# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:11:23 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 3-{(2S)-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxo-3-piperazin-1-ylpropyl}benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1cccc(C[C@H](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N4CCNCC4)c1
#
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
 FD3  FD3  3-{(2S)-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxo-3-piperazin-1-ylpropyl}benzenecarboximidamide  ligand  60  33  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FD3
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
 FD3  C65   C  CR6   0   0.182  -0.6625   0.9765   3.1207
 FD3  C66   C  CR16  0  -0.356  -0.8002  -0.3151   3.6145
 FD3  C64   C  CR16  0  -0.306   0.0252   1.9149   3.8833
 FD3  C63   C  CR16  0  -0.228   0.5653   1.5636   5.1118
 FD3  C62   C  CR16  0  -0.300   0.4340   0.2686   5.5898
 FD3  C61   C  CR6   0   0.033  -0.2562  -0.6834   4.8417
 FD3  C25   C  C     0   0.329  -0.4377  -2.0750   5.3443
 FD3  N43   N  NH2   0  -0.804   0.5952  -2.5498   6.0957
 FD3  N54   N  N     0  -0.642  -1.4791  -2.7900   5.1491
 FD3  C34   C  CH2   0  -0.531  -1.2129   1.3283   1.7703
 FD3  C31   C  CH1   0  -0.249  -0.2652   0.9016   0.6384
 FD3  C35   C  C     0   0.578  -0.9396   1.1773  -0.7144
 FD3  O36   O  O     0  -0.491  -0.8285   2.3016  -1.1865
 FD3  N81   N  NT    0  -0.452  -1.6398   0.1972  -1.3051
 FD3  C71   C  CH2   0  -0.325  -1.9005  -1.1280  -0.7698
 FD3  C72   C  CH2   0  -0.285  -3.3998  -1.3701  -0.6910
 FD3  C74   C  CH2   0  -0.292  -3.7670   0.1497  -2.5004
 FD3  C75   C  CH2   0  -0.306  -2.2744   0.4119  -2.5977
 FD3  N40   N  NH1   0  -0.598  -3.9902  -1.1939  -2.0017
 FD3  N29   N  NC1   0  -0.692   0.9737   1.6531   0.7383
 FD3  S12   S  S     0   1.376   2.3526   0.9608   0.1459
 FD3  O32   O  OS    0  -0.655   3.3602   2.0073   0.1585
 FD3  O33   O  OS    0  -0.647   2.5686  -0.2689   0.8881
 FD3  C2    C  CR6   0  -0.231   1.9806   0.5300  -1.5300
 FD3  C3    C  CR16  0  -0.222   2.0269   1.5391  -2.5159
 FD3  C4    C  CR16  0  -0.304   1.6010   1.2532  -3.7795
 FD3  C9    C  CR66  0   0.129   1.0837  -1.0406  -3.1140
 FD3  C10   C  CR66  0   0.130   1.1037  -0.0308  -4.1095
 FD3  C1    C  CR16  0  -0.297   1.5380  -0.7327  -1.8128
 FD3  C5    C  CR16  0  -0.308   0.6140  -0.3334  -5.3996
 FD3  C6    C  CR16  0  -0.246   0.1260  -1.5809  -5.6819
 FD3  C7    C  CR16  0  -0.256   0.1127  -2.5862  -4.6930
 FD3  C8    C  CR16  0  -0.303   0.5847  -2.3234  -3.4362
 FD3  H661  H  HCR6  0   0.250  -1.3288  -1.0536   3.0207
 FD3  H641  H  HCR6  0   0.253   0.1360   2.9280   3.5170
 FD3  H631  H  HCR6  0   0.261   1.0907   2.3034   5.7013
 FD3  H621  H  HCR6  0   0.263   0.8493   0.0092   6.5549
 FD3  H431  H  HNH2  0   0.384   0.5536  -3.5252   6.3453
 FD3  H432  H  HNH2  0   0.393   1.5228  -2.2102   5.9041
 FD3  H541  H  H     0   0.332  -2.1950  -2.2607   4.6657
 FD3  H341  H  HCH2  0   0.275  -2.1835   0.8480   1.6187
 FD3  H342  H  HCH2  0   0.278  -1.3878   2.4037   1.6949
