# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:00:37 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 5-methyl-6-[(quinolin-5-ylamino)methyl]pyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(CNc2cccc3ncccc23)cnc4nc(N)nc(N)c14
#
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
 LIH  LIH  5-methyl-6-[(quinolin-5-ylamino)methyl]pyrido[2,3-d]pyrimidine-2,4-diamine  ligand  42  25  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIH
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
 LIH  C4A   C  CR66  0  -0.187  -0.0263  -0.3342  -2.8984
 LIH  C4    C  CR6   0   0.461  -1.0521  -0.9542  -3.7134
 LIH  C2    C  CR6   0   0.541  -0.4048   0.3153  -5.4986
 LIH  C8A   C  CR66  0   0.356   0.6583   0.7321  -3.5453
 LIH  C5    C  CR6   0   0.203   0.3383  -0.6858  -1.5782
 LIH  C6    C  CR6   0  -0.051   1.2781   0.1133  -0.9375
 LIH  C7    C  CR16  0  -0.095   1.8234   1.1887  -1.6464
 LIH  C5A   C  CH3   0  -0.812  -0.2056  -1.8934  -0.8732
 LIH  C5'   C  CR6   0   0.347   0.7883  -0.0955   2.7450
 LIH  C6'   C  CR16  0  -0.377   1.9595  -0.5815   3.2958
 LIH  C7'   C  CR16  0  -0.246   2.0801  -0.7733   4.6836
 LIH  C8'   C  CR16  0  -0.332   1.0604  -0.4741   5.5435
 LIH  C9    C  CH2   0  -0.390   1.7274  -0.1145   0.4770
 LIH  C4'   C  CR16  0  -0.178  -1.5724   0.6185   3.1600
 LIH  C4X   C  CR66  0  -0.013  -0.3121   0.1880   3.6221
 LIH  C8X   C  CR66  0   0.205  -0.1588   0.0151   5.0232
 LIH  C2'   C  CR16  0  -0.084  -2.3032   0.7156   5.4261
 LIH  C3'   C  CR16  0  -0.326  -2.5703   0.8874   4.0566
 LIH  N3    N  N     0  -0.505  -1.1924  -0.6446  -4.9843
 LIH  N1    N  N     0  -0.498   0.4675   1.0489  -4.8357
 LIH  N8    N  N     0  -0.433   1.5588   1.4883  -2.8927
 LIH  N1'   N  N     0  -0.439  -1.1587   0.2932   5.8944
 LIH  N10   N  NH1   0  -0.685   0.6287   0.0883   1.3953
 LIH  N4    N  NH2   0  -0.820  -1.9140  -1.8635  -3.2392
 LIH  N2    N  NH2   0  -0.817  -0.5377   0.5329  -6.8192
 LIH  H71   H  HCR6  0   0.262   2.5435   1.8295  -1.1435
 LIH  H5A1  H  HCH3  0   0.268  -1.1945  -1.7031  -0.4492
 LIH  H5A2  H  HCH3  0   0.267  -0.2735  -2.7507  -1.5405
 LIH  H5A3  H  HCH3  0   0.283   0.4262  -2.1860  -0.0397
 LIH  H6'1  H  HCR6  0   0.276   2.8113  -0.8073   2.6695
 LIH  H7'1  H  HCR6  0   0.258   3.0170  -1.1529   5.0707
 LIH  H8'1  H  HCR6  0   0.250   1.1602  -0.6048   6.6127
 LIH  H91   H  HCH2  0   0.257   2.1078  -1.1331   0.5994
 LIH  H92   H  HCH2  0   0.256   2.5712   0.5529   0.6966
