# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:05:54 2020
#   Inital geometry file: a 166 line input string
#   Ligand name: N-[(2S)-1-({5-[(diaminomethylidene)amino]pentyl}amino)-1-oxo-3-phenylpropan-2-yl]-4-hydroxy-2-oxo-1,2-dihydroquinoline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)=NCCCCCNC(=O)[C@H](Cc1ccccc1)NC(=O)c2ccc3NC(=O)C=C(O)c3c2
#
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
 J1J  J1J  N-[(2S)-1-({5-[(diaminomethylidene)amino]pentyl}amino)-1-oxo-3-phenylpropan-2-yl]-4-hydroxy-2-oxo-1,2-dihydroquinoline-6-carboxamide  ligand  65  35  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J1J
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
 J1J  C25   C  C     0   0.554    1.8967  -0.2698  -0.4836
 J1J  O26   O  O     0  -0.479    1.7507  -0.9929  -1.4583
 J1J  C27   C  CR6   0  -0.032    3.2364   0.2891  -0.1367
 J1J  C28   C  CR16  0  -0.287    3.6081   0.6195   1.1740
 J1J  C29   C  CR16  0  -0.307    4.8676   1.0936   1.4569
 J1J  C30   C  CR66  0   0.397    5.7975   1.2624   0.4260
 J1J  C31   C  CR66  0  -0.039    5.4404   0.9343  -0.8910
 J1J  C32   C  CR16  0  -0.329    4.1632   0.4368  -1.1518
 J1J  C33   C  CR6   0   0.480    6.4384   1.1267  -1.9167
 J1J  C34   C  CR16  0  -0.591    7.6694   1.6035  -1.6036
 J1J  C35   C  CR6   0   0.519    8.0372   1.9338  -0.2496
 J1J  O36   O  O     0  -0.497    9.1354   2.3602   0.0867
 J1J  N37   N  NR16  0  -0.763    7.0489   1.7367   0.6887
 J1J  O38   O  OH1   0  -0.595    6.0566   0.8063  -3.1487
 J1J  N24   N  NH1   0  -0.652    0.8852   0.0868   0.3295
 J1J  C22   C  C     0   0.558   -1.4669   0.6568   0.2900
 J1J  O23   O  O     0  -0.494   -1.2737   1.6558   0.9693
 J1J  C20   C  CH2   0  -0.516   -0.7094  -1.4522   1.3966
 J1J  C17   C  CR6   0   0.143    0.3184  -2.5455   1.4375
 J1J  C16   C  CR16  0  -0.310    1.4114  -2.4647   2.2956
 J1J  C18   C  CR16  0  -0.292    0.2230  -3.6392   0.5802
 J1J  C15   C  CR16  0  -0.240    2.3892  -3.4512   2.2972
 J1J  C19   C  CR16  0  -0.241    1.1946  -4.6293   0.5804
 J1J  C14   C  CR16  0  -0.271    2.2835  -4.5366   1.4387
 J1J  C2    C  CH2   0  -0.330   -8.7690   1.5889  -0.8735
 J1J  C3    C  CH2   0  -0.430   -7.5417   0.6774  -0.8375
 J1J  C4    C  CH2   0  -0.423   -6.2405   1.4451  -0.6483
 J1J  C5    C  CH2   0  -0.457   -5.0222   0.5316  -0.6105
 J1J  N7    N  NH2   0  -0.836  -10.3158   0.4181   1.1734
 J1J  C8    C  C     0   0.544  -10.6131   0.3165  -0.1650
 J1J  C21   C  CH1   0  -0.212   -0.4382  -0.4683   0.2394
 J1J  N10   N  NH2   0  -0.829  -11.7118  -0.4739  -0.4274
 J1J  C12   C  CH2   0  -0.245   -3.7315   1.3116  -0.4178
 J1J  N13   N  NH1   0  -0.637   -2.5859   0.4244  -0.4020
 J1J  N26   N  N     0  -0.483   -9.9935   0.8727  -1.1369
 J1J  H24   H  HNH1  0   0.400    1.0376   0.7772   1.0479
 J1J  H28   H  HCR6  0   0.264    2.9202   0.4807   1.9980
 J1J  H32   H  HCR6  0   0.272    3.8878   0.1710  -2.1629
 J1J  H29   H  HCR6  0   0.287    5.1456   1.3283   2.4762
 J1J  H37   H  HNR6  0   0.416    7.2863   1.9554   1.6470
 J1J  H34   H  HCR6  0   0.287    8.4229   1.7479  -2.3680
 J1J  H38   H  HOH1  0   0.490    6.7651   0.9676  -3.7845
