# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 03:52:29 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-(2,3-dimethyl-1-benzofuran-5-yl)pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc2ccc(cc2c1C)c3cc(N)nc(N)c3
#
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
 RK5  RK5  4-(2,3-dimethyl-1-benzofuran-5-yl)pyridine-2,6-diamine  ligand  34  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RK5
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
 RK5  C1   C  CH3   0  -0.755  32.9360  19.5699  24.0267
 RK5  C2   C  CR5   0   0.317  32.9283  20.9688  23.5451
 RK5  C3   C  CR5   0  -0.050  32.6545  21.5229  22.3404
 RK5  C4   C  CH3   0  -0.750  32.2595  20.8497  21.0731
 RK5  C5   C  CR56  0   0.095  32.8280  22.9418  22.5202
 RK5  C6   C  CR16  0  -0.424  32.7008  24.0548  21.6952
 RK5  C7   C  CR6   0   0.069  32.9441  25.3197  22.2239
 RK5  C8   C  CR16  0  -0.320  33.3161  25.4505  23.5741
 RK5  C9   C  CR16  0  -0.331  33.4522  24.3542  24.4102
 RK5  C10  C  CR56  0   0.348  33.1985  23.1150  23.8528
 RK5  O1   O  O     0  -0.461  33.2610  21.9200  24.4724
 RK5  C11  C  CR6   0   0.203  32.8093  26.5220  21.3737
 RK5  C12  C  CR16  0  -0.491  33.1956  26.4886  20.0385
 RK5  C13  C  CR6   0   0.460  33.0377  27.6484  19.2711
 RK5  N1   N  NH2   0  -0.838  33.3494  27.6530  17.9411
 RK5  N2   N  N     0  -0.506  32.5471  28.7821  19.7682
 RK5  C14  C  CR6   0   0.460  32.1840  28.8123  21.0490
 RK5  N3   N  NH2   0  -0.838  31.7307  30.0109  21.5226
 RK5  C15  C  CR16  0  -0.492  32.2902  27.7019  21.8948
 RK5  H1   H  HCH3  0   0.258  32.2333  19.4279  24.8499
 RK5  H2   H  HCH3  0   0.259  32.6539  18.8900  23.2261
 RK5  H3   H  HCH3  0   0.258  33.9247  19.2764  24.3846
 RK5  H4   H  HCH3  0   0.243  32.9606  21.0830  20.2698
 RK5  H5   H  HCH3  0   0.248  32.2276  19.7666  21.1790
 RK5  H6   H  HCH3  0   0.243  31.2729  21.1788  20.7416
 RK5  H7   H  HCR6  0   0.251  32.3957  23.9394  20.6623
 RK5  H8   H  HCR6  0   0.255  33.5233  26.4354  23.9724
 RK5  H9   H  HCR6  0   0.267  33.7478  24.4697  25.4447
 RK5  H10  H  HCR6  0   0.250  33.6305  25.6008  19.5984
 RK5  H11  H  HNH2  0   0.377  33.4980  28.5560  17.5215
 RK5  H12  H  HNH2  0   0.386  33.9722  26.9365  17.6073
 RK5  H13  H  HNH2  0   0.377  31.3990  30.6634  20.8313
 RK5  H14  H  HNH2  0   0.386  31.1853  29.9975  22.3684
 RK5  H15  H  HCR6  0   0.249  31.9509  27.7661  22.9203

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
 RK5  N1   C13  single    1.366  0.020  1.366
 RK5  C13  N2   aromatic  1.332  0.020  1.332
 RK5  C13  C12  aromatic  1.400  0.020  1.400
 RK5  N2   C14  aromatic  1.332  0.020  1.332
 RK5  C12  C11  aromatic  1.390  0.020  1.390
 RK5  C4   C3   single    1.488  0.020  1.488
 RK5  C14  N3   single    1.366  0.020  1.366
 RK5  C14  C15  aromatic  1.400  0.020  1.400
 RK5  C11  C15  aromatic  1.390  0.020  1.390
 RK5  C11  C7   single    1.479  0.020  1.479
 RK5  C6   C7   aromatic  1.392  0.020  1.392
 RK5  C6   C5   aromatic  1.391  0.020  1.391
 RK5  C7   C8   aromatic  1.407  0.020  1.407
 RK5  C3   C5   aromatic  1.441  0.020  1.441
 RK5  C3   C2   aromatic  1.354  0.020  1.354
