# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 14:28:08 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-(4-carbamimidoylbenzyl)-1-(3-phenylpropanoyl)-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
 27U  27U  N-(4-carbamimidoylbenzyl)-1-(3-phenylpropanoyl)-L-prolinamide  ligand  54  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_27U
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
 27U  C3    C  C     0   0.584  -2.3553   0.2174  -0.4770
 27U  O1    O  O     0  -0.506  -1.8694  -0.7628  -1.0296
 27U  C2    C  CH2   0  -0.588  -3.8289   0.3207  -0.1521
 27U  C1    C  CH2   0  -0.500  -4.5974  -0.9627  -0.4527
 27U  C17   C  CR6   0   0.127  -6.0558  -0.8078  -0.1197
 27U  C18   C  CR16  0  -0.308  -6.9359  -0.2341  -1.0357
 27U  C19   C  CR16  0  -0.239  -8.2768  -0.0571  -0.7233
 27U  C20   C  CR16  0  -0.274  -8.7617  -0.4528   0.5171
 27U  C21   C  CR16  0  -0.239  -7.8951  -1.0262   1.4381
 27U  C22   C  CR16  0  -0.312  -6.5540  -1.2003   1.1202
 27U  N1    N  NT    0  -0.485  -1.5898   1.2667  -0.1331
 27U  C7    C  CH1   0  -0.172  -0.1677   1.2531  -0.4117
 27U  C8    C  C     0   0.559   0.5207   0.0625   0.2418
 27U  O2    O  O     0  -0.488   0.2193  -0.3130   1.3626
 27U  C6    C  CH2   0  -0.481   0.3307   2.5723   0.1978
 27U  C5    C  CH2   0  -0.473  -0.9001   3.4714   0.1556
 27U  C4    C  CH2   0  -0.270  -2.0382   2.5123   0.4762
 27U  N2    N  NH1   0  -0.638   1.5211  -0.4592  -0.4866
 27U  C9    C  CH2   0  -0.330   2.3896  -1.5184  -0.0429
 27U  C10   C  CR6   0   0.084   3.8412  -1.1120   0.0202
 27U  C15   C  CR16  0  -0.290   4.8326  -2.0669  -0.1941
 27U  C14   C  CR16  0  -0.260   6.1730  -1.7324  -0.1115
 27U  C13   C  CR6   0   0.034   6.5624  -0.4251   0.1724
 27U  C16   C  C     0   0.333   8.0112  -0.0896   0.2402
 27U  N3    N  N     0  -0.652   8.8440  -1.0211   0.5083
 27U  N4    N  NH2   0  -0.823   8.3152   1.2286   0.0501
 27U  C12   C  CR16  0  -0.276   5.5720   0.5299   0.3904
 27U  C11   C  CR16  0  -0.280   4.2289   0.1892   0.3172
 27U  H2    H  HCH2  0   0.274  -3.9513   0.5962   0.8998
 27U  H2A   H  HCH2  0   0.277  -4.2578   1.1511  -0.7230
 27U  H1    H  HCH2  0   0.249  -4.4844  -1.2169  -1.5080
 27U  H1A   H  HCH2  0   0.249  -4.1726  -1.7900   0.1187
 27U  H18   H  HCR6  0   0.246  -6.5679   0.0754  -2.0075
 27U  H19   H  HCR6  0   0.253  -8.9447   0.3860  -1.4512
 27U  H20   H  HCR6  0   0.253  -9.8078  -0.3194   0.7612
 27U  H21   H  HCR6  0   0.253  -8.2631  -1.3440   2.4054
 27U  H22   H  HCR6  0   0.246  -5.8875  -1.6544   1.8447
 27U  H7    H  HCH1  0   0.274   0.0050   1.2453  -1.4932
 27U  H6    H  HCH2  0   0.252   0.6424   2.4180   1.2333
 27U  H6A   H  HCH2  0   0.266   1.1803   2.9728  -0.3526
 27U  H5    H  HCH2  0   0.258  -0.8444   4.2983   0.8620
 27U  H5A   H  HCH2  0   0.245  -1.0339   3.8886  -0.8442
 27U  H4    H  HCH2  0   0.258  -2.9876   2.8411   0.0552
 27U  H4A   H  HCH2  0   0.243  -2.1695   2.3952   1.5563
 27U  HN2   H  HNH1  0   0.404   1.6635  -0.1131  -1.4225
 27U  H9    H  HCH2  0   0.274   2.0552  -1.8393   0.9443
 27U  H9A   H  HCH2  0   0.266   2.2844  -2.3823  -0.7034
 27U  H15   H  HCR6  0   0.254   4.5525  -3.0851  -0.4380
 27U  H14   H  HCR6  0   0.255   6.9299  -2.4853  -0.2845
 27U  HN3   H  H     0   0.323   9.7996  -0.6746   0.4922
 27U  HN4   H  HNH2  0   0.395   7.7009   1.7847  -0.5218