 LIH  H4'1  H  HCR6  0   0.261  -1.7717   0.7275   2.1019
 LIH  H2'1  H  HCR6  0   0.262  -3.0779   0.9317   6.1547
 LIH  H3'1  H  HCR6  0   0.271  -3.5462   1.2173   3.7295
 LIH  H101  H  HNH1  0   0.388   0.0069   0.8324   1.1225
 LIH  H41   H  HNH2  0   0.403  -2.6537  -2.1585  -3.8557
 LIH  H42   H  HNH2  0   0.423  -2.0777  -1.9916  -2.2588
 LIH  H21   H  HNH2  0   0.395  -1.3115   0.1233  -7.3116
 LIH  H22   H  HNH2  0   0.395  -0.0956   1.3359  -7.2306

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
 LIH  C4A  C4    aromatic  1.449  0.020  1.449
 LIH  C4A  C8A   aromatic  1.423  0.020  1.423
 LIH  C4A  C5    aromatic  1.414  0.020  1.414
 LIH  C4   N3    aromatic  1.316  0.020  1.316
 LIH  C4   N4    single    1.340  0.020  1.340
 LIH  C2   N3    aromatic  1.344  0.020  1.344
 LIH  C2   N1    aromatic  1.319  0.020  1.319
 LIH  C2   N2    single    1.345  0.020  1.345
 LIH  C8A  N1    aromatic  1.342  0.020  1.342
 LIH  C8A  N8    aromatic  1.345  0.020  1.345
 LIH  C5   C6    aromatic  1.390  0.020  1.390
 LIH  C5   C5A   single    1.500  0.020  1.500
 LIH  C6   C7    aromatic  1.399  0.020  1.399
 LIH  C6   C9    single    1.502  0.020  1.502
 LIH  C7   N8    aromatic  1.309  0.020  1.309
 LIH  C7   H71   single    0.930  0.020  1.080
 LIH  C5A  H5A1  single    0.970  0.020  1.090
 LIH  C5A  H5A2  single    0.970  0.020  1.090
 LIH  C5A  H5A3  single    0.970  0.020  1.090
 LIH  C5'  C6'   aromatic  1.382  0.020  1.382
 LIH  C5'  C4X   aromatic  1.435  0.020  1.435
 LIH  C5'  N10   single    1.372  0.020  1.372
 LIH  C6'  C7'   aromatic  1.406  0.020  1.406
 LIH  C6'  H6'1  single    0.930  0.020  1.080
 LIH  C7'  C8'   aromatic  1.367  0.020  1.367
 LIH  C7'  H7'1  single    0.930  0.020  1.080
 LIH  C8'  C8X   aromatic  1.413  0.020  1.413
 LIH  C8'  H8'1  single    0.930  0.020  1.080
 LIH  C9   N10   single    1.446  0.020  1.446
 LIH  C9   H91   single    0.970  0.020  1.090
 LIH  C9   H92   single    0.970  0.020  1.090
 LIH  C4'  C4X   aromatic  1.410  0.020  1.410
 LIH  C4'  C3'   aromatic  1.368  0.020  1.368
 LIH  C4'  H4'1  single    0.930  0.020  1.080
 LIH  C4X  C8X   aromatic  1.420  0.020  1.420
 LIH  C8X  N1'   aromatic  1.355  0.020  1.355
 LIH  C2'  C3'   aromatic  1.406  0.020  1.406
 LIH  C2'  N1'   aromatic  1.307  0.020  1.307
 LIH  C2'  H2'1  single    0.930  0.020  1.080
 LIH  C3'  H3'1  single    0.930  0.020  1.080
 LIH  N10  H101  single    0.890  0.020  1.040
 LIH  N4   H41   single    0.890  0.020  1.040
 LIH  N4   H42   single    0.890  0.020  1.040
