# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:03:35 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[(5-methyl-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]-~{N}-(4-pyridin-2-yloxyphenyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2ccccc2c3nnc(SCC(=O)Nc4ccc(Oc5ccccn5)cc4)nc13
#
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
 NV5  NV5  2-[(5-methyl-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]-~{N}-(4-pyridin-2-yloxyphenyl)ethanamide  ligand  50  32  .  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_NV5
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
 NV5  C4   C  CR16  0  -0.254   90.6010  40.4788  10.1777
 NV5  C5   C  CR16  0  -0.265   89.3767  40.3096   9.5245
 NV5  C6   C  CR16  0  -0.315   88.8448  41.3224   8.7437
 NV5  C7   C  CR56  0   0.024   89.5586  42.5084   8.6245
 NV5  C10  C  CH2   0  -0.755   91.0709  48.3843   6.8269
 NV5  C13  C  CR16  0  -0.310   94.3611  47.7796   9.2926
 NV5  C15  C  CR6   0   0.361   96.1265  48.1594   7.7213
 NV5  C17  C  CR16  0  -0.387   99.6824  48.4075   7.1832
 NV5  C20  C  CR16  0  -0.059   99.1425  50.5730   8.7344
 NV5  C21  C  CR16  0  -0.308   95.2862  48.9517   6.9585
 NV5  C22  C  CR16  0  -0.281   93.9797  49.1662   7.3706
 NV5  C3   C  CR16  0  -0.309   91.3284  41.6553  10.0710
 NV5  C9   C  CR6   0   0.224   89.5536  46.1234   6.9508
 NV5  C19  C  CR16  0  -0.346  100.4475  50.3622   8.3379
 NV5  C2   C  CR56  0   0.377   90.7913  42.6636   9.2855
 NV5  C11  C  C     0   0.550   91.0072  48.6713   8.3171
 NV5  C16  C  CR6   0   0.515   98.4054  48.7282   7.6466
 NV5  C14  C  CR16  0  -0.305   95.6737  47.5843   8.8972
 NV5  C12  C  CR6   0   0.323   93.4981  48.5606   8.5274
 NV5  N1   N  NR5   0  -0.608   91.3208  43.9207   9.0153
 NV5  C8   C  CR56  0   0.087   89.3447  43.7465   7.9259
 NV5  N2   N  N     0  -0.231   88.3797  44.1740   7.1521
 NV5  N3   N  N     0  -0.308   88.4844  45.3883   6.6513
 NV5  S1   S  S2    0   0.128   89.5358  47.7006   6.1919
 NV5  O1   O  O     0  -0.455   89.9498  48.8354   8.8932
 NV5  N4   N  NH1   0  -0.720   92.1843  48.7575   8.9869
 NV5  C18  C  CR16  0  -0.147  100.7142  49.2490   7.5428
 NV5  N5   N  N     0  -0.440   98.1336  49.7691   8.3956
 NV5  N6   N  N     0  -0.429   90.5801  45.7871   7.7239
 NV5  C23  C  CR56  0   0.550   90.4650  44.5750   8.2110
 NV5  H1   H  HCR6  0   0.269   90.9934  39.6731  10.7839
 NV5  H2   H  HCR6  0   0.264   88.8411  39.3761   9.6314
 NV5  H3   H  HCR6  0   0.264   87.8965  41.1944   8.2388
 NV5  H4   H  HCH2  0   0.320   91.9052  47.7376   6.5600
 NV5  H5   H  HCH2  0   0.341   91.2007  49.3223   6.2814
 NV5  H6   H  HCR6  0   0.281   94.0066  47.3218  10.2076
 NV5  H8   H  HCR6  0   0.267   98.8854  51.4248   9.3534
 NV5  H9   H  HCR6  0   0.277   95.6469  49.4158   6.0498
 NV5  H10  H  HCR6  0   0.279   93.3491  49.8248   6.7901
