# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:03:08 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-(4-phenylpiperazin-1-yl)-6-propylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1nc(N)nc(N)c1N2CCN(CC2)c3ccccc3
#
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
 BOJ  BOJ  5-(4-phenylpiperazin-1-yl)-6-propylpyrimidine-2,4-diamine  ligand  47  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BOJ
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
 BOJ  C15  C  CR16  0  -0.245  -5.7594   0.1024   1.1349
 BOJ  C1   C  CH2   0  -0.428   2.1293  -2.7578   0.6147
 BOJ  C3   C  CR6   0   0.256   2.7905  -0.5529  -0.3804
 BOJ  C8   C  CH2   0  -0.300  -1.4839  -0.2893   1.0391
 BOJ  C4   C  CR6   0   0.066   1.9541   0.5185  -0.1061
 BOJ  C5   C  CR6   0   0.479   2.6007   1.7489   0.1645
 BOJ  C6   C  CR6   0   0.509   4.6232   0.7527  -0.0981
 BOJ  C7   C  CH2   0  -0.297  -0.1403   0.4017   1.1657
 BOJ  C9   C  CH2   0  -0.309  -1.5580   0.2545  -1.3034
 BOJ  N3   N  NH2   0  -0.831   1.9054   2.8800   0.3988
 BOJ  N    N  N     0  -0.510   3.9268   1.8541   0.1725
 BOJ  N2   N  NH2   0  -0.825   5.9738   0.8790  -0.1300
 BOJ  N1   N  N     0  -0.505   4.1223  -0.4480  -0.3779
 BOJ  C    C  CH3   0  -0.665   1.5787  -4.1491   0.3389
 BOJ  N4   N  NT    0  -0.515   0.5537   0.3510  -0.1021
 BOJ  C10  C  CH2   0  -0.286  -0.2077   0.9409  -1.1812
 BOJ  N5   N  NT    0  -0.518  -2.2628   0.3053  -0.0390
 BOJ  C11  C  CR6   0   0.360  -3.6375   0.0607  -0.0416
 BOJ  C16  C  CR16  0  -0.325  -4.3907   0.3031   1.1175
 BOJ  C14  C  CR16  0  -0.288  -6.4304  -0.3360  -0.0021
 BOJ  C13  C  CR16  0  -0.243  -5.6979  -0.5743  -1.1538
 BOJ  C12  C  CR16  0  -0.357  -4.3205  -0.3893  -1.1773
 BOJ  H1   H  HCR6  0   0.251  -6.3101   0.3071   2.0445
 BOJ  H2   H  HCH2  0   0.223   3.1153  -2.8322   1.0812
 BOJ  H3   H  HCH2  0   0.227   1.4857  -2.2442   1.3337
 BOJ  H4   H  HCH2  0   0.231   2.8941  -2.4229  -1.3698
 BOJ  H5   H  HCH2  0   0.239   1.2475  -1.8352  -1.1148
 BOJ  H6   H  HCH2  0   0.215  -1.3220  -1.3621   0.8532
 BOJ  H7   H  HCH2  0   0.253  -2.0164  -0.1986   1.9840
 BOJ  H8   H  HCH2  0   0.198  -0.3147   1.4289   1.5287
 BOJ  H9   H  HCH2  0   0.247   0.4539  -0.1119   1.9228
 BOJ  H10  H  HCH2  0   0.250  -2.1382   0.7772  -2.0646
 BOJ  H11  H  HCH2  0   0.212  -1.4079  -0.7799  -1.6494
 BOJ  H12  H  HNH2  0   0.403   0.9217   2.8492   0.5957
 BOJ  H13  H  HNH2  0   0.392   2.4048   3.6797   0.7492
 BOJ  H14  H  HNH2  0   0.385   6.3767   1.6887   0.3095
 BOJ  H15  H  HNH2  0   0.386   6.5183   0.0356  -0.0741
 BOJ  H16  H  HCH3  0   0.218   0.5770  -4.0970  -0.0921
 BOJ  H17  H  HCH3  0   0.219   2.2130  -4.6928  -0.3635
 BOJ  H18  H  HCH3  0   0.230   1.5145  -4.7391   1.2536
 BOJ  H19  H  HCH2  0   0.247   0.3382   0.8104  -2.1166
 BOJ  H20  H  HCH2  0   0.200  -0.3762   2.0219  -1.0504
