# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:36:27 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4,4'-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(OCCCCCOc2ccc(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
 PNT  PNT  4,4'-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide  ligand  49  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNT
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
 PNT  C1    C  CR6   0   0.387   -4.8622  -0.5980  -0.0055
 PNT  C2    C  CR16  0  -0.336   -5.9286  -1.5013   0.0569
 PNT  C3    C  CR16  0  -0.259   -7.2293  -1.0485  -0.0044
 PNT  C4    C  CR6   0   0.023   -7.5175   0.3138  -0.1181
 PNT  C5    C  CR16  0  -0.277   -6.4497   1.2017  -0.1856
 PNT  C6    C  CR16  0  -0.372   -5.1329   0.7619  -0.1331
 PNT  C7    C  CH2   0  -0.172   -2.5018  -0.2659  -0.0049
 PNT  C8    C  CH2   0  -0.456   -1.2541  -1.1166   0.1017
 PNT  C9    C  C     0   0.330   -8.9315   0.7645  -0.1806
 PNT  C10   C  CH2   0  -0.440    0.0078  -0.2666   0.0138
 PNT  C1'   C  CR6   0   0.387    4.8797  -0.5800   0.0145
 PNT  C2'   C  CR16  0  -0.336    5.9478  -1.4805   0.0845
 PNT  C3'   C  CR16  0  -0.258    7.2475  -1.0253   0.0202
 PNT  C4'   C  CR6   0   0.023    7.5328   0.3365  -0.1042
 PNT  C5'   C  CR16  0  -0.277    6.4632   1.2218  -0.1786
 PNT  C6'   C  CR16  0  -0.372    5.1475   0.7795  -0.1233
 PNT  C7'   C  CH2   0  -0.171    2.5178  -0.2550   0.0068
 PNT  C8'   C  CH2   0  -0.456    1.2731  -1.1104   0.1107
 PNT  C9'   C  C     0   0.330    8.9462   0.7886  -0.1696
 PNT  O1    O  O2    0  -0.472   -3.6301  -1.1260   0.0651
 PNT  O1'   O  O2    0  -0.472    3.6488  -1.1106   0.0875
 PNT  N1    N  N     0  -0.656   -9.8276  -0.0649  -0.5599
 PNT  N2    N  NH2   0  -0.824   -9.1426   2.0786   0.1360
 PNT  N1'   N  N     0  -0.656    9.8426  -0.0414  -0.5473
 PNT  N2'   N  NH2   0  -0.824    9.1562   2.1034   0.1437
 PNT  H2    H  HCR6  0   0.263   -5.7240  -2.5601   0.1564
 PNT  H3    H  HCR6  0   0.256   -8.0429  -1.7593   0.0446
 PNT  H5    H  HCR6  0   0.259   -6.6219   2.2644  -0.3006
 PNT  H6    H  HCR6  0   0.282   -4.3404   1.4942  -0.1950
 PNT  H71   H  HCH2  0   0.224   -2.5320   0.4690   0.8078
 PNT  H72   H  HCH2  0   0.223   -2.5047   0.2871  -0.9513
 PNT  H81   H  HCH2  0   0.234   -1.2641  -1.6641   1.0487
 PNT  H82   H  HCH2  0   0.234   -1.2509  -1.8608  -0.6998
 PNT  H101  H  HCH2  0   0.226    0.0095   0.2888  -0.9299
 PNT  H102  H  HCH2  0   0.227    0.0030   0.4826   0.8120
 PNT  H2'   H  HCR6  0   0.263    5.7452  -2.5389   0.1919
 PNT  H3'   H  HCR6  0   0.256    8.0629  -1.7336   0.0750
 PNT  H5'   H  HCR6  0   0.259    6.6331   2.2842  -0.3008
 PNT  H6'   H  HCR6  0   0.282    4.3532   1.5093  -0.1926
 PNT  H7'1  H  HCH2  0   0.223    2.5236   0.2929  -0.9426
 PNT  H7'2  H  HCH2  0   0.224    2.5406   0.4844   0.8157
 PNT  H8'1  H  HCH2  0   0.234    1.2808  -1.6544   1.0597
 PNT  H8'2  H  HCH2  0   0.233    1.2770  -1.8576  -0.6881
 PNT  HN1   H  H     0   0.322  -10.7530   0.3542  -0.5235