 NV5  H14  H  HCR6  0   0.281   92.2738  41.7724  10.5839
 NV5  H15  H  HCR6  0   0.270  101.2308  51.0436   8.6379
 NV5  H16  H  HCR6  0   0.277   96.3345  46.9715   9.4963
 NV5  H17  H  HNH1  0   0.407   92.0776  48.8590   9.9873
 NV5  H18  H  HCR6  0   0.279  101.7218  49.0418   7.2075
 NV5  C1   C  CH3   0  -0.546   92.5738  44.4292   9.5182
 NV5  O2   O  O2    0  -0.521   97.4030  47.8952   7.2844
 NV5  H7   H  HCR6  0   0.280   99.8474  47.5331   6.5684
 NV5  H11  H  HCH3  0   0.268   93.3746  43.7195   9.3186
 NV5  H12  H  HCH3  0   0.271   92.8006  45.3623   9.0103
 NV5  H13  H  HCH3  0   0.267   92.5168  44.6122  10.5907

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
 NV5  N3   N2   aromatic  1.318  0.020  1.318
 NV5  N3   C9   aromatic  1.332  0.020  1.332
 NV5  C10  S1   single    1.796  0.020  1.796
 NV5  C10  C11  single    1.519  0.020  1.519
 NV5  S1   C9   single    1.750  0.020  1.750
 NV5  N2   C8   aromatic  1.309  0.020  1.309
 NV5  C18  C17  aromatic  1.379  0.020  1.379
 NV5  C18  C19  aromatic  1.394  0.020  1.394
 NV5  C9   N6   aromatic  1.328  0.020  1.328
 NV5  C21  C22  aromatic  1.387  0.020  1.387
 NV5  C21  C15  aromatic  1.384  0.020  1.384
 NV5  C17  C16  aromatic  1.396  0.020  1.396
 NV5  C22  C12  aromatic  1.392  0.020  1.392
 NV5  C19  C20  aromatic  1.380  0.020  1.380
 NV5  C8   C7   aromatic  1.438  0.020  1.438
 NV5  C8   C23  aromatic  1.422  0.020  1.422
 NV5  C11  O1   double    1.215  0.020  1.215
 NV5  C11  N4   single    1.357  0.020  1.357
 NV5  C6   C7   aromatic  1.389  0.020  1.389
 NV5  C6   C5   aromatic  1.385  0.020  1.385
 NV5  C16  O2   single    1.353  0.020  1.353
 NV5  C16  N5   aromatic  1.311  0.020  1.311
 NV5  N6   C23  aromatic  1.311  0.020  1.311
 NV5  C20  N5   aromatic  1.334  0.020  1.334
 NV5  C7   C2   aromatic  1.407  0.020  1.407
 NV5  O2   C15  single    1.375  0.020  1.375
 NV5  C15  C14  aromatic  1.385  0.020  1.385
 NV5  C23  N1   aromatic  1.344  0.020  1.344
 NV5  C12  N4   single    1.406  0.020  1.406
 NV5  C12  C13  aromatic  1.393  0.020  1.393
 NV5  C5   C4   aromatic  1.398  0.020  1.398
 NV5  C2   N1   aromatic  1.391  0.020  1.391
 NV5  C2   C3   aromatic  1.386  0.020  1.386
 NV5  N1   C1   single    1.443  0.020  1.443
 NV5  C14  C13  aromatic  1.385  0.020  1.385
 NV5  C4   C3   aromatic  1.387  0.020  1.387
 NV5  C4   H1   single    0.930  0.020  1.080
 NV5  C5   H2   single    0.930  0.020  1.080
 NV5  C6   H3   single    0.930  0.020  1.080
 NV5  C10  H4   single    0.970  0.020  1.090
 NV5  C10  H5   single    0.970  0.020  1.090
 NV5  C13  H6   single    0.930  0.020  1.080
 NV5  C17  H7   single    0.930  0.020  1.080
 NV5  C20  H8   single    0.930  0.020  1.080
 NV5  C21  H9   single    0.930  0.020  1.080
 NV5  C22  H10  single    0.930  0.020  1.080
 NV5  C1   H11  single    0.970  0.020  1.090