 BOJ  H21  H  HCR6  0   0.258  -3.9051   0.6774   2.0094
 BOJ  H22  H  HCR6  0   0.248  -7.5021  -0.4834   0.0127
 BOJ  H23  H  HCR6  0   0.252  -6.1945  -0.9228  -2.0508
 BOJ  H24  H  HCR6  0   0.265  -3.7862  -0.6124  -2.0908
 BOJ  C2   C  CH2   0  -0.474   2.2352  -1.9169  -0.6599

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
 BOJ  C9   C10  single    1.520  0.020  1.520
 BOJ  C9   N5   single    1.449  0.020  1.449
 BOJ  C12  C13  aromatic  1.390  0.020  1.390
 BOJ  C12  C11  aromatic  1.400  0.020  1.400
 BOJ  C13  C14  aromatic  1.386  0.020  1.386
 BOJ  C10  N4   single    1.446  0.020  1.446
 BOJ  N5   C11  single    1.396  0.020  1.396
 BOJ  N5   C8   single    1.457  0.020  1.457
 BOJ  C11  C16  aromatic  1.403  0.020  1.403
 BOJ  C14  C15  aromatic  1.391  0.020  1.391
 BOJ  C8   C7   single    1.516  0.020  1.516
 BOJ  C16  C15  aromatic  1.383  0.020  1.383
 BOJ  N4   C7   single    1.446  0.020  1.446
 BOJ  N4   C4   single    1.410  0.020  1.410
 BOJ  N3   C5   single    1.348  0.020  1.348
 BOJ  C4   C5   aromatic  1.416  0.020  1.416
 BOJ  C4   C3   aromatic  1.387  0.020  1.387
 BOJ  C5   N    aromatic  1.330  0.020  1.330
 BOJ  C2   C3   single    1.499  0.020  1.499
 BOJ  C2   C1   single    1.531  0.020  1.531
 BOJ  C3   N1   aromatic  1.336  0.020  1.336
 BOJ  N    C6   aromatic  1.331  0.020  1.331
 BOJ  C1   C    single    1.522  0.020  1.522
 BOJ  N1   C6   aromatic  1.331  0.020  1.331
 BOJ  C6   N2   single    1.357  0.020  1.357
 BOJ  C15  H1   single    0.930  0.020  1.080
 BOJ  C1   H2   single    0.970  0.020  1.090
 BOJ  C1   H3   single    0.970  0.020  1.090
 BOJ  C2   H4   single    0.970  0.020  1.090
 BOJ  C2   H5   single    0.970  0.020  1.090
 BOJ  C8   H6   single    0.970  0.020  1.090
 BOJ  C8   H7   single    0.970  0.020  1.090
 BOJ  C7   H8   single    0.970  0.020  1.090
 BOJ  C7   H9   single    0.970  0.020  1.090
 BOJ  C9   H10  single    0.970  0.020  1.090
 BOJ  C9   H11  single    0.970  0.020  1.090
 BOJ  N3   H12  single    0.890  0.020  1.040
 BOJ  N3   H13  single    0.890  0.020  1.040
 BOJ  N2   H14  single    0.890  0.020  1.040
 BOJ  N2   H15  single    0.890  0.020  1.040
 BOJ  C    H16  single    0.970  0.020  1.090
 BOJ  C    H17  single    0.970  0.020  1.090
 BOJ  C    H18  single    0.970  0.020  1.090
 BOJ  C10  H19  single    0.970  0.020  1.090
 BOJ  C10  H20  single    0.970  0.020  1.090
 BOJ  C16  H21  single    0.930  0.020  1.080
 BOJ  C14  H22  single    0.930  0.020  1.080
 BOJ  C13  H23  single    0.930  0.020  1.080
 BOJ  C12  H24  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
 BOJ  H1   C15  C14  120.06  3.000
 BOJ  H1   C15  C16  119.09  3.000
 BOJ  C14  C15  C16  120.84  3.000
 BOJ  H3   C1   H2   106.40  3.000
 BOJ  H3   C1   C    109.62  3.000
 BOJ  H2   C1   C    109.96  3.000
 BOJ  H3   C1   C2   109.29  3.000
 BOJ  H2   C1   C2   109.29  3.000