 FD3  H311  H  HCH1  0   0.293  -0.0176  -0.1505   0.7782
 FD3  H711  H  HCH2  0   0.255  -1.4417  -1.8721  -1.4284
 FD3  H712  H  HCH2  0   0.259  -1.4674  -1.2613   0.2172
 FD3  H721  H  HCH2  0   0.248  -3.5715  -2.3918  -0.3484
 FD3  H722  H  HCH2  0   0.200  -3.8240  -0.6937   0.0695
 FD3  H741  H  HCH2  0   0.243  -4.2075   0.2458  -3.4941
 FD3  H742  H  HCH2  0   0.202  -4.2202   0.9256  -1.8635
 FD3  H751  H  HCH2  0   0.268  -2.0802   1.4258  -2.9342
 FD3  H752  H  HCH2  0   0.243  -1.8208  -0.2737  -3.3215
 FD3  H401  H  HNH1  0   0.360  -4.9822  -1.3849  -1.9585
 FD3  H291  H  HNC1  0   0.406   0.8742   2.6178   0.4328
 FD3  H31   H  HCR6  0   0.280   2.3878   2.5291  -2.2731
 FD3  H41   H  HCR6  0   0.268   1.6271   2.0195  -4.5438
 FD3  H11   H  HCR6  0   0.291   1.5102  -1.5025  -1.0523
 FD3  H51   H  HCR6  0   0.264   0.6256   0.4362  -6.1612
 FD3  H61   H  HCR6  0   0.267  -0.2512  -1.8033  -6.6714
 FD3  H71   H  HCR6  0   0.266  -0.2722  -3.5679  -4.9349
 FD3  H81   H  HCR6  0   0.267   0.5800  -3.0944  -2.6756

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
 FD3  C65  C66   aromatic  1.390  0.020  1.390
 FD3  C65  C64   aromatic  1.391  0.020  1.391
 FD3  C65  C34   single    1.500  0.020  1.500
 FD3  C66  C61   aromatic  1.392  0.020  1.392
 FD3  C66  H661  single    0.930  0.020  1.080
 FD3  C64  C63   aromatic  1.387  0.020  1.387
 FD3  C64  H641  single    0.930  0.020  1.080
 FD3  C63  C62   aromatic  1.387  0.020  1.387
 FD3  C63  H631  single    0.930  0.020  1.080
 FD3  C62  C61   aromatic  1.394  0.020  1.394
 FD3  C62  H621  single    0.930  0.020  1.080
 FD3  C61  C25   single    1.491  0.020  1.491
 FD3  C25  N43   single    1.363  0.020  1.363
 FD3  C25  N54   double    1.278  0.020  1.278
 FD3  N43  H431  single    0.890  0.020  1.040
 FD3  N43  H432  single    0.890  0.020  1.040
 FD3  N54  H541  single    0.890  0.020  1.040
 FD3  C34  C31   single    1.537  0.020  1.537
 FD3  C34  H341  single    0.970  0.020  1.090
 FD3  C34  H342  single    0.970  0.020  1.090
 FD3  C31  C35   single    1.537  0.020  1.537
 FD3  C31  N29   single    1.452  0.020  1.452
 FD3  C31  H311  single    0.970  0.020  1.090
 FD3  C35  O36   double    1.224  0.020  1.224
 FD3  C35  N81   single    1.342  0.020  1.342
 FD3  N81  C71   single    1.453  0.020  1.453
 FD3  N81  C75   single    1.456  0.020  1.456
 FD3  C71  C72   single    1.521  0.020  1.521
 FD3  C71  H711  single    0.970  0.020  1.090
 FD3  C71  H712  single    0.970  0.020  1.090
 FD3  C72  N40   single    1.448  0.020  1.448
 FD3  C72  H721  single    0.970  0.020  1.090
 FD3  C72  H722  single    0.970  0.020  1.090
 FD3  C74  C75   single    1.519  0.020  1.519
 FD3  C74  N40   single    1.451  0.020  1.451
 FD3  C74  H741  single    0.970  0.020  1.090
 FD3  C74  H742  single    0.970  0.020  1.090
 FD3  C75  H751  single    0.970  0.020  1.090
 FD3  C75  H752  single    0.970  0.020  1.090
 FD3  N40  H401  single    0.890  0.020  1.040
 FD3  N29  S12   single    1.653  0.020  1.653
 FD3  N29  H291  single    0.890  0.020  1.040
 FD3  S12  O32   double    1.453  0.020  1.453