 J1J  H21   H  HCH1  0   0.289   -0.5095  -1.0065  -0.7065
 J1J  H13   H  HNH1  0   0.403   -2.6229  -0.3890  -0.9964
 J1J  H201  H  HCH2  0   0.266   -1.7103  -1.8705   1.2693
 J1J  H202  H  HCH2  0   0.263   -0.7118  -0.8989   2.3390
 J1J  H16   H  HCR6  0   0.246    1.4975  -1.6262   2.9768
 J1J  H18   H  HCR6  0   0.245   -0.6218  -3.7176  -0.0951
 J1J  H15   H  HCR6  0   0.253    3.2319  -3.3719   2.9720
 J1J  H19   H  HCR6  0   0.252    1.1020  -5.4750  -0.0890
 J1J  H14   H  HCR6  0   0.253    3.0428  -5.3079   1.4401
 J1J  H21C  H  HCH2  0   0.189   -8.7979   2.1872   0.0508
 J1J  H22C  H  HCH2  0   0.219   -8.6253   2.3177  -1.6771
 J1J  H31C  H  HCH2  0   0.210   -7.6506  -0.0572  -0.0325
 J1J  H32C  H  HCH2  0   0.217   -7.5020   0.1045  -1.7692
 J1J  H41C  H  HCH2  0   0.217   -6.1250   2.1733  -1.4581
 J1J  H42C  H  HCH2  0   0.217   -6.2879   2.0255   0.2797
 J1J  H51C  H  HCH2  0   0.229   -5.1298  -0.1947   0.2004
 J1J  H52C  H  HCH2  0   0.227   -4.9706  -0.0428  -1.5418
 J1J  H121  H  HCH2  0   0.234   -3.6226   2.0564  -1.2129
 J1J  H122  H  HCH2  0   0.242   -3.7599   1.8555   0.5268
 J1J  H71N  H  HNH2  0   0.389  -10.6401  -0.3291   1.7658
 J1J  H72N  H  HNH2  0   0.395   -9.3859   0.7148   1.4159
 J1J  H101  H  HNH2  0   0.378  -12.4334  -0.4837   0.2768
 J1J  H102  H  HNH2  0   0.374  -12.0862  -0.3401  -1.3530

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
 J1J  C25  O26   double    1.222  0.020  1.222
 J1J  C25  C27   single    1.492  0.020  1.492
 J1J  C25  N24   single    1.346  0.020  1.346
 J1J  C27  C28   aromatic  1.402  0.020  1.402
 J1J  C27  C32   aromatic  1.382  0.020  1.382
 J1J  C28  C29   aromatic  1.375  0.020  1.375
 J1J  C29  C30   aromatic  1.399  0.020  1.399
 J1J  C30  C31   aromatic  1.403  0.020  1.403
 J1J  C30  N37   single    1.364  0.020  1.364
 J1J  C31  C32   aromatic  1.395  0.020  1.395
 J1J  C31  C33   single    1.444  0.020  1.444
 J1J  C33  C34   double    1.357  0.020  1.357
 J1J  C33  O38   single    1.329  0.020  1.329
 J1J  C34  C35   single    1.441  0.020  1.441
 J1J  C35  O36   double    1.225  0.020  1.225
 J1J  C35  N37   single    1.377  0.020  1.377
 J1J  N24  C21   single    1.438  0.020  1.438
 J1J  C22  O23   double    1.223  0.020  1.223
 J1J  C22  C21   single    1.525  0.020  1.525
 J1J  C22  N13   single    1.336  0.020  1.336
 J1J  C20  C17   single    1.501  0.020  1.501
 J1J  C20  C21   single    1.543  0.020  1.543
 J1J  C17  C16   aromatic  1.392  0.020  1.392
 J1J  C17  C18   aromatic  1.393  0.020  1.393
 J1J  C16  C15   aromatic  1.389  0.020  1.389
 J1J  C18  C19   aromatic  1.387  0.020  1.387
 J1J  C15  C14   aromatic  1.388  0.020  1.388
 J1J  C19  C14   aromatic  1.390  0.020  1.390
 J1J  C2   C3    single    1.529  0.020  1.529
 J1J  C2   N26   single    1.443  0.020  1.443
 J1J  C3   C4    single    1.523  0.020  1.523
 J1J  C4   C5    single    1.523  0.020  1.523
 J1J  C5   C12   single    1.520  0.020  1.520
 J1J  N7   C8    single    1.375  0.020  1.375
 J1J  C8   N10   single    1.379  0.020  1.379
 J1J  C8   N26   double    1.280  0.020  1.280
