# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:43:04 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-azanyl-2-butoxy-8-[[3-(pyrrolidin-1-ylmethyl)phenyl]methyl]-5,7-dihydropteridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCOc1nc(N)c2NC(=O)CN(Cc3cccc(CN4CCCC4)c3)c2n1
#
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
 9JR  9JR  4-azanyl-2-butoxy-8-[[3-(pyrrolidin-1-ylmethyl)phenyl]methyl]-5,7-dihydropteridin-6-one  ligand  60  30  .  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_9JR
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
 9JR  N    N  NT    0  -0.494   0.2898  -1.8104  -0.6031
 9JR  C    C  CR6   0   0.551   1.5652  -1.5836  -0.1986
 9JR  O    O  O     0  -0.471  -0.3125  -5.0703   0.6521
 9JR  C1   C  CR6   0   0.106   2.1974  -2.5755   0.5550
 9JR  C10  C  CH2   0  -0.421  -0.4417  -0.8466  -1.4064
 9JR  C11  C  CR6   0   0.142  -1.2914   0.0906  -0.5824
 9JR  C12  C  CR16  0  -0.299  -2.8878   1.7661   0.9748
 9JR  C13  C  CR6   0   0.113  -3.4602   0.6579   0.3566
 9JR  C14  C  CR16  0  -0.229  -1.5356   2.0350   0.8170
 9JR  C15  C  CR16  0  -0.372  -2.6512  -0.1611  -0.4230
 9JR  C16  C  CR16  0  -0.316  -0.7359   1.2010   0.0466
 9JR  C17  C  CH2   0  -0.324  -4.9177   0.3294   0.5491
 9JR  C18  C  CH2   0  -0.275  -7.1599   1.2129   0.7561
 9JR  C19  C  CH2   0  -0.466  -7.8993   2.4614   0.2739
 9JR  C2   C  CH2   0  -0.416  -0.5112  -2.7284   0.1825
 9JR  C20  C  CH2   0  -0.272  -5.8192   2.0549  -0.9124
 9JR  C21  C  CH2   0  -0.464  -7.0001   3.0254  -0.8478
 9JR  C3   C  C     0   0.499   0.2425  -3.9913   0.5421
 9JR  C4   C  CR6   0   0.580   3.4240  -0.3234  -0.0881
 9JR  C5   C  CR6   0   0.444   3.4771  -2.2941   1.0213
 9JR  C6   C  CH2   0  -0.148   5.3380   1.0825  -0.0465
 9JR  C7   C  CH2   0  -0.456   5.7186   2.4569  -0.5555
 9JR  C8   C  CH2   0  -0.430   7.1450   2.8216  -0.1592
 9JR  C9   C  CH3   0  -0.660   7.5443   4.2134  -0.6289
 9JR  N1   N  NH1   0  -0.714   1.5586  -3.8069   0.7571
 9JR  N2   N  N     0  -0.520   2.1863  -0.4562  -0.5340
 9JR  N3   N  N     0  -0.523   4.0929  -1.1534   0.6810
 9JR  N4   N  NH2   0  -0.831   4.1788  -3.1750   1.7749
 9JR  N5   N  NR5   0  -0.423  -5.7730   1.4829   0.4219
 9JR  O1   O  O2    0  -0.461   4.0039   0.8098  -0.4731
 9JR  H1   H  HCH2  0   0.281   0.2753  -0.2909  -2.0069
 9JR  H2   H  HCH2  0   0.275  -1.0782  -1.4094  -2.0937
 9JR  H3   H  HCR6  0   0.245  -3.5081   2.4246   1.5703
 9JR  H4   H  HCR6  0   0.251  -1.1008   2.9034   1.2956
 9JR  H5   H  HCR6  0   0.244  -3.0940  -1.0164  -0.9238
 9JR  H6   H  HCR6  0   0.256   0.3188   1.4133  -0.0737
 9JR  H7   H  HCH2  0   0.206  -5.2035  -0.4736  -0.1528
 9JR  H8   H  HCH2  0   0.250  -5.0561  -0.0842   1.5536
 9JR  H9   H  HCH2  0   0.233  -7.2751   1.0266   1.8262