 LIH  N2   H21   single    0.890  0.020  1.040
 LIH  N2   H22   single    0.890  0.020  1.040

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
 LIH  C5    C4A  C8A   119.13  3.000
 LIH  C5    C4A  C4    126.95  3.000
 LIH  C8A   C4A  C4    113.92  3.000
 LIH  N4    C4   N3    115.67  3.000
 LIH  N4    C4   C4A   123.14  3.000
 LIH  N3    C4   C4A   121.20  3.000
 LIH  N2    C2   N1    117.97  3.000
 LIH  N2    C2   N3    115.68  3.000
 LIH  N1    C2   N3    126.35  3.000
 LIH  N8    C8A  N1    115.40  3.000
 LIH  N8    C8A  C4A   121.53  3.000
 LIH  N1    C8A  C4A   123.07  3.000
 LIH  C5A   C5   C6    119.42  3.000
 LIH  C5A   C5   C4A   123.05  3.000
 LIH  C6    C5   C4A   117.50  3.000
 LIH  C9    C6   C7    118.52  3.000
 LIH  C9    C6   C5    123.32  3.000
 LIH  C7    C6   C5    118.16  3.000
 LIH  H71   C7   N8    116.06  3.000
 LIH  H71   C7   C6    118.49  3.000
 LIH  N8    C7   C6    125.44  3.000
 LIH  H5A3  C5A  H5A2  107.13  3.000
 LIH  H5A3  C5A  H5A1  106.00  3.000
 LIH  H5A2  C5A  H5A1  108.58  3.000
 LIH  H5A3  C5A  C5    111.51  3.000
 LIH  H5A2  C5A  C5    111.62  3.000
 LIH  H5A1  C5A  C5    111.72  3.000
 LIH  N10   C5'  C4X   119.06  3.000
 LIH  N10   C5'  C6'   122.53  3.000
 LIH  C4X   C5'  C6'   118.39  3.000
 LIH  H6'1  C6'  C7'   118.40  3.000
 LIH  H6'1  C6'  C5'   120.67  3.000
 LIH  C7'   C6'  C5'   120.91  3.000
 LIH  H7'1  C7'  C8'   119.83  3.000
 LIH  H7'1  C7'  C6'   118.36  3.000
 LIH  C8'   C7'  C6'   121.80  3.000
 LIH  H8'1  C8'  C8X   119.04  3.000
 LIH  H8'1  C8'  C7'   121.77  3.000
 LIH  C8X   C8'  C7'   119.20  3.000
 LIH  H92   C9   H91   106.04  3.000
 LIH  H92   C9   N10   111.82  3.000
 LIH  H91   C9   N10   108.88  3.000
 LIH  H92   C9   C6    109.04  3.000
 LIH  H91   C9   C6    110.53  3.000
 LIH  N10   C9   C6    110.46  3.000
 LIH  H4'1  C4'  C3'   119.12  3.000
 LIH  H4'1  C4'  C4X   121.05  3.000
 LIH  C3'   C4'  C4X   119.82  3.000
 LIH  C8X   C4X  C4'   117.20  3.000
 LIH  C8X   C4X  C5'   119.74  3.000
 LIH  C4'   C4X  C5'   123.05  3.000
 LIH  N1'   C8X  C4X   121.98  3.000
 LIH  N1'   C8X  C8'   118.10  3.000
 LIH  C4X   C8X  C8'   119.91  3.000
 LIH  H2'1  C2'  N1'   116.68  3.000
 LIH  H2'1  C2'  C3'   119.61  3.000
 LIH  N1'   C2'  C3'   123.71  3.000
 LIH  H3'1  C3'  C2'   120.25  3.000
 LIH  H3'1  C3'  C4'   121.34  3.000
 LIH  C2'   C3'  C4'   118.41  3.000
 LIH  C2    N3   C4    118.38  3.000
 LIH  C8A   N1   C2    116.49  3.000
 LIH  C7    N8   C8A   117.95  3.000
