# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 07:52:14 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5-(aminomethyl)-6-(2,4-dichlorophenyl)-2-(3,5-dimethoxyphenyl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)cc(c1)c2nc(N)c(CN)c(n2)c3ccc(Cl)cc3Cl
#
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
 5AP  5AP  5-(aminomethyl)-6-(2,4-dichlorophenyl)-2-(3,5-dimethoxyphenyl)pyrimidin-4-amine  ligand  45  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5AP
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
 5AP  CL2   CL  CL    0  -0.110   1.3473  -1.9782  -1.6403
 5AP  C17   C   CR6   0  -0.111   0.9624  -0.6149  -2.6307
 5AP  C16   C   CR16  0  -0.152   1.7588  -0.3780  -3.7404
 5AP  C14   C   CR6   0  -0.057   1.4468   0.6883  -4.5674
 5AP  CL1   CL  CL    0  -0.112   2.4394   0.9966  -5.9489
 5AP  C13   C   CR16  0  -0.190   0.3543   1.5004  -4.3124
 5AP  C12   C   CR16  0  -0.289  -0.4285   1.2366  -3.2007
 5AP  C11   C   CR6   0   0.091  -0.1393   0.1848  -2.3356
 5AP  C10   C   CR6   0   0.229  -0.9652  -0.0260  -1.1213
 5AP  C19   C   CR6   0  -0.036  -2.3186  -0.2874  -1.1998
 5AP  C20   C   CH2   0  -0.407  -3.0778  -0.3982  -2.4901
 5AP  N21   N   NH2   0  -0.780  -3.7339   0.8630  -2.8204
 5AP  C22   C   CR6   0   0.487  -2.9752  -0.4110   0.0503
 5AP  N23   N   NH2   0  -0.837  -4.3025  -0.6194   0.1353
 5AP  N9    N   N     0  -0.448  -0.3052   0.0816   0.0353
 5AP  C2    C   CR6   0   0.389  -1.0091  -0.0656   1.1419
 5AP  N1    N   N     0  -0.479  -2.3119  -0.3010   1.1989
 5AP  C3    C   CR6   0   0.019  -0.2783   0.0405   2.4280
 5AP  C4    C   CR16  0  -0.428   1.1120   0.0321   2.4268
 5AP  C5    C   CR6   0   0.452   1.7997   0.1277   3.6319
 5AP  O25   O   O2    0  -0.475   3.1432   0.0984   3.5490
 5AP  C28   C   CH3   0  -0.440   3.9054   0.2306   4.7321
 5AP  C6    C   CR16  0  -0.535   1.1089   0.2453   4.8379
 5AP  C7    C   CR6   0   0.450  -0.2856   0.2579   4.8220
 5AP  C8    C   CR16  0  -0.427  -0.9815   0.1476   3.6222
 5AP  O26   O   O2    0  -0.475  -1.0372   0.3767   5.9325
 5AP  C29   C   CH3   0  -0.439  -0.3925   0.5375   7.1802
 5AP  H16   H   HCR6  0   0.303   2.6038  -1.0175  -3.9537
 5AP  H13   H   HCR6  0   0.287   0.1129   2.3263  -4.9665
 5AP  H12   H   HCR6  0   0.277  -1.2949   1.8554  -3.0049
 5AP  H201  H   HCH2  0   0.225  -3.7666  -1.2532  -2.4324
 5AP  H202  H   HCH2  0   0.258  -2.3851  -0.6409  -3.2961
 5AP  H211  H   HNH2  0   0.357  -4.2343   0.7539  -3.6940
 5AP  H212  H   HNH2  0   0.343  -4.4395   1.0772  -2.1262
 5AP  H231  H   HNH2  0   0.399  -4.6869  -0.8478   1.0370
 5AP  H232  H   HNH2  0   0.408  -4.8290  -0.9396  -0.6589
 5AP  H4    H   HCR6  0   0.257   1.6582  -0.0596   1.4978
 5AP  H281  H   HCH3  0   0.262   4.9494   0.1940   4.4313
 5AP  H282  H   HCH3  0   0.229   3.7175   1.1827   5.2351
 5AP  H283  H   HCH3  0   0.230   3.7148  -0.5831   5.4367
 5AP  H6    H   HCR6  0   0.303   1.6489   0.3242   5.7705
 5AP  H8    H   HCR6  0   0.253  -2.0629   0.1539   3.6246
 5AP  H291  H   HCH3  0   0.262  -1.1796   0.6464   7.9220
 5AP  H292  H   HCH3  0   0.229   0.2175  -0.3312   7.4417
