# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:36:32 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(Oc2ccc(cc2)c3[nH]c4cc(ccc4c3)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
 5CZ  5CZ  2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide  ligand  47  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5CZ
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
 5CZ  C2   C  CR6   0   0.055  -0.6996  -1.0932  -0.3796
 5CZ  C3   C  CR16  0  -0.307   0.0287  -0.2441  -1.2169
 5CZ  C7   C  CR16  0  -0.320  -0.0247  -2.1414   0.2489
 5CZ  C8   C  CR5   0   0.380  -2.1322  -0.9173  -0.1687
 5CZ  C9   C  CR15  0  -0.453  -3.0640  -1.8301   0.2637
 5CZ  C10  C  CR56  0   0.084  -4.3227  -1.1682   0.2839
 5CZ  C11  C  CR56  0   0.364  -4.0941   0.1563  -0.1515
 5CZ  C20  C  CR6   0   0.358   4.2948  -0.8216  -0.5836
 5CZ  C21  C  CR16  0  -0.318   5.5686  -0.9548  -1.1303
 5CZ  C22  C  CR16  0  -0.266   6.5796  -0.1030  -0.7305
 5CZ  C24  C  CR16  0  -0.283   5.0693   1.0143   0.7485
 5CZ  N29  N  N     0  -0.655   8.4543   1.9376  -0.1771
 5CZ  C30  C  CR16  0  -0.338  -5.6268  -1.5479   0.6225
 5CZ  C31  C  CR16  0  -0.296  -6.6405  -0.6178   0.5335
 5CZ  C32  C  CR6   0  -0.021  -6.3956   0.7017   0.0985
 5CZ  C33  C  CR16  0  -0.361  -5.1120   1.0962  -0.2486
 5CZ  C34  C  C     0   0.330  -7.5097   1.6836  -0.0132
 5CZ  C4   C  CR16  0  -0.284   1.3858  -0.4301  -1.4174
 5CZ  C5   C  CR6   0   0.304   2.0335  -1.4781  -0.7786
 5CZ  C6   C  CR16  0  -0.297   1.3321  -2.3354   0.0554
 5CZ  N12  N  NR15  0  -0.757  -2.7630   0.2734  -0.4217
 5CZ  O19  O  O2    0  -0.507   3.3631  -1.7207  -1.0010
 5CZ  C23  C  CR6   0   0.035   6.3507   0.8934   0.2186
 5CZ  C25  C  CR16  0  -0.325   4.0420   0.1666   0.3588
 5CZ  C26  C  C     0   0.336   7.4639   1.7947   0.6187
 5CZ  N27  N  NH2   0  -0.825   7.2964   2.4402   1.8106
 5CZ  N35  N  N     0  -0.647  -7.5875   2.6019  -0.9009
 5CZ  N38  N  NH2   0  -0.805  -8.5126   1.5247   0.8969
 5CZ  H1   H  HCR6  0   0.261  -0.4589   0.5644  -1.7461
 5CZ  H2   H  HCR6  0   0.263  -0.5595  -2.8076   0.9133
 5CZ  H3   H  HCR5  0   0.257  -2.8732  -2.8628   0.5100
 5CZ  H4   H  HCR6  0   0.272   5.7604  -1.7287  -1.8628
 5CZ  H5   H  HCR6  0   0.260   7.5673  -0.2107  -1.1577
 5CZ  H6   H  HCR6  0   0.263   4.8409   1.7886   1.4698
 5CZ  H7   H  H     0   0.323   9.1624   2.5457   0.2253
 5CZ  H8   H  HCR6  0   0.252  -5.8417  -2.5579   0.9474
 5CZ  H9   H  HCR6  0   0.255  -7.6505  -0.9157   0.7821
 5CZ  H10  H  HCR6  0   0.267  -4.9013   2.1106  -0.5658
