# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 14:26:16 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-methyl-N~1~-[3-(pyridin-4-yl)-2,6-naphthyridin-1-yl]propane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(N)CNc1nc(cc2cnccc12)c3ccncc3
#
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
 07U  07U  2-methyl-N~1~-[3-(pyridin-4-yl)-2,6-naphthyridin-1-yl]propane-1,2-diamine  ligand  41  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_07U
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
 07U  N1   N  NH1   0  -0.680   1.9628  -0.2699   0.1756
 07U  C6   C  CT    0   0.002   3.5435  -2.0993  -0.0851
 07U  C10  C  CH3   0  -0.645   3.6942  -3.6049   0.1366
 07U  C20  C  CR6   0   0.257  -1.5217   0.2803   0.0064
 07U  C21  C  CR16  0  -0.450  -1.6685   1.6404   0.0335
 07U  C24  C  CR16  0  -0.094  -0.5436   3.8476   0.1271
 07U  C3   C  CH2   0  -0.220   2.0930  -1.7041   0.2212
 07U  N7   N  NH2   0  -0.790   4.4033  -1.3065   0.7957
 07U  C14  C  CH3   0  -0.637   3.8961  -1.7505  -1.5294
 07U  C18  C  CR6   0   0.506   0.7879   0.3750   0.1383
 07U  N19  N  N     0  -0.511  -0.3169  -0.3295   0.0690
 07U  C23  C  CR66  0   0.123  -0.5015   2.4350   0.1059
 07U  N26  N  N     0  -0.395   0.5194   4.6067   0.1795
 07U  C27  C  CR16  0  -0.080   1.7250   4.0102   0.2137
 07U  C29  C  CR16  0  -0.372   1.8943   2.6485   0.2011
 07U  C31  C  CR66  0   0.050   0.7617   1.8223   0.1521
 07U  C32  C  CR6   0   0.158  -2.6836  -0.6328  -0.0705
 07U  C33  C  CR16  0  -0.356  -2.5291  -1.9994   0.1552
 07U  C35  C  CR16  0  -0.060  -3.6374  -2.8279   0.0844
 07U  N37  N  N     0  -0.406  -4.8635  -2.4005  -0.1945
 07U  C38  C  CR16  0  -0.064  -5.0109  -1.0989  -0.4166
 07U  C40  C  CR16  0  -0.404  -3.9706  -0.1864  -0.3685
 07U  H1   H  HNH1  0   0.397   2.8079   0.2210   0.4307
 07U  H2   H  HCH3  0   0.222   3.0232  -4.1777  -0.5063
 07U  H3   H  HCH3  0   0.231   4.7157  -3.9231  -0.0805
 07U  H4   H  HCH3  0   0.226   3.4741  -3.8727   1.1725
 07U  H5   H  HCR6  0   0.262  -2.6362   2.1213   0.0099
 07U  H6   H  HCR6  0   0.270  -1.5084   4.3456   0.0958
 07U  H7   H  HCH2  0   0.230   1.8046  -2.0926   1.2074
 07U  H8   H  HCH2  0   0.242   1.4193  -2.1614  -0.5045
 07U  H9   H  HNH2  0   0.347   4.2922  -1.6156   1.7555
 07U  H10  H  HNH2  0   0.351   5.3760  -1.4700   0.5633
 07U  H12  H  HCH3  0   0.231   3.7652  -0.6867  -1.7291
 07U  H13  H  HCH3  0   0.229   4.9366  -2.0054  -1.7412
 07U  H14  H  HCH3  0   0.227   3.2711  -2.3066  -2.2289
 07U  H15  H  HCR6  0   0.272   2.5847   4.6674   0.2527
 07U  H16  H  HCR6  0   0.264   2.9004   2.2518   0.2258
 07U  H17  H  HCR6  0   0.271  -1.5579  -2.4121   0.3871
 07U  H18  H  HCR6  0   0.263  -3.5242  -3.8917   0.2628
