# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 14:17:12 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 4,4'-[hexane-1,6-diylbis(oxy)]dibenzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(OCCCCCCOc2ccc(cc2)C(N)=N)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
 DID  DID  4,4'-[hexane-1,6-diylbis(oxy)]dibenzenecarboximidamide  ligand  52  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DID
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
 DID  C4    C  CR6   0  -0.017   0.1471   0.0377    8.2297
 DID  C5    C  CR16  0  -0.275  -1.1781  -0.0931    7.8086
 DID  C6    C  CR16  0  -0.338  -1.5063  -0.0746    6.4688
 DID  C1    C  CR6   0   0.390  -0.5101   0.0850    5.5006
 DID  C2    C  CR16  0  -0.370   0.8153   0.2268    5.9066
 DID  C3    C  CR16  0  -0.267   1.1298   0.1954    7.2583
 DID  C9    C  C     0   0.327   0.4795   0.0215    9.6788
 DID  N1    N  NH2   0  -0.805   1.7123  -0.4808    9.9799
 DID  N2    N  N     0  -0.646  -0.2763   0.4688   10.6085
 DID  O1    O  O2    0  -0.472  -0.9168   0.0863    4.2218
 DID  C7    C  CH2   0  -0.173   0.0539   0.1638    3.1860
 DID  C8    C  CH2   0  -0.456  -0.6578   0.0409    1.8558
 DID  C10   C  CH2   0  -0.427   0.3268   0.0993    0.6937
 DID  C11   C  CH2   0  -0.426  -0.3599  -0.0252   -0.6603
 DID  C8'   C  CH2   0  -0.456   0.6265   0.0372   -1.8206
 DID  C7'   C  CH2   0  -0.173  -0.0770  -0.1072   -3.1531
 DID  O1'   O  O2    0  -0.473   0.8975  -0.0174   -4.1836
 DID  C1'   C  CR6   0   0.387   0.5004  -0.0567   -5.4654
 DID  C6'   C  CR16  0  -0.371  -0.8160  -0.2462   -5.8779
 DID  C5'   C  CR16  0  -0.277  -1.1191  -0.2613   -7.2336
 DID  C4'   C  CR6   0   0.022  -0.1348  -0.0937   -8.2014
 DID  C3'   C  CR16  0  -0.259   1.1827   0.0828   -7.7720
 DID  C2'   C  CR16  0  -0.336   1.4999   0.1065   -6.4304
 DID  C9'   C  C     0   0.332  -0.4378  -0.1168   -9.6557
 DID  N1'   N  NH2   0  -0.825  -1.7396   0.1361   -9.9873
 DID  N2'   N  N     0  -0.657   0.4987  -0.4086  -10.4764
 DID  H5    H  HCR6  0   0.262  -1.9684  -0.2356    8.5353
 DID  H6    H  HCR6  0   0.266  -2.5366  -0.1943    6.1577
 DID  H2    H  HCR6  0   0.282   1.6150   0.3638    5.1924
 DID  H3    H  HCR6  0   0.265   2.1661   0.3162    7.5472
 DID  HN11  H  HNH2  0   0.382   1.9073  -0.6110   10.9599
 DID  HN12  H  HNH2  0   0.391   2.0886  -1.2020    9.3873
 DID  HN2   H  H     0   0.330  -1.1022   0.9096   10.2210
 DID  H71   H  HCH2  0   0.223   0.5927   1.1170    3.2406
 DID  H72   H  HCH2  0   0.223   0.7912  -0.6394    3.2983
 DID  H81   H  HCH2  0   0.231  -1.2093  -0.9033    1.8232
 DID  H82   H  HCH2  0   0.232  -1.3918   0.8455    1.7565
 DID  H101  H  HCH2  0   0.221   0.8858   1.0403    0.7314
 DID  H102  H  HCH2  0   0.221   1.0661  -0.7011    0.8000
 DID  H111  H  HCH2  0   0.221  -0.9159  -0.9680   -0.6989
 DID  H112  H  HCH2  0   0.221  -1.1015   0.7730   -0.7669
 DID  H8'1  H  HCH2  0   0.231   1.1655   0.9888   -1.7934
 DID  H8'2  H  HCH2  0   0.231   1.3708  -0.7568   -1.7127
 DID  H7'1  H  HCH2  0   0.223  -0.5967  -1.0711   -3.2034
 DID  H7'2  H  HCH2  0   0.223  -0.8299   0.6803   -3.2750
 DID  H6'   H  HCR6  0   0.281  -1.6179  -0.3883   -5.1672