 LIH  C2'   N1'  C8X   118.83  3.000
 LIH  H101  N10  C9    113.61  3.000
 LIH  H101  N10  C5'   115.93  3.000
 LIH  C9    N10  C5'   121.18  3.000
 LIH  H42   N4   H41   116.20  3.000
 LIH  H42   N4   C4    122.56  3.000
 LIH  H41   N4   C4    117.04  3.000
 LIH  H22   N2   H21   117.65  3.000
 LIH  H22   N2   C2    119.20  3.000
 LIH  H21   N2   C2    119.43  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
 LIH  CONST_01  C2    N3   C4   C4A    0.00   0.0  0
 LIH  CONST_02  C2    N1   C8A  C4A    0.00   0.0  0
 LIH  CONST_03  C7    N8   C8A  C4A    0.00   0.0  0
 LIH  CONST_04  C7    C6   C5   C4A    0.00   0.0  0
 LIH  CONST_05  N1    C8A  C4A  C4     0.00   0.0  0
 LIH  CONST_06  N8    C8A  C4A  C4   180.00   0.0  0
 LIH  CONST_07  C6    C5   C4A  C4   180.00   0.0  0
 LIH  CONST_08  N1    C2   N3   C4     0.00   0.0  0
 LIH  CONST_09  N8    C8A  N1   C2   180.00   0.0  0
 LIH  CONST_10  N3    C4   C4A  C8A    0.00   0.0  0
 LIH  CONST_11  C6    C5   C4A  C8A    0.00   0.0  0
 LIH  CONST_12  N3    C2   N1   C8A    0.00   0.0  0
 LIH  CONST_13  C6    C7   N8   C8A    0.00   0.0  0
 LIH  CONST_14  N3    C4   C4A  C5   180.00   0.0  0
 LIH  CONST_15  N1    C8A  C4A  C5   180.00   0.0  0
 LIH  CONST_16  N8    C8A  C4A  C5     0.00   0.0  0
 LIH  CONST_17  N8    C7   C6   C5     0.00   0.0  0
 LIH  CONST_18  N1    C8A  N8   C7   180.00   0.0  0
 LIH  CONST_19  C8'   C7'  C6'  C5'    0.00   0.0  0
 LIH  CONST_20  C3'   C4'  C4X  C5'  180.00   0.0  0
 LIH  CONST_21  C8'   C8X  C4X  C5'    0.00   0.0  0
 LIH  CONST_22  N1'   C8X  C4X  C5'  180.00   0.0  0
 LIH  CONST_23  C4'   C4X  C5'  C6'  180.00   0.0  0
 LIH  CONST_24  C8X   C4X  C5'  C6'    0.00   0.0  0
 LIH  CONST_25  C8X   C8'  C7'  C6'    0.00   0.0  0
 LIH  CONST_26  C4X   C5'  C6'  C7'    0.00   0.0  0
 LIH  CONST_27  C4X   C8X  C8'  C7'    0.00   0.0  0
 LIH  CONST_28  N1'   C8X  C8'  C7'  180.00   0.0  0
 LIH  CONST_29  C4'   C4X  C8X  C8'  180.00   0.0  0
 LIH  CONST_30  C2'   N1'  C8X  C8'  180.00   0.0  0
 LIH  CONST_31  N1'   C8X  C4X  C4'    0.00   0.0  0
 LIH  CONST_32  N1'   C2'  C3'  C4'    0.00   0.0  0
 LIH  CONST_33  C2'   C3'  C4'  C4X    0.00   0.0  0
 LIH  CONST_34  C2'   N1'  C8X  C4X    0.00   0.0  0
 LIH  CONST_35  C3'   C4'  C4X  C8X    0.00   0.0  0
 LIH  CONST_36  C3'   C2'  N1'  C8X    0.00   0.0  0
 LIH  CONST_37  C9    C6   C5   C4A  180.00   0.0  0
 LIH  CONST_38  C5A   C5   C4A  C4     0.00   0.0  0
 LIH  CONST_39  N2    C2   N3   C4   180.00   0.0  0