 07U  H19  H  HCR6  0   0.265  -6.0130  -0.7563  -0.6494
 07U  H20  H  HCR6  0   0.266  -4.1812   0.8533  -0.5764

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
 07U  N7   C6   single    1.464  0.020  1.464
 07U  C14  C6   single    1.527  0.020  1.527
 07U  C10  C6   single    1.529  0.020  1.529
 07U  C6   C3   single    1.534  0.020  1.534
 07U  C3   N1   single    1.441  0.020  1.441
 07U  N1   C18  single    1.341  0.020  1.341
 07U  C18  N19  aromatic  1.312  0.020  1.312
 07U  C18  C31  aromatic  1.448  0.020  1.448
 07U  N19  C20  aromatic  1.352  0.020  1.352
 07U  C29  C31  aromatic  1.403  0.020  1.403
 07U  C29  C27  aromatic  1.372  0.020  1.372
 07U  C31  C23  aromatic  1.405  0.020  1.405
 07U  C40  C38  aromatic  1.385  0.020  1.385
 07U  C40  C32  aromatic  1.394  0.020  1.394
 07U  C27  N26  aromatic  1.346  0.020  1.346
 07U  C20  C32  single    1.480  0.020  1.480
 07U  C20  C21  aromatic  1.368  0.020  1.368
 07U  C38  N37  aromatic  1.329  0.020  1.329
 07U  C32  C33  aromatic  1.394  0.020  1.394
 07U  C23  C21  aromatic  1.414  0.020  1.414
 07U  C23  C24  aromatic  1.413  0.020  1.413
 07U  N37  C35  aromatic  1.328  0.020  1.328
 07U  C33  C35  aromatic  1.385  0.020  1.385
 07U  N26  C24  aromatic  1.307  0.020  1.307
 07U  N1   H1   single    0.860  0.020  1.020
 07U  C10  H2   single    0.970  0.020  1.090
 07U  C10  H3   single    0.970  0.020  1.090
 07U  C10  H4   single    0.970  0.020  1.090
 07U  C21  H5   single    0.930  0.020  1.080
 07U  C24  H6   single    0.930  0.020  1.080
 07U  C3   H7   single    0.970  0.020  1.090
 07U  C3   H8   single    0.970  0.020  1.090
 07U  N7   H9   single    0.890  0.020  1.040
 07U  N7   H10  single    0.890  0.020  1.040
 07U  C14  H12  single    0.970  0.020  1.090
 07U  C14  H13  single    0.970  0.020  1.090
 07U  C14  H14  single    0.970  0.020  1.090
 07U  C27  H15  single    0.930  0.020  1.080
 07U  C29  H16  single    0.930  0.020  1.080
 07U  C33  H17  single    0.930  0.020  1.080
 07U  C35  H18  single    0.930  0.020  1.080
 07U  C38  H19  single    0.930  0.020  1.080
 07U  C40  H20  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
 07U  H1   N1   C18  120.43  3.000
 07U  H1   N1   C3   113.59  3.000
 07U  C18  N1   C3   123.97  3.000
 07U  C14  C6   N7   108.04  3.000
 07U  C14  C6   C3   110.38  3.000
 07U  N7   C6   C3   107.20  3.000
 07U  C3   C6   C10  108.53  3.000
 07U  C14  C6   C10  109.83  3.000
 07U  N7   C6   C10  112.83  3.000
 07U  H4   C10  H3   107.80  3.000
 07U  H4   C10  H2   107.82  3.000
 07U  H3   C10  H2   107.76  3.000
 07U  H4   C10  C6   111.04  3.000
 07U  H3   C10  C6   110.50  3.000
 07U  H2   C10  C6   111.76  3.000
 07U  C32  C20  N19  115.08  3.000
