# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 13:54:18 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-(2-hydroxyphenyl)-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1c2cnc3[nH]c4cnc(cc4c3c2)C#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
 3XL  3XL  3-(2-hydroxyphenyl)-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile  ligand  32  22  .  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_3XL
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
 3XL  N4   N  NS    0  -0.248  -5.7106  -3.0014  -0.4492
 3XL  C17  C  CSP   0   0.049  -5.0397  -2.0741  -0.3206
 3XL  C9   C  CR6   0   0.173  -4.2035  -0.9202  -0.1595
 3XL  N3   N  N     0  -0.412  -4.8504   0.2477  -0.0373
 3XL  C8   C  CR16  0  -0.095  -4.1518   1.3510   0.1143
 3XL  C6   C  CR56  0   0.286  -2.7579   1.3129   0.1481
 3XL  N2   N  NR15  0  -0.755  -1.8510   2.3170   0.2957
 3XL  C3   C  CR56  0   0.475  -0.5910   1.7852   0.2693
 3XL  N1   N  N     0  -0.424   0.5294   2.4742   0.3886
 3XL  C2   C  CR16  0  -0.075   1.6431   1.7625   0.3310
 3XL  C10  C  CR16  0  -0.385  -2.8255  -1.0719  -0.1392
 3XL  C7   C  CR56  0   0.144  -2.0771   0.0845   0.0201
 3XL  C4   C  CR56  0   0.017  -0.6783   0.3905   0.0990
 3XL  C5   C  CR16  0  -0.270   0.5062  -0.3299   0.0392
 3XL  C1   C  CR6   0  -0.010   1.7012   0.3682   0.1537
 3XL  C11  C  CR6   0  -0.056   2.9979  -0.3390   0.1338
 3XL  C16  C  CR16  0  -0.285   3.2228  -1.4170   0.9874
 3XL  C15  C  CR16  0  -0.272   4.4253  -2.1081   0.9865
 3XL  C14  C  CR16  0  -0.249   5.4311  -1.7150   0.1149
 3XL  C13  C  CR16  0  -0.376   5.2299  -0.6506  -0.7507
 3XL  C12  C  CR6   0   0.326   4.0185   0.0347  -0.7508
 3XL  O1   O  OH1   0  -0.623   3.7740   1.0539  -1.5969
 3XL  H1   H  HCR6  0   0.291  -4.6968   2.2828   0.2116
 3XL  H2   H  HNR5  0   0.424  -2.0635   3.2966   0.4037
 3XL  H3   H  HCR6  0   0.265   2.5637   2.3224   0.4474
 3XL  H4   H  HCR6  0   0.290  -2.3709  -2.0475  -0.2451
 3XL  H5   H  HCR6  0   0.271   0.5032  -1.4037  -0.1022
 3XL  H6   H  HCR6  0   0.257   2.4386  -1.7086   1.6757
 3XL  H7   H  HCR6  0   0.255   4.5747  -2.9385   1.6633
 3XL  H8   H  HCR6  0   0.262   6.3791  -2.2367   0.1030
 3XL  H9   H  HCR6  0   0.272   6.0159  -0.3547  -1.4367
 3XL  H10  H  HOH1  0   0.477   4.5433   1.2186  -2.1538

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
 3XL  N4   C17  triple    1.152  0.020  1.152
 3XL  C17  C9   single    1.434  0.020  1.434
 3XL  C9   C10  aromatic  1.386  0.020  1.386
 3XL  C9   N3   aromatic  1.341  0.020  1.341
 3XL  O1   C12  single    1.347  0.020  1.347
 3XL  C10  C7   aromatic  1.387  0.020  1.387
 3XL  N3   C8   aromatic  1.315  0.020  1.315
 3XL  C7   C6   aromatic  1.410  0.020  1.410
 3XL  C7   C4   aromatic  1.434  0.020  1.434
 3XL  C13  C12  aromatic  1.392  0.020  1.392
 3XL  C13  C14  aromatic  1.387  0.020  1.387
 3XL  C8   C6   aromatic  1.395  0.020  1.395
 3XL  C12  C11  aromatic  1.401  0.020  1.401
 3XL  C6   N2   aromatic  1.361  0.020  1.361
 3XL  C5   C4   aromatic  1.388  0.020  1.388
 3XL  C5   C1   aromatic  1.389  0.020  1.389
 3XL  C4   C3   aromatic  1.408  0.020  1.408
 3XL  C14  C15  aromatic  1.388  0.020  1.388
