5465   5.1150  -0.3432
 49U  H4    H  HCH2  0   0.242   3.1288   2.7009  -2.1098
 49U  H4A   H  HCH2  0   0.257   3.8272   3.1072  -0.5393
 49U  HN23  H  HNH1  0   0.406  -1.8875   3.0814  -0.0342
 49U  H24   H  HCH2  0   0.273  -3.7300   2.5949  -1.3835
 49U  H24A  H  HCH2  0   0.270  -2.7175   1.6742  -2.4686
 49U  H30   H  HCR6  0   0.255  -5.2786   0.6304  -1.7192
 49U  H29   H  HCR6  0   0.261  -6.0758  -1.4449  -0.7065
 49U  HN46  H  H     0   0.331  -3.0325  -3.9074   0.9417
 49U  HN47  H  HNH2  0   0.392  -6.5555  -2.2943   1.5030
 49U  HN4A  H  HNH2  0   0.383  -6.3741  -3.9446   1.8187
 49U  H27   H  HCR6  0   0.259  -2.3587  -1.8292   1.3963
 49U  H26   H  HCR6  0   0.271  -1.5715   0.2488   0.3902

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
 49U  C2   C3    single    1.524  0.020  1.524
 49U  C2   C1    single    1.538  0.020  1.538
 49U  C24  N23   single    1.438  0.020  1.438
 49U  C24  C25   single    1.511  0.020  1.511
 49U  N23  C7    single    1.343  0.020  1.343
 49U  C3   C4    single    1.521  0.020  1.521
 49U  C26  C25   aromatic  1.390  0.020  1.390
 49U  C26  C27   aromatic  1.388  0.020  1.388
 49U  C7   O22   double    1.219  0.020  1.219
 49U  C7   C1    single    1.522  0.020  1.522
 49U  C1   N1    single    1.449  0.020  1.449
 49U  C25  C30   aromatic  1.393  0.020  1.393
 49U  C27  C28   aromatic  1.392  0.020  1.392
 49U  C4   N1    single    1.457  0.020  1.457
 49U  N1   C14   single    1.345  0.020  1.345
 49U  C30  C29   aromatic  1.385  0.020  1.385
 49U  C28  C29   aromatic  1.395  0.020  1.395
 49U  C28  C9    single    1.489  0.020  1.489
 49U  C14  O32   double    1.226  0.020  1.226
 49U  C14  C5    single    1.511  0.020  1.511
 49U  N47  C9    single    1.364  0.020  1.364
 49U  C9   N46   double    1.278  0.020  1.278
 49U  C5   C21   single    1.521  0.020  1.521
 49U  C45  C44   single    1.529  0.020  1.529
 49U  C45  C47   single    1.527  0.020  1.527
 49U  C44  C21   single    1.522  0.020  1.522
 49U  C44  C49   single    1.534  0.020  1.534
 49U  C47  C48   single    1.542  0.020  1.542
 49U  C48  C49   single    1.544  0.020  1.544
 49U  N23  HN23  single    0.860  0.020  1.020
 49U  C24  H24   single    0.970  0.020  1.090
 49U  C24  H24A  single    0.970  0.020  1.090
 49U  C26  H26   single    0.930  0.020  1.080
 49U  C27  H27   single    0.930  0.020  1.080
 49U  N46  HN46  single    0.890  0.020  1.040
 49U  N47  HN47  single    0.890  0.020  1.040
 49U  N47  HN4A  single    0.890  0.020  1.040
 49U  C29  H29   single    0.930  0.020  1.080
 49U  C30  H30   single    0.930  0.020  1.080
 49U  C1   H1    single    0.970  0.020  1.090
 49U  C2   H2    single    0.970  0.020  1.090
 49U  C2   H2A   single    0.970  0.020  1.090
 49U  C3   H3    single    0.970  0.020  1.090
 49U  C3   H3A   single    0.970  0.020  1.090
 49U  C4   H4    single    0.970  0.020  1.090
 49U  C4   H4A   single    0.970  0.020  1.090
 49U  C5   H5    single    0.970  0.020  1.090
 49U  C5   H5A   single    0.970  0.020  1.090
 49U  C21  H21   single    0.970  0.020  1.090
 49U  C21  H21A  single    0.970  0.020  1.090
 49U  C44  H44   single    0.970  0.020  1.090
 49U  C49  H49   single    0.970  0.020  1.090
 49U  C49  H49A  single    0.970  0.020  1.090
 49U  C48  H48   single    0.970  0.020  1.090
 49U  C48  H48A  single    0.970  0.020  1.090
 49U  C47  H47   single    0.970  0.020  1.090
 49U  C47  H47A  single    0.970  0.020  1.090
 49U  C45  H45   single    0.970  0.020  1.090