 DID  H5'   H  HCR6  0   0.259  -2.1499  -0.4291   -7.5188
 DID  H3'   H  HCR6  0   0.255   1.9654   0.2131   -8.5070
 DID  H2'   H  HCR6  0   0.263   2.5247   0.2572   -6.1141
 DID  H1'1  H  HNH2  0   0.389  -1.9473   0.2682  -10.9644
 DID  H1'2  H  HNH2  0   0.393  -2.2789   0.7321   -9.3813
 DID  H1    H  H     0   0.321   0.1723  -0.3535  -11.4375

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
 DID  C4   C5    aromatic  1.397  0.020  1.397
 DID  C4   C3    aromatic  1.391  0.020  1.391
 DID  C4   C9    single    1.487  0.020  1.487
 DID  C5   C6    aromatic  1.380  0.020  1.380
 DID  C5   H5    single    0.930  0.020  1.080
 DID  C6   C1    aromatic  1.398  0.020  1.398
 DID  C6   H6    single    0.930  0.020  1.080
 DID  C1   C2    aromatic  1.393  0.020  1.393
 DID  C1   O1    single    1.342  0.020  1.342
 DID  C2   C3    aromatic  1.388  0.020  1.388
 DID  C2   H2    single    0.930  0.020  1.080
 DID  C3   H3    single    0.930  0.020  1.080
 DID  C9   N1    single    1.365  0.020  1.365
 DID  C9   N2    double    1.279  0.020  1.279
 DID  N1   HN11  single    0.890  0.020  1.040
 DID  N1   HN12  single    0.890  0.020  1.040
 DID  N2   HN2   single    0.890  0.020  1.040
 DID  O1   C7    single    1.422  0.020  1.422
 DID  C7   C8    single    1.514  0.020  1.514
 DID  C7   H71   single    0.970  0.020  1.090
 DID  C7   H72   single    0.970  0.020  1.090
 DID  C8   C10   single    1.524  0.020  1.524
 DID  C8   H81   single    0.970  0.020  1.090
 DID  C8   H82   single    0.970  0.020  1.090
 DID  C10  C11   single    1.523  0.020  1.523
 DID  C10  H101  single    0.970  0.020  1.090
 DID  C10  H102  single    0.970  0.020  1.090
 DID  C11  C8'   single    1.524  0.020  1.524
 DID  C11  H111  single    0.970  0.020  1.090
 DID  C11  H112  single    0.970  0.020  1.090
 DID  C8'  C7'   single    1.514  0.020  1.514
 DID  C8'  H8'1  single    0.970  0.020  1.090
 DID  C8'  H8'2  single    0.970  0.020  1.090
 DID  C7'  O1'   single    1.421  0.020  1.421
 DID  C7'  H7'1  single    0.970  0.020  1.090
 DID  C7'  H7'2  single    0.970  0.020  1.090
 DID  O1'  C1'   single    1.343  0.020  1.343
 DID  C1'  C6'   aromatic  1.392  0.020  1.392
 DID  C1'  C2'   aromatic  1.399  0.020  1.399
 DID  C6'  C5'   aromatic  1.389  0.020  1.389
 DID  C6'  H6'   single    0.930  0.020  1.080
 DID  C5'  C4'   aromatic  1.390  0.020  1.390
 DID  C5'  H5'   single    0.930  0.020  1.080
 DID  C4'  C3'   aromatic  1.397  0.020  1.397
 DID  C4'  C9'   single    1.486  0.020  1.486
 DID  C3'  C2'   aromatic  1.379  0.020  1.379
 DID  C3'  H3'   single    0.930  0.020  1.080
 DID  C2'  H2'   single    0.930  0.020  1.080
 DID  C9'  N1'   single    1.367  0.020  1.367
 DID  C9'  N2'   double    1.279  0.020  1.279
 DID  N1'  H1'1  single    0.890  0.020  1.040
 DID  N1'  H1'2  single    0.890  0.020  1.040
 DID  N2'  H1    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
 DID  C9    C4   C3    121.60  3.000
 DID  C9    C4   C5    120.33  3.000
 DID  C3    C4   C5    118.06  3.000
 DID  H5    C5   C6    118.67  3.000
 DID  H5    C5   C4    120.16  3.000
 DID  C6    C5   C4    121.15  3.000
 DID  H6    C6   C1    119.45  3.000
