# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:39:13 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-[5-(6-methylpyridin-2-yl)-2,3-dihydro-1H-pyrazol-4-yl]-1,5-naphthyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(n1)C2=C(CNN2)c3ccc4ncccc4n3
#
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
 460  460  2-[5-(6-methylpyridin-2-yl)-2,3-dihydro-1H-pyrazol-4-yl]-1,5-naphthyridine  ligand  37  22  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_460
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
 460  C1    C  CH3   0  -0.724   3.1957   1.9960  -0.0720
 460  C2    C  CR6   0   0.231   2.7037   0.9008  -0.9686
 460  C3    C  CR16  0  -0.334   3.5871  -0.0054  -1.5570
 460  C4    C  CR16  0  -0.152   3.0867  -0.9737  -2.4090
 460  C5    C  CR16  0  -0.318   1.7201  -1.0256  -2.6384
 460  C6    C  CR6   0   0.166   0.9130  -0.1027  -1.9836
 460  N7    N  N     0  -0.421   1.3967   0.8457  -1.1879
 460  C8    C  CR5   0   0.364  -0.5458  -0.1335  -2.1768
 460  N9    N  NR15  0  -0.535  -1.0270  -0.2644  -3.4730
 460  N10   N  NR15  0  -0.477  -2.4464  -0.2724  -3.4294
 460  C12   C  CH2   0  -0.311  -2.8332   0.1050  -2.0628
 460  C13   C  CR5   0  -0.131  -1.5463  -0.0350  -1.2795
 460  C14   C  CR6   0   0.159  -1.4587  -0.0495   0.1664
 460  C15   C  CR16  0  -0.320  -2.5308   0.4889   0.9357
 460  C16   C  CR16  0  -0.196  -2.4476   0.5024   2.2953
 460  C17   C  CR66  0   0.183  -1.2941  -0.0230   2.9196
 460  N18   N  N     0  -0.427  -1.1898  -0.0102   4.2662
 460  C19   C  CR16  0  -0.093  -0.1056  -0.5085   4.8015
 460  C20   C  CR16  0  -0.319   0.9574  -1.0589   4.0538
 460  C21   C  CR16  0  -0.202   0.8660  -1.0828   2.6911
 460  C22   C  CR66  0   0.173  -0.2895  -0.5515   2.0738
 460  N23   N  N     0  -0.455  -0.3926  -0.5713   0.7335
 460  H11   H  HCH3  0   0.253   3.2150   2.9491  -0.6047
 460  H12   H  HCH3  0   0.249   2.5360   2.1165   0.7864
 460  H13   H  HCH3  0   0.243   4.2042   1.7995   0.2879
 460  H3    H  HCR6  0   0.264   4.6474   0.0573  -1.3502
 460  H4    H  HCR6  0   0.271   3.7500  -1.6832  -2.8859
 460  H5    H  HCR6  0   0.267   1.2872  -1.7715  -3.2908
 460  HN9   H  HNR5  0   0.383  -0.6705   0.4247  -4.1259
 460  H10   H  HNR5  0   0.369  -2.7237  -1.2333  -3.5857
 460  H121  H  HCH2  0   0.250  -3.6322  -0.5525  -1.7155
 460  H122  H  HCH2  0   0.233  -3.2202   1.1314  -2.0206
 460  H15   H  HCR6  0   0.271  -3.4025   0.8948   0.4397
 460  H16   H  HCR6  0   0.272  -3.2442   0.9105   2.9047
 460  H19   H  HCR6  0   0.265  -0.0408  -0.4879   5.8840
 460  H20   H  HCR6  0   0.274   1.8248  -1.4512   4.5664
 460  H21   H  HCR6  0   0.271   1.6544  -1.4925   2.0725

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
 460  C1   C2    single    1.498  0.020  1.498
 460  C1   H11   single    0.970  0.020  1.090
 460  C1   H12   single    0.970  0.020  1.090
 460  C1   H13   single    0.970  0.020  1.090
 460  C2   C3    aromatic  1.396  0.020  1.396
 460  C2   N7    aromatic  1.326  0.020  1.326
 460  C3   C4    aromatic  1.383  0.020  1.383
 460  C3   H3    single    0.930  0.020  1.080
 460  C4   C5    aromatic  1.387  0.020  1.387
 460  C4   H4    single    0.930  0.020  1.080
 460  C5   C6    aromatic  1.390  0.020  1.390
 460  C5   H5    single    0.930  0.020  1.080
 460  C6   N7    aromatic  1.329  0.020  1.329
 460  C6   C8    single    1.472  0.020  1.472
 460  C8   N9    single    1.389  0.020  1.389
 460  C8   C13   double    1.348  0.020  1.348
