# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:29:59 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-(2-methyl-1,3-benzoxazol-6-yl)-3-(1,5-naphthyridin-4-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc2cc(NC(=O)Nc3ccnc4cccnc34)ccc2n1
#
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
 NVK  NVK  1-(2-methyl-1,3-benzoxazol-6-yl)-3-(1,5-naphthyridin-4-yl)urea  ligand  37  24  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NVK
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
 NVK  C1   C  CH3   0  -0.763   7.7038  -1.0359  -0.6047
 NVK  C10  C  CR6   0   0.438  -2.8064   0.6056  -0.0812
 NVK  C11  C  CR66  0   0.127  -3.9305  -0.2820  -0.0743
 NVK  C12  C  CR66  0   0.184  -5.2168   0.2518  -0.2887
 NVK  C13  C  CR16  0  -0.089  -4.3959   2.3492  -0.5013
 NVK  C14  C  CR16  0  -0.386  -3.0652   1.9407  -0.3002
 NVK  C15  C  CR16  0  -0.184  -6.2982  -0.6559  -0.2738
 NVK  C16  C  CR16  0  -0.326  -6.0552  -1.9833  -0.0566
 NVK  C17  C  CR16  0  -0.065  -4.7278  -2.4083   0.1459
 NVK  C2   C  CR5   0   0.471   6.3812  -0.5152  -0.2029
 NVK  C3   C  CR56  0   0.139   4.7315   0.5778   0.5460
 NVK  C4   C  CR56  0   0.358   4.2347  -0.5666  -0.0615
 NVK  C5   C  CR16  0  -0.427   2.8953  -0.8760  -0.1500
 NVK  C6   C  CR6   0   0.351   2.0171   0.0332   0.4383
 NVK  C7   C  CR16  0  -0.299   2.4959   1.1879   1.0799
 NVK  C8   C  CR16  0  -0.321   3.8499   1.4762   1.1310
 NVK  C9   C  C     0   0.738  -0.3552   0.6159   0.1827
 NVK  N1   N  N     0  -0.445   6.1118   0.5686   0.4317
 NVK  N2   N  NH1   0  -0.786   0.6499  -0.2798   0.4095
 NVK  N3   N  NH1   0  -0.781  -1.5900   0.0119   0.1342
 NVK  N4   N  N     0  -0.445  -5.4445   1.5676  -0.5020
 NVK  N5   N  N     0  -0.450  -3.7063  -1.5923   0.1378
 NVK  O1   O  O     0  -0.440   5.2953  -1.2608  -0.5375
 NVK  O2   O  O     0  -0.483  -0.1841   1.8112   0.0465
 NVK  H3   H  HCH3  0   0.274   7.7606  -1.1612  -1.6866
 NVK  H1   H  HCH3  0   0.271   8.4794  -0.3427  -0.2917
 NVK  H2   H  HCH3  0   0.274   7.8960  -2.0075  -0.1482
 NVK  H9   H  HCR6  0   0.268  -4.5808   3.4048  -0.6713
 NVK  H10  H  HCR6  0   0.292  -2.2860   2.6826  -0.3216
 NVK  H11  H  HCR6  0   0.280  -7.3006  -0.2805  -0.4359
 NVK  H12  H  HCR6  0   0.280  -6.8579  -2.7070  -0.0382
 NVK  H13  H  HCR6  0   0.275  -4.5166  -3.4575   0.3180
 NVK  H4   H  HCR6  0   0.290   2.5401  -1.7695  -0.6468
 NVK  H5   H  HCR6  0   0.273   1.8026   1.8622   1.5589
 NVK  H6   H  HCR6  0   0.269   4.2028   2.3712   1.6253
 NVK  H7   H  HNH1  0   0.417   0.4311  -1.2626   0.3470
 NVK  H8   H  HNH1  0   0.419  -1.6587  -0.9903   0.2728

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
 NVK  C8   C7   aromatic  1.385  0.020  1.385