 NV5  C1   H12  single    0.970  0.020  1.090
 NV5  C1   H13  single    0.970  0.020  1.090
 NV5  C3   H14  single    0.930  0.020  1.080
 NV5  C19  H15  single    0.930  0.020  1.080
 NV5  C14  H16  single    0.930  0.020  1.080
 NV5  N4   H17  single    0.860  0.020  1.020
 NV5  C18  H18  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
 NV5  H1   C4   C3   118.98  3.000
 NV5  H1   C4   C5   119.30  3.000
 NV5  C3   C4   C5   121.73  3.000
 NV5  H2   C5   C6   119.78  3.000
 NV5  H2   C5   C4   119.47  3.000
 NV5  C6   C5   C4   120.75  3.000
 NV5  H3   C6   C7   120.75  3.000
 NV5  H3   C6   C5   120.88  3.000
 NV5  C7   C6   C5   118.38  3.000
 NV5  C8   C7   C2   105.28  3.000
 NV5  C2   C7   C6   120.26  3.000
 NV5  C8   C7   C6   134.46  3.000
 NV5  H5   C10  H4   107.24  3.000
 NV5  H5   C10  S1   104.58  3.000
 NV5  H4   C10  S1   110.01  3.000
 NV5  H5   C10  C11  109.42  3.000
 NV5  H4   C10  C11  112.64  3.000
 NV5  S1   C10  C11  112.51  3.000
 NV5  H6   C13  C12  119.89  3.000
 NV5  H6   C13  C14  119.47  3.000
 NV5  C12  C13  C14  120.63  3.000
 NV5  O2   C15  C14  119.57  3.000
 NV5  C14  C15  C21  120.47  3.000
 NV5  O2   C15  C21  119.91  3.000
 NV5  H7   C17  C18  121.83  3.000
 NV5  H7   C17  C16  120.93  3.000
 NV5  C18  C17  C16  117.23  3.000
 NV5  H8   C20  N5   116.06  3.000
 NV5  H8   C20  C19  120.56  3.000
 NV5  N5   C20  C19  123.38  3.000
 NV5  H9   C21  C22  119.82  3.000
 NV5  H9   C21  C15  120.39  3.000
 NV5  C22  C21  C15  119.79  3.000
 NV5  H10  C22  C12  120.64  3.000
 NV5  H10  C22  C21  118.97  3.000
 NV5  C12  C22  C21  120.38  3.000
 NV5  H14  C3   C2   121.90  3.000
 NV5  H14  C3   C4   120.90  3.000
 NV5  C2   C3   C4   117.21  3.000
 NV5  N6   C9   S1   119.23  3.000
 NV5  N6   C9   N3   127.71  3.000
 NV5  S1   C9   N3   113.07  3.000
 NV5  H15  C19  C18  121.55  3.000
 NV5  H15  C19  C20  120.62  3.000
 NV5  C18  C19  C20  117.83  3.000
 NV5  N1   C2   C3   128.32  3.000
 NV5  C3   C2   C7   121.69  3.000
 NV5  N1   C2   C7   110.00  3.000
 NV5  N4   C11  O1   120.81  3.000
 NV5  N4   C11  C10  117.37  3.000
 NV5  O1   C11  C10  121.81  3.000
 NV5  N5   C16  O2   119.23  3.000
 NV5  N5   C16  C17  124.19  3.000
 NV5  O2   C16  C17  116.59  3.000
 NV5  H16  C14  C15  120.36  3.000
 NV5  H16  C14  C13  120.04  3.000
 NV5  C15  C14  C13  119.59  3.000
 NV5  N4   C12  C22  122.29  3.000
 NV5  N4   C12  C13  118.56  3.000
 NV5  C22  C12  C13  119.09  3.000
 NV5  C23  N1   C2   108.29  3.000
 NV5  C2   N1   C1   125.57  3.000
 NV5  C23  N1   C1   126.15  3.000
 NV5  C23  C8   N2   120.60  3.000
 NV5  C23  C8   C7   106.69  3.000
 NV5  N2   C8   C7   132.72  3.000
 NV5  N3   N2   C8   117.85  3.000
 NV5  N2   N3   C9   119.14  3.000
 NV5  C9   S1   C10  100.43  3.000
 NV5  H17  N4   C12  115.86  3.000
 NV5  H17  N4   C11  113.77  3.000