 460  N9   N10   single    1.420  0.020  1.420
 460  N9   HN9   single    0.890  0.020  1.040
 460  N10  C12   single    1.470  0.020  1.470
 460  N10  H10   single    0.890  0.020  1.040
 460  C12  C13   single    1.513  0.020  1.513
 460  C12  H121  single    0.970  0.020  1.090
 460  C12  H122  single    0.970  0.020  1.090
 460  C13  C14   single    1.449  0.020  1.449
 460  C14  C15   aromatic  1.425  0.020  1.425
 460  C14  N23   aromatic  1.315  0.020  1.315
 460  C15  C16   aromatic  1.362  0.020  1.362
 460  C15  H15   single    0.930  0.020  1.080
 460  C16  C17   aromatic  1.413  0.020  1.413
 460  C16  H16   single    0.930  0.020  1.080
 460  C17  N18   aromatic  1.351  0.020  1.351
 460  C17  C22   aromatic  1.416  0.020  1.416
 460  N18  C19   aromatic  1.308  0.020  1.308
 460  C19  C20   aromatic  1.411  0.020  1.411
 460  C19  H19   single    0.930  0.020  1.080
 460  C20  C21   aromatic  1.366  0.020  1.366
 460  C20  H20   single    0.930  0.020  1.080
 460  C21  C22   aromatic  1.414  0.020  1.414
 460  C21  H21   single    0.930  0.020  1.080
 460  C22  N23   aromatic  1.344  0.020  1.344

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
 460  H13   C1   H12   108.68  3.000
 460  H13   C1   H11   107.61  3.000
 460  H12   C1   H11   107.37  3.000
 460  H13   C1   C2    111.72  3.000
 460  H12   C1   C2    110.70  3.000
 460  H11   C1   C2    110.60  3.000
 460  N7    C2   C3    121.80  3.000
 460  N7    C2   C1    116.93  3.000
 460  C3    C2   C1    121.27  3.000
 460  H3    C3   C4    120.84  3.000
 460  H3    C3   C2    120.14  3.000
 460  C4    C3   C2    119.03  3.000
 460  H4    C4   C5    120.44  3.000
 460  H4    C4   C3    120.57  3.000
 460  C5    C4   C3    118.98  3.000
 460  H5    C5   C6    120.65  3.000
 460  H5    C5   C4    121.34  3.000
 460  C6    C5   C4    118.00  3.000
 460  C8    C6   N7    117.02  3.000
 460  C8    C6   C5    119.98  3.000
 460  N7    C6   C5    122.99  3.000
 460  C6    N7   C2    119.16  3.000
 460  C13   C8   N9    111.78  3.000
 460  C13   C8   C6    130.31  3.000
 460  N9    C8   C6    117.90  3.000
 460  HN9   N9   N10   112.03  3.000
 460  HN9   N9   C8    114.52  3.000
 460  N10   N9   C8    108.55  3.000
 460  H10   N10  C12   108.38  3.000
 460  H10   N10  N9    105.93  3.000
 460  C12   N10  N9    106.87  3.000
 460  H122  C12  H121  107.03  3.000
 460  H122  C12  C13   111.50  3.000
 460  H121  C12  C13   113.71  3.000
 460  H122  C12  N10   111.64  3.000
 460  H121  C12  N10   109.51  3.000
 460  C13   C12  N10   103.52  3.000
 460  C14   C13  C12   124.69  3.000
 460  C14   C13  C8    128.24  3.000
 460  C12   C13  C8    107.07  3.000
 460  N23   C14  C15   121.79  3.000
 460  N23   C14  C13   118.90  3.000
 460  C15   C14  C13   119.31  3.000
 460  H15   C15  C16   120.19  3.000
 460  H15   C15  C14   120.02  3.000
 460  C16   C15  C14   119.78  3.000
 460  H16   C16  C17   119.47  3.000
 460  H16   C16  C15   121.37  3.000
 460  C17   C16  C15   119.15  3.000
 460  C22   C17  N18   122.98  3.000
 460  C22   C17  C16   117.01  3.000
 460  N18   C17  C16   120.01  3.000
 460  C19   N18  C17   117.94  3.000
 460  H19   C19  C20   119.41  3.000
 460  H19   C19  N18   116.80  3.000
 460  C20   C19  N18   123.79  3.000
 460  H20   C20  C21   121.35  3.000
 460  H20   C20  C19   119.65  3.000
 460  C21   C20  C19   119.01  3.000
 460  H21   C21  C22   119.20  3.000
 460  H21   C21  C20   121.87  3.000