 5CZ  H11  H  HCR6  0   0.285   1.9307   0.2321  -2.0785
 5CZ  H12  H  HCR6  0   0.277   1.8445  -3.1496   0.5510
 5CZ  H13  H  HNR5  0   0.416  -2.3066   1.1336  -0.6768
 5CZ  H14  H  HCR6  0   0.283   3.0605   0.2901   0.7967
 5CZ  H15  H  HNH2  0   0.395   6.7396   1.9998   2.5241
 5CZ  H16  H  HNH2  0   0.391   8.0863   2.9484   2.1751
 5CZ  H17  H  H     0   0.330  -6.8283   2.5191  -1.5666
 5CZ  H18  H  HNH2  0   0.391  -8.2852   1.1386   1.7977
 5CZ  H19  H  HNH2  0   0.382  -9.2109   2.2507   0.9202

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
 5CZ  N35  C34  double    1.280  0.020  1.280
 5CZ  C34  N38  single    1.364  0.020  1.364
 5CZ  C34  C32  single    1.489  0.020  1.489
 5CZ  C32  C31  aromatic  1.411  0.020  1.411
 5CZ  C32  C33  aromatic  1.387  0.020  1.387
 5CZ  C31  C30  aromatic  1.379  0.020  1.379
 5CZ  C33  C11  aromatic  1.389  0.020  1.389
 5CZ  C30  C10  aromatic  1.400  0.020  1.400
 5CZ  C11  C10  aromatic  1.413  0.020  1.413
 5CZ  C11  N12  aromatic  1.363  0.020  1.363
 5CZ  C10  C9   aromatic  1.422  0.020  1.422
 5CZ  N12  C8   aromatic  1.371  0.020  1.371
 5CZ  C9   C8   aromatic  1.374  0.020  1.374
 5CZ  C8   C2   single    1.459  0.020  1.459
 5CZ  C2   C7   aromatic  1.396  0.020  1.396
 5CZ  C2   C3   aromatic  1.397  0.020  1.397
 5CZ  C7   C6   aromatic  1.384  0.020  1.384
 5CZ  C3   C4   aromatic  1.384  0.020  1.384
 5CZ  C6   C5   aromatic  1.387  0.020  1.387
 5CZ  C4   C5   aromatic  1.388  0.020  1.388
 5CZ  C5   O19  single    1.370  0.020  1.370
 5CZ  O19  C20  single    1.360  0.020  1.360
 5CZ  C20  C21  aromatic  1.393  0.020  1.393
 5CZ  C20  C25  aromatic  1.389  0.020  1.389
 5CZ  C21  C22  aromatic  1.381  0.020  1.381
 5CZ  C25  C24  aromatic  1.388  0.020  1.388
 5CZ  C22  C23  aromatic  1.395  0.020  1.395
 5CZ  C24  C23  aromatic  1.392  0.020  1.392
 5CZ  C23  C26  single    1.487  0.020  1.487
 5CZ  C26  N29  double    1.278  0.020  1.278
 5CZ  C26  N27  single    1.366  0.020  1.366
 5CZ  C3   H1   single    0.930  0.020  1.080
 5CZ  C7   H2   single    0.930  0.020  1.080
 5CZ  C9   H3   single    0.930  0.020  1.080
 5CZ  C21  H4   single    0.930  0.020  1.080
 5CZ  C22  H5   single    0.930  0.020  1.080
 5CZ  C24  H6   single    0.930  0.020  1.080
 5CZ  N29  H7   single    0.890  0.020  1.040
 5CZ  C30  H8   single    0.930  0.020  1.080
 5CZ  C31  H9   single    0.930  0.020  1.080
 5CZ  C33  H10  single    0.930  0.020  1.080
 5CZ  C4   H11  single    0.930  0.020  1.080
 5CZ  C6   H12  single    0.930  0.020  1.080
 5CZ  N12  H13  single    0.860  0.020  1.020