 FD3  S12  O33   double    1.453  0.020  1.453
 FD3  S12  C2    single    1.770  0.020  1.770
 FD3  C2   C3    aromatic  1.412  0.020  1.412
 FD3  C2   C1    aromatic  1.368  0.020  1.368
 FD3  C3   C4    aromatic  1.364  0.020  1.364
 FD3  C3   H31   single    0.930  0.020  1.080
 FD3  C4   C10   aromatic  1.416  0.020  1.416
 FD3  C4   H41   single    0.930  0.020  1.080
 FD3  C9   C10   aromatic  1.418  0.020  1.418
 FD3  C9   C1    aromatic  1.412  0.020  1.412
 FD3  C9   C8    aromatic  1.414  0.020  1.414
 FD3  C10  C5    aromatic  1.413  0.020  1.413
 FD3  C1   H11   single    0.930  0.020  1.080
 FD3  C5   C6    aromatic  1.369  0.020  1.369
 FD3  C5   H51   single    0.930  0.020  1.080
 FD3  C6   C7    aromatic  1.410  0.020  1.410
 FD3  C6   H61   single    0.930  0.020  1.080
 FD3  C7   C8    aromatic  1.368  0.020  1.368
 FD3  C7   H71   single    0.930  0.020  1.080
 FD3  C8   H81   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
 FD3  C34   C65  C64   121.11  3.000
 FD3  C34   C65  C66   120.10  3.000
 FD3  C64   C65  C66   118.76  3.000
 FD3  H661  C66  C61   119.52  3.000
 FD3  H661  C66  C65   119.10  3.000
 FD3  C61   C66  C65   121.36  3.000
 FD3  H641  C64  C63   119.78  3.000
 FD3  H641  C64  C65   119.75  3.000
 FD3  C63   C64  C65   120.47  3.000
 FD3  H631  C63  C62   119.78  3.000
 FD3  H631  C63  C64   119.89  3.000
 FD3  C62   C63  C64   120.33  3.000
 FD3  H621  C62  C61   120.34  3.000
 FD3  H621  C62  C63   119.66  3.000
 FD3  C61   C62  C63   119.98  3.000
 FD3  C25   C61  C62   121.13  3.000
 FD3  C25   C61  C66   119.78  3.000
 FD3  C62   C61  C66   119.09  3.000
 FD3  N54   C25  N43   120.45  3.000
 FD3  N54   C25  C61   124.74  3.000
 FD3  N43   C25  C61   114.77  3.000
 FD3  H432  N43  H431  114.32  3.000
 FD3  H432  N43  C25   118.43  3.000
 FD3  H431  N43  C25   116.27  3.000
 FD3  H541  N54  C25   110.87  3.000
 FD3  H342  C34  H341  106.31  3.000
 FD3  H342  C34  C31   108.75  3.000
 FD3  H341  C34  C31   108.87  3.000
 FD3  H342  C34  C65   110.60  3.000
 FD3  H341  C34  C65   110.33  3.000
 FD3  C31   C34  C65   111.81  3.000
 FD3  H311  C31  N29   107.27  3.000
 FD3  H311  C31  C35   112.69  3.000
 FD3  N29   C31  C35   110.00  3.000
 FD3  H311  C31  C34   108.29  3.000
 FD3  N29   C31  C34   109.37  3.000
 FD3  C35   C31  C34   109.14  3.000
 FD3  N81   C35  O36   123.26  3.000
 FD3  N81   C35  C31   119.05  3.000
 FD3  O36   C35  C31   117.67  3.000
 FD3  C75   N81  C71   112.55  3.000
 FD3  C75   N81  C35   120.70  3.000
 FD3  C71   N81  C35   126.71  3.000
 FD3  H712  C71  H711  107.24  3.000
 FD3  H712  C71  C72   109.06  3.000
 FD3  H711  C71  C72   109.65  3.000
 FD3  H712  C71  N81   112.04  3.000
 FD3  H711  C71  N81   108.86  3.000
 FD3  C72   C71  N81   109.95  3.000
 FD3  H722  C72  H721  107.30  3.000
 FD3  H722  C72  N40   113.13  3.000
 FD3  H721  C72  N40   109.51  3.000
 FD3  H722  C72  C71   108.50  3.000
 FD3  H721  C72  C71   108.68  3.000
 FD3  N40   C72  C71   109.61  3.000
 FD3  H742  C74  H741  107.37  3.000
 FD3  H742  C74  N40   112.98  3.000
 FD3  H741  C74  N40   109.42  3.000