 DID  H6    C6   C5    120.26  3.000
 DID  C1    C6   C5    120.29  3.000
 DID  O1    C1   C2    124.46  3.000
 DID  O1    C1   C6    116.36  3.000
 DID  C2    C1   C6    119.18  3.000
 DID  H2    C2   C3    118.60  3.000
 DID  H2    C2   C1    121.61  3.000
 DID  C3    C2   C1    119.79  3.000
 DID  H3    C3   C2    118.31  3.000
 DID  H3    C3   C4    120.17  3.000
 DID  C2    C3   C4    121.51  3.000
 DID  N2    C9   N1    120.14  3.000
 DID  N2    C9   C4    124.93  3.000
 DID  N1    C9   C4    114.90  3.000
 DID  HN12  N1   HN11  114.07  3.000
 DID  HN12  N1   C9    118.13  3.000
 DID  HN11  N1   C9    115.91  3.000
 DID  HN2   N2   C9    110.84  3.000
 DID  C7    O1   C1    119.17  3.000
 DID  H72   C7   H71   107.54  3.000
 DID  H72   C7   C8    110.29  3.000
 DID  H71   C7   C8    110.21  3.000
 DID  H72   C7   O1    110.17  3.000
 DID  H71   C7   O1    110.29  3.000
 DID  C8    C7   O1    108.35  3.000
 DID  H82   C8   H81   107.09  3.000
 DID  H82   C8   C10   109.64  3.000
 DID  H81   C8   C10   109.63  3.000
 DID  H82   C8   C7    109.61  3.000
 DID  H81   C8   C7    109.47  3.000
 DID  C10   C8   C7    111.30  3.000
 DID  H102  C10  H101  106.27  3.000
 DID  H102  C10  C11   109.32  3.000
 DID  H101  C10  C11   109.33  3.000
 DID  H102  C10  C8    109.52  3.000
 DID  H101  C10  C8    109.66  3.000
 DID  C11   C10  C8    112.54  3.000
 DID  H112  C11  H111  106.28  3.000
 DID  H112  C11  C8'   109.54  3.000
 DID  H111  C11  C8'   109.69  3.000
 DID  H112  C11  C10   109.40  3.000
 DID  H111  C11  C10   109.30  3.000
 DID  C8'   C11  C10   112.43  3.000
 DID  H8'2  C8'  H8'1  107.08  3.000
 DID  H8'2  C8'  C7'   109.51  3.000
 DID  H8'1  C8'  C7'   109.50  3.000
 DID  H8'2  C8'  C11   109.61  3.000
 DID  H8'1  C8'  C11   109.60  3.000
 DID  C7'   C8'  C11   111.43  3.000
 DID  H7'2  C7'  H7'1  107.52  3.000
 DID  H7'2  C7'  O1'   110.18  3.000
 DID  H7'1  C7'  O1'   110.32  3.000
 DID  H7'2  C7'  C8'   110.40  3.000
 DID  H7'1  C7'  C8'   110.15  3.000
 DID  O1'   C7'  C8'   108.27  3.000
 DID  C1'   O1'  C7'   119.19  3.000
 DID  C2'   C1'  C6'   119.15  3.000
 DID  C2'   C1'  O1'   116.35  3.000
 DID  C6'   C1'  O1'   124.50  3.000
 DID  H6'   C6'  C5'   118.58  3.000
 DID  H6'   C6'  C1'   121.64  3.000
 DID  C5'   C6'  C1'   119.79  3.000
 DID  H5'   C5'  C4'   120.62  3.000
 DID  H5'   C5'  C6'   117.80  3.000
 DID  C4'   C5'  C6'   121.56  3.000
 DID  C9'   C4'  C3'   119.68  3.000
 DID  C9'   C4'  C5'   122.34  3.000
 DID  C3'   C4'  C5'   117.97  3.000
 DID  H3'   C3'  C2'   119.52  3.000
 DID  H3'   C3'  C4'   119.27  3.000
 DID  C2'   C3'  C4'   121.21  3.000
 DID  H2'   C2'  C3'   120.28  3.000
 DID  H2'   C2'  C1'   119.40  3.000
 DID  C3'   C2'  C1'   120.32  3.000
 DID  N2'   C9'  N1'   125.72  3.000
 DID  N2'   C9'  C4'   118.84  3.000
 DID  N1'   C9'  C4'   115.39  3.000
 DID  H1'2  N1'  H1'1  113.31  3.000
 DID  H1'2  N1'  C9'   118.28  3.000
 DID  H1'1  N1'  C9'   117.11  3.000
 DID  H1    N2'  C9'   111.06  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
 DID  CONST_01  C1    C6   C5   C4      0.00   0.0  0
 DID  CONST_02  C1    C2   C3   C4      0.00   0.0  0