 J1J  C12  N13   single    1.449  0.020  1.449
 J1J  N24  H24   single    0.860  0.020  1.020
 J1J  C28  H28   single    0.930  0.020  1.080
 J1J  C32  H32   single    0.930  0.020  1.080
 J1J  C29  H29   single    0.930  0.020  1.080
 J1J  N37  H37   single    0.860  0.020  1.020
 J1J  C34  H34   single    0.930  0.020  1.080
 J1J  O38  H38   single    0.850  0.020  0.980
 J1J  C21  H21   single    0.970  0.020  1.090
 J1J  N13  H13   single    0.860  0.020  1.020
 J1J  C20  H201  single    0.970  0.020  1.090
 J1J  C20  H202  single    0.970  0.020  1.090
 J1J  C16  H16   single    0.930  0.020  1.080
 J1J  C18  H18   single    0.930  0.020  1.080
 J1J  C15  H15   single    0.930  0.020  1.080
 J1J  C19  H19   single    0.930  0.020  1.080
 J1J  C14  H14   single    0.930  0.020  1.080
 J1J  C2   H21C  single    0.970  0.020  1.090
 J1J  C2   H22C  single    0.970  0.020  1.090
 J1J  C3   H31C  single    0.970  0.020  1.090
 J1J  C3   H32C  single    0.970  0.020  1.090
 J1J  C4   H41C  single    0.970  0.020  1.090
 J1J  C4   H42C  single    0.970  0.020  1.090
 J1J  C5   H51C  single    0.970  0.020  1.090
 J1J  C5   H52C  single    0.970  0.020  1.090
 J1J  C12  H121  single    0.970  0.020  1.090
 J1J  C12  H122  single    0.970  0.020  1.090
 J1J  N7   H71N  single    0.890  0.020  1.040
 J1J  N7   H72N  single    0.890  0.020  1.040
 J1J  N10  H101  single    0.890  0.020  1.040
 J1J  N10  H102  single    0.890  0.020  1.040

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
 J1J  N24   C25  C27   115.78  3.000
 J1J  N24   C25  O26   123.28  3.000
 J1J  C27   C25  O26   120.94  3.000
 J1J  C32   C27  C28   118.92  3.000
 J1J  C32   C27  C25   118.11  3.000
 J1J  C28   C27  C25   122.93  3.000
 J1J  H28   C28  C29   118.02  3.000
 J1J  H28   C28  C27   120.86  3.000
 J1J  C29   C28  C27   121.09  3.000
 J1J  H29   C29  C30   119.81  3.000
 J1J  H29   C29  C28   120.25  3.000
 J1J  C30   C29  C28   119.93  3.000
 J1J  N37   C30  C31   119.71  3.000
 J1J  N37   C30  C29   120.67  3.000
 J1J  C31   C30  C29   119.62  3.000
 J1J  C33   C31  C32   123.19  3.000
 J1J  C33   C31  C30   117.36  3.000
 J1J  C32   C31  C30   119.45  3.000
 J1J  H32   C32  C31   119.71  3.000
 J1J  H32   C32  C27   119.32  3.000
 J1J  C31   C32  C27   120.97  3.000
 J1J  O38   C33  C34   124.01  3.000
 J1J  O38   C33  C31   115.33  3.000
 J1J  C34   C33  C31   120.66  3.000
 J1J  H34   C34  C35   117.05  3.000
 J1J  H34   C34  C33   121.02  3.000
 J1J  C35   C34  C33   121.93  3.000
 J1J  N37   C35  O36   120.41  3.000
 J1J  N37   C35  C34   115.10  3.000
 J1J  O36   C35  C34   124.50  3.000
 J1J  H37   N37  C35   116.51  3.000
 J1J  H37   N37  C30   118.24  3.000
 J1J  C35   N37  C30   125.24  3.000
 J1J  H38   O38  C33   111.06  3.000
 J1J  H24   N24  C21   116.64  3.000
 J1J  H24   N24  C25   119.89  3.000
 J1J  C21   N24  C25   123.47  3.000
 J1J  N13   C22  C21   114.79  3.000
 J1J  N13   C22  O23   124.19  3.000
 J1J  C21   C22  O23   120.94  3.000
 J1J  H202  C20  H201  107.00  3.000
 J1J  H202  C20  C21   108.92  3.000
 J1J  H201  C20  C21   108.53  3.000
 J1J  H202  C20  C17   110.30  3.000