 07U  C32  C20  C21  122.02  3.000
 07U  N19  C20  C21  122.90  3.000
 07U  H5   C21  C23  119.36  3.000
 07U  H5   C21  C20  122.54  3.000
 07U  C23  C21  C20  118.10  3.000
 07U  H6   C24  N26  117.20  3.000
 07U  H6   C24  C23  118.97  3.000
 07U  N26  C24  C23  123.83  3.000
 07U  H8   C3   H7   106.67  3.000
 07U  H8   C3   C6   110.07  3.000
 07U  H7   C3   C6   109.65  3.000
 07U  H8   C3   N1   109.91  3.000
 07U  H7   C3   N1   110.90  3.000
 07U  C6   C3   N1   109.60  3.000
 07U  H10  N7   H9   105.84  3.000
 07U  H10  N7   C6   109.78  3.000
 07U  H9   N7   C6   109.87  3.000
 07U  H14  C14  H13  107.62  3.000
 07U  H14  C14  H12  108.14  3.000
 07U  H13  C14  H12  107.85  3.000
 07U  H14  C14  C6   110.97  3.000
 07U  H13  C14  C6   110.49  3.000
 07U  H12  C14  C6   111.61  3.000
 07U  C31  C18  N19  121.46  3.000
 07U  C31  C18  N1   119.77  3.000
 07U  N19  C18  N1   118.76  3.000
 07U  C18  N19  C20  120.71  3.000
 07U  C31  C23  C24  117.53  3.000
 07U  C24  C23  C21  122.54  3.000
 07U  C31  C23  C21  119.93  3.000
 07U  C27  N26  C24  118.17  3.000
 07U  H15  C27  C29  120.31  3.000
 07U  H15  C27  N26  116.31  3.000
 07U  C29  C27  N26  123.38  3.000
 07U  H16  C29  C31  122.40  3.000
 07U  H16  C29  C27  118.58  3.000
 07U  C31  C29  C27  119.02  3.000
 07U  C29  C31  C23  118.06  3.000
 07U  C23  C31  C18  116.88  3.000
 07U  C29  C31  C18  125.06  3.000
 07U  C40  C32  C33  116.80  3.000
 07U  C33  C32  C20  120.64  3.000
 07U  C40  C32  C20  122.56  3.000
 07U  H17  C33  C35  120.11  3.000
 07U  H17  C33  C32  120.59  3.000
 07U  C35  C33  C32  119.30  3.000
 07U  H18  C35  N37  116.52  3.000
 07U  H18  C35  C33  119.65  3.000
 07U  N37  C35  C33  123.83  3.000
 07U  C38  N37  C35  116.93  3.000
 07U  H19  C38  C40  119.58  3.000
 07U  H19  C38  N37  116.62  3.000
 07U  C40  C38  N37  123.81  3.000
 07U  H20  C40  C38  118.73  3.000
 07U  H20  C40  C32  121.93  3.000
 07U  C38  C40  C32  119.33  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
 07U  CONST_01  C31  C18  N19  C20    0.00   0.0  0
 07U  CONST_02  C38  C40  C32  C20  180.00   0.0  0
 07U  CONST_03  C35  C33  C32  C20  180.00   0.0  0
 07U  CONST_04  C31  C23  C21  C20    0.00   0.0  0
 07U  CONST_05  C24  C23  C21  C20  180.00   0.0  0
 07U  CONST_06  C18  N19  C20  C21    0.00   0.0  0
 07U  CONST_07  C40  C32  C20  C21    0.00   0.0  0
 07U  CONST_08  C33  C32  C20  C21  180.00   0.0  0
 07U  CONST_09  C18  C31  C23  C21    0.00   0.0  0
 07U  CONST_10  C29  C31  C23  C21  180.00   0.0  0
 07U  CONST_11  N26  C24  C23  C21  180.00   0.0  0
 07U  CONST_12  C18  C31  C23  C24  180.00   0.0  0
 07U  CONST_13  C29  C31  C23  C24    0.00   0.0  0
 07U  CONST_14  C29  C27  N26  C24    0.00   0.0  0