 RK5  C5   C10  aromatic  1.394  0.020  1.394
 RK5  C2   C1   single    1.479  0.020  1.479
 RK5  C2   O1   aromatic  1.369  0.020  1.369
 RK5  C8   C9   aromatic  1.385  0.020  1.385
 RK5  C10  O1   aromatic  1.348  0.020  1.348
 RK5  C10  C9   aromatic  1.382  0.020  1.382
 RK5  C1   H1   single    0.970  0.020  1.090
 RK5  C1   H2   single    0.970  0.020  1.090
 RK5  C1   H3   single    0.970  0.020  1.090
 RK5  C4   H4   single    0.970  0.020  1.090
 RK5  C4   H5   single    0.970  0.020  1.090
 RK5  C4   H6   single    0.970  0.020  1.090
 RK5  C6   H7   single    0.930  0.020  1.080
 RK5  C8   H8   single    0.930  0.020  1.080
 RK5  C9   H9   single    0.930  0.020  1.080
 RK5  C12  H10  single    0.930  0.020  1.080
 RK5  N1   H11  single    0.890  0.020  1.040
 RK5  N1   H12  single    0.890  0.020  1.040
 RK5  N3   H13  single    0.890  0.020  1.040
 RK5  N3   H14  single    0.890  0.020  1.040
 RK5  C15  H15  single    0.930  0.020  1.080

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
 RK5  H3   C1   H2   107.95  3.000
 RK5  H3   C1   H1   107.50  3.000
 RK5  H2   C1   H1   107.87  3.000
 RK5  H3   C1   C2   111.45  3.000
 RK5  H2   C1   C2   110.50  3.000
 RK5  H1   C1   C2   111.41  3.000
 RK5  O1   C2   C3   111.55  3.000
 RK5  O1   C2   C1   115.79  3.000
 RK5  C3   C2   C1   132.66  3.000
 RK5  C5   C3   C4   125.71  3.000
 RK5  C5   C3   C2   105.53  3.000
 RK5  C4   C3   C2   128.76  3.000
 RK5  H6   C4   H5   107.64  3.000
 RK5  H6   C4   H4   107.02  3.000
 RK5  H5   C4   H4   107.64  3.000
 RK5  H6   C4   C3   111.22  3.000
 RK5  H5   C4   C3   112.02  3.000
 RK5  H4   C4   C3   111.07  3.000
 RK5  C10  C5   C6   119.45  3.000
 RK5  C10  C5   C3   105.89  3.000
 RK5  C6   C5   C3   134.66  3.000
 RK5  H7   C6   C7   120.53  3.000
 RK5  H7   C6   C5   120.40  3.000
 RK5  C7   C6   C5   119.06  3.000
 RK5  C11  C7   C8   120.02  3.000
 RK5  C8   C7   C6   119.68  3.000
 RK5  C11  C7   C6   120.29  3.000
 RK5  H8   C8   C9   118.63  3.000
 RK5  H8   C8   C7   119.24  3.000
 RK5  C9   C8   C7   122.11  3.000
 RK5  H9   C9   C10  122.09  3.000
 RK5  H9   C9   C8   121.29  3.000
 RK5  C10  C9   C8   116.62  3.000
 RK5  O1   C10  C9   126.95  3.000
 RK5  C9   C10  C5   123.07  3.000
 RK5  O1   C10  C5   109.98  3.000
 RK5  C10  O1   C2   107.06  3.000
 RK5  C15  C11  C12  118.95  3.000
 RK5  C15  C11  C7   120.57  3.000
 RK5  C12  C11  C7   120.48  3.000
 RK5  H10  C12  C13  120.14  3.000
 RK5  H10  C12  C11  121.46  3.000
 RK5  C13  C12  C11  118.38  3.000
 RK5  N2   C13  N1   116.41  3.000
 RK5  N2   C13  C12  122.84  3.000
 RK5  N1   C13  C12  120.72  3.000
 RK5  H12  N1   H11  114.14  3.000
 RK5  H12  N1   C13  117.50  3.000
 RK5  H11  N1   C13  116.26  3.000
 RK5  C14  N2   C13  118.61  3.000
 RK5  C15  C14  N3   120.77  3.000
 RK5  C15  C14  N2   122.85  3.000
 RK5  N3   C14  N2   116.35  3.000
 RK5  H14  N3   H13  114.03  3.000
 RK5  H14  N3   C14  117.35  3.000
 RK5  H13  N3   C14  116.09  3.000
 RK5  H15  C15  C14  120.12  3.000
 RK5  H15  C15  C11  121.50  3.000
 RK5  C14  C15  C11  118.36  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
 RK5  CONST_01  C6   C5   C3   C2    180.00   0.0  0