 NVK  C8   C3   aromatic  1.388  0.020  1.388
 NVK  N1   C3   aromatic  1.385  0.020  1.385
 NVK  N1   C2   aromatic  1.284  0.020  1.284
 NVK  C7   C6   aromatic  1.405  0.020  1.405
 NVK  C3   C4   aromatic  1.388  0.020  1.388
 NVK  O2   C9   double    1.215  0.020  1.215
 NVK  C13  C14  aromatic  1.406  0.020  1.406
 NVK  C13  N4   aromatic  1.308  0.020  1.308
 NVK  C14  C10  aromatic  1.377  0.020  1.377
 NVK  C2   C1   single    1.477  0.020  1.477
 NVK  C2   O1   aromatic  1.359  0.020  1.359
 NVK  C6   N2   single    1.403  0.020  1.403
 NVK  C6   C5   aromatic  1.394  0.020  1.394
 NVK  C9   N2   single    1.365  0.020  1.365
 NVK  C9   N3   single    1.375  0.020  1.375
 NVK  C4   O1   aromatic  1.354  0.020  1.354
 NVK  C4   C5   aromatic  1.377  0.020  1.377
 NVK  N4   C12  aromatic  1.352  0.020  1.352
 NVK  C10  N3   single    1.371  0.020  1.371
 NVK  C10  C11  aromatic  1.432  0.020  1.432
 NVK  C12  C11  aromatic  1.409  0.020  1.409
 NVK  C12  C15  aromatic  1.412  0.020  1.412
 NVK  C11  N5   aromatic  1.346  0.020  1.346
 NVK  C15  C16  aromatic  1.367  0.020  1.367
 NVK  N5   C17  aromatic  1.307  0.020  1.307
 NVK  C16  C17  aromatic  1.408  0.020  1.408
 NVK  C1   H3   single    0.970  0.020  1.090
 NVK  C1   H1   single    0.970  0.020  1.090
 NVK  C1   H2   single    0.970  0.020  1.090
 NVK  C13  H9   single    0.930  0.020  1.080
 NVK  C14  H10  single    0.930  0.020  1.080
 NVK  C15  H11  single    0.930  0.020  1.080
 NVK  C16  H12  single    0.930  0.020  1.080
 NVK  C17  H13  single    0.930  0.020  1.080
 NVK  C5   H4   single    0.930  0.020  1.080
 NVK  C7   H5   single    0.930  0.020  1.080
 NVK  C8   H6   single    0.930  0.020  1.080
 NVK  N2   H7   single    0.860  0.020  1.020
 NVK  N3   H8   single    0.860  0.020  1.020

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
 NVK  H2   C1   H1   108.79  3.000
 NVK  H2   C1   H3   107.68  3.000
 NVK  H1   C1   H3   108.78  3.000
 NVK  H2   C1   C2   110.98  3.000
 NVK  H1   C1   C2   109.63  3.000
 NVK  H3   C1   C2   110.91  3.000
 NVK  N3   C10  C14  127.70  3.000
 NVK  N3   C10  C11  115.30  3.000
 NVK  C14  C10  C11  116.99  3.000
 NVK  N5   C11  C12  123.01  3.000
 NVK  N5   C11  C10  118.24  3.000
 NVK  C12  C11  C10  118.75  3.000
 NVK  N4   C12  C15  119.88  3.000
 NVK  C15  C12  C11  117.00  3.000
 NVK  N4   C12  C11  123.12  3.000
 NVK  H9   C13  N4   116.41  3.000
 NVK  H9   C13  C14  117.78  3.000
 NVK  N4   C13  C14  125.81  3.000
 NVK  H10  C14  C13  118.82  3.000
 NVK  H10  C14  C10  122.36  3.000
 NVK  C13  C14  C10  118.82  3.000
 NVK  H11  C15  C16  121.68  3.000
 NVK  H11  C15  C12  118.99  3.000
 NVK  C16  C15  C12  119.33  3.000
 NVK  H12  C16  C17  119.70  3.000
 NVK  H12  C16  C15  121.39  3.000
