# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:38:20 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2,6-bis(3-carbamimidoylphenoxy)-3,5-difluoro-4-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(F)c(Oc2cccc(c2)C(N)=N)[nH+]c(Oc3cccc(c3)C(N)=N)c1F
#
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
 623  623  2,6-bis(3-carbamimidoylphenoxy)-3,5-difluoro-4-methylpyridinium  ligand  47  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_623
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
 623  C1    C  CR6   0   0.431  -1.1123   2.1092   0.0891
 623  F1    F  F     0  -0.266  -2.4182   2.2050   0.2956
 623  C2    C  CR6   0  -0.129  -0.3027   3.2266   0.2926
 623  C3    C  CR6   0   0.436   1.0432   3.0802   0.0324
 623  F3    F  F     0  -0.269   1.8847   4.0917   0.1839
 623  C4    C  CR6   0   0.571   1.5708   1.8739  -0.4068
 623  N5    N  NR16  1  -0.689   0.7370   0.8395  -0.5561
 623  C6    C  CR6   0   0.478  -0.5925   0.9091  -0.3251
 623  C7    C  CH3   0  -0.711  -0.8971   4.5112   0.7578
 623  O1    O  O2    0  -0.464   2.8563   1.7804  -0.6557
 623  O2    O  O2    0  -0.470  -1.2634  -0.1975  -0.5910
 623  C21   C  CR6   0   0.363  -2.2263  -0.6607   0.3001
 623  C22   C  CR16  0  -0.338  -3.3533  -1.2263  -0.2571
 623  C23   C  CR6   0   0.050  -4.3193  -1.7774   0.5797
 623  C24   C  CR16  0  -0.288  -4.1410  -1.7214   1.9598
 623  C25   C  CR16  0  -0.236  -3.0004  -1.1392   2.4944
 623  C26   C  CR16  0  -0.311  -2.0207  -0.6117   1.6683
 623  C27   C  C     0   0.345  -5.5285  -2.3960  -0.0359
 623  N21   N  N     0  -0.647  -5.9015  -1.9818  -1.1844
 623  N22   N  NH2   0  -0.822  -6.1544  -3.3329   0.7327
 623  C11   C  CR6   0   0.255   3.3912   0.5743  -1.1114
 623  C12   C  CR16  0  -0.273   3.5426   0.3951  -2.4757
 623  C13   C  CR16  0  -0.239   4.1116  -0.7901  -2.9131
 623  C14   C  CR16  0  -0.278   4.5009  -1.7641  -2.0032
 623  C15   C  CR6   0   0.050   4.3329  -1.5663  -0.6354
 623  C16   C  CR16  0  -0.307   3.7771  -0.3716  -0.1845
 623  C17   C  C     0   0.351   4.7491  -2.5841   0.3726
 623  N11   N  N     0  -0.646   5.0129  -2.1827   1.5550
 623  N12   N  NH2   0  -0.823   4.8553  -3.8589  -0.0972
 623  HN5   H  HNR6  0   0.485   1.1040  -0.0635  -0.8580
 623  H51   H  HCH3  0   0.294  -1.2953   4.3911   1.7660
 623  H52   H  HCH3  0   0.282  -0.1680   5.3145   0.7722
 623  H53   H  HCH3  0   0.289  -1.7218   4.8067   0.1105
 623  H22   H  HCR6  0   0.283  -3.4835  -1.2523  -1.3307
 623  H24   H  HCR6  0   0.269  -4.8935  -2.1140   2.6303
 623  H25   H  HCR6  0   0.278  -2.8670  -1.1004   3.5668
 623  H26   H  HCR6  0   0.298  -1.1199  -0.1874   2.0942
 623  H21   H  H     0   0.328  -6.7122  -2.4967  -1.5169
 623  H221  H  HNH2  0   0.398  -5.6037  -3.8594   1.3911
 623  H222  H  HNH2  0   0.394  -6.8876  -3.8720   0.2996
 623  H12   H  HCR6  0   0.298   3.2336   1.1616  -3.1741
 623  H13   H  HCR6  0   0.283   4.2549  -0.9550  -3.9719
 623  H14   H  HCR6  0   0.274   4.9552  -2.6722  -2.3760
 623  H16   H  HCR6  0   0.295   3.6555  -0.1955   0.8765
 623  HN11  H  H     0   0.331   5.2575  -2.9586   2.1641
 623  H121  H  HNH2  0   0.399   4.2758  -4.1390  -0.8713
