# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:13:49 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-[(1R)-2-{(2S)-2-[(4-carbamimidoylbenzyl)carbamoyl]azetidin-1-yl}-1-cyclohexyl-2-oxoethyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCN2C(=O)[C@H](NCC(O)=O)C3CCCCC3)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
 MEL  MEL  N-[(1R)-2-{(2S)-2-[(4-carbamimidoylbenzyl)carbamoyl]azetidin-1-yl}-1-cyclohexyl-2-oxoethyl]glycine  ligand  61  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MEL
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
 MEL  C1    C  CH1    0  -0.248   1.1473   0.3820  -4.3698
 MEL  C2    C  CH2    0  -0.430   2.5480   0.7747  -3.9012
 MEL  C3    C  CH2    0  -0.425   3.5728   0.6215  -5.0218
 MEL  C4    C  CH2    0  -0.429   3.5597  -0.7926  -5.5918
 MEL  C5    C  CH2    0  -0.429   2.1608  -1.1897  -6.0505
 MEL  C6    C  CH2    0  -0.428   1.1415  -1.0409  -4.9243
 MEL  N7    N  NH1    0  -0.610  -1.2910   0.3060  -3.6484
 MEL  C8    C  CH1    0  -0.164   0.0693   0.6510  -3.2924
 MEL  C9    C  C      0   0.526   0.3748  -0.0790  -1.9945
 MEL  O0    O  O      0  -0.501   0.1935  -1.2844  -1.8574
 MEL  N11   N  NT     0  -0.449   0.8507   0.6530  -0.9847
 MEL  C12   C  CH1    0  -0.189   1.1958   0.2006   0.3403
 MEL  C13   C  C      0   0.572  -0.0050  -0.2821   1.1341
 MEL  O14   O  O      0  -0.485  -1.1194   0.1748   0.9393
 MEL  N15   N  NH1    0  -0.630   0.2865  -1.1836   2.0847
 MEL  C16   C  CH2    0  -0.362  -0.6667  -1.6817   3.0462
 MEL  C17   C  CR6    0   0.110  -0.5174  -1.0638   4.4152
 MEL  C18   C  CR16   0  -0.284  -0.2997   0.3027   4.5745
 MEL  C19   C  CR16   0  -0.273  -0.1875   0.8581   5.8376
 MEL  C20   C  CR6    0  -0.008  -0.3023   0.0640   6.9776
 MEL  C21   C  CR16   0  -0.266  -0.5296  -1.3005   6.8208
 MEL  C22   C  CR16   0  -0.294  -0.6254  -1.8556   5.5528
 MEL  C23   C  C      0   0.329  -0.1584   0.6769   8.3281
 MEL  N24   N  N      0  -0.642   0.6372   1.6382   8.6056
 MEL  N25   N  NH2    0  -0.803  -0.9200   0.1046   9.3017
 MEL  C26   C  CH2    0  -0.525   1.6065   1.6609   0.6745
 MEL  C27   C  CH2    0  -0.253   1.1382   2.0597  -0.7391
 MEL  C28   C  CH2    0  -0.408  -1.8389   0.9952  -4.7956
 MEL  C29   C  C      0   0.391  -3.1063   0.3078  -5.3348
 MEL  O30   O  OC    -1  -0.622  -3.8257   0.9990  -6.0820
 MEL  O31   O  O      0  -0.606  -3.2842  -0.8857  -5.0199
 MEL  H11   H  HCH1   0   0.223   0.9020   1.0517  -5.2045
 MEL  H21   H  HCH2   0   0.226   2.5460   1.8080  -3.5416
 MEL  H22   H  HCH2   0   0.213   2.8545   0.1496  -3.0542
 MEL  H31   H  HCH2   0   0.209   3.3494   1.3398  -5.8181
 MEL  H32   H  HCH2   0   0.225   4.5708   0.8712  -4.6526
 MEL  H41   H  HCH2   0   0.225   4.2696  -0.8759  -6.4185
 MEL  H42   H  HCH2   0   0.207   3.8976  -1.4914  -4.8185
 MEL  H51   H  HCH2   0   0.207   1.8605  -0.5579  -6.8941