 J1J  H201  C20  C17   110.59  3.000
 J1J  C21   C20  C17   111.38  3.000
 J1J  C18   C17  C16   118.60  3.000
 J1J  C18   C17  C20   120.54  3.000
 J1J  C16   C17  C20   120.81  3.000
 J1J  H16   C16  C15   119.52  3.000
 J1J  H16   C16  C17   119.66  3.000
 J1J  C15   C16  C17   120.82  3.000
 J1J  H18   C18  C19   119.61  3.000
 J1J  H18   C18  C17   119.57  3.000
 J1J  C19   C18  C17   120.82  3.000
 J1J  H15   C15  C14   120.14  3.000
 J1J  H15   C15  C16   119.79  3.000
 J1J  C14   C15  C16   120.07  3.000
 J1J  H19   C19  C14   120.08  3.000
 J1J  H19   C19  C18   119.84  3.000
 J1J  C14   C19  C18   120.09  3.000
 J1J  H14   C14  C19   120.19  3.000
 J1J  H14   C14  C15   120.21  3.000
 J1J  C19   C14  C15   119.60  3.000
 J1J  H22C  C2   H21C  104.95  3.000
 J1J  H22C  C2   N26   107.93  3.000
 J1J  H21C  C2   N26   113.62  3.000
 J1J  H22C  C2   C3    107.99  3.000
 J1J  H21C  C2   C3    108.97  3.000
 J1J  N26   C2   C3    112.93  3.000
 J1J  H32C  C3   H31C  106.16  3.000
 J1J  H32C  C3   C4    109.80  3.000
 J1J  H31C  C3   C4    109.38  3.000
 J1J  H32C  C3   C2    108.73  3.000
 J1J  H31C  C3   C2    109.71  3.000
 J1J  C4    C3   C2    112.84  3.000
 J1J  H42C  C4   H41C  106.18  3.000
 J1J  H42C  C4   C5    109.35  3.000
 J1J  H41C  C4   C5    109.44  3.000
 J1J  H42C  C4   C3    109.60  3.000
 J1J  H41C  C4   C3    109.48  3.000
 J1J  C5    C4   C3    112.59  3.000
 J1J  H52C  C5   H51C  106.66  3.000
 J1J  H52C  C5   C12   109.69  3.000
 J1J  H51C  C5   C12   109.28  3.000
 J1J  H52C  C5   C4    109.33  3.000
 J1J  H51C  C5   C4    109.75  3.000
 J1J  C12   C5   C4    111.99  3.000
 J1J  H72N  N7   H71N  112.01  3.000
 J1J  H72N  N7   C8    117.16  3.000
 J1J  H71N  N7   C8    116.62  3.000
 J1J  N26   C8   N10   119.37  3.000
 J1J  N26   C8   N7    127.05  3.000
 J1J  N10   C8   N7    113.58  3.000
 J1J  H21   C21  C20   108.92  3.000
 J1J  H21   C21  C22   110.40  3.000
 J1J  C20   C21  C22   109.08  3.000
 J1J  H21   C21  N24   107.77  3.000
 J1J  C20   C21  N24   111.16  3.000
 J1J  C22   C21  N24   109.50  3.000
 J1J  H102  N10  H101  112.15  3.000
 J1J  H102  N10  C8    113.26  3.000
 J1J  H101  N10  C8    116.29  3.000
 J1J  H122  C12  H121  107.00  3.000
 J1J  H122  C12  N13   108.46  3.000
 J1J  H121  C12  N13   110.23  3.000
 J1J  H122  C12  C5    110.10  3.000
 J1J  H121  C12  C5    109.96  3.000
 J1J  N13   C12  C5    111.00  3.000
 J1J  H13   N13  C12   117.29  3.000
 J1J  H13   N13  C22   118.46  3.000
 J1J  C12   N13  C22   124.14  3.000
 J1J  C8    N26  C2    119.21  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
 J1J  CONST_01  C30  C29  C28  C27     0.00   0.0  0
 J1J  CONST_02  C30  C31  C32  C27     0.00   0.0  0
 J1J  CONST_03  C31  C32  C27  C28     0.00   0.0  0
 J1J  CONST_04  C31  C30  C29  C28     0.00   0.0  0
 J1J  CONST_05  C32  C27  C28  C29     0.00   0.0  0
 J1J  CONST_06  C32  C31  C30  C29     0.00   0.0  0
 J1J  CONST_07  C14  C15  C16  C17     0.00   0.0  0
 J1J  CONST_08  C14  C19  C18  C17     0.00   0.0  0
 J1J  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 J1J  CONST_10  C19  C14  C15  C16     0.00   0.0  0