 49U  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
 49U  H47A  C47  H47   106.81  3.000
 49U  H47A  C47  C48   112.68  3.000
 49U  H47   C47  C48   110.25  3.000
 49U  H47A  C47  C45   112.85  3.000
 49U  H47   C47  C45   109.41  3.000
 49U  C48   C47  C45   104.85  3.000
 49U  H45A  C45  H45   107.35  3.000
 49U  H45A  C45  C44   113.62  3.000
 49U  H45   C45  C44   109.31  3.000
 49U  H45A  C45  C47   112.72  3.000
 49U  H45   C45  C47   110.37  3.000
 49U  C44   C45  C47   103.44  3.000
 49U  H44   C44  C21   108.68  3.000
 49U  H44   C44  C49   108.39  3.000
 49U  C21   C44  C49   113.38  3.000
 49U  H44   C44  C45   107.94  3.000
 49U  C49   C44  C45   102.81  3.000
 49U  C21   C44  C45   115.28  3.000
 49U  H49A  C49  H49   106.60  3.000
 49U  H49A  C49  C48   110.13  3.000
 49U  H49   C49  C48   112.79  3.000
 49U  H49A  C49  C44   109.27  3.000
 49U  H49   C49  C44   111.93  3.000
 49U  C48   C49  C44   106.11  3.000
 49U  H48A  C48  H48   106.54  3.000
 49U  H48A  C48  C49   110.51  3.000
 49U  H48   C48  C49   111.96  3.000
 49U  H48A  C48  C47   110.82  3.000
 49U  H48   C48  C47   111.30  3.000
 49U  C49   C48  C47   105.78  3.000
 49U  H21A  C21  H21   106.41  3.000
 49U  H21A  C21  C5    110.10  3.000
 49U  H21   C21  C5    109.57  3.000
 49U  H21A  C21  C44   108.96  3.000
 49U  H21   C21  C44   109.40  3.000
 49U  C5    C21  C44   112.23  3.000
 49U  H5A   C5   H5    105.32  3.000
 49U  H5A   C5   C14   108.71  3.000
 49U  H5    C5   C14   108.40  3.000
 49U  H5A   C5   C21   109.55  3.000
 49U  H5    C5   C21   110.44  3.000
 49U  C14   C5   C21   114.04  3.000
 49U  N1    C14  O32   121.10  3.000
 49U  O32   C14  C5    122.69  3.000
 49U  N1    C14  C5    116.20  3.000
 49U  C4    N1   C1    112.86  3.000
 49U  C4    N1   C14   126.41  3.000
 49U  C1    N1   C14   120.73  3.000
 49U  H1    C1   C2    110.28  3.000
 49U  H1    C1   C7    110.38  3.000
 49U  C2    C1   C7    110.24  3.000
 49U  H1    C1   N1    110.30  3.000
 49U  C7    C1   N1    111.76  3.000
 49U  C2    C1   N1    103.70  3.000
 49U  N23   C7   O22   123.81  3.000
 49U  O22   C7   C1    121.85  3.000
 49U  N23   C7   C1    114.18  3.000
 49U  H2A   C2   H2    107.93  3.000
 49U  H2A   C2   C3    113.48  3.000
 49U  H2    C2   C3    109.77  3.000
 49U  H2A   C2   C1    111.59  3.000
 49U  H2    C2   C1    110.37  3.000
 49U  C3    C2   C1    103.67  3.000
 49U  H3A   C3   H3    108.00  3.000
 49U  H3A   C3   C4    109.95  3.000
 49U  H3    C3   C4    112.38  3.000
 49U  H3A   C3   C2    110.49  3.000
 49U  H3    C3   C2    112.89  3.000
 49U  C4    C3   C2    103.10  3.000
 49U  H4A   C4   H4    107.96  3.000
 49U  H4A   C4   C3    112.14  3.000
 49U  H4    C4   C3    111.52  3.000
 49U  H4A   C4   N1    111.45  3.000
 49U  H4    C4   N1    111.05  3.000
 49U  C3    C4   N1    102.73  3.000
 49U  HN23  N23  C24   117.68  3.000
 49U  HN23  N23  C7    118.63  3.000
 49U  C24   N23  C7    123.65  3.000
 49U  H24A  C24  H24   106.31  3.000
 49U  H24A  C24  C25   109.24  3.000
 49U  H24   C24  C25   109.22  3.000
 49U  H24A  C24  N23   108.67  3.000
 49U  H24   C24  N23   108.07  3.000
 49U  C25   C24  N23   114.97  3.000
 49U  C26   C25  C30   118.57  3.000
 49U  C30   C25  C24   118.79  3.000
 49U  C26   C25  C24   122.64  3.000
 49U  H30   C30  C29   119.24  3.000
 49U  H30   C30  C25   119.74  3.000
 49U  C29   C30  C25   121.02  3.000
 49U  H29   C29  C28   120.32  3.000
 49U  H29   C29  C30   119.24  3.000
