# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:00:53 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 6-[(Z)-2-(2,5-dimethoxyphenyl)ethenyl]-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(\C=C/c2cnc3nc(N)nc(N)c3c2C)c1
#
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
 LII  LII  6-[(Z)-2-(2,5-dimethoxyphenyl)ethenyl]-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine  ligand  44  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_LII
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
 LII  C4A   C  CR66  0  -0.184  -2.5535  -0.8245  -0.1380
 LII  C4    C  CR6   0   0.458  -3.9347  -0.8184   0.2960
 LII  C2    C  CR6   0   0.540  -4.3478   0.9979  -1.0273
 LII  C8A   C  CR66  0   0.352  -2.2626   0.1295  -1.1503
 LII  C5    C  CR6   0   0.197  -1.5106  -1.6494   0.3467
 LII  C6    C  CR6   0  -0.101  -0.2674  -1.5489  -0.2649
 LII  C7    C  CR16  0  -0.069  -0.1227  -0.6287  -1.3170
 LII  C5A   C  CH3   0  -0.821  -1.6652  -2.5778   1.5163
 LII  C9    C  C1    0  -0.276   0.8802  -2.3903   0.1079
 LII  C1'   C  CR6   0  -0.050   2.5838  -0.5691   0.3519
 LII  C2'   C  CR6   0   0.338   3.7702  -0.1907  -0.3011
 LII  C3'   C  CR16  0  -0.371   4.2029   1.1240  -0.2250
 LII  C4'   C  CR16  0  -0.378   3.4767   2.0741   0.4909
 LII  C5'   C  CR6   0   0.376   2.3082   1.7088   1.1441
 LII  C6'   C  CR16  0  -0.358   1.8769   0.3853   1.0685
 LII  C10   C  C1    0  -0.220   2.1338  -1.9682   0.3045
 LII  C2X   C  CH3   0  -0.434   5.6021  -0.8449  -1.6612
 LII  C5X   C  CH3   0  -0.434   1.9477   3.8930   1.9909
 LII  N3    N  N     0  -0.505  -4.7795   0.0975  -0.1285
 LII  N1    N  N     0  -0.496  -3.1539   1.0328  -1.5862
 LII  N8    N  N     0  -0.430  -1.0516   0.1863  -1.7380
 LII  N4    N  NH2   0  -0.822  -4.4407  -1.7218   1.1473
 LII  N16   N  NH2   0  -0.818  -5.2537   1.9140  -1.4159
 LII  O2'   O  O2    0  -0.467   4.4052  -1.1670  -0.9848
 LII  O5'   O  O2    0  -0.478   1.5392   2.5470   1.8755
 LII  H71   H  HCR6  0   0.262   0.8315  -0.5761  -1.8332
 LII  H51   H  HCH3  0   0.268  -2.1716  -3.5044   1.2329
 LII  H52   H  HCH3  0   0.281  -0.6953  -2.8614   1.9168
 LII  H53   H  HCH3  0   0.270  -2.2213  -2.1178   2.3312
 LII  H91   H  H     0   0.265   0.7006  -3.4581   0.1815
 LII  H3'1  H  HCR6  0   0.282   5.1107   1.4439  -0.7179
 LII  H4'1  H  HCR6  0   0.280   3.8527   3.0875   0.5226
 LII  H6'1  H  HCR6  0   0.260   0.9742   0.0972   1.5928
 LII  H101  H  H     0   0.257   2.8934  -2.7260   0.4637
 LII  H2A1  H  HCH3  0   0.226   5.4450  -0.0781  -2.4248
 LII  H2A2  H  HCH3  0   0.226   6.3820  -0.5031  -0.9752
 LII  H2A3  H  HCH3  0   0.258   5.9393  -1.7577  -2.1465
 LII  H5'1  H  HCH3  0   0.225   1.9730   4.3997   1.0218
 LII  H5'2  H  HCH3  0   0.257   1.2138   4.3879   2.6225
 LII  H5'3  H  HCH3  0   0.224   2.9319   3.9851   2.4592
 LII  H41   H  HNH2  0   0.421  -3.9928  -2.5990   1.3331
 LII  H42   H  HNH2  0   0.402  -5.4355  -1.6928   1.3013
 LII  H161  H  HNH2  0   0.395  -4.9531   2.7018  -1.9624