 5AP  H293  H   HCH3  0   0.229   0.2365   1.4312   7.2027

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
 5AP  CL2  C17   single    1.728  0.020  1.728
 5AP  C17  C16   aromatic  1.386  0.020  1.386
 5AP  C17  C11   aromatic  1.393  0.020  1.393
 5AP  C16  C14   aromatic  1.385  0.020  1.385
 5AP  C16  H16   single    0.930  0.020  1.080
 5AP  C14  CL1   single    1.729  0.020  1.729
 5AP  C14  C13   aromatic  1.385  0.020  1.385
 5AP  C13  C12   aromatic  1.385  0.020  1.385
 5AP  C13  H13   single    0.930  0.020  1.080
 5AP  C12  C11   aromatic  1.392  0.020  1.392
 5AP  C12  H12   single    0.930  0.020  1.080
 5AP  C11  C10   single    1.484  0.020  1.484
 5AP  C10  C19   aromatic  1.381  0.020  1.381
 5AP  C10  N9    aromatic  1.336  0.020  1.336
 5AP  C19  C20   single    1.501  0.020  1.501
 5AP  C19  C22   aromatic  1.417  0.020  1.417
 5AP  C20  N21   single    1.459  0.020  1.459
 5AP  C20  H201  single    0.970  0.020  1.090
 5AP  C20  H202  single    0.970  0.020  1.090
 5AP  N21  H211  single    0.890  0.020  1.040
 5AP  N21  H212  single    0.890  0.020  1.040
 5AP  C22  N23   single    1.346  0.020  1.346
 5AP  C22  N1    aromatic  1.331  0.020  1.331
 5AP  N23  H231  single    0.890  0.020  1.040
 5AP  N23  H232  single    0.890  0.020  1.040
 5AP  N9   C2    aromatic  1.320  0.020  1.320
 5AP  C2   N1    aromatic  1.325  0.020  1.325
 5AP  C2   C3    single    1.483  0.020  1.483
 5AP  C3   C4    aromatic  1.390  0.020  1.390
 5AP  C3   C8    aromatic  1.390  0.020  1.390
 5AP  C4   C5    aromatic  1.391  0.020  1.391
 5AP  C4   H4    single    0.930  0.020  1.080
 5AP  C5   O25   single    1.346  0.020  1.346
 5AP  C5   C6    aromatic  1.395  0.020  1.395
 5AP  O25  C28   single    1.414  0.020  1.414
 5AP  C28  H281  single    0.970  0.020  1.090
 5AP  C28  H282  single    0.970  0.020  1.090
 5AP  C28  H283  single    0.970  0.020  1.090
 5AP  C6   C7    aromatic  1.395  0.020  1.395
 5AP  C6   H6    single    0.930  0.020  1.080
 5AP  C7   C8    aromatic  1.391  0.020  1.391
 5AP  C7   O26   single    1.346  0.020  1.346
 5AP  C8   H8    single    0.930  0.020  1.080
 5AP  O26  C29   single    1.414  0.020  1.414
 5AP  C29  H291  single    0.970  0.020  1.090
 5AP  C29  H292  single    0.970  0.020  1.090
 5AP  C29  H293  single    0.970  0.020  1.090

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
 5AP  C11   C17  C16   121.73  3.000
 5AP  C11   C17  CL2   120.50  3.000
 5AP  C16   C17  CL2   117.74  3.000
 5AP  H16   C16  C14   120.92  3.000
 5AP  H16   C16  C17   120.40  3.000
 5AP  C14   C16  C17   118.69  3.000
 5AP  C13   C14  CL1   119.70  3.000
 5AP  C13   C14  C16   121.29  3.000
 5AP  CL1   C14  C16   119.02  3.000
 5AP  H13   C13  C12   120.33  3.000
 5AP  H13   C13  C14   120.86  3.000
 5AP  C12   C13  C14   118.81  3.000
 5AP  H12   C12  C11   119.06  3.000
 5AP  H12   C12  C13   119.26  3.000
 5AP  C11   C12  C13   121.68  3.000
 5AP  C10   C11  C12   120.02  3.000
 5AP  C10   C11  C17   122.15  3.000
 5AP  C12   C11  C17   117.80  3.000
 5AP  N9    C10  C19   123.28  3.000