 07U  CONST_15  C32  C20  N19  C18  180.00   0.0  0
 07U  CONST_16  C27  C29  C31  C18  180.00   0.0  0
 07U  CONST_17  C29  C31  C18  N19  180.00   0.0  0
 07U  CONST_18  C23  C31  C18  N19    0.00   0.0  0
 07U  CONST_19  C40  C32  C20  N19  180.00   0.0  0
 07U  CONST_20  C33  C32  C20  N19    0.00   0.0  0
 07U  CONST_21  C23  C21  C20  N19    0.00   0.0  0
 07U  CONST_22  C27  C29  C31  C23    0.00   0.0  0
 07U  CONST_23  C32  C20  C21  C23  180.00   0.0  0
 07U  CONST_24  C27  N26  C24  C23    0.00   0.0  0
 07U  CONST_25  C31  C29  C27  N26    0.00   0.0  0
 07U  CONST_26  C31  C23  C24  N26    0.00   0.0  0
 07U  CONST_27  N37  C38  C40  C32    0.00   0.0  0
 07U  CONST_28  N37  C35  C33  C32    0.00   0.0  0
 07U  CONST_29  C38  C40  C32  C33    0.00   0.0  0
 07U  CONST_30  C38  N37  C35  C33    0.00   0.0  0
 07U  CONST_31  C40  C38  N37  C35    0.00   0.0  0
 07U  CONST_32  C40  C32  C33  C35    0.00   0.0  0
 07U  CONST_33  C20  N19  C18  N1   180.00   0.0  0
 07U  CONST_34  C29  C31  C18  N1     0.00   0.0  0
 07U  CONST_35  C23  C31  C18  N1   180.00   0.0  0
 07U  CONST_36  H20  C40  C32  C20    0.00   0.0  0
 07U  CONST_37  H17  C33  C32  C20    0.00   0.0  0
 07U  CONST_38  H6   C24  C23  C21    0.00   0.0  0
 07U  CONST_39  H5   C21  C23  C24    0.00   0.0  0
 07U  CONST_40  H15  C27  N26  C24  180.00   0.0  0
 07U  CONST_41  H16  C29  C31  C18    0.00   0.0  0
 07U  CONST_42  H19  C38  C40  C32  180.00   0.0  0
 07U  CONST_43  H18  C35  C33  C32  180.00   0.0  0
 07U  CONST_44  N19  C18  N1   C3     0.00   0.0  0
 07U  CONST_45  C31  C18  N1   C3   180.00   0.0  0
 07U  CONST_46  H1   N1   C18  N19  180.00   0.0  0
 07U  Var_01    C18  N1   C3   C6   166.40  30.0  3
 07U  Var_02    N7   C6   C3   N1    51.02  30.0  2
 07U  Var_03    H9   N7   C6   C10  -49.91  30.0  3
 07U  Var_04    H12  C14  C6   C10  178.04  30.0  3
 07U  Var_05    H2   C10  C6   C3    59.56  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
 07U  plan-1  C20  0.020
 07U  plan-1  C32  0.020
 07U  plan-1  C33  0.020
 07U  plan-1  C35  0.020
 07U  plan-1  N37  0.020
 07U  plan-1  C38  0.020
 07U  plan-1  C40  0.020
 07U  plan-1  H17  0.020
 07U  plan-1  H18  0.020
 07U  plan-1  H19  0.020
 07U  plan-1  H20  0.020
 07U  plan-2  N1   0.020
 07U  plan-2  C20  0.020
 07U  plan-2  C21  0.020
 07U  plan-2  C24  0.020
 07U  plan-2  C18  0.020
 07U  plan-2  N19  0.020
 07U  plan-2  C23  0.020
 07U  plan-2  N26  0.020
 07U  plan-2  C27  0.020
 07U  plan-2  C29  0.020
 07U  plan-2  C31  0.020
 07U  plan-2  C32  0.020
 07U  plan-2  H5   0.020
 07U  plan-2  H6   0.020
 07U  plan-2  H15  0.020
 07U  plan-2  H16  0.020
 07U  plan-3  N1   0.020
 07U  plan-3  C3   0.020
 07U  plan-3  C18  0.020
 07U  plan-3  H1   0.020