 LII  H162  H  HNH2  0   0.395  -6.1141   2.0013  -0.9049

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
 LII  C4A  C4    aromatic  1.448  0.020  1.448
 LII  C4A  C8A   aromatic  1.421  0.020  1.421
 LII  C4A  C5    aromatic  1.415  0.020  1.415
 LII  C4   N3    aromatic  1.316  0.020  1.316
 LII  C4   N4    single    1.341  0.020  1.341
 LII  C2   N3    aromatic  1.343  0.020  1.343
 LII  C2   N1    aromatic  1.319  0.020  1.319
 LII  C2   N16   single    1.346  0.020  1.346
 LII  C8A  N1    aromatic  1.342  0.020  1.342
 LII  C8A  N8    aromatic  1.347  0.020  1.347
 LII  C5   C6    aromatic  1.389  0.020  1.389
 LII  C5   C5A   single    1.501  0.020  1.501
 LII  C6   C7    aromatic  1.405  0.020  1.405
 LII  C6   C9    single    1.471  0.020  1.471
 LII  C7   N8    aromatic  1.306  0.020  1.306
 LII  C7   H71   single    0.930  0.020  1.080
 LII  C5A  H51   single    0.970  0.020  1.090
 LII  C5A  H52   single    0.970  0.020  1.090
 LII  C5A  H53   single    0.970  0.020  1.090
 LII  C9   C10   double    1.337  0.020  1.337
 LII  C9   H91   single    0.930  0.020  1.080
 LII  C1'  C2'   aromatic  1.406  0.020  1.406
 LII  C1'  C6'   aromatic  1.387  0.020  1.387
 LII  C1'  C10   single    1.470  0.020  1.470
 LII  C2'  C3'   aromatic  1.386  0.020  1.386
 LII  C2'  O2'   single    1.350  0.020  1.350
 LII  C3'  C4'   aromatic  1.394  0.020  1.394
 LII  C3'  H3'1  single    0.930  0.020  1.080
 LII  C4'  C5'   aromatic  1.388  0.020  1.388
 LII  C4'  H4'1  single    0.930  0.020  1.080
 LII  C5'  C6'   aromatic  1.394  0.020  1.394
 LII  C5'  O5'   single    1.352  0.020  1.352
 LII  C6'  H6'1  single    0.930  0.020  1.080
 LII  C10  H101  single    0.930  0.020  1.080
 LII  C2X  O2'   single    1.412  0.020  1.412
 LII  C2X  H2A1  single    0.970  0.020  1.090
 LII  C2X  H2A2  single    0.970  0.020  1.090
 LII  C2X  H2A3  single    0.970  0.020  1.090
 LII  C5X  O5'   single    1.411  0.020  1.411
 LII  C5X  H5'1  single    0.970  0.020  1.090
 LII  C5X  H5'2  single    0.970  0.020  1.090
 LII  C5X  H5'3  single    0.970  0.020  1.090
 LII  N4   H41   single    0.890  0.020  1.040
 LII  N4   H42   single    0.890  0.020  1.040
 LII  N16  H161  single    0.890  0.020  1.040
 LII  N16  H162  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
 LII  C5    C4A  C8A   118.97  3.000
 LII  C5    C4A  C4    127.07  3.000
 LII  C8A   C4A  C4    113.95  3.000
 LII  N4    C4   N3    115.56  3.000
 LII  N4    C4   C4A   123.20  3.000
 LII  N3    C4   C4A   121.23  3.000
 LII  N16   C2   N1    117.97  3.000
 LII  N16   C2   N3    115.67  3.000
 LII  N1    C2   N3    126.31  3.000
 LII  N8    C8A  N1    115.27  3.000
 LII  N8    C8A  C4A   121.54  3.000
 LII  N1    C8A  C4A   123.19  3.000
 LII  C5A   C5   C6    118.68  3.000
 LII  C5A   C5   C4A   123.46  3.000
 LII  C6    C5   C4A   117.81  3.000
 LII  C9    C6   C7    118.94  3.000
 LII  C9    C6   C5    123.04  3.000
 LII  C7    C6   C5    117.98  3.000
 LII  H71   C7   N8    116.20  3.000
 LII  H71   C7   C6    118.56  3.000