 9JR  H10  H  HCH2  0   0.190  -7.5360   0.3211   0.2267
 9JR  H11  H  HCH2  0   0.233  -8.9022   2.2184  -0.0752
 9JR  H12  H  HCH2  0   0.234  -8.0061   3.1844   1.0830
 9JR  H13  H  HCH2  0   0.276  -0.8747  -2.2633   1.1097
 9JR  H14  H  HCH2  0   0.284  -1.3882  -3.0167  -0.3958
 9JR  H15  H  HCH2  0   0.191  -6.0015   1.2791  -1.6762
 9JR  H16  H  HCH2  0   0.234  -4.8770   2.5428  -1.1681
 9JR  H17  H  HCH2  0   0.233  -7.5149   3.0880  -1.8061
 9JR  H18  H  HCH2  0   0.234  -6.6592   4.0308  -0.5999
 9JR  H19  H  HCH2  0   0.220   6.0195   0.3218  -0.4387
 9JR  H20  H  HCH2  0   0.221   5.4004   1.0464   1.0445
 9JR  H21  H  HCH2  0   0.226   5.6226   2.4874  -1.6451
 9JR  H22  H  HCH2  0   0.226   5.0249   3.2012  -0.1529
 9JR  H23  H  HCH2  0   0.219   7.2494   2.7609   0.9281
 9JR  H24  H  HCH2  0   0.219   7.8383   2.0836  -0.5735
 9JR  H25  H  HCH3  0   0.219   6.9003   4.9781  -0.1915
 9JR  H26  H  HCH3  0   0.229   8.5717   4.4459  -0.3480
 9JR  H27  H  HCH3  0   0.219   7.4707   4.3014  -1.7142
 9JR  H28  H  HNH1  0   0.408   2.1189  -4.6298   0.9328
 9JR  H29  H  HNH2  0   0.398   3.6795  -3.8258   2.3590
 9JR  H30  H  HNH2  0   0.396   5.0289  -2.8247   2.1859

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
 9JR  O1   C6   single    1.427  0.020  1.427
 9JR  O1   C4   single    1.330  0.020  1.330
 9JR  C6   C7   single    1.514  0.020  1.514
 9JR  C14  C12  aromatic  1.388  0.020  1.388
 9JR  C14  C16  aromatic  1.389  0.020  1.389
 9JR  C18  C19  single    1.529  0.020  1.529
 9JR  C18  N5   single    1.452  0.020  1.452
 9JR  C12  C13  aromatic  1.392  0.020  1.392
 9JR  C19  C21  single    1.544  0.020  1.544
 9JR  N5   C17  single    1.442  0.020  1.442
 9JR  N5   C20  single    1.452  0.020  1.452
 9JR  C4   N3   aromatic  1.314  0.020  1.314
 9JR  C4   N2   aromatic  1.322  0.020  1.322
 9JR  N3   C5   aromatic  1.340  0.020  1.340
 9JR  C8   C7   single    1.525  0.020  1.525
 9JR  C8   C9   single    1.522  0.020  1.522
 9JR  C21  C20  single    1.530  0.020  1.530
 9JR  C16  C11  aromatic  1.392  0.020  1.392
 9JR  C13  C17  single    1.506  0.020  1.506
 9JR  C13  C15  aromatic  1.390  0.020  1.390
 9JR  N4   C5   single    1.355  0.020  1.355
 9JR  N2   C    aromatic  1.330  0.020  1.330
 9JR  C5   C1   aromatic  1.391  0.020  1.391
 9JR  C11  C15  aromatic  1.392  0.020  1.392
 9JR  C11  C10  single    1.510  0.020  1.510
 9JR  C    C1   aromatic  1.397  0.020  1.397
 9JR  C    N    single    1.357  0.020  1.357
 9JR  C1   N1   single    1.402  0.020  1.402
 9JR  C10  N    single    1.452  0.020  1.452
 9JR  N    C2   single    1.450  0.020  1.450
 9JR  N1   C3   single    1.346  0.020  1.346
 9JR  C3   C2   single    1.514  0.020  1.514