 DID  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 DID  CONST_04  C2    C1   C6   C5      0.00   0.0  0
 DID  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 DID  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 DID  CONST_07  C4'   C5'  C6'  C1'     0.00   0.0  0
 DID  CONST_08  C4'   C3'  C2'  C1'     0.00   0.0  0
 DID  CONST_09  C3'   C2'  C1'  C6'     0.00   0.0  0
 DID  CONST_10  C3'   C4'  C5'  C6'     0.00   0.0  0
 DID  CONST_11  C2'   C1'  C6'  C5'     0.00   0.0  0
 DID  CONST_12  C2'   C3'  C4'  C5'     0.00   0.0  0
 DID  CONST_13  O1    C1   C6   C5    180.00   0.0  0
 DID  CONST_14  C9    C4   C5   C6    180.00   0.0  0
 DID  CONST_15  C9    C4   C3   C2    180.00   0.0  0
 DID  CONST_16  O1    C1   C2   C3    180.00   0.0  0
 DID  CONST_17  C5'   C6'  C1'  O1'   180.00   0.0  0
 DID  CONST_18  C3'   C2'  C1'  O1'   180.00   0.0  0
 DID  CONST_19  C9'   C4'  C5'  C6'   180.00   0.0  0
 DID  CONST_20  C9'   C4'  C3'  C2'   180.00   0.0  0
 DID  CONST_21  H6    C6   C5   C4    180.00   0.0  0
 DID  CONST_22  H2    C2   C3   C4    180.00   0.0  0
 DID  CONST_23  H3    C3   C4   C5    180.00   0.0  0
 DID  CONST_24  H5    C5   C6   C1    180.00   0.0  0
 DID  CONST_25  H5'   C5'  C6'  C1'   180.00   0.0  0
 DID  CONST_26  H3'   C3'  C2'  C1'   180.00   0.0  0
 DID  CONST_27  H2'   C2'  C1'  C6'   180.00   0.0  0
 DID  CONST_28  H6'   C6'  C5'  C4'   180.00   0.0  0
 DID  CONST_29  HN11  N1   C9   C4    180.00   0.0  0
 DID  CONST_31  HN2   N2   C9   C4      0.00   0.0  0
 DID  CONST_32  H1'1  N1'  C9'  C4'   180.00   0.0  0
 DID  CONST_34  H1    N2'  C9'  C4'   180.00   0.0  0
 DID  Var_01    N1    C9   C4   C5    149.78  30.0  2
 DID  Var_02    C6'   C1'  O1'  C7'    -3.26  30.0  2
 DID  Var_03    N1'   C9'  C4'  C5'    21.03  30.0  2
 DID  Var_04    C8    C7   O1   C1    175.73  30.0  3
 DID  Var_05    H7'1  C7'  O1'  C1'    62.42  30.0  1
 DID  Var_06    C10   C8   C7   O1   -179.33  30.0  3
 DID  Var_07    C11   C10  C8   C7    179.86  30.0  3
 DID  Var_08    C8'   C11  C10  C8    179.85  30.0  3
 DID  Var_09    C7'   C8'  C11  C10   179.24  30.0  3
 DID  Var_10    O1'   C7'  C8'  C11   179.04  30.0  3

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
 DID  plan-1  C4    0.020
 DID  plan-1  C5    0.020
 DID  plan-1  C6    0.020
 DID  plan-1  C1    0.020
 DID  plan-1  C2    0.020
 DID  plan-1  C3    0.020
 DID  plan-1  C9    0.020
 DID  plan-1  O1    0.020
 DID  plan-1  H5    0.020
 DID  plan-1  H6    0.020
 DID  plan-1  H2    0.020
 DID  plan-1  H3    0.020
 DID  plan-2  O1'   0.020
 DID  plan-2  C1'   0.020
 DID  plan-2  C6'   0.020
 DID  plan-2  C5'   0.020
 DID  plan-2  C4'   0.020
 DID  plan-2  C3'   0.020
 DID  plan-2  C2'   0.020
 DID  plan-2  C9'   0.020
 DID  plan-2  H6'   0.020
 DID  plan-2  H5'   0.020
 DID  plan-2  H3'   0.020
 DID  plan-2  H2'   0.020
 DID  plan-3  C4    0.020
 DID  plan-3  C9    0.020
 DID  plan-3  N1    0.020
 DID  plan-3  N2    0.020
 DID  plan-3  HN11  0.020
 DID  plan-3  HN12  0.020
 DID  plan-3  HN2   0.020
 DID  plan-4  C4'   0.020
 DID  plan-4  C9'   0.020
 DID  plan-4  N1'   0.020
 DID  plan-4  N2'   0.020
 DID  plan-4  H1'1  0.020
 DID  plan-4  H1'2  0.020
 DID  plan-4  H1    0.020