 3XL  C11  C1   single    1.477  0.020  1.477
 3XL  C11  C16  aromatic  1.393  0.020  1.393
 3XL  C1   C2   aromatic  1.407  0.020  1.407
 3XL  N2   C3   aromatic  1.368  0.020  1.368
 3XL  C3   N1   aromatic  1.321  0.020  1.321
 3XL  C2   N1   aromatic  1.323  0.020  1.323
 3XL  C15  C16  aromatic  1.387  0.020  1.387
 3XL  C8   H1   single    0.930  0.020  1.080
 3XL  N2   H2   single    0.860  0.020  1.020
 3XL  C2   H3   single    0.930  0.020  1.080
 3XL  C10  H4   single    0.930  0.020  1.080
 3XL  C5   H5   single    0.930  0.020  1.080
 3XL  C16  H6   single    0.930  0.020  1.080
 3XL  C15  H7   single    0.930  0.020  1.080
 3XL  C14  H8   single    0.930  0.020  1.080
 3XL  C13  H9   single    0.930  0.020  1.080
 3XL  O1   H10  single    0.850  0.020  0.980

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
 3XL  C9   C17  N4   180.00  3.000
 3XL  C10  C9   N3   125.00  3.000
 3XL  N3   C9   C17  115.45  3.000
 3XL  C10  C9   C17  119.55  3.000
 3XL  C8   N3   C9   119.02  3.000
 3XL  H1   C8   C6   121.59  3.000
 3XL  H1   C8   N3   117.69  3.000
 3XL  C6   C8   N3   120.73  3.000
 3XL  C7   C6   N2   109.32  3.000
 3XL  N2   C6   C8   130.42  3.000
 3XL  C7   C6   C8   120.27  3.000
 3XL  H2   N2   C3   125.03  3.000
 3XL  H2   N2   C6   126.01  3.000
 3XL  C3   N2   C6   108.96  3.000
 3XL  C4   C3   N1   125.48  3.000
 3XL  N1   C3   N2   125.23  3.000
 3XL  C4   C3   N2   109.29  3.000
 3XL  C2   N1   C3   115.44  3.000
 3XL  H3   C2   C1   119.38  3.000
 3XL  H3   C2   N1   115.63  3.000
 3XL  C1   C2   N1   124.99  3.000
 3XL  H4   C10  C7   122.46  3.000
 3XL  H4   C10  C9   121.00  3.000
 3XL  C7   C10  C9   116.55  3.000
 3XL  C4   C7   C10  135.30  3.000
 3XL  C4   C7   C6   106.26  3.000
 3XL  C10  C7   C6   118.44  3.000
 3XL  C5   C4   C7   136.01  3.000
 3XL  C5   C4   C3   117.81  3.000
 3XL  C7   C4   C3   106.18  3.000
 3XL  H5   C5   C1   120.76  3.000
 3XL  H5   C5   C4   121.20  3.000
 3XL  C1   C5   C4   118.04  3.000
 3XL  C11  C1   C5   120.91  3.000
 3XL  C11  C1   C2   120.83  3.000
 3XL  C5   C1   C2   118.23  3.000
 3XL  C12  C11  C16  118.40  3.000
 3XL  C16  C11  C1   120.25  3.000
 3XL  C12  C11  C1   121.34  3.000
 3XL  H6   C16  C15  119.60  3.000
 3XL  H6   C16  C11  118.73  3.000
 3XL  C15  C16  C11  121.67  3.000
 3XL  H7   C15  C14  120.69  3.000
 3XL  H7   C15  C16  120.13  3.000
 3XL  C14  C15  C16  119.18  3.000
 3XL  H8   C14  C13  119.36  3.000
 3XL  H8   C14  C15  120.35  3.000
 3XL  C13  C14  C15  120.29  3.000
 3XL  H9   C13  C12  119.76  3.000
 3XL  H9   C13  C14  119.95  3.000
 3XL  C12  C13  C14  120.29  3.000
 3XL  O1   C12  C13  122.05  3.000
 3XL  C13  C12  C11  120.16  3.000
 3XL  O1   C12  C11  117.78  3.000
 3XL  H10  O1   C12  110.32  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
 3XL  CONST_01  C6   C7   C10  C9     0.00  0.0  0
 3XL  CONST_02  C4   C7   C10  C9   180.00  0.0  0
 3XL  CONST_03  C6   C8   N3   C9     0.00  0.0  0
 3XL  CONST_04  C7   C10  C9   N3     0.00  0.0  0
 3XL  CONST_05  C7   C6   C8   N3     0.00  0.0  0
 3XL  CONST_06  N2   C6   C8   N3   180.00  0.0  0
 3XL  CONST_07  C10  C9   N3   C8     0.00  0.0  0
 3XL  CONST_08  C10  C7   C6   C8     0.00  0.0  0