 460  C22   C21  C20   118.93  3.000
 460  N23   C22  C21   119.51  3.000
 460  N23   C22  C17   123.14  3.000
 460  C21   C22  C17   117.35  3.000
 460  C22   N23  C14   119.09  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
 460  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 460  CONST_02  C5   C6   N7   C2     0.00   0.0  0
 460  CONST_03  C6   N7   C2   C3     0.00   0.0  0
 460  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 460  CONST_05  N7   C2   C3   C4     0.00   0.0  0
 460  CONST_06  N7   C6   C5   C4     0.00   0.0  0
 460  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 460  CONST_08  C17  C22  N23  C14    0.00   0.0  0
 460  CONST_09  C21  C22  N23  C14  180.00   0.0  0
 460  CONST_10  C22  N23  C14  C15    0.00   0.0  0
 460  CONST_11  N18  C17  C16  C15  180.00   0.0  0
 460  CONST_12  C22  C17  C16  C15    0.00   0.0  0
 460  CONST_13  N23  C14  C15  C16    0.00   0.0  0
 460  CONST_14  C19  N18  C17  C16  180.00   0.0  0
 460  CONST_15  C21  C22  C17  C16  180.00   0.0  0
 460  CONST_16  N23  C22  C17  C16    0.00   0.0  0
 460  CONST_17  C20  C19  N18  C17    0.00   0.0  0
 460  CONST_18  C20  C21  C22  C17    0.00   0.0  0
 460  CONST_19  C21  C22  C17  N18    0.00   0.0  0
 460  CONST_20  N23  C22  C17  N18  180.00   0.0  0
 460  CONST_21  C21  C20  C19  N18    0.00   0.0  0
 460  CONST_22  C22  C17  N18  C19    0.00   0.0  0
 460  CONST_23  C22  C21  C20  C19    0.00   0.0  0
 460  CONST_24  N23  C22  C21  C20  180.00   0.0  0
 460  CONST_25  C8   C6   N7   C2   180.00   0.0  0
 460  CONST_26  C8   C6   C5   C4   180.00   0.0  0
 460  CONST_27  C16  C15  C14  C13  180.00   0.0  0
 460  CONST_28  C22  N23  C14  C13  180.00   0.0  0
 460  CONST_29  C4   C3   C2   C1   180.00   0.0  0
 460  CONST_30  C6   N7   C2   C1   180.00   0.0  0
 460  CONST_31  H4   C4   C3   C2   180.00   0.0  0
 460  CONST_32  H5   C5   C4   C3   180.00   0.0  0
 460  CONST_33  H3   C3   C4   C5   180.00   0.0  0
 460  CONST_34  H15  C15  C14  C13    0.00   0.0  0
 460  CONST_35  H16  C16  C15  C14  180.00   0.0  0
 460  CONST_36  H19  C19  N18  C17  180.00   0.0  0
 460  CONST_37  H21  C21  C22  C17  180.00   0.0  0
 460  CONST_38  H20  C20  C19  N18  180.00   0.0  0
 460  Var_01    N9   C8   C6   C5   -45.67  30.0  2
 460  Var_02    N10  N9   C8   C6   179.97  30.0  1
 460  Var_03    C12  C13  C8   C6   170.58  30.0  1
 460  Var_04    C12  N10  N9   C8    10.07  30.0  1
 460  Var_05    N10  C12  C13  C8    13.95  30.0  1
 460  Var_06    C15  C14  C13  C8   159.77  30.0  2
 460  Var_07    C13  C12  N10  N9   -14.32  30.0  1
 460  Var_08    H11  C1   C2   C3   102.07  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
 460  plan-1  C1   0.020
 460  plan-1  C2   0.020
 460  plan-1  C3   0.020
 460  plan-1  C4   0.020
 460  plan-1  C5   0.020
 460  plan-1  C6   0.020
 460  plan-1  N7   0.020
 460  plan-1  C8   0.020
 460  plan-1  H3   0.020
 460  plan-1  H4   0.020
 460  plan-1  H5   0.020
 460  plan-2  C8   0.020
 460  plan-2  N9   0.020
 460  plan-2  N10  0.020
 460  plan-2  HN9  0.020
 460  plan-3  C13  0.020
 460  plan-3  C14  0.020
 460  plan-3  C15  0.020
 460  plan-3  C16  0.020
 460  plan-3  C17  0.020
 460  plan-3  N18  0.020
 460  plan-3  C19  0.020
 460  plan-3  C20  0.020
 460  plan-3  C21  0.020
 460  plan-3  C22  0.020
 460  plan-3  N23  0.020
 460  plan-3  H15  0.020
 460  plan-3  H16  0.020
 460  plan-3  H19  0.020
 460  plan-3  H20  0.020
 460  plan-3  H21  0.020