 9JR  C3   O    double    1.218  0.020  1.218
 9JR  C10  H1   single    0.970  0.020  1.090
 9JR  C10  H2   single    0.970  0.020  1.090
 9JR  C12  H3   single    0.930  0.020  1.080
 9JR  C14  H4   single    0.930  0.020  1.080
 9JR  C15  H5   single    0.930  0.020  1.080
 9JR  C16  H6   single    0.930  0.020  1.080
 9JR  C17  H7   single    0.970  0.020  1.090
 9JR  C17  H8   single    0.970  0.020  1.090
 9JR  C18  H9   single    0.970  0.020  1.090
 9JR  C18  H10  single    0.970  0.020  1.090
 9JR  C19  H11  single    0.970  0.020  1.090
 9JR  C19  H12  single    0.970  0.020  1.090
 9JR  C2   H13  single    0.970  0.020  1.090
 9JR  C2   H14  single    0.970  0.020  1.090
 9JR  C20  H15  single    0.970  0.020  1.090
 9JR  C20  H16  single    0.970  0.020  1.090
 9JR  C21  H17  single    0.970  0.020  1.090
 9JR  C21  H18  single    0.970  0.020  1.090
 9JR  C6   H19  single    0.970  0.020  1.090
 9JR  C6   H20  single    0.970  0.020  1.090
 9JR  C7   H21  single    0.970  0.020  1.090
 9JR  C7   H22  single    0.970  0.020  1.090
 9JR  C8   H23  single    0.970  0.020  1.090
 9JR  C8   H24  single    0.970  0.020  1.090
 9JR  C9   H25  single    0.970  0.020  1.090
 9JR  C9   H26  single    0.970  0.020  1.090
 9JR  C9   H27  single    0.970  0.020  1.090
 9JR  N1   H28  single    0.860  0.020  1.020
 9JR  N4   H29  single    0.890  0.020  1.040
 9JR  N4   H30  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
 9JR  C2   N    C10  116.21  3.000
 9JR  C2   N    C    117.62  3.000
 9JR  C10  N    C    121.82  3.000
 9JR  N2   C    C1   121.77  3.000
 9JR  C1   C    N    117.87  3.000
 9JR  N2   C    N    120.36  3.000
 9JR  N1   C1   C5   123.28  3.000
 9JR  N1   C1   C    119.68  3.000
 9JR  C5   C1   C    116.98  3.000
 9JR  H2   C10  H1   107.44  3.000
 9JR  H2   C10  C11  109.58  3.000
 9JR  H1   C10  C11  110.80  3.000
 9JR  H2   C10  N    107.43  3.000
 9JR  H1   C10  N    108.20  3.000
 9JR  C11  C10  N    113.17  3.000
 9JR  C16  C11  C15  118.84  3.000
 9JR  C15  C11  C10  120.00  3.000
 9JR  C16  C11  C10  121.15  3.000
 9JR  H3   C12  C14  120.19  3.000
 9JR  H3   C12  C13  119.52  3.000
 9JR  C14  C12  C13  120.29  3.000
 9JR  C17  C13  C15  120.41  3.000
 9JR  C15  C13  C12  118.60  3.000
 9JR  C17  C13  C12  120.98  3.000
 9JR  H4   C14  C16  119.72  3.000
 9JR  H4   C14  C12  119.77  3.000
 9JR  C16  C14  C12  120.52  3.000
 9JR  H5   C15  C13  119.04  3.000
 9JR  H5   C15  C11  119.21  3.000
 9JR  C13  C15  C11  121.74  3.000
 9JR  H6   C16  C14  120.32  3.000
 9JR  H6   C16  C11  119.67  3.000
 9JR  C14  C16  C11  120.00  3.000
 9JR  H8   C17  H7   106.01  3.000
 9JR  H8   C17  N5   107.94  3.000
 9JR  H7   C17  N5   111.85  3.000
 9JR  H8   C17  C13  108.78  3.000
 9JR  H7   C17  C13  109.14  3.000