 PNT  HN2   H  HNH2  0   0.393   -8.5151   2.5148   0.7915
 PNT  HN3   H  HNH2  0   0.389  -10.0999   2.3726   0.2494
 PNT  HN'1  H  H     0   0.322   10.7677   0.3786  -0.5129
 PNT  HN'2  H  HNH2  0   0.393    8.5287   2.5395   0.7993
 PNT  HN'3  H  HNH2  0   0.389   10.1132   2.3985   0.2562

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
 PNT  C1   C2    aromatic  1.399  0.020  1.399
 PNT  C1   C6    aromatic  1.392  0.020  1.392
 PNT  C1   O1    single    1.342  0.020  1.342
 PNT  C2   C3    aromatic  1.379  0.020  1.379
 PNT  C2   H2    single    0.930  0.020  1.080
 PNT  C3   C4    aromatic  1.397  0.020  1.397
 PNT  C3   H3    single    0.930  0.020  1.080
 PNT  C4   C5    aromatic  1.390  0.020  1.390
 PNT  C4   C9    single    1.485  0.020  1.485
 PNT  C5   C6    aromatic  1.389  0.020  1.389
 PNT  C5   H5    single    0.930  0.020  1.080
 PNT  C6   H6    single    0.930  0.020  1.080
 PNT  C7   C8    single    1.514  0.020  1.514
 PNT  C7   O1    single    1.421  0.020  1.421
 PNT  C7   H71   single    0.970  0.020  1.090
 PNT  C7   H72   single    0.970  0.020  1.090
 PNT  C8   C10   single    1.524  0.020  1.524
 PNT  C8   H81   single    0.970  0.020  1.090
 PNT  C8   H82   single    0.970  0.020  1.090
 PNT  C9   N1    double    1.279  0.020  1.279
 PNT  C9   N2    single    1.368  0.020  1.368
 PNT  C10  C8'   single    1.524  0.020  1.524
 PNT  C10  H101  single    0.970  0.020  1.090
 PNT  C10  H102  single    0.970  0.020  1.090
 PNT  C1'  C2'   aromatic  1.399  0.020  1.399
 PNT  C1'  C6'   aromatic  1.393  0.020  1.393
 PNT  C1'  O1'   single    1.342  0.020  1.342
 PNT  C2'  C3'   aromatic  1.379  0.020  1.379
 PNT  C2'  H2'   single    0.930  0.020  1.080
 PNT  C3'  C4'   aromatic  1.397  0.020  1.397
 PNT  C3'  H3'   single    0.930  0.020  1.080
 PNT  C4'  C5'   aromatic  1.390  0.020  1.390
 PNT  C4'  C9'   single    1.485  0.020  1.485
 PNT  C5'  C6'   aromatic  1.389  0.020  1.389
 PNT  C5'  H5'   single    0.930  0.020  1.080
 PNT  C6'  H6'   single    0.930  0.020  1.080
 PNT  C7'  C8'   single    1.514  0.020  1.514
 PNT  C7'  O1'   single    1.420  0.020  1.420
 PNT  C7'  H7'1  single    0.970  0.020  1.090
 PNT  C7'  H7'2  single    0.970  0.020  1.090
 PNT  C8'  H8'1  single    0.970  0.020  1.090
 PNT  C8'  H8'2  single    0.970  0.020  1.090
 PNT  C9'  N1'   double    1.279  0.020  1.279
 PNT  C9'  N2'   single    1.368  0.020  1.368
 PNT  N1   HN1   single    0.890  0.020  1.040
 PNT  N2   HN2   single    0.890  0.020  1.040
 PNT  N2   HN3   single    0.890  0.020  1.040
 PNT  N1'  HN'1  single    0.890  0.020  1.040
 PNT  N2'  HN'2  single    0.890  0.020  1.040
 PNT  N2'  HN'3  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
 PNT  O1    C1   C6    124.57  3.000
 PNT  O1    C1   C2    116.32  3.000
 PNT  C6    C1   C2    119.11  3.000
 PNT  H2    C2   C3    120.22  3.000
 PNT  H2    C2   C1    119.43  3.000
 PNT  C3    C2   C1    120.34  3.000
 PNT  H3    C3   C4    119.30  3.000
 PNT  H3    C3   C2    119.47  3.000