 MEL  H52   H  HCH2   0   0.224   2.1614  -2.2181  -6.4207
 MEL  H61   H  HCH2   0   0.217   1.3710  -1.7579  -4.1309
 MEL  H62   H  HCH2   0   0.220   0.1454  -1.2988  -5.2949
 MEL  H71   H  HNH1   0   0.338  -1.3912  -0.6912  -3.7877
 MEL  H81   H  HCH1   0   0.248   0.0927   1.7306  -3.0997
 MEL  H121  H  HCH1   0   0.281   2.0171  -0.5208   0.3634
 MEL  H151  H  HNH1   0   0.407   1.2403  -1.4963   2.1764
 MEL  H161  H  HCH2   0   0.273  -0.5611  -2.7650   3.1197
 MEL  H162  H  HCH2   0   0.274  -1.6688  -1.4894   2.6618
 MEL  H181  H  HCR6   0   0.254  -0.2234   0.9505   3.7101
 MEL  H191  H  HCR6   0   0.262  -0.0306   1.9255   5.9337
 MEL  H211  H  HCR6   0   0.263  -0.6068  -1.9448   7.6873
 MEL  H221  H  HCR6   0   0.259  -0.7785  -2.9233   5.4509
 MEL  H241  H  H      0   0.332   1.2053   1.8759   7.8011
 MEL  H251  H  HNH2   0   0.384  -0.9374   0.5782  10.1909
 MEL  H252  H  HNH2   0   0.393  -1.7934  -0.3213   9.0404
 MEL  H261  H  HCH2   0   0.267   1.0580   2.1258   1.4907
 MEL  H262  H  HCH2   0   0.275   2.6731   1.7813   0.8437
 MEL  H271  H  HCH2   0   0.255   0.2558   2.6999  -0.7696
 MEL  H272  H  HCH2   0   0.255   1.9116   2.4815  -1.3805
 MEL  H281  H  HCH2   0   0.217  -2.0710   2.0313  -4.5290
 MEL  H282  H  HCH2   0   0.202  -1.1402   1.0564  -5.6469

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
 MEL  C1   C2    single    1.528  0.020  1.528
 MEL  C1   C6    single    1.527  0.020  1.527
 MEL  C1   C8    single    1.548  0.020  1.548
 MEL  C1   H11   single    0.970  0.020  1.090
 MEL  C2   C3    single    1.526  0.020  1.526
 MEL  C2   H21   single    0.970  0.020  1.090
 MEL  C2   H22   single    0.970  0.020  1.090
 MEL  C3   C4    single    1.525  0.020  1.525
 MEL  C3   H31   single    0.970  0.020  1.090
 MEL  C3   H32   single    0.970  0.020  1.090
 MEL  C4   C5    single    1.525  0.020  1.525
 MEL  C4   H41   single    0.970  0.020  1.090
 MEL  C4   H42   single    0.970  0.020  1.090
 MEL  C5   C6    single    1.526  0.020  1.526
 MEL  C5   H51   single    0.970  0.020  1.090
 MEL  C5   H52   single    0.970  0.020  1.090
 MEL  C6   H61   single    0.970  0.020  1.090
 MEL  C6   H62   single    0.970  0.020  1.090
 MEL  N7   C8    single    1.448  0.020  1.448
 MEL  N7   C28   single    1.446  0.020  1.446
 MEL  N7   H71   single    0.890  0.020  1.040
 MEL  C8   C9    single    1.520  0.020  1.520
 MEL  C8   H81   single    0.970  0.020  1.090
 MEL  C9   O0    double    1.227  0.020  1.227
 MEL  C9   N11   single    1.335  0.020  1.335
 MEL  N11  C12   single    1.442  0.020  1.442
 MEL  N11  C27   single    1.457  0.020  1.457
 MEL  C12  C13   single    1.518  0.020  1.518
 MEL  C12  C26   single    1.553  0.020  1.553
 MEL  C12  H121  single    0.970  0.020  1.090
 MEL  C13  O14   double    1.220  0.020  1.220
 MEL  C13  N15   single    1.342  0.020  1.342
 MEL  N15  C16   single    1.443  0.020  1.443