 623  H122  H  HNH2  0   0.396   5.0025  -4.5906   0.5801

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
 623  C1   F1    single    1.326  0.020  1.326
 623  C1   C2    aromatic  1.395  0.020  1.395
 623  C1   C6    aromatic  1.372  0.020  1.372
 623  C2   C3    aromatic  1.379  0.020  1.379
 623  C2   C7    single    1.490  0.020  1.490
 623  C3   F3    single    1.324  0.020  1.324
 623  C3   C4    aromatic  1.388  0.020  1.388
 623  C4   N5    aromatic  1.337  0.020  1.337
 623  C4   O1    single    1.313  0.020  1.313
 623  N5   C6    aromatic  1.351  0.020  1.351
 623  N5   HN5   single    0.860  0.020  1.020
 623  C6   O2    single    1.321  0.020  1.321
 623  C7   H51   single    0.970  0.020  1.090
 623  C7   H52   single    0.970  0.020  1.090
 623  C7   H53   single    0.970  0.020  1.090
 623  O1   C11   single    1.396  0.020  1.396
 623  O2   C21   single    1.391  0.020  1.391
 623  C21  C22   aromatic  1.379  0.020  1.379
 623  C21  C26   aromatic  1.384  0.020  1.384
 623  C22  C23   aromatic  1.392  0.020  1.392
 623  C22  H22   single    0.930  0.020  1.080
 623  C23  C24   aromatic  1.393  0.020  1.393
 623  C23  C27   single    1.491  0.020  1.491
 623  C24  C25   aromatic  1.388  0.020  1.388
 623  C24  H24   single    0.930  0.020  1.080
 623  C25  C26   aromatic  1.386  0.020  1.386
 623  C25  H25   single    0.930  0.020  1.080
 623  C26  H26   single    0.930  0.020  1.080
 623  C27  N21   double    1.277  0.020  1.277
 623  C27  N22   single    1.364  0.020  1.364
 623  N21  H21   single    0.890  0.020  1.040
 623  N22  H221  single    0.890  0.020  1.040
 623  N22  H222  single    0.890  0.020  1.040
 623  C11  C12   aromatic  1.384  0.020  1.384
 623  C11  C16   aromatic  1.379  0.020  1.379
 623  C12  C13   aromatic  1.385  0.020  1.385
 623  C12  H12   single    0.930  0.020  1.080
 623  C13  C14   aromatic  1.389  0.020  1.389
 623  C13  H13   single    0.930  0.020  1.080
 623  C14  C15   aromatic  1.392  0.020  1.392
 623  C14  H14   single    0.930  0.020  1.080
 623  C15  C16   aromatic  1.393  0.020  1.393
 623  C15  C17   single    1.492  0.020  1.492
 623  C16  H16   single    0.930  0.020  1.080
 623  C17  N11   double    1.276  0.020  1.276
 623  C17  N12   single    1.363  0.020  1.363
 623  N11  HN11  single    0.890  0.020  1.040
 623  N12  H121  single    0.890  0.020  1.040
 623  N12  H122  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
 623  C6    C1   C2    121.66  3.000
 623  C6    C1   F1    118.92  3.000
 623  C2    C1   F1    119.42  3.000
 623  C7    C2   C3    122.68  3.000
 623  C7    C2   C1    120.31  3.000
 623  C3    C2   C1    117.00  3.000
 623  C4    C3   F3    117.28  3.000
 623  C4    C3   C2    121.55  3.000
 623  F3    C3   C2    121.17  3.000
 623  O1    C4   N5    122.31  3.000
 623  O1    C4   C3    119.61  3.000
 623  N5    C4   C3    118.07  3.000
 623  HN5   N5   C6    116.75  3.000
 623  HN5   N5   C4    119.56  3.000
 623  C6    N5   C4    123.69  3.000
 623  O2    C6   N5    114.97  3.000
 623  O2    C6   C1    126.95  3.000
 623  N5    C6   C1    118.00  3.000
 623  H53   C7   H52   108.41  3.000
 623  H53   C7   H51   107.63  3.000