 49U  C28   C29  C30   120.43  3.000
 49U  C27   C28  C9    120.09  3.000
 49U  C9    C28  C29   121.39  3.000
 49U  C27   C28  C29   118.51  3.000
 49U  N47   C9   N46   120.36  3.000
 49U  N46   C9   C28   124.65  3.000
 49U  N47   C9   C28   114.95  3.000
 49U  HN46  N46  C9    110.75  3.000
 49U  HN4A  N47  HN47  114.08  3.000
 49U  HN4A  N47  C9    115.90  3.000
 49U  HN47  N47  C9    118.17  3.000
 49U  H27   C27  C26   118.97  3.000
 49U  H27   C27  C28   120.07  3.000
 49U  C26   C27  C28   120.95  3.000
 49U  H26   C26  C27   119.14  3.000
 49U  H26   C26  C25   120.34  3.000
 49U  C27   C26  C25   120.52  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
 49U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 49U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 49U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 49U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 49U  CONST_05  C26   C25  C30  C29     0.00   0.0  0
 49U  CONST_06  C26   C27  C28  C29     0.00   0.0  0
 49U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 49U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 49U  CONST_09  C9    C28  C29  C30   180.00   0.0  0
 49U  CONST_10  C26   C27  C28  C9    180.00   0.0  0
 49U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 49U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 49U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 49U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 49U  CONST_15  C1    N1   C14  C5    180.00   0.0  0
 49U  CONST_16  C4    N1   C14  C5      0.00   0.0  0
 49U  CONST_17  C1    N1   C14  O32     0.00   0.0  0
 49U  CONST_18  C4    N1   C14  O32   180.00   0.0  0
 49U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 49U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 49U  CONST_22  HN4A  N47  C9   C28   180.00   0.0  0
 49U  CONST_23  HN46  N46  C9   C28     0.00   0.0  0
 49U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 49U  Var_01    C44   C49  C48  C47    -8.53  30.0  1
 49U  Var_02    C49   C48  C47  C45   -17.06  30.0  1
 49U  Var_03    C48   C47  C45  C44    36.36  30.0  1
 49U  Var_04    C2    C3   C4   N1    -34.25  30.0  1
 49U  Var_05    C4    C3   C2   C1     36.65  30.0  1
 49U  Var_06    C3    C4   N1   C1     19.71  30.0  1
 49U  Var_07    C26   C25  C24  N23   -15.15  30.0  2
 49U  Var_08    N47   C9   C28  C29   -32.90  30.0  2
 49U  Var_09    C14   C5   C21  C44  -178.76  30.0  2
 49U  Var_10    N1    C14  C5   C21  -177.27  30.0  2
 49U  Var_11    C25   C24  N23  C7     93.82  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
 49U  chir_01  C44  C45  C21  C49  negativ
 49U  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
 49U  plan-1  C5    0.020
 49U  plan-1  C14   0.020
 49U  plan-1  O32   0.020
 49U  plan-1  N1    0.020
 49U  plan-1  C1    0.020
 49U  plan-1  C4    0.020
 49U  plan-2  C24   0.020
 49U  plan-2  C25   0.020
 49U  plan-2  C30   0.020
 49U  plan-2  C29   0.020
 49U  plan-2  C28   0.020
 49U  plan-2  C9    0.020
 49U  plan-2  C27   0.020
 49U  plan-2  C26   0.020
 49U  plan-2  H30   0.020
 49U  plan-2  H29   0.020
 49U  plan-2  H27   0.020
 49U  plan-2  H26   0.020
 49U  plan-3  C1    0.020
 49U  plan-3  C7    0.020
 49U  plan-3  O22   0.020
 49U  plan-3  N23   0.020
 49U  plan-3  C24   0.020
 49U  plan-3  HN23  0.020
 49U  plan-4  C28   0.020
 49U  plan-4  C9    0.020
 49U  plan-4  N46   0.020
 49U  plan-4  N47   0.020
 49U  plan-4  HN46  0.020
 49U  plan-4  HN47  0.020
 49U  plan-4  HN4A  0.020