 9JR  N5   C17  C13  112.84  3.000
 9JR  H10  C18  H9   107.24  3.000
 9JR  H10  C18  N5   111.44  3.000
 9JR  H9   C18  N5   110.98  3.000
 9JR  H10  C18  C19  110.11  3.000
 9JR  H9   C18  C19  113.40  3.000
 9JR  N5   C18  C19  103.74  3.000
 9JR  H12  C19  H11  107.18  3.000
 9JR  H12  C19  C21  110.73  3.000
 9JR  H11  C19  C21  112.63  3.000
 9JR  H12  C19  C18  110.78  3.000
 9JR  H11  C19  C18  111.35  3.000
 9JR  C21  C19  C18  104.23  3.000
 9JR  H14  C2   H13  107.07  3.000
 9JR  H14  C2   C3   107.83  3.000
 9JR  H13  C2   C3   108.50  3.000
 9JR  H14  C2   N    108.95  3.000
 9JR  H13  C2   N    111.83  3.000
 9JR  C3   C2   N    112.45  3.000
 9JR  H16  C20  H15  107.13  3.000
 9JR  H16  C20  N5   111.33  3.000
 9JR  H15  C20  N5   111.36  3.000
 9JR  H16  C20  C21  113.12  3.000
 9JR  H15  C20  C21  110.34  3.000
 9JR  N5   C20  C21  103.63  3.000
 9JR  H18  C21  H17  107.14  3.000
 9JR  H18  C21  C20  110.69  3.000
 9JR  H17  C21  C20  111.35  3.000
 9JR  H18  C21  C19  110.71  3.000
 9JR  H17  C21  C19  112.62  3.000
 9JR  C20  C21  C19  104.38  3.000
 9JR  N1   C3   C2   114.23  3.000
 9JR  C2   C3   O    122.24  3.000
 9JR  N1   C3   O    123.52  3.000
 9JR  O1   C4   N3   119.05  3.000
 9JR  N3   C4   N2   127.61  3.000
 9JR  O1   C4   N2   113.34  3.000
 9JR  N4   C5   N3   117.16  3.000
 9JR  N4   C5   C1   122.11  3.000
 9JR  N3   C5   C1   120.65  3.000
 9JR  H20  C6   H19  107.41  3.000
 9JR  H20  C6   O1   110.20  3.000
 9JR  H19  C6   O1   110.02  3.000
 9JR  H20  C6   C7   110.56  3.000
 9JR  H19  C6   C7   110.74  3.000
 9JR  O1   C6   C7   107.93  3.000
 9JR  H22  C7   H21  106.97  3.000
 9JR  H22  C7   C8   109.56  3.000
 9JR  H21  C7   C8   109.52  3.000
 9JR  H22  C7   C6   109.53  3.000
 9JR  H21  C7   C6   109.76  3.000
 9JR  C8   C7   C6   111.40  3.000
 9JR  H24  C8   H23  106.17  3.000
 9JR  H24  C8   C9   109.49  3.000
 9JR  H23  C8   C9   109.41  3.000
 9JR  H24  C8   C7   109.46  3.000
 9JR  H23  C8   C7   109.53  3.000
 9JR  C9   C8   C7   112.57  3.000
 9JR  H27  C9   H26  107.61  3.000
 9JR  H27  C9   H25  107.59  3.000
 9JR  H26  C9   H25  107.66  3.000
 9JR  H27  C9   C8   111.27  3.000
 9JR  H26  C9   C8   111.27  3.000
 9JR  H25  C9   C8   111.24  3.000
 9JR  H28  N1   C3   117.27  3.000
 9JR  H28  N1   C1   119.17  3.000
 9JR  C3   N1   C1   122.87  3.000
 9JR  C4   N2   C    115.93  3.000
 9JR  C5   N3   C4   116.88  3.000
 9JR  H30  N4   H29  113.99  3.000
 9JR  H30  N4   C5   115.97  3.000
 9JR  H29  N4   C5   119.07  3.000
 9JR  C20  N5   C18  104.73  3.000
 9JR  C20  N5   C17  114.52  3.000
 9JR  C18  N5   C17  113.43  3.000
 9JR  C6   O1   C4   118.94  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
 9JR  CONST_01  N3   C4   N2   C       0.00   0.0  0
