# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:41:13 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-(4-carbamimidoylphenyl)-1H-indole-6-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)c2[nH]c3cc(ccc3c2)C(N)=N
#
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
 DAP  DAP  2-(4-carbamimidoylphenyl)-1H-indole-6-carboximidamide  ligand  36  21  .  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_DAP
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
 DAP  N1    N  NR15  0  -0.757   0.6405   0.0804  -0.6564
 DAP  C2    C  CR5   0   0.378  -0.3836  -0.1232   0.2322
 DAP  C3    C  CR15  0  -0.448  -1.5289  -0.4149  -0.4690
 DAP  C4    C  CR16  0  -0.336  -1.9085  -0.5819  -3.0376
 DAP  C5    C  CR16  0  -0.303  -1.2554  -0.4432  -4.2434
 DAP  C6    C  CR6   0   0.016   0.1148  -0.1100  -4.3079
 DAP  C7    C  CR16  0  -0.347   0.8435   0.0765  -3.1436
 DAP  C8    C  CR56  0   0.371   0.1788  -0.0567  -1.9314
 DAP  C9    C  CR56  0   0.080  -1.1949  -0.3785  -1.8508
 DAP  C10   C  C     0   0.332   0.8089   0.0368  -5.6159
 DAP  N2    N  N     0  -0.656   2.0672  -0.1823  -5.6780
 DAP  N3    N  NH2   0  -0.823   0.0018   0.3605  -6.6713
 DAP  C1'   C  CR6   0   0.056  -0.1820  -0.0393   1.6736
 DAP  C2'   C  CR16  0  -0.312  -1.2736   0.1551   2.5245
 DAP  C3'   C  CR16  0  -0.269  -1.0991   0.2348   3.8927
 DAP  C4'   C  CR6   0  -0.006   0.1695   0.1205   4.4601
 DAP  C5'   C  CR16  0  -0.263   1.2591  -0.0788   3.6159
 DAP  C6'   C  CR16  0  -0.298   1.0870  -0.1545   2.2439
 DAP  C11   C  C     0   0.332   0.3399   0.2327   5.9353
 DAP  N4    N  N     0  -0.640  -0.3642   0.9848   6.6917
 DAP  N5    N  NH2   0  -0.805   1.3616  -0.5058   6.4533
 DAP  HN1   H  HNR5  0   0.416   1.5676   0.3895  -0.4146
 DAP  H3    H  HCR5  0   0.257  -2.4905  -0.6562  -0.0444
 DAP  H4    H  HCR6  0   0.251  -2.9584  -0.8446  -3.0128
 DAP  H5    H  HCR6  0   0.251  -1.8080  -0.6179  -5.1574
 DAP  H7    H  HCR6  0   0.259   1.8952   0.3263  -3.1899
 DAP  HN2   H  H     0   0.321   2.4230  -0.0032  -6.6135
 DAP  HN31  H  HNH2  0   0.389   0.4564   0.6121  -7.5350
 DAP  HN32  H  HNH2  0   0.393  -0.8295   0.8979  -6.4864
 DAP  H2'   H  HCR6  0   0.260  -2.2697   0.2571   2.1136
 DAP  H3'   H  HCR6  0   0.266  -1.9669   0.3762   4.5246
 DAP  H5'   H  HCR6  0   0.267   2.2583  -0.1639   4.0230
 DAP  H6'   H  HCR6  0   0.258   1.9595  -0.3206   1.6246
 DAP  HN4   H  H     0   0.333  -1.0060   1.5478   6.1460
 DAP  HN51  H  HNH2  0   0.385   1.4169  -0.5409   7.4588
 DAP  HN52  H  HNH2  0   0.393   1.6109  -1.3666   5.9955

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
 DAP  N1   C2    aromatic  1.371  0.020  1.371
 DAP  N1   C8    aromatic  1.363  0.020  1.363
 DAP  N1   HN1   single    0.860  0.020  1.020
 DAP  C2   C3    aromatic  1.374  0.020  1.374
 DAP  C2   C1'   single    1.458  0.020  1.458
 DAP  C3   C9    aromatic  1.422  0.020  1.422
 DAP  C3   H3    single    0.930  0.020  1.080
 DAP  C4   C5    aromatic  1.378  0.020  1.378
 DAP  C4   C9    aromatic  1.400  0.020  1.400
 DAP  C4   H4    single    0.930  0.020  1.080
 DAP  C5   C6    aromatic  1.412  0.020  1.412
 DAP  C5   H5    single    0.930  0.020  1.080
 DAP  C6   C7    aromatic  1.386  0.020  1.386
 DAP  C6   C10   single    1.488  0.020  1.488
 DAP  C7   C8    aromatic  1.389  0.020  1.389
 DAP  C7   H7    single    0.930  0.020  1.080
 DAP  C8   C9    aromatic  1.413  0.020  1.413
