# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:16:51 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-{4-[3-(2-methoxypyrimidin-5-yl)phenyl]piperazin-1-yl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cn1)c2cccc(c2)N3CCN(CC3)c4cnc(N)nc4N
#
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
 BOD  BOD  5-{4-[3-(2-methoxypyrimidin-5-yl)phenyl]piperazin-1-yl}pyrimidine-2,4-diamine  ligand  50  28  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BOD
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
 BOD  C18  C  CR6   0   0.469   5.4137  -0.3754  -0.9326
 BOD  C17  C  CR6   0   0.527   6.8872  -1.4269   0.4443
 BOD  C16  C  CR16  0  -0.050   4.8762  -0.8895   1.3060
 BOD  C12  C  CH2   0  -0.288   2.1031  -0.6786  -0.1685
 BOD  C11  C  CH2   0  -0.309   0.8479   0.0137  -0.6597
 BOD  C9   C  CR6   0   0.403  -0.7661   1.6741   0.1016
 BOD  N5   N  N     0  -0.507   6.6133  -0.9220  -0.7590
 BOD  C13  C  CH2   0  -0.282   2.8850   1.3896   0.7512
 BOD  C8   C  CR16  0  -0.371  -1.0279   3.0473   0.0167
 BOD  C6   C  CR16  0  -0.347  -3.4115   2.6499   0.0219
 BOD  N7   N  NH2   0  -0.823   8.1298  -1.9412   0.6174
 BOD  C4   C  CR16  0  -0.024  -4.2669  -0.9056  -0.4893
 BOD  N1   N  N     0  -0.455  -5.2739  -1.7666  -0.4496
 BOD  C2   C  CR16  0  -0.044  -5.4812   0.5931   0.8375
 BOD  C3   C  CR6   0  -0.080  -4.2963   0.3261   0.1508
 BOD  N4   N  N     0  -0.489   6.0729  -1.4438   1.5009
 BOD  N6   N  NH2   0  -0.816   5.0957   0.1145  -2.1388
 BOD  C15  C  CR6   0   0.077   4.4687  -0.3263   0.1214
 BOD  N3   N  NT    0  -0.516   3.2046   0.2666  -0.1107
 BOD  C14  C  CH2   0  -0.318   1.6313   2.0939   0.2631
 BOD  N2   N  NT    0  -0.524   0.5257   1.1615   0.1776
 BOD  C7   C  CR16  0  -0.226  -2.3339   3.5168  -0.0114
 BOD  C10  C  CR16  0  -0.411  -1.8670   0.8069   0.1552
 BOD  C5   C  CR6   0   0.118  -3.1740   1.2761   0.1049
 BOD  N    N  N     0  -0.426  -6.4966  -0.2483   0.8846
 BOD  C1   C  CR6   0   0.592  -6.3401  -1.3959   0.2362
 BOD  O    O  O2    0  -0.448  -7.3822  -2.2083   0.3178
 BOD  C    C  CH3   0  -0.417  -7.3130  -3.4694  -0.3376
 BOD  H1   H  HCR6  0   0.258   4.2018  -0.8980   2.1587
 BOD  H2   H  HCH2  0   0.208   1.9042  -1.1386   0.8121
 BOD  H3   H  HCH2  0   0.249   2.3556  -1.4810  -0.8634
 BOD  H4   H  HCH2  0   0.221   0.9914   0.3274  -1.7040
 BOD  H5   H  HCH2  0   0.256   0.0347  -0.7078  -0.6476
 BOD  H6   H  HCH2  0   0.206   2.7346   1.0817   1.7974
 BOD  H7   H  HCH2  0   0.249   3.7127   2.0998   0.7351
 BOD  H8   H  HCR6  0   0.270  -0.2226   3.7655  -0.0403
 BOD  H9   H  HCR6  0   0.250  -4.4220   3.0335  -0.0369
 BOD  H10  H  HNH2  0   0.387   8.2795  -2.5342   1.4155
 BOD  H11  H  HNH2  0   0.387   8.6591  -2.1710  -0.2061
 BOD  H13  H  HCR6  0   0.277  -5.6033   1.5247   1.3808
 BOD  H14  H  HNH2  0   0.395   4.2450   0.6452  -2.2252
 BOD  H15  H  HNH2  0   0.391   5.8089   0.2284  -2.8377
 BOD  H16  H  HCH2  0   0.255   1.3942   2.8815   0.9788
 BOD  H17  H  HCH2  0   0.216   1.8377   2.5727  -0.7061
 BOD  H18  H  HCR6  0   0.256  -2.5051   4.5833  -0.0840
 BOD  H19  H  HCR6  0   0.261  -1.7041  -0.2557   0.2840
 BOD  H20  H  HCH3  0   0.251  -8.2622  -3.9584  -0.1359