 3XL  CONST_09  C4   C7   C6   C8   180.00  0.0  0
 3XL  CONST_10  C3   N2   C6   C8   180.00  0.0  0
 3XL  CONST_11  C5   C4   C7   C6   180.00  0.0  0
 3XL  CONST_12  C3   C4   C7   C6     0.00  0.0  0
 3XL  CONST_13  C4   C3   N2   C6     0.00  0.0  0
 3XL  CONST_14  N1   C3   N2   C6   180.00  0.0  0
 3XL  CONST_15  C10  C7   C6   N2   180.00  0.0  0
 3XL  CONST_16  C4   C7   C6   N2     0.00  0.0  0
 3XL  CONST_17  C7   C4   C3   N2     0.00  0.0  0
 3XL  CONST_18  C5   C4   C3   N2   180.00  0.0  0
 3XL  CONST_19  C2   N1   C3   N2   180.00  0.0  0
 3XL  CONST_20  C10  C7   C4   C3   180.00  0.0  0
 3XL  CONST_21  C1   C5   C4   C3     0.00  0.0  0
 3XL  CONST_22  C7   C6   N2   C3     0.00  0.0  0
 3XL  CONST_23  C1   C2   N1   C3     0.00  0.0  0
 3XL  CONST_24  C7   C4   C3   N1   180.00  0.0  0
 3XL  CONST_25  C5   C4   C3   N1     0.00  0.0  0
 3XL  CONST_26  C5   C1   C2   N1     0.00  0.0  0
 3XL  CONST_27  C11  C1   C2   N1   180.00  0.0  0
 3XL  CONST_28  C4   C5   C1   C2     0.00  0.0  0
 3XL  CONST_31  C4   C3   N1   C2     0.00  0.0  0
 3XL  CONST_32  C5   C4   C7   C10    0.00  0.0  0
 3XL  CONST_33  C1   C5   C4   C7   180.00  0.0  0
 3XL  CONST_34  C11  C1   C5   C4   180.00  0.0  0
 3XL  CONST_37  C13  C12  C11  C1   180.00  0.0  0
 3XL  CONST_38  C15  C16  C11  C1   180.00  0.0  0
 3XL  CONST_39  C14  C13  C12  C11    0.00  0.0  0
 3XL  CONST_40  C14  C15  C16  C11    0.00  0.0  0
 3XL  CONST_41  C13  C12  C11  C16    0.00  0.0  0
 3XL  CONST_42  C13  C14  C15  C16    0.00  0.0  0
 3XL  CONST_43  C12  C13  C14  C15    0.00  0.0  0
 3XL  CONST_44  C12  C11  C16  C15    0.00  0.0  0
 3XL  CONST_45  C7   C10  C9   C17  180.00  0.0  0
 3XL  CONST_46  C8   N3   C9   C17  180.00  0.0  0
 3XL  CONST_47  O1   C12  C11  C1     0.00  0.0  0
 3XL  CONST_48  O1   C12  C11  C16  180.00  0.0  0
 3XL  CONST_49  O1   C12  C13  C14  180.00  0.0  0
 3XL  CONST_50  H1   C8   N3   C9   180.00  0.0  0
 3XL  CONST_51  H4   C10  C9   N3   180.00  0.0  0
 3XL  CONST_52  H2   N2   C6   C8     0.00  0.0  0
 3XL  CONST_53  H5   C5   C4   C3   180.00  0.0  0
 3XL  CONST_54  H3   C2   N1   C3   180.00  0.0  0
 3XL  CONST_55  H6   C16  C11  C1     0.00  0.0  0
 3XL  CONST_56  H9   C13  C12  C11  180.00  0.0  0
 3XL  CONST_57  H7   C15  C16  C11  180.00  0.0  0
 3XL  CONST_58  H8   C14  C15  C16  180.00  0.0  0

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
 3XL  plan-1  C1   0.020
 3XL  plan-1  C11  0.020
 3XL  plan-1  C16  0.020
 3XL  plan-1  C15  0.020
 3XL  plan-1  C14  0.020
 3XL  plan-1  C13  0.020
 3XL  plan-1  C12  0.020
 3XL  plan-1  O1   0.020
 3XL  plan-1  H6   0.020
 3XL  plan-1  H7   0.020
 3XL  plan-1  H8   0.020
 3XL  plan-1  H9   0.020
 3XL  plan-2  N4   0.020
 3XL  plan-2  C17  0.020
 3XL  plan-2  C9   0.020
 3XL  plan-2  N3   0.020
 3XL  plan-2  C8   0.020
 3XL  plan-2  C6   0.020
 3XL  plan-2  N2   0.020
 3XL  plan-2  C3   0.020
 3XL  plan-2  N1   0.020
 3XL  plan-2  C2   0.020
 3XL  plan-2  C10  0.020
 3XL  plan-2  C7   0.020
 3XL  plan-2  C4   0.020
 3XL  plan-2  C5   0.020
 3XL  plan-2  C1   0.020
 3XL  plan-2  C11  0.020
 3XL  plan-2  H1   0.020
 3XL  plan-2  H2   0.020
 3XL  plan-2  H3   0.020
 3XL  plan-2  H4   0.020
 3XL  plan-2  H5   0.020