 J1J  CONST_11  C15  C16  C17  C18     0.00   0.0  0
 J1J  CONST_12  C15  C14  C19  C18     0.00   0.0  0
 J1J  CONST_13  C34  C35  N37  C30     0.00   0.0  0
 J1J  CONST_14  C29  C28  C27  C25   180.00   0.0  0
 J1J  CONST_15  C31  C32  C27  C25   180.00   0.0  0
 J1J  CONST_16  C15  C16  C17  C20   180.00   0.0  0
 J1J  CONST_17  C19  C18  C17  C20   180.00   0.0  0
 J1J  CONST_18  O36  C35  N37  C30   180.00   0.0  0
 J1J  CONST_19  H29  C29  C28  C27   180.00   0.0  0
 J1J  CONST_20  H32  C32  C27  C28   180.00   0.0  0
 J1J  CONST_21  H28  C28  C29  C30   180.00   0.0  0
 J1J  CONST_22  H15  C15  C16  C17   180.00   0.0  0
 J1J  CONST_23  H19  C19  C18  C17   180.00   0.0  0
 J1J  CONST_24  H18  C18  C17  C16   180.00   0.0  0
 J1J  CONST_25  H14  C14  C15  C16   180.00   0.0  0
 J1J  CONST_26  H16  C16  C17  C18   180.00   0.0  0
 J1J  CONST_27  H37  N37  C35  C34   180.00   0.0  0
 J1J  CONST_28  C21  N24  C25  C27   180.00   0.0  0
 J1J  CONST_29  H24  N24  C25  C27     0.00   0.0  0
 J1J  CONST_30  C21  N24  C25  O26     0.00   0.0  0
 J1J  CONST_31  C12  N13  C22  O23     0.00   0.0  0
 J1J  CONST_32  C12  N13  C22  C21   180.00   0.0  0
 J1J  CONST_33  N7   C8   N26  C2      0.00   0.0  0
 J1J  CONST_34  N10  C8   N26  C2    180.00   0.0  0
 J1J  CONST_35  H13  N13  C22  O23   180.00   0.0  0
 J1J  Var_01    C28  C27  C25  O26  -152.25  30.0  2
 J1J  Var_02    C21  C20  C17  C16    97.23  30.0  2
 J1J  Var_03    C5   C12  N13  C22  -149.35  30.0  1
 J1J  Var_04    C5   C4   C3   C2    179.89  30.0  3
 J1J  Var_05    C12  C5   C4   C3   -179.86  30.0  3
 J1J  Var_06    N26  C2   C3   C4    176.32  30.0  1
 J1J  Var_07    N13  C12  C5   C4   -179.27  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
 J1J  chir_01  C21  N24  C22  C20  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
 J1J  plan-1  C20   0.020
 J1J  plan-1  C17   0.020
 J1J  plan-1  C16   0.020
 J1J  plan-1  C18   0.020
 J1J  plan-1  C15   0.020
 J1J  plan-1  C19   0.020
 J1J  plan-1  C14   0.020
 J1J  plan-1  H16   0.020
 J1J  plan-1  H18   0.020
 J1J  plan-1  H15   0.020
 J1J  plan-1  H19   0.020
 J1J  plan-1  H14   0.020
 J1J  plan-2  C25   0.020
 J1J  plan-2  C27   0.020
 J1J  plan-2  C28   0.020
 J1J  plan-2  C29   0.020
 J1J  plan-2  C30   0.020
 J1J  plan-2  C31   0.020
 J1J  plan-2  C32   0.020
 J1J  plan-2  C33   0.020
 J1J  plan-2  C34   0.020
 J1J  plan-2  C35   0.020
 J1J  plan-2  O36   0.020
 J1J  plan-2  N37   0.020
 J1J  plan-2  O38   0.020
 J1J  plan-2  H28   0.020
 J1J  plan-2  H32   0.020
 J1J  plan-2  H29   0.020
 J1J  plan-2  H37   0.020
 J1J  plan-2  H34   0.020
 J1J  plan-3  C25   0.020
 J1J  plan-3  O26   0.020
 J1J  plan-3  C27   0.020
 J1J  plan-3  N24   0.020
 J1J  plan-3  C21   0.020
 J1J  plan-3  H24   0.020
 J1J  plan-4  C22   0.020
 J1J  plan-4  O23   0.020
 J1J  plan-4  C21   0.020
 J1J  plan-4  C12   0.020
 J1J  plan-4  N13   0.020
 J1J  plan-4  H13   0.020
 J1J  plan-5  C2    0.020
 J1J  plan-5  N7    0.020
 J1J  plan-5  C8    0.020
 J1J  plan-5  N10   0.020
 J1J  plan-5  N26   0.020
 J1J  plan-5  H71N  0.020
 J1J  plan-5  H72N  0.020
 J1J  plan-5  H101  0.020
 J1J  plan-5  H102  0.020