 LII  N8    C7   C6    125.24  3.000
 LII  H53   C5A  H52   106.87  3.000
 LII  H53   C5A  H51   108.40  3.000
 LII  H52   C5A  H51   106.72  3.000
 LII  H53   C5A  C5    112.00  3.000
 LII  H52   C5A  C5    110.89  3.000
 LII  H51   C5A  C5    111.71  3.000
 LII  H91   C9   C10   117.10  3.000
 LII  H91   C9   C6    116.80  3.000
 LII  C10   C9   C6    126.02  3.000
 LII  C10   C1'  C6'   121.02  3.000
 LII  C10   C1'  C2'   119.95  3.000
 LII  C6'   C1'  C2'   119.00  3.000
 LII  O2'   C2'  C3'   124.52  3.000
 LII  O2'   C2'  C1'   115.93  3.000
 LII  C3'   C2'  C1'   119.55  3.000
 LII  H3'1  C3'  C4'   118.03  3.000
 LII  H3'1  C3'  C2'   121.17  3.000
 LII  C4'   C3'  C2'   120.80  3.000
 LII  H4'1  C4'  C5'   121.71  3.000
 LII  H4'1  C4'  C3'   118.21  3.000
 LII  C5'   C4'  C3'   120.08  3.000
 LII  O5'   C5'  C6'   116.22  3.000
 LII  O5'   C5'  C4'   124.77  3.000
 LII  C6'   C5'  C4'   119.01  3.000
 LII  H6'1  C6'  C5'   118.96  3.000
 LII  H6'1  C6'  C1'   119.46  3.000
 LII  C5'   C6'  C1'   121.57  3.000
 LII  H101  C10  C1'   116.47  3.000
 LII  H101  C10  C9    117.23  3.000
 LII  C1'   C10  C9    126.29  3.000
 LII  H2A3  C2X  H2A2  108.73  3.000
 LII  H2A3  C2X  H2A1  108.76  3.000
 LII  H2A2  C2X  H2A1  108.74  3.000
 LII  H2A3  C2X  O2'   106.57  3.000
 LII  H2A2  C2X  O2'   112.04  3.000
 LII  H2A1  C2X  O2'   111.89  3.000
 LII  H5'3  C5X  H5'2  108.68  3.000
 LII  H5'3  C5X  H5'1  108.63  3.000
 LII  H5'2  C5X  H5'1  108.63  3.000
 LII  H5'3  C5X  O5'   112.07  3.000
 LII  H5'2  C5X  O5'   106.63  3.000
 LII  H5'1  C5X  O5'   112.08  3.000
 LII  C2    N3   C4    118.41  3.000
 LII  C8A   N1   C2    116.48  3.000
 LII  C7    N8   C8A   118.20  3.000
 LII  H42   N4   H41   116.00  3.000
 LII  H42   N4   C4    116.78  3.000
 LII  H41   N4   C4    122.61  3.000
 LII  H162  N16  H161  117.70  3.000
 LII  H162  N16  C2    119.27  3.000
 LII  H161  N16  C2    119.30  3.000
 LII  C2X   O2'  C2'   118.44  3.000
 LII  C5X   O5'  C5'   118.09  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
 LII  CONST_01  C2    N3   C4   C4A     0.00   0.0  0
 LII  CONST_02  C2    N1   C8A  C4A     0.00   0.0  0
 LII  CONST_03  C7    N8   C8A  C4A     0.00   0.0  0
 LII  CONST_04  C7    C6   C5   C4A     0.00   0.0  0
 LII  CONST_05  N1    C8A  C4A  C4      0.00   0.0  0
 LII  CONST_06  N8    C8A  C4A  C4    180.00   0.0  0
 LII  CONST_07  C6    C5   C4A  C4    180.00   0.0  0
 LII  CONST_08  N1    C2   N3   C4      0.00   0.0  0
 LII  CONST_09  N8    C8A  N1   C2    180.00   0.0  0
 LII  CONST_10  N3    C4   C4A  C8A     0.00   0.0  0
 LII  CONST_11  C6    C5   C4A  C8A     0.00   0.0  0
 LII  CONST_12  N3    C2   N1   C8A     0.00   0.0  0
 LII  CONST_13  C6    C7   N8   C8A     0.00   0.0  0
 LII  CONST_14  N3    C4   C4A  C5    180.00   0.0  0
 LII  CONST_15  N1    C8A  C4A  C5    180.00   0.0  0
 LII  CONST_16  N8    C8A  C4A  C5      0.00   0.0  0
 LII  CONST_17  N8    C7   C6   C5      0.00   0.0  0
 LII  CONST_18  N1    C8A  N8   C7    180.00   0.0  0