 623  H52   C7   H51   108.34  3.000
 623  H53   C7   C2    110.51  3.000
 623  H52   C7   C2    111.99  3.000
 623  H51   C7   C2    109.83  3.000
 623  C11   O1   C4    119.91  3.000
 623  C21   O2   C6    120.09  3.000
 623  C26   C21  C22   122.37  3.000
 623  C26   C21  O2    121.23  3.000
 623  C22   C21  O2    116.32  3.000
 623  H22   C22  C23   120.24  3.000
 623  H22   C22  C21   120.63  3.000
 623  C23   C22  C21   119.13  3.000
 623  C27   C23  C24   121.98  3.000
 623  C27   C23  C22   118.61  3.000
 623  C24   C23  C22   119.41  3.000
 623  H24   C24  C25   119.03  3.000
 623  H24   C24  C23   120.70  3.000
 623  C25   C24  C23   120.26  3.000
 623  H25   C25  C26   119.36  3.000
 623  H25   C25  C24   119.90  3.000
 623  C26   C25  C24   120.74  3.000
 623  H26   C26  C25   120.18  3.000
 623  H26   C26  C21   121.74  3.000
 623  C25   C26  C21   118.08  3.000
 623  N22   C27  N21   126.57  3.000
 623  N22   C27  C23   115.11  3.000
 623  N21   C27  C23   118.28  3.000
 623  H21   N21  C27   111.28  3.000
 623  H222  N22  H221  113.53  3.000
 623  H222  N22  C27   117.33  3.000
 623  H221  N22  C27   118.47  3.000
 623  C16   C11  C12   122.87  3.000
 623  C16   C11  O1    118.71  3.000
 623  C12   C11  O1    118.40  3.000
 623  H12   C12  C13   121.30  3.000
 623  H12   C12  C11   120.87  3.000
 623  C13   C12  C11   117.83  3.000
 623  H13   C13  C14   119.84  3.000
 623  H13   C13  C12   119.61  3.000
 623  C14   C13  C12   120.55  3.000
 623  H14   C14  C15   120.56  3.000
 623  H14   C14  C13   118.74  3.000
 623  C15   C14  C13   120.68  3.000
 623  C17   C15  C16   118.55  3.000
 623  C17   C15  C14   122.23  3.000
 623  C16   C15  C14   119.21  3.000
 623  H16   C16  C15   120.12  3.000
 623  H16   C16  C11   121.04  3.000
 623  C15   C16  C11   118.84  3.000
 623  N12   C17  N11   126.69  3.000
 623  N12   C17  C15   115.28  3.000
 623  N11   C17  C15   117.98  3.000
 623  HN11  N11  C17   111.40  3.000
 623  H122  N12  H121  113.50  3.000
 623  H122  N12  C17   117.32  3.000
 623  H121  N12  C17   118.71  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
 623  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 623  CONST_02  C4    N5   C6   C1     0.00   0.0  0
 623  CONST_03  N5    C6   C1   C2     0.00   0.0  0
 623  CONST_04  N5    C4   C3   C2     0.00   0.0  0
 623  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 623  CONST_06  C6    N5   C4   C3     0.00   0.0  0
 623  CONST_07  C24   C23  C22  C21    0.00   0.0  0
 623  CONST_08  C24   C25  C26  C21    0.00   0.0  0
 623  CONST_09  C25   C26  C21  C22    0.00   0.0  0
 623  CONST_10  C25   C24  C23  C22    0.00   0.0  0
 623  CONST_11  C26   C21  C22  C23    0.00   0.0  0
 623  CONST_12  C26   C25  C24  C23    0.00   0.0  0
 623  CONST_13  C14   C13  C12  C11    0.00   0.0  0
 623  CONST_14  C14   C15  C16  C11    0.00   0.0  0
 623  CONST_15  C15   C16  C11  C12    0.00   0.0  0
 623  CONST_16  C15   C14  C13  C12    0.00   0.0  0
 623  CONST_17  C16   C11  C12  C13    0.00   0.0  0
 623  CONST_18  C16   C15  C14  C13    0.00   0.0  0
 623  CONST_19  F3    C3   C2   C1   180.00   0.0  0