 BOD  H21  H  HCH3  0   0.235  -7.1858  -3.3574  -1.4146
 BOD  H22  H  HCH3  0   0.235  -6.5001  -4.0823   0.0524
 BOD  H12  H  HCR6  0   0.272  -3.4023  -1.2075  -1.0713

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
 BOD  C7   C8   aromatic  1.388  0.020  1.388
 BOD  C7   C6   aromatic  1.383  0.020  1.383
 BOD  C8   C9   aromatic  1.401  0.020  1.401
 BOD  C14  C13  single    1.519  0.020  1.519
 BOD  C14  N2   single    1.449  0.020  1.449
 BOD  C6   C5   aromatic  1.397  0.020  1.397
 BOD  C13  N3   single    1.451  0.020  1.451
 BOD  C9   N2   single    1.392  0.020  1.392
 BOD  C9   C10  aromatic  1.402  0.020  1.402
 BOD  N2   C11  single    1.457  0.020  1.457
 BOD  C5   C10  aromatic  1.390  0.020  1.390
 BOD  C5   C3   single    1.471  0.020  1.471
 BOD  N6   C18  single    1.340  0.020  1.340
 BOD  C2   C3   aromatic  1.395  0.020  1.395
 BOD  C2   N    aromatic  1.320  0.020  1.320
 BOD  N3   C15  single    1.415  0.020  1.415
 BOD  N3   C12  single    1.453  0.020  1.453
 BOD  C11  C12  single    1.515  0.020  1.515
 BOD  C3   C4   aromatic  1.388  0.020  1.388
 BOD  C18  C15  aromatic  1.417  0.020  1.417
 BOD  C18  N5   aromatic  1.330  0.020  1.330
 BOD  C15  C16  aromatic  1.373  0.020  1.373
 BOD  N    C1   aromatic  1.327  0.020  1.327
 BOD  N5   C17  aromatic  1.333  0.020  1.333
 BOD  C4   N1   aromatic  1.326  0.020  1.326
 BOD  C16  N4   aromatic  1.333  0.020  1.333
 BOD  C1   N1   aromatic  1.321  0.020  1.321
 BOD  C1   O    single    1.324  0.020  1.324
 BOD  C17  N4   aromatic  1.334  0.020  1.334
 BOD  C17  N7   single    1.356  0.020  1.356
 BOD  O    C    single    1.423  0.020  1.423
 BOD  C16  H1   single    0.930  0.020  1.080
 BOD  C12  H2   single    0.970  0.020  1.090
 BOD  C12  H3   single    0.970  0.020  1.090
 BOD  C11  H4   single    0.970  0.020  1.090
 BOD  C11  H5   single    0.970  0.020  1.090
 BOD  C13  H6   single    0.970  0.020  1.090
 BOD  C13  H7   single    0.970  0.020  1.090
 BOD  C8   H8   single    0.930  0.020  1.080
 BOD  C6   H9   single    0.930  0.020  1.080
 BOD  N7   H10  single    0.890  0.020  1.040
 BOD  N7   H11  single    0.890  0.020  1.040
 BOD  C4   H12  single    0.930  0.020  1.080
 BOD  C2   H13  single    0.930  0.020  1.080
 BOD  N6   H14  single    0.890  0.020  1.040
 BOD  N6   H15  single    0.890  0.020  1.040
 BOD  C14  H16  single    0.970  0.020  1.090
 BOD  C14  H17  single    0.970  0.020  1.090
 BOD  C7   H18  single    0.930  0.020  1.080
 BOD  C10  H19  single    0.930  0.020  1.080
 BOD  C    H20  single    0.970  0.020  1.090
 BOD  C    H21  single    0.970  0.020  1.090
 BOD  C    H22  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
 BOD  C15  C18  N6   119.92  3.000
 BOD  C15  C18  N5   121.26  3.000
 BOD  N6   C18  N5   118.81  3.000
 BOD  N4   C17  N7   116.97  3.000
 BOD  N7   C17  N5   116.56  3.000
 BOD  N4   C17  N5   126.45  3.000
 BOD  H1   C16  C15  119.71  3.000
 BOD  H1   C16  N4   116.03  3.000
 BOD  C15  C16  N4   124.26  3.000
 BOD  H3   C12  H2   107.56  3.000
 BOD  H3   C12  N3   109.17  3.000
 BOD  H2   C12  N3   111.92  3.000
 BOD  H3   C12  C11  108.74  3.000
 BOD  H2   C12  C11  109.27  3.000