 5CZ  C25  H14  single    0.930  0.020  1.080
 5CZ  N27  H15  single    0.890  0.020  1.040
 5CZ  N27  H16  single    0.890  0.020  1.040
 5CZ  N35  H17  single    0.890  0.020  1.040
 5CZ  N38  H18  single    0.890  0.020  1.040
 5CZ  N38  H19  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
 5CZ  C8   C2   C7   120.01  3.000
 5CZ  C7   C2   C3   118.30  3.000
 5CZ  C8   C2   C3   121.69  3.000
 5CZ  H1   C3   C4   118.11  3.000
 5CZ  H1   C3   C2   120.80  3.000
 5CZ  C4   C3   C2   121.07  3.000
 5CZ  H2   C7   C6   118.94  3.000
 5CZ  H2   C7   C2   119.98  3.000
 5CZ  C6   C7   C2   121.07  3.000
 5CZ  N12  C8   C9   108.84  3.000
 5CZ  C9   C8   C2   129.15  3.000
 5CZ  N12  C8   C2   122.00  3.000
 5CZ  H3   C9   C10  126.79  3.000
 5CZ  H3   C9   C8   126.00  3.000
 5CZ  C10  C9   C8   107.19  3.000
 5CZ  C30  C10  C11  118.65  3.000
 5CZ  C11  C10  C9   106.78  3.000
 5CZ  C30  C10  C9   134.57  3.000
 5CZ  N12  C11  C33  130.06  3.000
 5CZ  N12  C11  C10  107.43  3.000
 5CZ  C33  C11  C10  122.51  3.000
 5CZ  C25  C20  O19  123.63  3.000
 5CZ  C25  C20  C21  120.07  3.000
 5CZ  O19  C20  C21  116.29  3.000
 5CZ  H4   C21  C22  120.46  3.000
 5CZ  H4   C21  C20  119.74  3.000
 5CZ  C22  C21  C20  119.80  3.000
 5CZ  H5   C22  C23  119.32  3.000
 5CZ  H5   C22  C21  119.52  3.000
 5CZ  C23  C22  C21  121.16  3.000
 5CZ  H6   C24  C25  117.89  3.000
 5CZ  H6   C24  C23  120.67  3.000
 5CZ  C25  C24  C23  121.44  3.000
 5CZ  H7   N29  C26  111.11  3.000
 5CZ  H8   C30  C31  120.19  3.000
 5CZ  H8   C30  C10  120.70  3.000
 5CZ  C31  C30  C10  119.11  3.000
 5CZ  H9   C31  C32  119.37  3.000
 5CZ  H9   C31  C30  119.07  3.000
 5CZ  C32  C31  C30  121.55  3.000
 5CZ  C34  C32  C33  119.08  3.000
 5CZ  C33  C32  C31  120.25  3.000
 5CZ  C34  C32  C31  120.66  3.000
 5CZ  H10  C33  C32  121.30  3.000
 5CZ  H10  C33  C11  120.76  3.000
 5CZ  C32  C33  C11  117.92  3.000
 5CZ  N38  C34  N35  120.13  3.000
 5CZ  N38  C34  C32  115.05  3.000
 5CZ  N35  C34  C32  124.80  3.000
 5CZ  H11  C4   C5   120.53  3.000
 5CZ  H11  C4   C3   119.97  3.000
 5CZ  C5   C4   C3   119.49  3.000
 5CZ  O19  C5   C6   118.63  3.000
 5CZ  O19  C5   C4   120.81  3.000
 5CZ  C6   C5   C4   120.51  3.000
 5CZ  H12  C6   C5   120.08  3.000
 5CZ  H12  C6   C7   120.37  3.000
 5CZ  C5   C6   C7   119.56  3.000
 5CZ  H13  N12  C11  124.50  3.000
 5CZ  H13  N12  C8   125.47  3.000
 5CZ  C11  N12  C8   109.76  3.000
 5CZ  C5   O19  C20  119.87  3.000
 5CZ  C26  C23  C24  122.28  3.000
 5CZ  C26  C23  C22  119.55  3.000
 5CZ  C24  C23  C22  118.17  3.000
 5CZ  H14  C25  C24  119.22  3.000