 BOJ  C    C1   C2   112.11  3.000
 BOJ  N1   C3   C4   122.70  3.000
 BOJ  N1   C3   C2   116.18  3.000
 BOJ  C4   C3   C2   121.10  3.000
 BOJ  H7   C8   H6   107.45  3.000
 BOJ  H7   C8   N5   110.29  3.000
 BOJ  H6   C8   N5   110.57  3.000
 BOJ  H7   C8   C7   108.85  3.000
 BOJ  H6   C8   C7   109.14  3.000
 BOJ  N5   C8   C7   110.46  3.000
 BOJ  N4   C4   C5   123.78  3.000
 BOJ  C5   C4   C3   115.71  3.000
 BOJ  N4   C4   C3   120.51  3.000
 BOJ  N    C5   N3   116.53  3.000
 BOJ  N    C5   C4   121.67  3.000
 BOJ  N3   C5   C4   121.78  3.000
 BOJ  N1   C6   N2   116.99  3.000
 BOJ  N2   C6   N    116.65  3.000
 BOJ  N1   C6   N    126.33  3.000
 BOJ  H9   C7   H8   107.22  3.000
 BOJ  H9   C7   N4   109.30  3.000
 BOJ  H8   C7   N4   113.39  3.000
 BOJ  H9   C7   C8   109.03  3.000
 BOJ  H8   C7   C8   108.16  3.000
 BOJ  N4   C7   C8   109.64  3.000
 BOJ  H11  C9   H10  107.66  3.000
 BOJ  H11  C9   N5   111.93  3.000
 BOJ  H10  C9   N5   109.49  3.000
 BOJ  H11  C9   C10  109.18  3.000
 BOJ  H10  C9   C10  108.21  3.000
 BOJ  N5   C9   C10  110.26  3.000
 BOJ  H13  N3   H12  116.27  3.000
 BOJ  H13  N3   C5   118.14  3.000
 BOJ  H12  N3   C5   120.92  3.000
 BOJ  C6   N    C5   117.06  3.000
 BOJ  H15  N2   H14  115.74  3.000
 BOJ  H15  N2   C6   117.36  3.000
 BOJ  H14  N2   C6   117.62  3.000
 BOJ  C6   N1   C3   116.52  3.000
 BOJ  H18  C    H17  107.73  3.000
 BOJ  H18  C    H16  107.63  3.000
 BOJ  H17  C    H16  107.64  3.000
 BOJ  H18  C    C1   111.35  3.000
 BOJ  H17  C    C1   111.22  3.000
 BOJ  H16  C    C1   111.10  3.000
 BOJ  C10  N4   C7   112.77  3.000
 BOJ  C7   N4   C4   118.35  3.000
 BOJ  C10  N4   C4   118.17  3.000
 BOJ  H20  C10  H19  107.20  3.000
 BOJ  H20  C10  N4   113.08  3.000
 BOJ  H19  C10  N4   109.11  3.000
 BOJ  H20  C10  C9   108.47  3.000
 BOJ  H19  C10  C9   108.77  3.000
 BOJ  N4   C10  C9   110.09  3.000
 BOJ  C11  N5   C9   118.12  3.000
 BOJ  C11  N5   C8   117.15  3.000
 BOJ  C9   N5   C8   111.81  3.000
 BOJ  C12  C11  C16  117.64  3.000
 BOJ  C16  C11  N5   119.77  3.000
 BOJ  C12  C11  N5   122.57  3.000
 BOJ  H21  C16  C11  119.97  3.000
 BOJ  H21  C16  C15  118.93  3.000
 BOJ  C11  C16  C15  121.08  3.000
 BOJ  H22  C14  C13  120.77  3.000
 BOJ  H22  C14  C15  120.63  3.000
 BOJ  C13  C14  C15  118.59  3.000
 BOJ  H23  C13  C12  118.90  3.000
 BOJ  H23  C13  C14  120.10  3.000
 BOJ  C12  C13  C14  121.00  3.000
 BOJ  H24  C12  C13  118.44  3.000
 BOJ  H24  C12  C11  120.71  3.000
 BOJ  C13  C12  C11  120.84  3.000
 BOJ  H5   C2   H4   108.06  3.000
 BOJ  H5   C2   C3   110.19  3.000
 BOJ  H4   C2   C3   108.61  3.000
 BOJ  H5   C2   C1   109.02  3.000
 BOJ  H4   C2   C1   109.16  3.000
 BOJ  C3   C2   C1   111.73  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
 BOJ  CONST_01  C12  C13  C14  C15     0.00   0.0  0
 BOJ  CONST_02  C12  C11  C16  C15     0.00   0.0  0