 27U  HN4A  H  HNH2  0   0.391   9.2884   1.4656  -0.0600
 27U  H12   H  HCR6  0   0.257   5.8351   1.5500   0.6394
 27U  H11   H  HCR6  0   0.250   3.4826   0.9546   0.4897

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
 27U  C1   C2    single    1.526  0.020  1.526
 27U  C1   C17   single    1.504  0.020  1.504
 27U  C2   C3    single    1.512  0.020  1.512
 27U  C3   O1    double    1.226  0.020  1.226
 27U  C3   N1    single    1.344  0.020  1.344
 27U  N1   C4    single    1.457  0.020  1.457
 27U  N1   C7    single    1.449  0.020  1.449
 27U  C4   C5    single    1.522  0.020  1.522
 27U  C5   C6    single    1.525  0.020  1.525
 27U  C6   C7    single    1.536  0.020  1.536
 27U  C7   C8    single    1.523  0.020  1.523
 27U  C8   N2    single    1.343  0.020  1.343
 27U  C8   O2    double    1.220  0.020  1.220
 27U  N2   C9    single    1.440  0.020  1.440
 27U  C9   C10   single    1.509  0.020  1.509
 27U  C10  C11   aromatic  1.390  0.020  1.390
 27U  C10  C15   aromatic  1.393  0.020  1.393
 27U  C11  C12   aromatic  1.388  0.020  1.388
 27U  C12  C13   aromatic  1.393  0.020  1.393
 27U  C13  C14   aromatic  1.393  0.020  1.393
 27U  C13  C16   single    1.489  0.020  1.489
 27U  C14  C15   aromatic  1.384  0.020  1.384
 27U  C16  N3    double    1.278  0.020  1.278
 27U  C16  N4    single    1.366  0.020  1.366
 27U  C17  C18   aromatic  1.394  0.020  1.394
 27U  C17  C22   aromatic  1.393  0.020  1.393
 27U  C18  C19   aromatic  1.388  0.020  1.388
 27U  C19  C20   aromatic  1.389  0.020  1.389
 27U  C20  C21   aromatic  1.389  0.020  1.389
 27U  C21  C22   aromatic  1.389  0.020  1.389
 27U  C1   H1    single    0.970  0.020  1.090
 27U  C1   H1A   single    0.970  0.020  1.090
 27U  C2   H2    single    0.970  0.020  1.090
 27U  C2   H2A   single    0.970  0.020  1.090
 27U  C4   H4    single    0.970  0.020  1.090
 27U  C4   H4A   single    0.970  0.020  1.090
 27U  C5   H5    single    0.970  0.020  1.090
 27U  C5   H5A   single    0.970  0.020  1.090
 27U  C6   H6    single    0.970  0.020  1.090
 27U  C6   H6A   single    0.970  0.020  1.090
 27U  C7   H7    single    0.970  0.020  1.090
 27U  N2   HN2   single    0.860  0.020  1.020
 27U  C9   H9    single    0.970  0.020  1.090
 27U  C9   H9A   single    0.970  0.020  1.090
 27U  C11  H11   single    0.930  0.020  1.080
 27U  C12  H12   single    0.930  0.020  1.080
 27U  C14  H14   single    0.930  0.020  1.080
 27U  C15  H15   single    0.930  0.020  1.080
 27U  N3   HN3   single    0.890  0.020  1.040
 27U  N4   HN4   single    0.890  0.020  1.040
 27U  N4   HN4A  single    0.890  0.020  1.040
 27U  C18  H18   single    0.930  0.020  1.080
 27U  C19  H19   single    0.930  0.020  1.080
 27U  C20  H20   single    0.930  0.020  1.080
 27U  C21  H21   single    0.930  0.020  1.080
 27U  C22  H22   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
 27U  N1    C3   C2   116.54  3.000
 27U  N1    C3   O1   120.93  3.000
 27U  C2    C3   O1   122.53  3.000
 27U  H2A   C2   H2   105.45  3.000
 27U  H2A   C2   C1   109.74  3.000
 27U  H2    C2   C1   110.17  3.000
 27U  H2A   C2   C3   108.75  3.000
 27U  H2    C2   C3   109.43  3.000
 27U  C1    C2   C3   113.01  3.000
 27U  H1A   C1   H1   106.82  3.000
 27U  H1A   C1   C17  109.85  3.000
 27U  H1    C1   C17  109.78  3.000
 27U  H1A   C1   C2   109.78  3.000
 27U  H1    C1   C2   109.53  3.000