 DAP  C10  N2    double    1.279  0.020  1.279
 DAP  C10  N3    single    1.368  0.020  1.368
 DAP  N2   HN2   single    0.890  0.020  1.040
 DAP  N3   HN31  single    0.890  0.020  1.040
 DAP  N3   HN32  single    0.890  0.020  1.040
 DAP  C1'  C2'   aromatic  1.398  0.020  1.398
 DAP  C1'  C6'   aromatic  1.396  0.020  1.396
 DAP  C2'  C3'   aromatic  1.382  0.020  1.382
 DAP  C2'  H2'   single    0.930  0.020  1.080
 DAP  C3'  C4'   aromatic  1.394  0.020  1.394
 DAP  C3'  H3'   single    0.930  0.020  1.080
 DAP  C4'  C5'   aromatic  1.393  0.020  1.393
 DAP  C4'  C11   single    1.489  0.020  1.489
 DAP  C5'  C6'   aromatic  1.385  0.020  1.385
 DAP  C5'  H5'   single    0.930  0.020  1.080
 DAP  C6'  H6'   single    0.930  0.020  1.080
 DAP  C11  N4    double    1.278  0.020  1.278
 DAP  C11  N5    single    1.363  0.020  1.363
 DAP  N4   HN4   single    0.890  0.020  1.040
 DAP  N5   HN51  single    0.890  0.020  1.040
 DAP  N5   HN52  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
 DAP  HN1   N1   C8    124.58  3.000
 DAP  HN1   N1   C2    125.29  3.000
 DAP  C8    N1   C2    109.77  3.000
 DAP  C1'   C2   C3    129.20  3.000
 DAP  C1'   C2   N1    121.93  3.000
 DAP  C3    C2   N1    108.86  3.000
 DAP  H3    C3   C9    126.71  3.000
 DAP  H3    C3   C2    126.13  3.000
 DAP  C9    C3   C2    107.13  3.000
 DAP  H4    C4   C9    120.68  3.000
 DAP  H4    C4   C5    120.27  3.000
 DAP  C9    C4   C5    119.05  3.000
 DAP  H5    C5   C6    119.68  3.000
 DAP  H5    C5   C4    118.73  3.000
 DAP  C6    C5   C4    121.58  3.000
 DAP  C10   C6   C7    118.67  3.000
 DAP  C10   C6   C5    121.08  3.000
 DAP  C7    C6   C5    120.25  3.000
 DAP  H7    C7   C8    121.64  3.000
 DAP  H7    C7   C6    120.41  3.000
 DAP  C8    C7   C6    117.94  3.000
 DAP  C9    C8   C7    122.47  3.000
 DAP  C9    C8   N1    107.39  3.000
 DAP  C7    C8   N1    130.14  3.000
 DAP  C8    C9   C4    118.70  3.000
 DAP  C8    C9   C3    106.84  3.000
 DAP  C4    C9   C3    134.46  3.000
 DAP  N3    C10  N2    125.72  3.000
 DAP  N3    C10  C6    115.24  3.000
 DAP  N2    C10  C6    119.00  3.000
 DAP  HN2   N2   C10   111.03  3.000
 DAP  HN32  N3   HN31  113.36  3.000
 DAP  HN32  N3   C10   118.16  3.000
 DAP  HN31  N3   C10   117.02  3.000
 DAP  C6'   C1'  C2'   118.21  3.000
 DAP  C6'   C1'  C2    121.66  3.000
 DAP  C2'   C1'  C2    120.13  3.000
 DAP  H2'   C2'  C3'   119.13  3.000
 DAP  H2'   C2'  C1'   120.05  3.000
 DAP  C3'   C2'  C1'   120.82  3.000
 DAP  H3'   C3'  C4'   120.15  3.000
 DAP  H3'   C3'  C2'   118.97  3.000
 DAP  C4'   C3'  C2'   120.88  3.000
 DAP  C11   C4'  C5'   121.45  3.000
 DAP  C11   C4'  C3'   120.07  3.000
 DAP  C5'   C4'  C3'   118.48  3.000
 DAP  H5'   C5'  C6'   118.89  3.000
 DAP  H5'   C5'  C4'   120.37  3.000
 DAP  C6'   C5'  C4'   120.74  3.000
 DAP  H6'   C6'  C5'   118.35  3.000
 DAP  H6'   C6'  C1'   120.76  3.000
 DAP  C5'   C6'  C1'   120.87  3.000
 DAP  N5    C11  N4    120.46  3.000
 DAP  N5    C11  C4'   114.93  3.000
 DAP  N4    C11  C4'   124.57  3.000
 DAP  HN4   N4   C11   110.94  3.000
 DAP  HN52  N5   HN51  114.24  3.000
 DAP  HN52  N5   C11   118.45  3.000
 DAP  HN51  N5   C11   116.06  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
 DAP  CONST_01  C9    C3   C2   N1      0.00   0.0  0
 DAP  CONST_04  C6    C7   C8   N1    180.00   0.0  0
 DAP  CONST_05  C3    C9   C8   N1      0.00   0.0  0
 DAP  CONST_06  C4    C9   C8   N1    180.00   0.0  0