 LIH  CONST_40  N4    C4   N3   C2   180.00   0.0  0
 LIH  CONST_41  N4    C4   C4A  C8A  180.00   0.0  0
 LIH  CONST_42  C5A   C5   C4A  C8A  180.00   0.0  0
 LIH  CONST_43  N2    C2   N1   C8A  180.00   0.0  0
 LIH  CONST_44  N4    C4   C4A  C5     0.00   0.0  0
 LIH  CONST_45  C5A   C5   C6   C7   180.00   0.0  0
 LIH  CONST_46  N10   C5'  C6'  C7'  180.00   0.0  0
 LIH  CONST_47  N8    C7   C6   C9   180.00   0.0  0
 LIH  CONST_48  N10   C5'  C4X  C4'    0.00   0.0  0
 LIH  CONST_49  N10   C5'  C4X  C8X  180.00   0.0  0
 LIH  CONST_50  H71   C7   N8   C8A  180.00   0.0  0
 LIH  CONST_51  H7'1  C7'  C6'  C5'  180.00   0.0  0
 LIH  CONST_52  H4'1  C4'  C4X  C5'    0.00   0.0  0
 LIH  CONST_53  H8'1  C8'  C7'  C6'  180.00   0.0  0
 LIH  CONST_54  H6'1  C6'  C7'  C8'  180.00   0.0  0
 LIH  CONST_55  H2'1  C2'  C3'  C4'  180.00   0.0  0
 LIH  CONST_56  H3'1  C3'  C4'  C4X  180.00   0.0  0
 LIH  CONST_57  C9    N10  C5'  C6'    0.00   0.0  0
 LIH  CONST_58  C4X   C5'  N10  C9   180.00   0.0  0
 LIH  CONST_59  H41   N4   C4   C4A  180.00   0.0  0
 LIH  CONST_62  H21   N2   C2   N3     0.00   0.0  0
 LIH  CONST_63  H22   N2   C2   N3   180.00   0.0  0
 LIH  Var_01    N10   C9   C6   C5   -64.88  30.0  2
 LIH  Var_02    C5'   N10  C9   C6   178.38  30.0  3
 LIH  Var_03    H5A1  C5A  C5   C4A  -81.41  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
 LIH  plan-1  C4A   0.020
 LIH  plan-1  C4    0.020
 LIH  plan-1  C2    0.020
 LIH  plan-1  C8A   0.020
 LIH  plan-1  C5    0.020
 LIH  plan-1  C6    0.020
 LIH  plan-1  C7    0.020
 LIH  plan-1  C5A   0.020
 LIH  plan-1  C9    0.020
 LIH  plan-1  N3    0.020
 LIH  plan-1  N1    0.020
 LIH  plan-1  N8    0.020
 LIH  plan-1  N4    0.020
 LIH  plan-1  N2    0.020
 LIH  plan-1  H71   0.020
 LIH  plan-2  C5'   0.020
 LIH  plan-2  C6'   0.020
 LIH  plan-2  C7'   0.020
 LIH  plan-2  C8'   0.020
 LIH  plan-2  C4'   0.020
 LIH  plan-2  C4X   0.020
 LIH  plan-2  C8X   0.020
 LIH  plan-2  C2'   0.020
 LIH  plan-2  C3'   0.020
 LIH  plan-2  N1'   0.020
 LIH  plan-2  N10   0.020
 LIH  plan-2  H6'1  0.020
 LIH  plan-2  H7'1  0.020
 LIH  plan-2  H8'1  0.020
 LIH  plan-2  H4'1  0.020
 LIH  plan-2  H2'1  0.020
 LIH  plan-2  H3'1  0.020
 LIH  plan-3  C5'   0.020
 LIH  plan-3  C9    0.020
 LIH  plan-3  N10   0.020
 LIH  plan-3  H101  0.020
 LIH  plan-4  C4    0.020
 LIH  plan-4  N4    0.020
 LIH  plan-4  H41   0.020
 LIH  plan-4  H42   0.020
 LIH  plan-5  C2    0.020
 LIH  plan-5  N2    0.020
 LIH  plan-5  H21   0.020
 LIH  plan-5  H22   0.020