 RK5  CONST_02  C10  C5   C3   C2      0.00   0.0  0
 RK5  CONST_03  C5   C10  O1   C2      0.00   0.0  0
 RK5  CONST_04  C9   C10  O1   C2    180.00   0.0  0
 RK5  CONST_05  C7   C6   C5   C3    180.00   0.0  0
 RK5  CONST_06  O1   C10  C5   C3      0.00   0.0  0
 RK5  CONST_07  C9   C10  C5   C3    180.00   0.0  0
 RK5  CONST_08  C10  O1   C2   C3      0.00   0.0  0
 RK5  CONST_09  C11  C7   C6   C5    180.00   0.0  0
 RK5  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 RK5  CONST_11  O1   C2   C3   C5      0.00   0.0  0
 RK5  CONST_12  C8   C9   C10  C5      0.00   0.0  0
 RK5  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 RK5  CONST_16  O1   C10  C5   C6    180.00   0.0  0
 RK5  CONST_17  C9   C10  C5   C6      0.00   0.0  0
 RK5  CONST_18  C13  C12  C11  C7    180.00   0.0  0
 RK5  CONST_19  C14  C15  C11  C7    180.00   0.0  0
 RK5  CONST_20  C10  C5   C6   C7      0.00   0.0  0
 RK5  CONST_21  C10  C9   C8   C7      0.00   0.0  0
 RK5  CONST_24  O1   C10  C9   C8    180.00   0.0  0
 RK5  CONST_25  C11  C7   C8   C9    180.00   0.0  0
 RK5  CONST_26  N2   C13  C12  C11     0.00   0.0  0
 RK5  CONST_27  N2   C14  C15  C11     0.00   0.0  0
 RK5  CONST_28  C14  N2   C13  C12     0.00   0.0  0
 RK5  CONST_29  C14  C15  C11  C12     0.00   0.0  0
 RK5  CONST_30  C15  C14  N2   C13     0.00   0.0  0
 RK5  CONST_31  C15  C11  C12  C13     0.00   0.0  0
 RK5  CONST_32  C5   C3   C2   C1    180.00   0.0  0
 RK5  CONST_33  C10  O1   C2   C1    180.00   0.0  0
 RK5  CONST_34  C6   C5   C3   C4      0.00   0.0  0
 RK5  CONST_35  C10  C5   C3   C4    180.00   0.0  0
 RK5  CONST_36  O1   C2   C3   C4    180.00   0.0  0
 RK5  CONST_37  N1   C13  C12  C11   180.00   0.0  0
 RK5  CONST_38  N3   C14  C15  C11   180.00   0.0  0
 RK5  CONST_39  N3   C14  N2   C13   180.00   0.0  0
 RK5  CONST_40  C14  N2   C13  N1    180.00   0.0  0
 RK5  CONST_41  H7   C6   C5   C3      0.00   0.0  0
 RK5  CONST_42  H9   C9   C10  C5    180.00   0.0  0
 RK5  CONST_43  H8   C8   C7   C6    180.00   0.0  0
 RK5  CONST_44  H10  C12  C11  C7      0.00   0.0  0
 RK5  CONST_45  H15  C15  C11  C7      0.00   0.0  0
 RK5  Var_01    H4   C4   C3   C2   -122.16  30.0  2
 RK5  Var_02    H1   C1   C2   C3   -120.41  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
 RK5  plan-1  C7   0.020
 RK5  plan-1  C11  0.020
 RK5  plan-1  C12  0.020
 RK5  plan-1  C13  0.020
 RK5  plan-1  N1   0.020
 RK5  plan-1  N2   0.020
 RK5  plan-1  C14  0.020
 RK5  plan-1  N3   0.020
 RK5  plan-1  C15  0.020
 RK5  plan-1  H10  0.020
 RK5  plan-1  H15  0.020
 RK5  plan-2  C1   0.020
 RK5  plan-2  C2   0.020
 RK5  plan-2  C3   0.020
 RK5  plan-2  C4   0.020
 RK5  plan-2  C5   0.020
 RK5  plan-2  C6   0.020
 RK5  plan-2  C7   0.020
 RK5  plan-2  C8   0.020
 RK5  plan-2  C9   0.020
 RK5  plan-2  C10  0.020
 RK5  plan-2  O1   0.020
 RK5  plan-2  C11  0.020
 RK5  plan-2  H7   0.020
 RK5  plan-2  H8   0.020
 RK5  plan-2  H9   0.020
 RK5  plan-3  C13  0.020
 RK5  plan-3  N1   0.020
 RK5  plan-3  H11  0.020
 RK5  plan-3  H12  0.020
 RK5  plan-4  C14  0.020
 RK5  plan-4  N3   0.020
 RK5  plan-4  H13  0.020
 RK5  plan-4  H14  0.020