 DAP  CONST_07  C7    C8   N1   C2    180.00   0.0  0
 DAP  CONST_08  C9    C8   N1   C2      0.00   0.0  0
 DAP  CONST_09  C4    C9   C3   C2    180.00   0.0  0
 DAP  CONST_10  C8    C9   C3   C2      0.00   0.0  0
 DAP  CONST_11  C3'   C2'  C1'  C2    180.00   0.0  0
 DAP  CONST_12  C5'   C6'  C1'  C2    180.00   0.0  0
 DAP  CONST_13  C8    N1   C2   C3      0.00   0.0  0
 DAP  CONST_16  C5    C4   C9   C3    180.00   0.0  0
 DAP  CONST_17  C7    C8   C9   C3    180.00   0.0  0
 DAP  CONST_18  C7    C6   C5   C4      0.00   0.0  0
 DAP  CONST_19  C7    C8   C9   C4      0.00   0.0  0
 DAP  CONST_20  C8    C9   C4   C5      0.00   0.0  0
 DAP  CONST_21  C8    C7   C6   C5      0.00   0.0  0
 DAP  CONST_22  C9    C4   C5   C6      0.00   0.0  0
 DAP  CONST_23  C9    C8   C7   C6      0.00   0.0  0
 DAP  CONST_24  C1'   C2   N1   C8    180.00   0.0  0
 DAP  CONST_25  C1'   C2   C3   C9    180.00   0.0  0
 DAP  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 DAP  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 DAP  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 DAP  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 DAP  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 DAP  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 DAP  CONST_32  C10   C6   C5   C4    180.00   0.0  0
 DAP  CONST_33  C10   C6   C7   C8    180.00   0.0  0
 DAP  CONST_34  C11   C4'  C3'  C2'   180.00   0.0  0
 DAP  CONST_35  C11   C4'  C5'  C6'   180.00   0.0  0
 DAP  CONST_36  H3    C3   C2   N1    180.00   0.0  0
 DAP  CONST_37  H7    C7   C8   N1      0.00   0.0  0
 DAP  CONST_38  H2'   C2'  C1'  C2      0.00   0.0  0
 DAP  CONST_39  H6'   C6'  C1'  C2      0.00   0.0  0
 DAP  CONST_40  HN1   N1   C2   C3    180.00   0.0  0
 DAP  CONST_41  H4    C4   C9   C3      0.00   0.0  0
 DAP  CONST_42  H5    C5   C6   C7    180.00   0.0  0
 DAP  CONST_43  H3'   C3'  C2'  C1'   180.00   0.0  0
 DAP  CONST_44  H5'   C5'  C6'  C1'   180.00   0.0  0
 DAP  CONST_45  HN2   N2   C10  C6    180.00   0.0  0
 DAP  CONST_46  HN31  N3   C10  C6    180.00   0.0  0
 DAP  CONST_48  HN4   N4   C11  C4'     0.00   0.0  0
 DAP  CONST_49  HN51  N5   C11  C4'   180.00   0.0  0
 DAP  Var_01    N2    C10  C6   C5   -152.87  30.0  2
 DAP  Var_02    N4    C11  C4'  C3'   -33.69  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
 DAP  plan-1  C2    0.020
 DAP  plan-1  C1'   0.020
 DAP  plan-1  C2'   0.020
 DAP  plan-1  C3'   0.020
 DAP  plan-1  C4'   0.020
 DAP  plan-1  C5'   0.020
 DAP  plan-1  C6'   0.020
 DAP  plan-1  C11   0.020
 DAP  plan-1  H2'   0.020
 DAP  plan-1  H3'   0.020
 DAP  plan-1  H5'   0.020
 DAP  plan-1  H6'   0.020
 DAP  plan-2  N1    0.020
 DAP  plan-2  C2    0.020
 DAP  plan-2  C3    0.020
 DAP  plan-2  C4    0.020
 DAP  plan-2  C5    0.020
 DAP  plan-2  C6    0.020
 DAP  plan-2  C7    0.020
 DAP  plan-2  C8    0.020
 DAP  plan-2  C9    0.020
 DAP  plan-2  C10   0.020
 DAP  plan-2  C1'   0.020
 DAP  plan-2  HN1   0.020
 DAP  plan-2  H3    0.020
 DAP  plan-2  H4    0.020
 DAP  plan-2  H5    0.020
 DAP  plan-2  H7    0.020
 DAP  plan-3  C6    0.020
 DAP  plan-3  C10   0.020
 DAP  plan-3  N2    0.020
 DAP  plan-3  N3    0.020
 DAP  plan-3  HN2   0.020
 DAP  plan-3  HN31  0.020
 DAP  plan-3  HN32  0.020
 DAP  plan-4  C4'   0.020
 DAP  plan-4  C11   0.020
 DAP  plan-4  N4    0.020
 DAP  plan-4  N5    0.020
 DAP  plan-4  HN4   0.020
 DAP  plan-4  HN51  0.020
 DAP  plan-4  HN52  0.020