 PNT  C4    C3   C2    121.23  3.000
 PNT  C9    C4   C5    122.36  3.000
 PNT  C9    C4   C3    119.71  3.000
 PNT  C5    C4   C3    117.92  3.000
 PNT  H5    C5   C6    117.74  3.000
 PNT  H5    C5   C4    120.66  3.000
 PNT  C6    C5   C4    121.59  3.000
 PNT  H6    C6   C5    118.58  3.000
 PNT  H6    C6   C1    121.63  3.000
 PNT  C5    C6   C1    119.80  3.000
 PNT  H72   C7   H71   107.57  3.000
 PNT  H72   C7   O1    110.24  3.000
 PNT  H71   C7   O1    110.34  3.000
 PNT  H72   C7   C8    110.27  3.000
 PNT  H71   C7   C8    110.32  3.000
 PNT  O1    C7   C8    108.11  3.000
 PNT  H82   C8   H81   107.09  3.000
 PNT  H82   C8   C10   109.56  3.000
 PNT  H81   C8   C10   109.67  3.000
 PNT  H82   C8   C7    109.46  3.000
 PNT  H81   C8   C7    109.55  3.000
 PNT  C10   C8   C7    111.41  3.000
 PNT  N2    C9   N1    125.71  3.000
 PNT  N2    C9   C4    115.38  3.000
 PNT  N1    C9   C4    118.87  3.000
 PNT  H102  C10  H101  106.34  3.000
 PNT  H102  C10  C8'   109.64  3.000
 PNT  H101  C10  C8'   109.53  3.000
 PNT  H102  C10  C8    109.63  3.000
 PNT  H101  C10  C8    109.51  3.000
 PNT  C8'   C10  C8    112.03  3.000
 PNT  O1'   C1'  C6'   124.59  3.000
 PNT  O1'   C1'  C2'   116.30  3.000
 PNT  C6'   C1'  C2'   119.12  3.000
 PNT  H2'   C2'  C3'   120.24  3.000
 PNT  H2'   C2'  C1'   119.43  3.000
 PNT  C3'   C2'  C1'   120.33  3.000
 PNT  H3'   C3'  C4'   119.27  3.000
 PNT  H3'   C3'  C2'   119.49  3.000
 PNT  C4'   C3'  C2'   121.24  3.000
 PNT  C9'   C4'  C5'   122.40  3.000
 PNT  C9'   C4'  C3'   119.67  3.000
 PNT  C5'   C4'  C3'   117.93  3.000
 PNT  H5'   C5'  C6'   117.74  3.000
 PNT  H5'   C5'  C4'   120.67  3.000
 PNT  C6'   C5'  C4'   121.58  3.000
 PNT  H6'   C6'  C5'   118.59  3.000
 PNT  H6'   C6'  C1'   121.61  3.000
 PNT  C5'   C6'  C1'   119.80  3.000
 PNT  H7'2  C7'  H7'1  107.57  3.000
 PNT  H7'2  C7'  O1'   110.35  3.000
 PNT  H7'1  C7'  O1'   110.25  3.000
 PNT  H7'2  C7'  C8'   110.34  3.000
 PNT  H7'1  C7'  C8'   110.26  3.000
 PNT  O1'   C7'  C8'   108.09  3.000
 PNT  H8'2  C8'  H8'1  107.08  3.000
 PNT  H8'2  C8'  C7'   109.45  3.000
 PNT  H8'1  C8'  C7'   109.56  3.000
 PNT  H8'2  C8'  C10   109.56  3.000
 PNT  H8'1  C8'  C10   109.66  3.000
 PNT  C7'   C8'  C10   111.44  3.000
 PNT  N2'   C9'  N1'   125.73  3.000
 PNT  N2'   C9'  C4'   115.37  3.000
 PNT  N1'   C9'  C4'   118.85  3.000
 PNT  C7    O1   C1    119.23  3.000
 PNT  C7'   O1'  C1'   119.27  3.000
 PNT  HN1   N1   C9    111.10  3.000
 PNT  HN3   N2   HN2   113.10  3.000
 PNT  HN3   N2   C9    116.93  3.000
 PNT  HN2   N2   C9    118.07  3.000
 PNT  HN'1  N1'  C9'   111.09  3.000
 PNT  HN'3  N2'  HN'2  113.09  3.000
 PNT  HN'3  N2'  C9'   116.92  3.000
 PNT  HN'2  N2'  C9'   118.03  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
 PNT  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 PNT  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PNT  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PNT  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PNT  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 PNT  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PNT  CONST_07  C4'   C3'  C2'  C1'     0.00   0.0  0