 27U  C17   C1   C2   110.99  3.000
 27U  C22   C17  C18  118.37  3.000
 27U  C22   C17  C1   121.00  3.000
 27U  C18   C17  C1   120.61  3.000
 27U  H18   C18  C19  119.55  3.000
 27U  H18   C18  C17  119.48  3.000
 27U  C19   C18  C17  120.97  3.000
 27U  H19   C19  C20  120.10  3.000
 27U  H19   C19  C18  119.78  3.000
 27U  C20   C19  C18  120.12  3.000
 27U  H20   C20  C21  120.30  3.000
 27U  H20   C20  C19  120.23  3.000
 27U  C21   C20  C19  119.47  3.000
 27U  H21   C21  C22  119.72  3.000
 27U  H21   C21  C20  120.12  3.000
 27U  C22   C21  C20  120.16  3.000
 27U  H22   C22  C21  119.54  3.000
 27U  H22   C22  C17  119.54  3.000
 27U  C21   C22  C17  120.92  3.000
 27U  C4    N1   C7   112.98  3.000
 27U  C7    N1   C3   120.17  3.000
 27U  C4    N1   C3   126.81  3.000
 27U  H7    C7   C6   110.29  3.000
 27U  H7    C7   C8   110.30  3.000
 27U  C6    C7   C8   110.76  3.000
 27U  H7    C7   N1   110.16  3.000
 27U  C8    C7   N1   111.62  3.000
 27U  C6    C7   N1   103.53  3.000
 27U  N2    C8   O2   124.25  3.000
 27U  O2    C8   C7   121.55  3.000
 27U  N2    C8   C7   114.07  3.000
 27U  H6A   C6   H6   107.97  3.000
 27U  H6A   C6   C5   113.52  3.000
 27U  H6    C6   C5   109.87  3.000
 27U  H6A   C6   C7   111.62  3.000
 27U  H6    C6   C7   110.33  3.000
 27U  C5    C6   C7   103.50  3.000
 27U  H5A   C5   H5   108.07  3.000
 27U  H5A   C5   C4   110.00  3.000
 27U  H5    C5   C4   112.33  3.000
 27U  H5A   C5   C6   110.47  3.000
 27U  H5    C5   C6   112.86  3.000
 27U  C4    C5   C6   103.07  3.000
 27U  H4A   C4   H4   108.01  3.000
 27U  H4A   C4   C5   111.41  3.000
 27U  H4    C4   C5   112.33  3.000
 27U  H4A   C4   N1   110.99  3.000
 27U  H4    C4   N1   111.38  3.000
 27U  C5    C4   N1   102.73  3.000
 27U  HN2   N2   C9   116.98  3.000
 27U  HN2   N2   C8   118.38  3.000
 27U  C9    N2   C8   124.61  3.000
 27U  H9A   C9   H9   106.56  3.000
 27U  H9A   C9   C10  109.32  3.000
 27U  H9    C9   C10  109.66  3.000
 27U  H9A   C9   N2   109.72  3.000
 27U  H9    C9   N2   108.09  3.000
 27U  C10   C9   N2   113.27  3.000
 27U  C11   C10  C15  118.43  3.000
 27U  C15   C10  C9   119.58  3.000
 27U  C11   C10  C9   121.97  3.000
 27U  H15   C15  C14  119.39  3.000
 27U  H15   C15  C10  119.64  3.000
 27U  C14   C15  C10  120.96  3.000
 27U  H14   C14  C13  119.35  3.000
 27U  H14   C14  C15  120.00  3.000
 27U  C13   C14  C15  120.64  3.000
 27U  C12   C13  C16  122.03  3.000
 27U  C16   C13  C14  119.52  3.000
 27U  C12   C13  C14  118.45  3.000
 27U  N4    C16  N3   125.99  3.000
 27U  N4    C16  C13  115.32  3.000
 27U  N3    C16  C13  118.65  3.000
 27U  HN3   N3   C16  111.15  3.000
 27U  HN4A  N4   HN4  113.41  3.000
 27U  HN4A  N4   C16  117.19  3.000
 27U  HN4   N4   C16  118.45  3.000
 27U  H12   C12  C11  118.60  3.000
 27U  H12   C12  C13  120.61  3.000
 27U  C11   C12  C13  120.77  3.000
 27U  H11   C11  C12  119.03  3.000
 27U  H11   C11  C10  120.23  3.000
 27U  C12   C11  C10  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
 27U  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 27U  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 27U  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 27U  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 27U  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 27U  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 27U  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 27U  CONST_08  C13   C14  C15  C10     0.00   0.0  0