 BOD  N3   C12  C11  110.11  3.000
 BOD  H5   C11  H4   107.31  3.000
 BOD  H5   C11  N2   110.55  3.000
 BOD  H4   C11  N2   110.48  3.000
 BOD  H5   C11  C12  108.23  3.000
 BOD  H4   C11  C12  109.28  3.000
 BOD  N2   C11  C12  110.91  3.000
 BOD  C10  C9   N2   119.92  3.000
 BOD  C10  C9   C8   117.51  3.000
 BOD  N2   C9   C8   122.54  3.000
 BOD  C17  N5   C18  117.31  3.000
 BOD  H7   C13  H6   107.45  3.000
 BOD  H7   C13  C14  108.64  3.000
 BOD  H6   C13  C14  108.81  3.000
 BOD  H7   C13  N3   109.14  3.000
 BOD  H6   C13  N3   112.22  3.000
 BOD  C14  C13  N3   110.48  3.000
 BOD  H8   C8   C7   118.38  3.000
 BOD  H8   C8   C9   121.04  3.000
 BOD  C7   C8   C9   120.58  3.000
 BOD  H9   C6   C5   120.70  3.000
 BOD  H9   C6   C7   120.25  3.000
 BOD  C5   C6   C7   119.04  3.000
 BOD  H11  N7   H10  115.91  3.000
 BOD  H11  N7   C17  117.68  3.000
 BOD  H10  N7   C17  117.48  3.000
 BOD  H12  C4   C3   120.72  3.000
 BOD  H12  C4   N1   116.15  3.000
 BOD  C3   C4   N1   123.12  3.000
 BOD  C1   N1   C4   116.52  3.000
 BOD  H13  C2   N    116.29  3.000
 BOD  H13  C2   C3   120.40  3.000
 BOD  N    C2   C3   123.30  3.000
 BOD  C5   C3   C2   122.66  3.000
 BOD  C2   C3   C4   114.49  3.000
 BOD  C5   C3   C4   122.85  3.000
 BOD  C16  N4   C17  115.27  3.000
 BOD  H15  N6   H14  118.71  3.000
 BOD  H15  N6   C18  119.92  3.000
 BOD  H14  N6   C18  118.07  3.000
 BOD  N3   C15  C16  125.33  3.000
 BOD  C16  C15  C18  115.44  3.000
 BOD  N3   C15  C18  119.23  3.000
 BOD  C15  N3   C13  115.05  3.000
 BOD  C15  N3   C12  114.28  3.000
 BOD  C13  N3   C12  111.10  3.000
 BOD  H17  C14  H16  107.74  3.000
 BOD  H17  C14  N2   111.78  3.000
 BOD  H16  C14  N2   109.73  3.000
 BOD  H17  C14  C13  109.27  3.000
 BOD  H16  C14  C13  107.68  3.000
 BOD  N2   C14  C13  110.51  3.000
 BOD  C14  N2   C9   118.32  3.000
 BOD  C9   N2   C11  117.65  3.000
 BOD  C14  N2   C11  111.85  3.000
 BOD  H18  C7   C6   119.72  3.000
 BOD  H18  C7   C8   118.90  3.000
 BOD  C6   C7   C8   121.36  3.000
 BOD  H19  C10  C5   118.51  3.000
 BOD  H19  C10  C9   119.56  3.000
 BOD  C5   C10  C9   121.88  3.000
 BOD  C10  C5   C3   119.89  3.000
 BOD  C3   C5   C6   120.49  3.000
 BOD  C10  C5   C6   119.62  3.000
 BOD  C1   N    C2   116.30  3.000
 BOD  O    C1   N    114.05  3.000
 BOD  O    C1   N1   119.68  3.000
 BOD  N    C1   N1   126.26  3.000
 BOD  C    O    C1   118.50  3.000
 BOD  H22  C    H21  108.91  3.000
 BOD  H22  C    H20  109.38  3.000
 BOD  H21  C    H20  109.36  3.000
 BOD  H22  C    O    111.70  3.000
 BOD  H21  C    O    111.69  3.000
 BOD  H20  C    O    105.72  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
 BOD  CONST_01  N4   C16  C15  C18     0.00   0.0  0
 BOD  CONST_02  N4   C17  N5   C18     0.00   0.0  0
 BOD  CONST_03  C15  C18  N5   C17     0.00   0.0  0
 BOD  CONST_04  C15  C16  N4   C17     0.00   0.0  0
 BOD  CONST_05  N5   C18  C15  C16     0.00   0.0  0
 BOD  CONST_06  N5   C17  N4   C16     0.00   0.0  0
 BOD  CONST_07  C6   C7   C8   C9      0.00   0.0  0
 BOD  CONST_08  C6   C5   C10  C9      0.00   0.0  0
 BOD  CONST_09  C3   C5   C10  C9    180.00   0.0  0
 BOD  CONST_10  C5   C6   C7   C8      0.00   0.0  0