 MEL  N15  H151  single    0.860  0.020  1.020
 MEL  C16  C17   single    1.509  0.020  1.509
 MEL  C16  H161  single    0.970  0.020  1.090
 MEL  C16  H162  single    0.970  0.020  1.090
 MEL  C17  C18   aromatic  1.393  0.020  1.393
 MEL  C17  C22   aromatic  1.390  0.020  1.390
 MEL  C18  C19   aromatic  1.384  0.020  1.384
 MEL  C18  H181  single    0.930  0.020  1.080
 MEL  C19  C20   aromatic  1.394  0.020  1.394
 MEL  C19  H191  single    0.930  0.020  1.080
 MEL  C20  C21   aromatic  1.392  0.020  1.392
 MEL  C20  C23   single    1.490  0.020  1.490
 MEL  C21  C22   aromatic  1.387  0.020  1.387
 MEL  C21  H211  single    0.930  0.020  1.080
 MEL  C22  H221  single    0.930  0.020  1.080
 MEL  C23  N24   double    1.278  0.020  1.278
 MEL  C23  N25   single    1.362  0.020  1.362
 MEL  N24  H241  single    0.890  0.020  1.040
 MEL  N25  H251  single    0.890  0.020  1.040
 MEL  N25  H252  single    0.890  0.020  1.040
 MEL  C26  C27   single    1.542  0.020  1.542
 MEL  C26  H261  single    0.970  0.020  1.090
 MEL  C26  H262  single    0.970  0.020  1.090
 MEL  C27  H271  single    0.970  0.020  1.090
 MEL  C27  H272  single    0.970  0.020  1.090
 MEL  C28  C29   single    1.539  0.020  1.539
 MEL  C28  H281  single    0.970  0.020  1.090
 MEL  C28  H282  single    0.970  0.020  1.090
 MEL  C29  O30   deloc     1.246  0.020  1.246
 MEL  C29  O31   deloc     1.247  0.020  1.247

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
 MEL  H11   C1   C8    105.52  3.000
 MEL  H11   C1   C6    106.94  3.000
 MEL  C8    C1   C6    114.34  3.000
 MEL  H11   C1   C2    106.33  3.000
 MEL  C8    C1   C2    112.35  3.000
 MEL  C6    C1   C2    110.75  3.000
 MEL  H22   C2   H21   106.56  3.000
 MEL  H22   C2   C3    108.80  3.000
 MEL  H21   C2   C3    109.72  3.000
 MEL  H22   C2   C1    110.28  3.000
 MEL  H21   C2   C1    109.99  3.000
 MEL  C3    C2   C1    111.37  3.000
 MEL  H32   C3   H31   106.38  3.000
 MEL  H32   C3   C4    110.24  3.000
 MEL  H31   C3   C4    109.55  3.000
 MEL  H32   C3   C2    110.01  3.000
 MEL  H31   C3   C2    109.33  3.000
 MEL  C4    C3   C2    111.21  3.000
 MEL  H42   C4   H41   106.56  3.000
 MEL  H42   C4   C5    109.22  3.000
 MEL  H41   C4   C5    110.40  3.000
 MEL  H42   C4   C3    108.96  3.000
 MEL  H41   C4   C3    110.36  3.000
 MEL  C5    C4   C3    111.22  3.000
 MEL  H52   C5   H51   106.37  3.000
 MEL  H52   C5   C6    110.00  3.000
 MEL  H51   C5   C6    109.19  3.000
 MEL  H52   C5   C4    110.27  3.000
 MEL  H51   C5   C4    109.44  3.000
 MEL  C6    C5   C4    111.43  3.000
 MEL  H62   C6   H61   106.40  3.000
 MEL  H62   C6   C5    109.59  3.000
 MEL  H61   C6   C5    109.34  3.000
 MEL  H62   C6   C1    110.26  3.000
 MEL  H61   C6   C1    110.28  3.000
 MEL  C5    C6   C1    110.87  3.000
 MEL  H71   N7   C28   108.84  3.000
 MEL  H71   N7   C8    111.21  3.000
 MEL  C28   N7   C8    115.94  3.000