 5CZ  H14  C25  C20  121.41  3.000
 5CZ  C24  C25  C20  119.37  3.000
 5CZ  N27  C26  C23  115.43  3.000
 5CZ  N27  C26  N29  125.83  3.000
 5CZ  C23  C26  N29  118.69  3.000
 5CZ  H16  N27  H15  113.46  3.000
 5CZ  H16  N27  C26  117.25  3.000
 5CZ  H15  N27  C26  118.67  3.000
 5CZ  H17  N35  C34  110.59  3.000
 5CZ  H19  N38  H18  114.36  3.000
 5CZ  H19  N38  C34  116.18  3.000
 5CZ  H18  N38  C34  118.43  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
 5CZ  CONST_01  C11  N12  C8   C2    180.00   0.0  0
 5CZ  CONST_02  C10  C9   C8   C2    180.00   0.0  0
 5CZ  CONST_03  C5   C6   C7   C2      0.00   0.0  0
 5CZ  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5CZ  CONST_07  C6   C7   C2   C3      0.00   0.0  0
 5CZ  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 5CZ  CONST_11  C4   C3   C2   C7      0.00   0.0  0
 5CZ  CONST_12  C4   C5   C6   C7      0.00   0.0  0
 5CZ  CONST_13  C33  C11  N12  C8    180.00   0.0  0
 5CZ  CONST_14  C10  C11  N12  C8      0.00   0.0  0
 5CZ  CONST_15  C30  C10  C9   C8    180.00   0.0  0
 5CZ  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 5CZ  CONST_17  C6   C7   C2   C8    180.00   0.0  0
 5CZ  CONST_18  C4   C3   C2   C8    180.00   0.0  0
 5CZ  CONST_19  C31  C30  C10  C9    180.00   0.0  0
 5CZ  CONST_20  C33  C11  C10  C9    180.00   0.0  0
 5CZ  CONST_21  N12  C11  C10  C9      0.00   0.0  0
 5CZ  CONST_22  C11  N12  C8   C9      0.00   0.0  0
 5CZ  CONST_23  C32  C31  C30  C10     0.00   0.0  0
 5CZ  CONST_24  C32  C33  C11  C10     0.00   0.0  0
 5CZ  CONST_25  N12  C8   C9   C10     0.00   0.0  0
 5CZ  CONST_26  C31  C32  C33  C11     0.00   0.0  0
 5CZ  CONST_27  C31  C30  C10  C11     0.00   0.0  0
 5CZ  CONST_28  C23  C22  C21  C20     0.00   0.0  0
 5CZ  CONST_29  C23  C24  C25  C20     0.00   0.0  0
 5CZ  CONST_30  C24  C25  C20  C21     0.00   0.0  0
 5CZ  CONST_31  C24  C23  C22  C21     0.00   0.0  0
 5CZ  CONST_32  C25  C20  C21  C22     0.00   0.0  0
 5CZ  CONST_33  C25  C24  C23  C22     0.00   0.0  0
 5CZ  CONST_34  C33  C32  C31  C30     0.00   0.0  0
 5CZ  CONST_35  C33  C11  C10  C30     0.00   0.0  0
 5CZ  CONST_36  N12  C11  C10  C30   180.00   0.0  0
 5CZ  CONST_37  N12  C11  C33  C32   180.00   0.0  0
 5CZ  CONST_38  O19  C5   C4   C3    180.00   0.0  0
 5CZ  CONST_39  O19  C5   C6   C7    180.00   0.0  0
 5CZ  CONST_40  C34  C32  C33  C11   180.00   0.0  0
 5CZ  CONST_41  C26  C23  C22  C21   180.00   0.0  0
 5CZ  CONST_42  O19  C20  C21  C22   180.00   0.0  0
 5CZ  CONST_43  O19  C20  C25  C24   180.00   0.0  0
 5CZ  CONST_44  C34  C32  C31  C30   180.00   0.0  0