 BOD  CONST_11  C5   C10  C9   C8      0.00   0.0  0
 BOD  CONST_15  N    C2   C3   C4      0.00   0.0  0
 BOD  CONST_16  N    C1   N1   C4      0.00   0.0  0
 BOD  CONST_17  C5   C3   C4   N1    180.00   0.0  0
 BOD  CONST_18  C2   C3   C4   N1      0.00   0.0  0
 BOD  CONST_19  C2   N    C1   N1      0.00   0.0  0
 BOD  CONST_21  C7   C6   C5   C3    180.00   0.0  0
 BOD  CONST_22  C1   N    C2   C3      0.00   0.0  0
 BOD  CONST_23  C1   N1   C4   C3      0.00   0.0  0
 BOD  CONST_24  C10  C9   C8   C7      0.00   0.0  0
 BOD  CONST_25  C10  C5   C6   C7      0.00   0.0  0
 BOD  CONST_26  N    C2   C3   C5    180.00   0.0  0
 BOD  CONST_27  N3   C15  C18  N5    180.00   0.0  0
 BOD  CONST_28  N3   C15  C16  N4    180.00   0.0  0
 BOD  CONST_29  C7   C8   C9   N2    180.00   0.0  0
 BOD  CONST_30  C5   C10  C9   N2    180.00   0.0  0
 BOD  CONST_31  N7   C17  N5   C18   180.00   0.0  0
 BOD  CONST_32  N6   C18  N5   C17   180.00   0.0  0
 BOD  CONST_33  N6   C18  C15  C16   180.00   0.0  0
 BOD  CONST_34  N7   C17  N4   C16   180.00   0.0  0
 BOD  CONST_35  O    C1   N1   C4    180.00   0.0  0
 BOD  CONST_36  O    C1   N    C2    180.00   0.0  0
 BOD  CONST_37  N3   C15  C18  N6      0.00   0.0  0
 BOD  CONST_38  H1   C16  C15  C18   180.00   0.0  0
 BOD  CONST_39  H18  C7   C8   C9    180.00   0.0  0
 BOD  CONST_40  H9   C6   C7   C8    180.00   0.0  0
 BOD  CONST_41  H19  C10  C9   C8    180.00   0.0  0
 BOD  CONST_42  H8   C8   C7   C6    180.00   0.0  0
 BOD  CONST_43  H13  C2   C3   C4    180.00   0.0  0
 BOD  CONST_44  H12  C4   C3   C2    180.00   0.0  0
 BOD  CONST_45  H14  N6   C18  N5    180.00   0.0  0
 BOD  CONST_46  H15  N6   C18  N5      0.00   0.0  0
 BOD  Var_01    C13  N3   C15  C18  -121.15  30.0  2
 BOD  Var_02    C14  C13  N3   C12   -58.01  30.0  1
 BOD  Var_03    C14  N2   C11  C12    55.59  30.0  1
 BOD  Var_04    C13  C14  N2   C11   -55.39  30.0  1
 BOD  Var_05    C8   C9   N2   C11  -135.15  30.0  3
 BOD  Var_06    N2   C14  C13  N3     56.24  30.0  1
 BOD  Var_07    N2   C11  C12  N3    -56.01  30.0  1
 BOD  Var_08    H20  C    O    C1    179.85  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
 BOD  plan-1  C18  0.020
 BOD  plan-1  C17  0.020
 BOD  plan-1  C16  0.020
 BOD  plan-1  N5   0.020
 BOD  plan-1  N7   0.020
 BOD  plan-1  N4   0.020
 BOD  plan-1  N6   0.020
 BOD  plan-1  C15  0.020
 BOD  plan-1  N3   0.020
 BOD  plan-1  H1   0.020
 BOD  plan-2  C4   0.020
 BOD  plan-2  N1   0.020
 BOD  plan-2  C2   0.020
 BOD  plan-2  C3   0.020
 BOD  plan-2  C5   0.020
 BOD  plan-2  N    0.020
 BOD  plan-2  C1   0.020
 BOD  plan-2  O    0.020
 BOD  plan-2  H13  0.020
 BOD  plan-2  H12  0.020
 BOD  plan-3  C9   0.020
 BOD  plan-3  C8   0.020
 BOD  plan-3  C6   0.020
 BOD  plan-3  C3   0.020
 BOD  plan-3  N2   0.020
 BOD  plan-3  C7   0.020
 BOD  plan-3  C10  0.020
 BOD  plan-3  C5   0.020
 BOD  plan-3  H8   0.020
 BOD  plan-3  H9   0.020
 BOD  plan-3  H18  0.020
 BOD  plan-3  H19  0.020
 BOD  plan-4  C17  0.020
 BOD  plan-4  N7   0.020
 BOD  plan-4  H10  0.020
 BOD  plan-4  H11  0.020
 BOD  plan-5  C18  0.020
 BOD  plan-5  N6   0.020
 BOD  plan-5  H14  0.020
 BOD  plan-5  H15  0.020