 MEL  H81   C8   C9    108.56  3.000
 MEL  H81   C8   N7    107.33  3.000
 MEL  C9    C8   N7    106.52  3.000
 MEL  H81   C8   C1    106.17  3.000
 MEL  C9    C8   C1    111.77  3.000
 MEL  N7    C8   C1    116.22  3.000
 MEL  N11   C9   O0    120.47  3.000
 MEL  N11   C9   C8    117.01  3.000
 MEL  O0    C9   C8    122.52  3.000
 MEL  C27   N11  C12    95.79  3.000
 MEL  C27   N11  C9    136.67  3.000
 MEL  C12   N11  C9    127.47  3.000
 MEL  H121  C12  C26   114.65  3.000
 MEL  H121  C12  C13   111.92  3.000
 MEL  C26   C12  C13   113.29  3.000
 MEL  H121  C12  N11   113.97  3.000
 MEL  C26   C12  N11    88.05  3.000
 MEL  C13   C12  N11   113.01  3.000
 MEL  N15   C13  O14   124.26  3.000
 MEL  N15   C13  C12   114.33  3.000
 MEL  O14   C13  C12   121.33  3.000
 MEL  H151  N15  C16   117.22  3.000
 MEL  H151  N15  C13   118.58  3.000
 MEL  C16   N15  C13   124.09  3.000
 MEL  H162  C16  H161  106.73  3.000
 MEL  H162  C16  C17   109.78  3.000
 MEL  H161  C16  C17   109.62  3.000
 MEL  H162  C16  N15   108.15  3.000
 MEL  H161  C16  N15   108.90  3.000
 MEL  C17   C16  N15   113.44  3.000
 MEL  C22   C17  C18   118.51  3.000
 MEL  C22   C17  C16   120.09  3.000
 MEL  C18   C17  C16   121.38  3.000
 MEL  H181  C18  C19   118.86  3.000
 MEL  H181  C18  C17   120.44  3.000
 MEL  C19   C18  C17   120.70  3.000
 MEL  H191  C19  C20   120.04  3.000
 MEL  H191  C19  C18   119.21  3.000
 MEL  C20   C19  C18   120.73  3.000
 MEL  C23   C20  C21   121.40  3.000
 MEL  C23   C20  C19   119.93  3.000
 MEL  C21   C20  C19   118.66  3.000
 MEL  H211  C21  C22   119.24  3.000
 MEL  H211  C21  C20   120.32  3.000
 MEL  C22   C21  C20   120.42  3.000
 MEL  H221  C22  C21   119.33  3.000
 MEL  H221  C22  C17   119.69  3.000
 MEL  C21   C22  C17   120.97  3.000
 MEL  N25   C23  N24   120.58  3.000
 MEL  N25   C23  C20   114.90  3.000
 MEL  N24   C23  C20   124.49  3.000
 MEL  H241  N24  C23   110.67  3.000
 MEL  H252  N25  H251  114.40  3.000
 MEL  H252  N25  C23   118.52  3.000
 MEL  H251  N25  C23   116.29  3.000
 MEL  H262  C26  H261  109.31  3.000
 MEL  H262  C26  C27   114.34  3.000
 MEL  H261  C26  C27   115.11  3.000
 MEL  H262  C26  C12   113.40  3.000
 MEL  H261  C26  C12   115.47  3.000
 MEL  C27   C26  C12    88.03  3.000
 MEL  H272  C27  H271  109.30  3.000
 MEL  H272  C27  C26   115.11  3.000
 MEL  H271  C27  C26   115.04  3.000
 MEL  H272  C27  N11   114.50  3.000
 MEL  H271  C27  N11   113.73  3.000
 MEL  C26   C27  N11    87.98  3.000
 MEL  H282  C28  H281  105.65  3.000
 MEL  H282  C28  C29   106.02  3.000
 MEL  H281  C28  C29   109.47  3.000
 MEL  H282  C28  N7    113.50  3.000
 MEL  H281  C28  N7    109.76  3.000
 MEL  C29   C28  N7    112.15  3.000
 MEL  O31   C29  O30   126.85  3.000
 MEL  O31   C29  C28   117.16  3.000
 MEL  O30   C29  C28   115.95  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