 FD3  H742  C74  C75   108.65  3.000
 FD3  H741  C74  C75   108.86  3.000
 FD3  N40   C74  C75   109.46  3.000
 FD3  H752  C75  H751  107.79  3.000
 FD3  H752  C75  C74   109.96  3.000
 FD3  H751  C75  C74   110.91  3.000
 FD3  H752  C75  N81   108.29  3.000
 FD3  H751  C75  N81   109.57  3.000
 FD3  C74   C75  N81   110.24  3.000
 FD3  H401  N40  C74   109.91  3.000
 FD3  H401  N40  C72   109.78  3.000
 FD3  C74   N40  C72   111.17  3.000
 FD3  H291  N29  S12   111.80  3.000
 FD3  H291  N29  C31   112.75  3.000
 FD3  S12   N29  C31   118.05  3.000
 FD3  C2    S12  O33   108.00  3.000
 FD3  C2    S12  O32   109.23  3.000
 FD3  O33   S12  O32   120.15  3.000
 FD3  C2    S12  N29   105.43  3.000
 FD3  O33   S12  N29   107.19  3.000
 FD3  O32   S12  N29   105.89  3.000
 FD3  C1    C2   C3    121.75  3.000
 FD3  C1    C2   S12   119.25  3.000
 FD3  C3    C2   S12   118.72  3.000
 FD3  H31   C3   C4    120.28  3.000
 FD3  H31   C3   C2    120.58  3.000
 FD3  C4    C3   C2    119.15  3.000
 FD3  H41   C4   C10   119.06  3.000
 FD3  H41   C4   C3    119.88  3.000
 FD3  C10   C4   C3    121.05  3.000
 FD3  C8    C9   C1    121.43  3.000
 FD3  C8    C9   C10   119.42  3.000
 FD3  C1    C9   C10   119.14  3.000
 FD3  C5    C10  C9    118.92  3.000
 FD3  C5    C10  C4    121.93  3.000
 FD3  C9    C10  C4    119.15  3.000
 FD3  H11   C1   C9    118.95  3.000
 FD3  H11   C1   C2    121.30  3.000
 FD3  C9    C1   C2    119.74  3.000
 FD3  H51   C5   C6    120.42  3.000
 FD3  H51   C5   C10   119.10  3.000
 FD3  C6    C5   C10   120.47  3.000
 FD3  H61   C6   C7    119.44  3.000
 FD3  H61   C6   C5    120.01  3.000
 FD3  C7    C6   C5    120.55  3.000
 FD3  H71   C7   C8    120.16  3.000
 FD3  H71   C7   C6    119.57  3.000
 FD3  C8    C7   C6    120.27  3.000
 FD3  H81   C8   C7    120.46  3.000
 FD3  H81   C8   C9    119.17  3.000
 FD3  C7    C8   C9    120.37  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
 FD3  CONST_01  C62   C61  C66  C65    0.00   0.0  0
 FD3  CONST_02  C62   C63  C64  C65    0.00   0.0  0
 FD3  CONST_03  C63   C64  C65  C66    0.00   0.0  0
 FD3  CONST_04  C63   C62  C61  C66    0.00   0.0  0
 FD3  CONST_05  C61   C66  C65  C64    0.00   0.0  0
 FD3  CONST_06  C61   C62  C63  C64    0.00   0.0  0
 FD3  CONST_07  C10   C4   C3   C2     0.00   0.0  0
 FD3  CONST_08  C10   C9   C1   C2     0.00   0.0  0
 FD3  CONST_09  C8    C9   C1   C2   180.00   0.0  0
 FD3  CONST_10  C9    C1   C2   C3     0.00   0.0  0
 FD3  CONST_11  C9    C10  C4   C3     0.00   0.0  0
 FD3  CONST_12  C5    C10  C4   C3   180.00   0.0  0
 FD3  CONST_13  C1    C2   C3   C4     0.00   0.0  0
 FD3  CONST_14  C1    C9   C10  C4     0.00   0.0  0
 FD3  CONST_15  C8    C9   C10  C4   180.00   0.0  0
 FD3  CONST_16  C6    C5   C10  C4   180.00   0.0  0
 FD3  CONST_17  C6    C5   C10  C9     0.00   0.0  0
 FD3  CONST_18  C6    C7   C8   C9     0.00   0.0  0
 FD3  CONST_19  C7    C8   C9   C10    0.00   0.0  0
 FD3  CONST_20  C7    C6   C5   C10    0.00   0.0  0
 FD3  CONST_21  C5    C10  C9   C1   180.00   0.0  0
 FD3  CONST_22  C7    C8   C9   C1   180.00   0.0  0