 NV5  C12  N4   C11  129.83  3.000
 NV5  H18  C18  C19  120.53  3.000
 NV5  H18  C18  C17  119.94  3.000
 NV5  C19  C18  C17  119.53  3.000
 NV5  C16  N5   C20  117.83  3.000
 NV5  C23  N6   C9   112.48  3.000
 NV5  N6   C23  C8   122.22  3.000
 NV5  N6   C23  N1   128.04  3.000
 NV5  C8   C23  N1   109.74  3.000
 NV5  H13  C1   H12  109.08  3.000
 NV5  H13  C1   H11  109.18  3.000
 NV5  H12  C1   H11  108.71  3.000
 NV5  H13  C1   N1   110.91  3.000
 NV5  H12  C1   N1   108.73  3.000
 NV5  H11  C1   N1   110.19  3.000
 NV5  C16  O2   C15  118.99  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
 NV5  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 NV5  CONST_02  C7   C2   C3   C4     0.00   0.0  0
 NV5  CONST_03  N1   C2   C3   C4   180.00   0.0  0
 NV5  CONST_04  C8   C7   C6   C5   180.00   0.0  0
 NV5  CONST_05  C2   C7   C6   C5     0.00   0.0  0
 NV5  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 NV5  CONST_07  N2   C8   C7   C6     0.00   0.0  0
 NV5  CONST_08  C23  C8   C7   C6   180.00   0.0  0
 NV5  CONST_09  N1   C2   C7   C6   180.00   0.0  0
 NV5  CONST_10  C3   C2   C7   C6     0.00   0.0  0
 NV5  CONST_11  C3   C4   C5   C6     0.00   0.0  0
 NV5  CONST_12  N3   N2   C8   C7   180.00   0.0  0
 NV5  CONST_13  N6   C23  C8   C7   180.00   0.0  0
 NV5  CONST_14  N1   C23  C8   C7     0.00   0.0  0
 NV5  CONST_15  C23  N1   C2   C7     0.00   0.0  0
 NV5  CONST_16  C21  C22  C12  C13    0.00   0.0  0
 NV5  CONST_17  C21  C15  C14  C13    0.00   0.0  0
 NV5  CONST_18  C12  C22  C21  C15    0.00   0.0  0
 NV5  CONST_19  C12  C13  C14  C15    0.00   0.0  0
 NV5  CONST_20  C20  C19  C18  C17    0.00   0.0  0
 NV5  CONST_21  C20  N5   C16  C17    0.00   0.0  0
 NV5  CONST_22  C14  C15  C21  C22    0.00   0.0  0
 NV5  CONST_23  C14  C13  C12  C22    0.00   0.0  0
 NV5  CONST_24  C8   C7   C2   C3   180.00   0.0  0
 NV5  CONST_25  C23  N1   C2   C3   180.00   0.0  0
 NV5  CONST_26  C8   N2   N3   C9     0.00   0.0  0
 NV5  CONST_27  C8   C23  N6   C9     0.00   0.0  0
 NV5  CONST_28  N1   C23  N6   C9   180.00   0.0  0
 NV5  CONST_29  C16  C17  C18  C19    0.00   0.0  0
 NV5  CONST_30  C16  N5   C20  C19    0.00   0.0  0
 NV5  CONST_31  N2   C8   C7   C2   180.00   0.0  0
 NV5  CONST_32  C23  C8   C7   C2     0.00   0.0  0
 NV5  CONST_33  C8   C23  N1   C2     0.00   0.0  0
 NV5  CONST_34  N6   C23  N1   C2   180.00   0.0  0
 NV5  CONST_35  N2   C8   C23  N1   180.00   0.0  0
 NV5  CONST_36  C8   C7   C2   N1     0.00   0.0  0
 NV5  CONST_37  N6   C9   N3   N2     0.00   0.0  0
 NV5  CONST_38  N6   C23  C8   N2     0.00   0.0  0
 NV5  CONST_39  C23  C8   N2   N3     0.00   0.0  0
 NV5  CONST_40  C23  N6   C9   N3     0.00   0.0  0
 NV5  CONST_41  N5   C16  C17  C18    0.00   0.0  0
 NV5  CONST_42  N5   C20  C19  C18    0.00   0.0  0
 NV5  CONST_43  C1   N1   C2   C7   180.00   0.0  0