 5AP  N9    C10  C11   114.97  3.000
 5AP  C19   C10  C11   121.74  3.000
 5AP  C22   C19  C20   121.15  3.000
 5AP  C22   C19  C10   114.86  3.000
 5AP  C20   C19  C10   123.96  3.000
 5AP  H202  C20  H201  105.30  3.000
 5AP  H202  C20  N21   108.10  3.000
 5AP  H201  C20  N21   113.72  3.000
 5AP  H202  C20  C19   109.30  3.000
 5AP  H201  C20  C19   109.21  3.000
 5AP  N21   C20  C19   110.98  3.000
 5AP  H212  N21  H211  105.65  3.000
 5AP  H212  N21  C20   109.93  3.000
 5AP  H211  N21  C20   108.92  3.000
 5AP  N1    C22  N23   116.72  3.000
 5AP  N1    C22  C19   121.54  3.000
 5AP  N23   C22  C19   121.73  3.000
 5AP  H232  N23  H231  115.82  3.000
 5AP  H232  N23  C22   121.05  3.000
 5AP  H231  N23  C22   117.92  3.000
 5AP  C2    N9   C10   116.96  3.000
 5AP  C3    C2   N1    117.38  3.000
 5AP  C3    C2   N9    117.15  3.000
 5AP  N1    C2   N9    125.47  3.000
 5AP  C2    N1   C22   117.87  3.000
 5AP  C8    C3   C4    120.47  3.000
 5AP  C8    C3   C2    120.08  3.000
 5AP  C4    C3   C2    119.45  3.000
 5AP  H4    C4   C5    120.02  3.000
 5AP  H4    C4   C3    120.41  3.000
 5AP  C5    C4   C3    119.56  3.000
 5AP  C6    C5   O25   123.32  3.000
 5AP  C6    C5   C4    120.67  3.000
 5AP  O25   C5   C4    116.01  3.000
 5AP  C28   O25  C5    118.98  3.000
 5AP  H283  C28  H282  108.77  3.000
 5AP  H283  C28  H281  108.71  3.000
 5AP  H282  C28  H281  108.76  3.000
 5AP  H283  C28  O25   112.08  3.000
 5AP  H282  C28  O25   111.96  3.000
 5AP  H281  C28  O25   106.45  3.000
 5AP  H6    C6   C7    120.59  3.000
 5AP  H6    C6   C5    120.33  3.000
 5AP  C7    C6   C5    119.09  3.000
 5AP  O26   C7   C8    116.05  3.000
 5AP  O26   C7   C6    123.34  3.000
 5AP  C8    C7   C6    120.61  3.000
 5AP  H8    C8   C7    119.85  3.000
 5AP  H8    C8   C3    120.54  3.000
 5AP  C7    C8   C3    119.60  3.000
 5AP  C29   O26  C7    118.91  3.000
 5AP  H293  C29  H292  108.88  3.000
 5AP  H293  C29  H291  108.70  3.000
 5AP  H292  C29  H291  108.69  3.000
 5AP  H293  C29  O26   111.94  3.000
 5AP  H292  C29  O26   112.04  3.000
 5AP  H291  C29  O26   106.46  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
 5AP  CONST_01  C13   C14  C16  C17     0.00   0.0  0
 5AP  CONST_02  C13   C12  C11  C17     0.00   0.0  0
 5AP  CONST_05  C12   C11  C17  C16     0.00   0.0  0
 5AP  CONST_06  C10   C11  C17  C16   180.00   0.0  0
 5AP  CONST_07  C12   C13  C14  C16     0.00   0.0  0
 5AP  CONST_08  C11   C17  C16  C14     0.00   0.0  0
 5AP  CONST_09  C11   C12  C13  C14     0.00   0.0  0
 5AP  CONST_10  C10   C11  C12  C13   180.00   0.0  0
 5AP  CONST_13  C22   C19  C10  C11   180.00   0.0  0
 5AP  CONST_14  C2    N9   C10  C11   180.00   0.0  0
 5AP  CONST_15  N1    C22  C19  C10     0.00   0.0  0
 5AP  CONST_16  N1    C2   N9   C10     0.00   0.0  0
 5AP  CONST_17  C3    C2   N9   C10   180.00   0.0  0
 5AP  CONST_18  C2    N9   C10  C19     0.00   0.0  0
 5AP  CONST_19  C2    N1   C22  C19     0.00   0.0  0
 5AP  CONST_20  N9    C10  C19  C22     0.00   0.0  0
 5AP  CONST_21  N9    C2   N1   C22     0.00   0.0  0
 5AP  CONST_22  C3    C2   N1   C22   180.00   0.0  0