 623  CONST_20  C3    C2   C1   F1   180.00   0.0  0
 623  CONST_21  N5    C6   C1   F1   180.00   0.0  0
 623  CONST_22  O2    C6   C1   C2   180.00   0.0  0
 623  CONST_23  O1    C4   C3   C2   180.00   0.0  0
 623  CONST_24  N5    C4   C3   F3   180.00   0.0  0
 623  CONST_25  C7    C2   C3   C4   180.00   0.0  0
 623  CONST_26  O2    C6   N5   C4   180.00   0.0  0
 623  CONST_27  C7    C2   C1   C6   180.00   0.0  0
 623  CONST_28  O1    C4   N5   C6   180.00   0.0  0
 623  CONST_29  C13   C12  C11  O1   180.00   0.0  0
 623  CONST_30  C15   C16  C11  O1   180.00   0.0  0
 623  CONST_31  C23   C22  C21  O2   180.00   0.0  0
 623  CONST_32  C25   C26  C21  O2   180.00   0.0  0
 623  CONST_33  C27   C23  C22  C21  180.00   0.0  0
 623  CONST_34  C27   C23  C24  C25  180.00   0.0  0
 623  CONST_35  C17   C15  C16  C11  180.00   0.0  0
 623  CONST_36  C17   C15  C14  C13  180.00   0.0  0
 623  CONST_37  HN5   N5   C6   C1   180.00   0.0  0
 623  CONST_38  H25   C25  C26  C21  180.00   0.0  0
 623  CONST_39  H26   C26  C21  C22  180.00   0.0  0
 623  CONST_40  H24   C24  C23  C22  180.00   0.0  0
 623  CONST_41  H22   C22  C23  C24  180.00   0.0  0
 623  CONST_42  H13   C13  C12  C11  180.00   0.0  0
 623  CONST_43  H16   C16  C11  C12  180.00   0.0  0
 623  CONST_44  H14   C14  C13  C12  180.00   0.0  0
 623  CONST_45  H12   C12  C13  C14  180.00   0.0  0
 623  CONST_46  H21   N21  C27  C23  180.00   0.0  0
 623  CONST_48  H222  N22  C27  C23  180.00   0.0  0
 623  CONST_49  HN11  N11  C17  C15  180.00   0.0  0
 623  CONST_51  H122  N12  C17  C15  180.00   0.0  0
 623  Var_01    C12   C11  O1   C4    94.97  30.0  2
 623  Var_02    C22   C21  O2   C6   142.81  30.0  2
 623  Var_03    N21   C27  C23  C22  -26.25  30.0  2
 623  Var_04    N11   C17  C15  C14  155.49  30.0  2
 623  Var_05    H51   C7   C2   C1    65.52  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
 623  plan-1  C1    0.020
 623  plan-1  F1    0.020
 623  plan-1  C2    0.020
 623  plan-1  C3    0.020
 623  plan-1  F3    0.020
 623  plan-1  C4    0.020
 623  plan-1  N5    0.020
 623  plan-1  C6    0.020
 623  plan-1  C7    0.020
 623  plan-1  O1    0.020
 623  plan-1  O2    0.020
 623  plan-1  HN5   0.020
 623  plan-2  O2    0.020
 623  plan-2  C21   0.020
 623  plan-2  C22   0.020
 623  plan-2  C23   0.020
 623  plan-2  C24   0.020
 623  plan-2  C25   0.020
 623  plan-2  C26   0.020
 623  plan-2  C27   0.020
 623  plan-2  H22   0.020
 623  plan-2  H24   0.020
 623  plan-2  H25   0.020
 623  plan-2  H26   0.020
 623  plan-3  O1    0.020
 623  plan-3  C11   0.020
 623  plan-3  C12   0.020
 623  plan-3  C13   0.020
 623  plan-3  C14   0.020
 623  plan-3  C15   0.020
 623  plan-3  C16   0.020
 623  plan-3  C17   0.020
 623  plan-3  H12   0.020
 623  plan-3  H13   0.020
 623  plan-3  H14   0.020
 623  plan-3  H16   0.020
 623  plan-4  C23   0.020
 623  plan-4  C27   0.020
 623  plan-4  N21   0.020
 623  plan-4  N22   0.020
 623  plan-4  H21   0.020
 623  plan-4  H221  0.020
 623  plan-4  H222  0.020
 623  plan-5  C15   0.020
 623  plan-5  C17   0.020
 623  plan-5  N11   0.020
 623  plan-5  N12   0.020
 623  plan-5  HN11  0.020
 623  plan-5  H121  0.020
 623  plan-5  H122  0.020