 NV5  CONST_44  O2   C15  C14  C13  180.00   0.0  0
 NV5  CONST_45  O2   C16  N5   C20  180.00   0.0  0
 NV5  CONST_46  N4   C12  C22  C21  180.00   0.0  0
 NV5  CONST_47  O2   C15  C21  C22  180.00   0.0  0
 NV5  CONST_48  C8   C23  N1   C1   180.00   0.0  0
 NV5  CONST_49  N6   C23  N1   C1     0.00   0.0  0
 NV5  CONST_50  C3   C2   N1   C1     0.00   0.0  0
 NV5  CONST_51  N4   C12  C13  C14  180.00   0.0  0
 NV5  CONST_52  S1   C9   N3   N2   180.00   0.0  0
 NV5  CONST_53  C23  N6   C9   S1   180.00   0.0  0
 NV5  CONST_54  C18  C17  C16  O2   180.00   0.0  0
 NV5  CONST_55  H3   C6   C5   C4   180.00   0.0  0
 NV5  CONST_56  H14  C3   C4   C5   180.00   0.0  0
 NV5  CONST_57  H1   C4   C5   C6   180.00   0.0  0
 NV5  CONST_58  H2   C5   C6   C7   180.00   0.0  0
 NV5  CONST_59  H10  C22  C12  C13  180.00   0.0  0
 NV5  CONST_60  H6   C13  C14  C15  180.00   0.0  0
 NV5  CONST_61  H15  C19  C18  C17  180.00   0.0  0
 NV5  CONST_62  H18  C18  C19  C20  180.00   0.0  0
 NV5  CONST_63  H16  C14  C15  C21  180.00   0.0  0
 NV5  CONST_64  H7   C17  C18  C19  180.00   0.0  0
 NV5  CONST_65  H8   C20  N5   C16  180.00   0.0  0
 NV5  CONST_66  H9   C21  C15  C14  180.00   0.0  0
 NV5  CONST_70  C12  N4   C11  C10    0.00   0.0  0
 NV5  CONST_71  O1   C11  N4   C12  180.00   0.0  0
 NV5  Var_01    C17  C16  O2   C15  179.56  30.0  2
 NV5  Var_02    C14  C15  O2   C16  -92.37  30.0  2
 NV5  Var_03    N3   C9   S1   C10  179.26  30.0  2
 NV5  Var_04    H11  C1   N1   C2    51.59  30.0  2
 NV5  Var_05    C11  C10  S1   C9   -69.11  30.0  2
 NV5  Var_06    O1   C11  C10  S1   -22.29  30.0  3

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
 NV5  plan-1  C13  0.020
 NV5  plan-1  C15  0.020
 NV5  plan-1  C21  0.020
 NV5  plan-1  C22  0.020
 NV5  plan-1  C14  0.020
 NV5  plan-1  C12  0.020
 NV5  plan-1  N4   0.020
 NV5  plan-1  H6   0.020
 NV5  plan-1  H9   0.020
 NV5  plan-1  H10  0.020
 NV5  plan-1  H16  0.020
 NV5  plan-1  O2   0.020
 NV5  plan-2  C17  0.020
 NV5  plan-2  C20  0.020
 NV5  plan-2  C19  0.020
 NV5  plan-2  C16  0.020
 NV5  plan-2  C18  0.020
 NV5  plan-2  N5   0.020
 NV5  plan-2  H8   0.020
 NV5  plan-2  H15  0.020
 NV5  plan-2  H18  0.020
 NV5  plan-2  O2   0.020
 NV5  plan-2  H7   0.020
 NV5  plan-3  C4   0.020
 NV5  plan-3  C5   0.020
 NV5  plan-3  C6   0.020
 NV5  plan-3  C7   0.020
 NV5  plan-3  C3   0.020
 NV5  plan-3  C9   0.020
 NV5  plan-3  C2   0.020
 NV5  plan-3  N1   0.020
 NV5  plan-3  C8   0.020
 NV5  plan-3  N2   0.020
 NV5  plan-3  N3   0.020
 NV5  plan-3  S1   0.020
 NV5  plan-3  N6   0.020
 NV5  plan-3  C23  0.020
 NV5  plan-3  H1   0.020
 NV5  plan-3  H2   0.020
 NV5  plan-3  H3   0.020
 NV5  plan-3  H14  0.020
 NV5  plan-3  C1   0.020
 NV5  plan-4  C10  0.020
 NV5  plan-4  C11  0.020
 NV5  plan-4  C12  0.020
 NV5  plan-4  O1   0.020
 NV5  plan-4  N4   0.020
 NV5  plan-4  H17  0.020