 5CZ  CONST_45  C26  C23  C24  C25   180.00   0.0  0
 5CZ  CONST_46  H13  N12  C8   C2      0.00   0.0  0
 5CZ  CONST_47  H3   C9   C8   C2      0.00   0.0  0
 5CZ  CONST_48  H12  C6   C7   C2    180.00   0.0  0
 5CZ  CONST_49  H11  C4   C3   C2    180.00   0.0  0
 5CZ  CONST_50  H2   C7   C2   C3    180.00   0.0  0
 5CZ  CONST_51  H1   C3   C2   C7    180.00   0.0  0
 5CZ  CONST_52  H8   C30  C10  C9      0.00   0.0  0
 5CZ  CONST_53  H9   C31  C30  C10   180.00   0.0  0
 5CZ  CONST_54  H10  C33  C11  C10   180.00   0.0  0
 5CZ  CONST_55  H5   C22  C21  C20   180.00   0.0  0
 5CZ  CONST_56  H6   C24  C25  C20   180.00   0.0  0
 5CZ  CONST_57  H14  C25  C20  C21   180.00   0.0  0
 5CZ  CONST_58  H4   C21  C22  C23   180.00   0.0  0
 5CZ  CONST_59  H17  N35  C34  C32     0.00   0.0  0
 5CZ  CONST_61  H19  N38  C34  C32   180.00   0.0  0
 5CZ  CONST_62  H7   N29  C26  C23   180.00   0.0  0
 5CZ  CONST_64  H16  N27  C26  C23   180.00   0.0  0
 5CZ  Var_01    C6   C5   O19  C20  -115.86  30.0  2
 5CZ  Var_02    C25  C20  O19  C5     17.49  30.0  2
 5CZ  Var_03    N29  C26  C23  C22    22.02  30.0  2
 5CZ  Var_04    N35  C34  C32  C31  -145.70  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
 5CZ  plan-1  C2   0.020
 5CZ  plan-1  C3   0.020
 5CZ  plan-1  C7   0.020
 5CZ  plan-1  C8   0.020
 5CZ  plan-1  C4   0.020
 5CZ  plan-1  C5   0.020
 5CZ  plan-1  C6   0.020
 5CZ  plan-1  O19  0.020
 5CZ  plan-1  H1   0.020
 5CZ  plan-1  H2   0.020
 5CZ  plan-1  H11  0.020
 5CZ  plan-1  H12  0.020
 5CZ  plan-2  C20  0.020
 5CZ  plan-2  C21  0.020
 5CZ  plan-2  C22  0.020
 5CZ  plan-2  C24  0.020
 5CZ  plan-2  O19  0.020
 5CZ  plan-2  C23  0.020
 5CZ  plan-2  C25  0.020
 5CZ  plan-2  C26  0.020
 5CZ  plan-2  H4   0.020
 5CZ  plan-2  H5   0.020
 5CZ  plan-2  H6   0.020
 5CZ  plan-2  H14  0.020
 5CZ  plan-3  C2   0.020
 5CZ  plan-3  C8   0.020
 5CZ  plan-3  C9   0.020
 5CZ  plan-3  C10  0.020
 5CZ  plan-3  C11  0.020
 5CZ  plan-3  C30  0.020
 5CZ  plan-3  C31  0.020
 5CZ  plan-3  C32  0.020
 5CZ  plan-3  C33  0.020
 5CZ  plan-3  C34  0.020
 5CZ  plan-3  N12  0.020
 5CZ  plan-3  H3   0.020
 5CZ  plan-3  H8   0.020
 5CZ  plan-3  H9   0.020
 5CZ  plan-3  H10  0.020
 5CZ  plan-3  H13  0.020
 5CZ  plan-4  C32  0.020
 5CZ  plan-4  C34  0.020
 5CZ  plan-4  N35  0.020
 5CZ  plan-4  N38  0.020
 5CZ  plan-4  H17  0.020
 5CZ  plan-4  H18  0.020
 5CZ  plan-4  H19  0.020
 5CZ  plan-5  N29  0.020
 5CZ  plan-5  C23  0.020
 5CZ  plan-5  C26  0.020
 5CZ  plan-5  N27  0.020
 5CZ  plan-5  H7   0.020
 5CZ  plan-5  H15  0.020
 5CZ  plan-5  H16  0.020