 NVK  C17  C16  C15  118.91  3.000
 NVK  H13  C17  N5   116.93  3.000
 NVK  H13  C17  C16  119.90  3.000
 NVK  N5   C17  C16  123.17  3.000
 NVK  O1   C2   N1   114.64  3.000
 NVK  O1   C2   C1   117.07  3.000
 NVK  N1   C2   C1   128.29  3.000
 NVK  N1   C3   C8   132.23  3.000
 NVK  N1   C3   C4   108.37  3.000
 NVK  C8   C3   C4   119.40  3.000
 NVK  O1   C4   C5   128.60  3.000
 NVK  C5   C4   C3   124.16  3.000
 NVK  O1   C4   C3   107.23  3.000
 NVK  H4   C5   C6   121.69  3.000
 NVK  H4   C5   C4   122.28  3.000
 NVK  C6   C5   C4   116.03  3.000
 NVK  N2   C6   C7   121.66  3.000
 NVK  N2   C6   C5   117.37  3.000
 NVK  C7   C6   C5   120.92  3.000
 NVK  H5   C7   C8   118.78  3.000
 NVK  H5   C7   C6   119.81  3.000
 NVK  C8   C7   C6   121.40  3.000
 NVK  H6   C8   C7   120.53  3.000
 NVK  H6   C8   C3   121.40  3.000
 NVK  C7   C8   C3   118.07  3.000
 NVK  O2   C9   N3   123.67  3.000
 NVK  N3   C9   N2   112.26  3.000
 NVK  O2   C9   N2   124.08  3.000
 NVK  C3   N1   C2   104.80  3.000
 NVK  H7   N2   C9   117.98  3.000
 NVK  H7   N2   C6   115.47  3.000
 NVK  C9   N2   C6   125.07  3.000
 NVK  H8   N3   C9   119.34  3.000
 NVK  H8   N3   C10  112.92  3.000
 NVK  C9   N3   C10  127.74  3.000
 NVK  C13  N4   C12  116.51  3.000
 NVK  C17  N5   C11  118.58  3.000
 NVK  C4   O1   C2   104.95  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
 NVK  CONST_01  N4   C13  C14  C10     0.00   0.0  0
 NVK  CONST_02  N4   C12  C11  C10     0.00   0.0  0
 NVK  CONST_03  C15  C12  C11  C10   180.00   0.0  0
 NVK  CONST_04  C17  N5   C11  C10   180.00   0.0  0
 NVK  CONST_05  C13  C14  C10  C11     0.00   0.0  0
 NVK  CONST_06  C13  N4   C12  C11     0.00   0.0  0
 NVK  CONST_07  C16  C15  C12  C11     0.00   0.0  0
 NVK  CONST_08  C16  C17  N5   C11     0.00   0.0  0
 NVK  CONST_09  C14  C13  N4   C12     0.00   0.0  0
 NVK  CONST_10  C14  C10  C11  C12     0.00   0.0  0
 NVK  CONST_11  C17  N5   C11  C12     0.00   0.0  0
 NVK  CONST_12  C17  C16  C15  C12     0.00   0.0  0
 NVK  CONST_13  C15  C12  N4   C13   180.00   0.0  0
 NVK  CONST_14  N5   C11  C10  C14   180.00   0.0  0
 NVK  CONST_15  N5   C11  C12  C15     0.00   0.0  0
 NVK  CONST_16  N5   C17  C16  C15     0.00   0.0  0
 NVK  CONST_17  N4   C12  C15  C16   180.00   0.0  0
 NVK  CONST_18  C8   C3   N1   C2    180.00   0.0  0
 NVK  CONST_19  C4   C3   N1   C2      0.00   0.0  0
 NVK  CONST_20  C3   C4   O1   C2      0.00   0.0  0
 NVK  CONST_21  C5   C4   O1   C2    180.00   0.0  0
 NVK  CONST_22  C6   C7   C8   C3      0.00   0.0  0
 NVK  CONST_23  O1   C2   N1   C3      0.00   0.0  0
 NVK  CONST_24  C6   C5   C4   C3      0.00   0.0  0
 NVK  CONST_25  C7   C8   C3   C4      0.00   0.0  0