 5AP  CONST_23  C4    C3   C2   N9      0.00   0.0  0
 5AP  CONST_24  C8    C3   C2   N9    180.00   0.0  0
 5AP  CONST_25  C5    C4   C3   C2    180.00   0.0  0
 5AP  CONST_26  C7    C8   C3   C2    180.00   0.0  0
 5AP  CONST_27  C4    C3   C2   N1    180.00   0.0  0
 5AP  CONST_28  C8    C3   C2   N1      0.00   0.0  0
 5AP  CONST_29  C6    C5   C4   C3      0.00   0.0  0
 5AP  CONST_30  C6    C7   C8   C3      0.00   0.0  0
 5AP  CONST_31  C7    C8   C3   C4      0.00   0.0  0
 5AP  CONST_32  C7    C6   C5   C4      0.00   0.0  0
 5AP  CONST_33  C8    C3   C4   C5      0.00   0.0  0
 5AP  CONST_34  C8    C7   C6   C5      0.00   0.0  0
 5AP  CONST_35  C14   C16  C17  CL2   180.00   0.0  0
 5AP  CONST_36  C12   C11  C17  CL2   180.00   0.0  0
 5AP  CONST_37  C10   C11  C17  CL2     0.00   0.0  0
 5AP  CONST_38  CL1   C14  C16  C17   180.00   0.0  0
 5AP  CONST_39  C12   C13  C14  CL1   180.00   0.0  0
 5AP  CONST_40  C20   C19  C10  C11     0.00   0.0  0
 5AP  CONST_41  N23   C22  C19  C10   180.00   0.0  0
 5AP  CONST_42  N9    C10  C19  C20   180.00   0.0  0
 5AP  CONST_43  N1    C22  C19  C20   180.00   0.0  0
 5AP  CONST_44  C2    N1   C22  N23   180.00   0.0  0
 5AP  CONST_45  O25   C5   C4   C3    180.00   0.0  0
 5AP  CONST_46  O26   C7   C8   C3    180.00   0.0  0
 5AP  CONST_47  O26   C7   C6   C5    180.00   0.0  0
 5AP  CONST_48  C7    C6   C5   O25   180.00   0.0  0
 5AP  CONST_49  H12   C12  C11  C17   180.00   0.0  0
 5AP  CONST_50  H13   C13  C14  C16   180.00   0.0  0
 5AP  CONST_51  H16   C16  C14  C13   180.00   0.0  0
 5AP  CONST_52  H4    C4   C3   C2      0.00   0.0  0
 5AP  CONST_53  H8    C8   C3   C2      0.00   0.0  0
 5AP  CONST_54  H6    C6   C5   C4    180.00   0.0  0
 5AP  CONST_55  H231  N23  C22  C19   180.00   0.0  0
 5AP  Var_01    N21   C20  C19  C10   -96.67  30.0  2
 5AP  Var_02    C6    C5   O25  C28    -1.87  30.0  2
 5AP  Var_03    H211  N21  C20  C19   179.93  30.0  3
 5AP  Var_04    H281  C28  O25  C5   -179.19  30.0  3
 5AP  Var_05    H291  C29  O26  C7    178.10  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
 5AP  plan-1  CL2   0.020
 5AP  plan-1  C17   0.020
 5AP  plan-1  C16   0.020
 5AP  plan-1  C14   0.020
 5AP  plan-1  CL1   0.020
 5AP  plan-1  C13   0.020
 5AP  plan-1  C12   0.020
 5AP  plan-1  C11   0.020
 5AP  plan-1  C10   0.020
 5AP  plan-1  H16   0.020
 5AP  plan-1  H13   0.020
 5AP  plan-1  H12   0.020
 5AP  plan-2  C11   0.020
 5AP  plan-2  C10   0.020
 5AP  plan-2  C19   0.020
 5AP  plan-2  C20   0.020
 5AP  plan-2  C22   0.020
 5AP  plan-2  N23   0.020
 5AP  plan-2  N9    0.020
 5AP  plan-2  C2    0.020
 5AP  plan-2  N1    0.020
 5AP  plan-2  C3    0.020
 5AP  plan-3  C2    0.020
 5AP  plan-3  C3    0.020
 5AP  plan-3  C4    0.020
 5AP  plan-3  C5    0.020
 5AP  plan-3  O25   0.020
 5AP  plan-3  C6    0.020
 5AP  plan-3  C7    0.020
 5AP  plan-3  C8    0.020
 5AP  plan-3  O26   0.020
 5AP  plan-3  H4    0.020
 5AP  plan-3  H6    0.020
 5AP  plan-3  H8    0.020
 5AP  plan-4  C22   0.020
 5AP  plan-4  N23   0.020
 5AP  plan-4  H231  0.020
 5AP  plan-4  H232  0.020