 MEL  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 MEL  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 MEL  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 MEL  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 MEL  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 MEL  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 MEL  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 MEL  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 MEL  CONST_09  C23   C20  C19  C18   180.00   0.0  0
 MEL  CONST_10  C23   C20  C21  C22   180.00   0.0  0
 MEL  CONST_11  H191  C19  C18  C17   180.00   0.0  0
 MEL  CONST_12  H211  C21  C22  C17   180.00   0.0  0
 MEL  CONST_13  H221  C22  C17  C18   180.00   0.0  0
 MEL  CONST_14  H181  C18  C19  C20   180.00   0.0  0
 MEL  CONST_15  C12   N11  C9   C8    180.00   0.0  0
 MEL  CONST_16  C27   N11  C9   C8      0.00   0.0  0
 MEL  CONST_17  C12   N11  C9   O0      0.00   0.0  0
 MEL  CONST_18  C27   N11  C9   O0    180.00   0.0  0
 MEL  CONST_19  C16   N15  C13  C12   180.00   0.0  0
 MEL  CONST_20  H151  N15  C13  C12     0.00   0.0  0
 MEL  CONST_21  H241  N24  C23  C20     0.00   0.0  0
 MEL  CONST_22  H251  N25  C23  C20   180.00   0.0  0
 MEL  CONST_24  C16   N15  C13  O14     0.00   0.0  0
 MEL  Var_01    C4    C3   C2   C1    -55.42  30.0  1
 MEL  Var_02    C4    C5   C6   C1     56.07  30.0  1
 MEL  Var_03    C5    C4   C3   C2     54.88  30.0  1
 MEL  Var_04    C6    C5   C4   C3    -55.40  30.0  1
 MEL  Var_05    C12   C26  C27  N11    -2.84  30.0  1
 MEL  Var_06    C18   C17  C16  N15    42.98  30.0  2
 MEL  Var_07    N24   C23  C20  C19   -35.08  30.0  2
 MEL  Var_08    C17   C16  N15  C13  -102.61  30.0  3
 MEL  Var_09    O30   C29  C28  N7    162.33  30.0  3
 MEL  Var_10    C29   C28  N7   C8    164.14  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
 MEL  chir_01  C1   C2   C6   C8   negativ
 MEL  chir_02  C8   N7   C1   C9   positiv
 MEL  chir_03  C12  N11  C13  C26  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
 MEL  plan-1  C8    0.020
 MEL  plan-1  C9    0.020
 MEL  plan-1  O0    0.020
 MEL  plan-1  N11   0.020
 MEL  plan-1  C12   0.020
 MEL  plan-1  C27   0.020
 MEL  plan-2  C16   0.020
 MEL  plan-2  C17   0.020
 MEL  plan-2  C18   0.020
 MEL  plan-2  C19   0.020
 MEL  plan-2  C20   0.020
 MEL  plan-2  C21   0.020
 MEL  plan-2  C22   0.020
 MEL  plan-2  C23   0.020
 MEL  plan-2  H181  0.020
 MEL  plan-2  H191  0.020
 MEL  plan-2  H211  0.020
 MEL  plan-2  H221  0.020
 MEL  plan-3  C12   0.020
 MEL  plan-3  C13   0.020
 MEL  plan-3  O14   0.020
 MEL  plan-3  N15   0.020
 MEL  plan-3  C16   0.020
 MEL  plan-3  H151  0.020
 MEL  plan-4  C20   0.020
 MEL  plan-4  C23   0.020
 MEL  plan-4  N24   0.020
 MEL  plan-4  N25   0.020
 MEL  plan-4  H241  0.020
 MEL  plan-4  H251  0.020
 MEL  plan-4  H252  0.020
 MEL  plan-5  C28   0.020
 MEL  plan-5  C29   0.020
 MEL  plan-5  O30   0.020
 MEL  plan-5  O31   0.020