 BOJ  CONST_03  N    C5   C4   C3      0.00   0.0  0
 BOJ  CONST_04  N    C6   N1   C3      0.00   0.0  0
 BOJ  CONST_05  C6   N    C5   C4      0.00   0.0  0
 BOJ  CONST_06  C6   N1   C3   C4      0.00   0.0  0
 BOJ  CONST_07  N1   C3   C4   C5      0.00   0.0  0
 BOJ  CONST_08  N1   C6   N    C5      0.00   0.0  0
 BOJ  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 BOJ  CONST_10  C14  C15  C16  C11     0.00   0.0  0
 BOJ  CONST_11  C13  C12  C11  C16     0.00   0.0  0
 BOJ  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 BOJ  CONST_13  N5   C11  C16  C15   180.00   0.0  0
 BOJ  CONST_14  N4   C4   C5   N     180.00   0.0  0
 BOJ  CONST_15  N4   C4   C3   N1    180.00   0.0  0
 BOJ  CONST_16  C13  C12  C11  N5    180.00   0.0  0
 BOJ  CONST_17  N4   C4   C3   C2      0.00   0.0  0
 BOJ  CONST_18  C5   C4   C3   C2    180.00   0.0  0
 BOJ  CONST_19  C6   N1   C3   C2    180.00   0.0  0
 BOJ  CONST_20  N3   C5   C4   C3    180.00   0.0  0
 BOJ  CONST_21  N2   C6   N1   C3    180.00   0.0  0
 BOJ  CONST_22  N2   C6   N    C5    180.00   0.0  0
 BOJ  CONST_23  N3   C5   N    C6    180.00   0.0  0
 BOJ  CONST_24  N4   C4   C5   N3      0.00   0.0  0
 BOJ  CONST_25  H23  C13  C14  C15   180.00   0.0  0
 BOJ  CONST_26  H24  C12  C11  N5      0.00   0.0  0
 BOJ  CONST_27  H21  C16  C11  N5      0.00   0.0  0
 BOJ  CONST_28  H1   C15  C16  C11   180.00   0.0  0
 BOJ  CONST_29  H22  C14  C15  C16   180.00   0.0  0
 BOJ  CONST_30  H12  N3   C5   C4      0.00   0.0  0
 BOJ  CONST_31  H13  N3   C5   C4    180.00   0.0  0
 BOJ  Var_01    C10  N4   C4   C3   -108.85  30.0  2
 BOJ  Var_02    C10  C9   N5   C8    -56.64  30.0  1
 BOJ  Var_03    C12  C11  N5   C8   -130.25  30.0  2
 BOJ  Var_04    C9   C10  N4   C4    159.11  30.0  1
 BOJ  Var_05    C9   N5   C8   C7     57.12  30.0  1
 BOJ  Var_06    N5   C9   C10  N4     55.44  30.0  1
 BOJ  Var_07    N5   C8   C7   N4    -55.85  30.0  1
 BOJ  Var_08    C4   C3   C2   C1    -91.93  30.0  2
 BOJ  Var_09    C    C1   C2   C3   -179.46  30.0  3
 BOJ  Var_10    H16  C    C1   C2    -60.40  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
 BOJ  plan-1  C3   0.020
 BOJ  plan-1  C4   0.020
 BOJ  plan-1  C5   0.020
 BOJ  plan-1  C6   0.020
 BOJ  plan-1  N3   0.020
 BOJ  plan-1  N    0.020
 BOJ  plan-1  N2   0.020
 BOJ  plan-1  N1   0.020
 BOJ  plan-1  N4   0.020
 BOJ  plan-1  C2   0.020
 BOJ  plan-2  C15  0.020
 BOJ  plan-2  N5   0.020
 BOJ  plan-2  C11  0.020
 BOJ  plan-2  C16  0.020
 BOJ  plan-2  C14  0.020
 BOJ  plan-2  C13  0.020
 BOJ  plan-2  C12  0.020
 BOJ  plan-2  H1   0.020
 BOJ  plan-2  H21  0.020
 BOJ  plan-2  H22  0.020
 BOJ  plan-2  H23  0.020
 BOJ  plan-2  H24  0.020
 BOJ  plan-3  C5   0.020
 BOJ  plan-3  N3   0.020
 BOJ  plan-3  H12  0.020
 BOJ  plan-3  H13  0.020
 BOJ  plan-4  C6   0.020
 BOJ  plan-4  N2   0.020
 BOJ  plan-4  H14  0.020
 BOJ  plan-4  H15  0.020