 PNT  CONST_08  C4'   C5'  C6'  C1'     0.00   0.0  0
 PNT  CONST_09  C5'   C6'  C1'  C2'     0.00   0.0  0
 PNT  CONST_10  C5'   C4'  C3'  C2'     0.00   0.0  0
 PNT  CONST_11  C6'   C1'  C2'  C3'     0.00   0.0  0
 PNT  CONST_12  C6'   C5'  C4'  C3'     0.00   0.0  0
 PNT  CONST_13  C9    C4   C3   C2    180.00   0.0  0
 PNT  CONST_14  O1    C1   C2   C3    180.00   0.0  0
 PNT  CONST_15  O1    C1   C6   C5    180.00   0.0  0
 PNT  CONST_16  C9    C4   C5   C6    180.00   0.0  0
 PNT  CONST_17  C9'   C4'  C3'  C2'   180.00   0.0  0
 PNT  CONST_18  O1'   C1'  C2'  C3'   180.00   0.0  0
 PNT  CONST_19  O1'   C1'  C6'  C5'   180.00   0.0  0
 PNT  CONST_20  C9'   C4'  C5'  C6'   180.00   0.0  0
 PNT  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 PNT  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 PNT  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 PNT  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 PNT  CONST_25  H3'   C3'  C2'  C1'   180.00   0.0  0
 PNT  CONST_26  H5'   C5'  C6'  C1'   180.00   0.0  0
 PNT  CONST_27  H6'   C6'  C1'  C2'   180.00   0.0  0
 PNT  CONST_28  H2'   C2'  C3'  C4'   180.00   0.0  0
 PNT  CONST_29  HN1   N1   C9   C4    180.00   0.0  0
 PNT  CONST_31  HN3   N2   C9   C4    180.00   0.0  0
 PNT  CONST_32  HN'1  N1'  C9'  C4'   180.00   0.0  0
 PNT  CONST_34  HN'3  N2'  C9'  C4'   180.00   0.0  0
 PNT  Var_01    N1    C9   C4   C3    -22.41  30.0  2
 PNT  Var_02    N1'   C9'  C4'  C3'    22.69  30.0  2
 PNT  Var_03    C8    C7   O1   C1    179.87  30.0  1
 PNT  Var_04    C8'   C7'  O1'  C1'   179.81  30.0  1
 PNT  Var_05    C8'   C10  C8   C7   -179.64  30.0  3
 PNT  Var_06    C7'   C8'  C10  C8    179.38  30.0  3
 PNT  Var_07    O1    C7   C8   C10   179.16  30.0  1
 PNT  Var_08    O1'   C7'  C8'  C10  -179.25  30.0  2

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
 PNT  plan-1  C1    0.020
 PNT  plan-1  C2    0.020
 PNT  plan-1  C3    0.020
 PNT  plan-1  C4    0.020
 PNT  plan-1  C5    0.020
 PNT  plan-1  C6    0.020
 PNT  plan-1  C9    0.020
 PNT  plan-1  O1    0.020
 PNT  plan-1  H2    0.020
 PNT  plan-1  H3    0.020
 PNT  plan-1  H5    0.020
 PNT  plan-1  H6    0.020
 PNT  plan-2  C1'   0.020
 PNT  plan-2  C2'   0.020
 PNT  plan-2  C3'   0.020
 PNT  plan-2  C4'   0.020
 PNT  plan-2  C5'   0.020
 PNT  plan-2  C6'   0.020
 PNT  plan-2  C9'   0.020
 PNT  plan-2  O1'   0.020
 PNT  plan-2  H2'   0.020
 PNT  plan-2  H3'   0.020
 PNT  plan-2  H5'   0.020
 PNT  plan-2  H6'   0.020
 PNT  plan-3  C4    0.020
 PNT  plan-3  C9    0.020
 PNT  plan-3  N1    0.020
 PNT  plan-3  N2    0.020
 PNT  plan-3  HN1   0.020
 PNT  plan-3  HN2   0.020
 PNT  plan-3  HN3   0.020
 PNT  plan-4  C4'   0.020
 PNT  plan-4  C9'   0.020
 PNT  plan-4  N1'   0.020
 PNT  plan-4  N2'   0.020
 PNT  plan-4  HN'1  0.020
 PNT  plan-4  HN'2  0.020
 PNT  plan-4  HN'3  0.020