 NVK  CONST_26  N1   C2   O1   C4      0.00   0.0  0
 NVK  CONST_27  C7   C6   C5   C4      0.00   0.0  0
 NVK  CONST_28  C8   C7   C6   C5      0.00   0.0  0
 NVK  CONST_29  C8   C3   C4   C5      0.00   0.0  0
 NVK  CONST_30  N1   C3   C4   C5    180.00   0.0  0
 NVK  CONST_31  O1   C4   C5   C6    180.00   0.0  0
 NVK  CONST_32  N1   C3   C8   C7    180.00   0.0  0
 NVK  CONST_33  O1   C4   C3   C8    180.00   0.0  0
 NVK  CONST_34  O1   C4   C3   N1      0.00   0.0  0
 NVK  CONST_35  N5   C11  C12  N4    180.00   0.0  0
 NVK  CONST_36  C3   N1   C2   C1    180.00   0.0  0
 NVK  CONST_37  C4   O1   C2   C1    180.00   0.0  0
 NVK  CONST_38  N3   C10  C11  C12   180.00   0.0  0
 NVK  CONST_39  N3   C10  C14  C13   180.00   0.0  0
 NVK  CONST_40  N2   C6   C5   C4    180.00   0.0  0
 NVK  CONST_41  N2   C6   C7   C8    180.00   0.0  0
 NVK  CONST_42  N5   C11  C10  N3      0.00   0.0  0
 NVK  CONST_43  H9   C13  C14  C10   180.00   0.0  0
 NVK  CONST_44  H10  C14  C10  C11   180.00   0.0  0
 NVK  CONST_45  H11  C15  C12  C11   180.00   0.0  0
 NVK  CONST_46  H13  C17  N5   C11   180.00   0.0  0
 NVK  CONST_47  H12  C16  C15  C12   180.00   0.0  0
 NVK  CONST_48  H5   C7   C8   C3    180.00   0.0  0
 NVK  CONST_49  H4   C5   C4   C3    180.00   0.0  0
 NVK  CONST_50  H6   C8   C3   C4    180.00   0.0  0
 NVK  CONST_51  C9   N3   C10  C11   180.00   0.0  0
 NVK  CONST_52  C9   N3   C10  C14     0.00   0.0  0
 NVK  CONST_55  H8   N3   C10  C11     0.00   0.0  0
 NVK  CONST_57  O2   C9   N3   C10     0.00   0.0  0
 NVK  CONST_58  O2   C9   N2   C6      0.00   0.0  0
 NVK  CONST_59  N2   C9   N3   C10   180.00   0.0  0
 NVK  CONST_60  N3   C9   N2   C6    180.00   0.0  0
 NVK  Var_01    H3   C1   C2   N1   -120.92  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
 NVK  plan-1  C1   0.020
 NVK  plan-1  C2   0.020
 NVK  plan-1  C3   0.020
 NVK  plan-1  C4   0.020
 NVK  plan-1  C5   0.020
 NVK  plan-1  C6   0.020
 NVK  plan-1  C7   0.020
 NVK  plan-1  C8   0.020
 NVK  plan-1  N1   0.020
 NVK  plan-1  N2   0.020
 NVK  plan-1  O1   0.020
 NVK  plan-1  H4   0.020
 NVK  plan-1  H5   0.020
 NVK  plan-1  H6   0.020
 NVK  plan-2  C10  0.020
 NVK  plan-2  C11  0.020
 NVK  plan-2  C12  0.020
 NVK  plan-2  C13  0.020
 NVK  plan-2  C14  0.020
 NVK  plan-2  C15  0.020
 NVK  plan-2  C16  0.020
 NVK  plan-2  C17  0.020
 NVK  plan-2  N3   0.020
 NVK  plan-2  N4   0.020
 NVK  plan-2  N5   0.020
 NVK  plan-2  H9   0.020
 NVK  plan-2  H10  0.020
 NVK  plan-2  H11  0.020
 NVK  plan-2  H12  0.020
 NVK  plan-2  H13  0.020
 NVK  plan-3  C10  0.020
 NVK  plan-3  C6   0.020
 NVK  plan-3  C9   0.020
 NVK  plan-3  N2   0.020
 NVK  plan-3  N3   0.020
 NVK  plan-3  O2   0.020
 NVK  plan-3  H7   0.020
 NVK  plan-3  H8   0.020