 FD3  CONST_23  C8    C9   C10  C5     0.00   0.0  0
 FD3  CONST_24  C8    C7   C6   C5     0.00   0.0  0
 FD3  CONST_25  C25   C61  C66  C65  180.00   0.0  0
 FD3  CONST_26  C34   C65  C64  C63  180.00   0.0  0
 FD3  CONST_27  C25   C61  C62  C63  180.00   0.0  0
 FD3  CONST_28  C34   C65  C66  C61  180.00   0.0  0
 FD3  CONST_29  C4    C3   C2   S12  180.00   0.0  0
 FD3  CONST_30  C9    C1   C2   S12  180.00   0.0  0
 FD3  CONST_31  H631  C63  C64  C65  180.00   0.0  0
 FD3  CONST_32  H641  C64  C65  C66  180.00   0.0  0
 FD3  CONST_33  H621  C62  C61  C66  180.00   0.0  0
 FD3  CONST_34  H661  C66  C65  C64  180.00   0.0  0
 FD3  CONST_35  H41   C4   C3   C2   180.00   0.0  0
 FD3  CONST_36  H11   C1   C2   C3   180.00   0.0  0
 FD3  CONST_37  H51   C5   C10  C4     0.00   0.0  0
 FD3  CONST_38  H71   C7   C8   C9   180.00   0.0  0
 FD3  CONST_39  H31   C3   C4   C10  180.00   0.0  0
 FD3  CONST_40  H81   C8   C9   C10  180.00   0.0  0
 FD3  CONST_41  H61   C6   C5   C10  180.00   0.0  0
 FD3  CONST_42  C71   N81  C35  C31    0.00   0.0  0
 FD3  CONST_43  C75   N81  C35  C31  180.00   0.0  0
 FD3  CONST_44  C71   N81  C35  O36  180.00   0.0  0
 FD3  CONST_45  C75   N81  C35  O36    0.00   0.0  0
 FD3  CONST_46  H431  N43  C25  C61  180.00   0.0  0
 FD3  CONST_48  H541  N54  C25  C61    0.00   0.0  0
 FD3  Var_01    N40   C72  C71  N81   56.72  30.0  1
 FD3  Var_02    N40   C74  C75  N81  -56.35  30.0  1
 FD3  Var_03    C74   C75  N81  C71   55.55  30.0  1
 FD3  Var_04    C74   N40  C72  C71  -60.08  30.0  1
 FD3  Var_05    C75   N81  C71  C72  -55.55  30.0  1
 FD3  Var_06    C75   C74  N40  C72   59.82  30.0  1
 FD3  Var_07    C31   C34  C65  C66  -81.29  30.0  2
 FD3  Var_08    N43   C25  C61  C66  147.75  30.0  2
 FD3  Var_09    C3    C2   S12  N29   79.81  30.0  2
 FD3  Var_10    C2    S12  N29  C31   54.39  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
 FD3  chir_01  C31  C34  C35  N29  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
 FD3  plan-1  C65   0.020
 FD3  plan-1  C66   0.020
 FD3  plan-1  C64   0.020
 FD3  plan-1  C63   0.020
 FD3  plan-1  C62   0.020
 FD3  plan-1  C61   0.020
 FD3  plan-1  C25   0.020
 FD3  plan-1  C34   0.020
 FD3  plan-1  H661  0.020
 FD3  plan-1  H641  0.020
 FD3  plan-1  H631  0.020
 FD3  plan-1  H621  0.020
 FD3  plan-2  S12   0.020
 FD3  plan-2  C2    0.020
 FD3  plan-2  C3    0.020
 FD3  plan-2  C4    0.020
 FD3  plan-2  C9    0.020
 FD3  plan-2  C10   0.020
 FD3  plan-2  C1    0.020
 FD3  plan-2  C5    0.020
 FD3  plan-2  C6    0.020
 FD3  plan-2  C7    0.020
 FD3  plan-2  C8    0.020
 FD3  plan-2  H31   0.020
 FD3  plan-2  H41   0.020
 FD3  plan-2  H11   0.020
 FD3  plan-2  H51   0.020
 FD3  plan-2  H61   0.020
 FD3  plan-2  H71   0.020
 FD3  plan-2  H81   0.020
 FD3  plan-3  C31   0.020
 FD3  plan-3  C35   0.020
 FD3  plan-3  O36   0.020
 FD3  plan-3  N81   0.020
 FD3  plan-3  C71   0.020
 FD3  plan-3  C75   0.020
 FD3  plan-4  C61   0.020
 FD3  plan-4  C25   0.020
 FD3  plan-4  N43   0.020
 FD3  plan-4  N54   0.020
 FD3  plan-4  H431  0.020
 FD3  plan-4  H432  0.020
 FD3  plan-4  H541  0.020