 27U  CONST_09  C12   C11  C10  C15     0.00   0.0  0
 27U  CONST_10  C12   C13  C14  C15     0.00   0.0  0
 27U  CONST_11  C11   C12  C13  C14     0.00   0.0  0
 27U  CONST_12  C11   C10  C15  C14     0.00   0.0  0
 27U  CONST_13  C19   C18  C17  C1    180.00   0.0  0
 27U  CONST_14  C21   C22  C17  C1    180.00   0.0  0
 27U  CONST_15  C12   C11  C10  C9    180.00   0.0  0
 27U  CONST_16  C14   C15  C10  C9    180.00   0.0  0
 27U  CONST_17  C16   C13  C14  C15   180.00   0.0  0
 27U  CONST_18  C11   C12  C13  C16   180.00   0.0  0
 27U  CONST_19  H19   C19  C18  C17   180.00   0.0  0
 27U  CONST_20  H21   C21  C22  C17   180.00   0.0  0
 27U  CONST_21  H22   C22  C17  C18   180.00   0.0  0
 27U  CONST_22  H20   C20  C19  C18   180.00   0.0  0
 27U  CONST_23  H18   C18  C19  C20   180.00   0.0  0
 27U  CONST_24  H12   C12  C11  C10   180.00   0.0  0
 27U  CONST_25  H14   C14  C15  C10   180.00   0.0  0
 27U  CONST_26  H11   C11  C10  C15   180.00   0.0  0
 27U  CONST_27  H15   C15  C14  C13   180.00   0.0  0
 27U  CONST_28  C4    N1   C3   O1    180.00   0.0  0
 27U  CONST_29  C7    N1   C3   O1      0.00   0.0  0
 27U  CONST_30  C4    N1   C3   C2      0.00   0.0  0
 27U  CONST_31  C7    N1   C3   C2    180.00   0.0  0
 27U  CONST_32  C9    N2   C8   C7    180.00   0.0  0
 27U  CONST_33  HN2   N2   C8   C7      0.00   0.0  0
 27U  CONST_34  HN3   N3   C16  C13   180.00   0.0  0
 27U  CONST_36  HN4A  N4   C16  C13   180.00   0.0  0
 27U  CONST_37  C9    N2   C8   O2      0.00   0.0  0
 27U  Var_01    C6    C5   C4   N1    -33.69  30.0  1
 27U  Var_02    C5    C4   N1   C7     17.99  30.0  1
 27U  Var_03    C4    C5   C6   C7     37.38  30.0  1
 27U  Var_04    C18   C17  C1   C2     84.21  30.0  2
 27U  Var_05    C11   C10  C9   N2     31.58  30.0  2
 27U  Var_06    N3    C16  C13  C14   -24.42  30.0  2
 27U  Var_07    C17   C1   C2   C3   -179.73  30.0  2
 27U  Var_08    N1    C3   C2   C1   -174.47  30.0  3
 27U  Var_09    C10   C9   N2   C8   -118.86  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
 27U  chir_01  C7  N1  C6  C8  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
 27U  plan-1  C1    0.020
 27U  plan-1  C17   0.020
 27U  plan-1  C18   0.020
 27U  plan-1  C19   0.020
 27U  plan-1  C20   0.020
 27U  plan-1  C21   0.020
 27U  plan-1  C22   0.020
 27U  plan-1  H18   0.020
 27U  plan-1  H19   0.020
 27U  plan-1  H20   0.020
 27U  plan-1  H21   0.020
 27U  plan-1  H22   0.020
 27U  plan-2  C9    0.020
 27U  plan-2  C10   0.020
 27U  plan-2  C15   0.020
 27U  plan-2  C14   0.020
 27U  plan-2  C13   0.020
 27U  plan-2  C16   0.020
 27U  plan-2  C12   0.020
 27U  plan-2  C11   0.020
 27U  plan-2  H15   0.020
 27U  plan-2  H14   0.020
 27U  plan-2  H12   0.020
 27U  plan-2  H11   0.020
 27U  plan-3  C7    0.020
 27U  plan-3  C8    0.020
 27U  plan-3  O2    0.020
 27U  plan-3  N2    0.020
 27U  plan-3  C9    0.020
 27U  plan-3  HN2   0.020
 27U  plan-4  C3    0.020
 27U  plan-4  O1    0.020
 27U  plan-4  C2    0.020
 27U  plan-4  N1    0.020
 27U  plan-4  C7    0.020
 27U  plan-4  C4    0.020
 27U  plan-5  C13   0.020
 27U  plan-5  C16   0.020
 27U  plan-5  N3    0.020
 27U  plan-5  N4    0.020
 27U  plan-5  HN3   0.020
 27U  plan-5  HN4   0.020
 27U  plan-5  HN4A  0.020