 LII  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 LII  CONST_20  C4'   C5'  C6'  C1'     0.00   0.0  0
 LII  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 LII  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 LII  CONST_23  C6'   C1'  C2'  C3'     0.00   0.0  0
 LII  CONST_24  C6'   C5'  C4'  C3'     0.00   0.0  0
 LII  CONST_25  C9    C6   C5   C4A   180.00   0.0  0
 LII  CONST_26  C5A   C5   C4A  C4      0.00   0.0  0
 LII  CONST_27  N16   C2   N3   C4    180.00   0.0  0
 LII  CONST_28  N4    C4   N3   C2    180.00   0.0  0
 LII  CONST_29  N4    C4   C4A  C8A   180.00   0.0  0
 LII  CONST_30  C5A   C5   C4A  C8A   180.00   0.0  0
 LII  CONST_31  N16   C2   N1   C8A   180.00   0.0  0
 LII  CONST_32  N4    C4   C4A  C5      0.00   0.0  0
 LII  CONST_33  C5A   C5   C6   C7    180.00   0.0  0
 LII  CONST_34  N8    C7   C6   C9    180.00   0.0  0
 LII  CONST_35  O5'   C5'  C6'  C1'   180.00   0.0  0
 LII  CONST_36  C10   C1'  C2'  C3'   180.00   0.0  0
 LII  CONST_37  O5'   C5'  C4'  C3'   180.00   0.0  0
 LII  CONST_38  O2'   C2'  C3'  C4'   180.00   0.0  0
 LII  CONST_39  C10   C1'  C6'  C5'   180.00   0.0  0
 LII  CONST_40  O2'   C2'  C1'  C6'   180.00   0.0  0
 LII  CONST_41  H71   C7   N8   C8A   180.00   0.0  0
 LII  CONST_42  H3'1  C3'  C2'  C1'   180.00   0.0  0
 LII  CONST_43  H6'1  C6'  C1'  C2'   180.00   0.0  0
 LII  CONST_44  H4'1  C4'  C3'  C2'   180.00   0.0  0
 LII  CONST_46  H42   N4   C4   C4A   180.00   0.0  0
 LII  CONST_47  H161  N16  C2   N3    180.00   0.0  0
 LII  CONST_48  H162  N16  C2   N3      0.00   0.0  0
 LII  Var_01    C1'   C10  C9   C6      8.10   0.0  2
 LII  Var_02    C10   C9   C6   C5   -134.64  30.0  2
 LII  Var_03    C2'   C1'  C10  C9   -137.16  30.0  3
 LII  Var_04    H51   C5A  C5   C4A    79.60  30.0  2
 LII  Var_05    H2A1  C2X  O2'  C2'   -60.76  30.0  3
 LII  Var_06    H5'1  C5X  O5'  C5'    62.13  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
 LII  plan-1  C1'   0.020
 LII  plan-1  C2'   0.020
 LII  plan-1  C3'   0.020
 LII  plan-1  C4'   0.020
 LII  plan-1  C5'   0.020
 LII  plan-1  C6'   0.020
 LII  plan-1  C10   0.020
 LII  plan-1  O2'   0.020
 LII  plan-1  O5'   0.020
 LII  plan-1  H3'1  0.020
 LII  plan-1  H4'1  0.020
 LII  plan-1  H6'1  0.020
 LII  plan-2  C4A   0.020
 LII  plan-2  C4    0.020
 LII  plan-2  C2    0.020
 LII  plan-2  C8A   0.020
 LII  plan-2  C5    0.020
 LII  plan-2  C6    0.020
 LII  plan-2  C7    0.020
 LII  plan-2  C5A   0.020
 LII  plan-2  C9    0.020
 LII  plan-2  N3    0.020
 LII  plan-2  N1    0.020
 LII  plan-2  N8    0.020
 LII  plan-2  N4    0.020
 LII  plan-2  N16   0.020
 LII  plan-2  H71   0.020
 LII  plan-3  C4    0.020
 LII  plan-3  N4    0.020
 LII  plan-3  H41   0.020
 LII  plan-3  H42   0.020
 LII  plan-4  C2    0.020
 LII  plan-4  N16   0.020
 LII  plan-4  H161  0.020
 LII  plan-4  H162  0.020
 LII  plan-5  C6    0.020
 LII  plan-5  C9    0.020
 LII  plan-5  C1'   0.020
 LII  plan-5  C10   0.020
 LII  plan-5  H91   0.020
 LII  plan-5  H101  0.020