 9JR  CONST_02  N3   C5   C1   C       0.00   0.0  0
 9JR  CONST_03  C4   N3   C5   C1      0.00   0.0  0
 9JR  CONST_04  C4   N2   C    C1      0.00   0.0  0
 9JR  CONST_05  C12  C14  C16  C11     0.00   0.0  0
 9JR  CONST_06  C12  C13  C15  C11     0.00   0.0  0
 9JR  CONST_07  C16  C14  C12  C13     0.00   0.0  0
 9JR  CONST_08  C16  C11  C15  C13     0.00   0.0  0
 9JR  CONST_09  C15  C13  C12  C14     0.00   0.0  0
 9JR  CONST_10  C15  C11  C16  C14     0.00   0.0  0
 9JR  CONST_11  N2   C4   N3   C5      0.00   0.0  0
 9JR  CONST_12  N2   C    C1   C5      0.00   0.0  0
 9JR  CONST_13  C2   C3   N1   C1      0.00   0.0  0
 9JR  CONST_14  O1   C4   N2   C     180.00   0.0  0
 9JR  CONST_15  N4   C5   C1   C     180.00   0.0  0
 9JR  CONST_16  C14  C16  C11  C10   180.00   0.0  0
 9JR  CONST_17  C13  C15  C11  C10   180.00   0.0  0
 9JR  CONST_18  C17  C13  C15  C11   180.00   0.0  0
 9JR  CONST_19  C17  C13  C12  C14   180.00   0.0  0
 9JR  CONST_20  N4   C5   N3   C4    180.00   0.0  0
 9JR  CONST_21  O1   C4   N3   C5    180.00   0.0  0
 9JR  CONST_22  N4   C5   C1   N1      0.00   0.0  0
 9JR  CONST_23  C1   N1   C3   O     180.00   0.0  0
 9JR  CONST_24  H4   C14  C16  C11   180.00   0.0  0
 9JR  CONST_25  H6   C16  C14  C12   180.00   0.0  0
 9JR  CONST_26  H5   C15  C13  C12   180.00   0.0  0
 9JR  CONST_27  H3   C12  C13  C15   180.00   0.0  0
 9JR  CONST_28  H28  N1   C3   C2    180.00   0.0  0
 9JR  CONST_30  H30  N4   C5   C1    180.00   0.0  0
 9JR  Var_01    N1   C3   C2   N      34.20  30.0  1
 9JR  Var_02    C3   N1   C1   C     -16.35  30.0  1
 9JR  Var_03    C3   C2   N    C     -45.28  30.0  1
 9JR  Var_04    C2   N    C    C1     25.22  30.0  1
 9JR  Var_05    C20  C21  C19  C18    -0.13  30.0  1
 9JR  Var_06    C21  C20  N5   C18    42.86  30.0  1
 9JR  Var_07    C20  N5   C18  C19   -43.00  30.0  1
 9JR  Var_08    N5   C20  C21  C19   -25.30  30.0  1
 9JR  Var_09    N5   C18  C19  C21    25.53  30.0  1
 9JR  Var_10    C16  C11  C10  N      80.85  30.0  2
 9JR  Var_11    C11  C10  N    C     -94.04  30.0  1
 9JR  Var_12    N5   C17  C13  C12    45.52  30.0  2
 9JR  Var_13    C18  N5   C17  C13  -173.30  30.0  2
 9JR  Var_14    N3   C4   O1   C6      0.48  30.0  2
 9JR  Var_15    C7   C6   O1   C4   -176.81  30.0  3
 9JR  Var_16    C9   C8   C7   C6   -178.61  30.0  2
 9JR  Var_17    O1   C6   C7   C8   -179.17  30.0  2
 9JR  Var_18    H25  C9   C8   C7     60.83  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
 9JR  plan-1  C10  0.020
 9JR  plan-1  C11  0.020
 9JR  plan-1  C12  0.020
 9JR  plan-1  C13  0.020
 9JR  plan-1  C14  0.020
 9JR  plan-1  C15  0.020
 9JR  plan-1  C16  0.020
 9JR  plan-1  C17  0.020
 9JR  plan-1  H3   0.020
 9JR  plan-1  H4   0.020
 9JR  plan-1  H5   0.020
 9JR  plan-1  H6   0.020
 9JR  plan-2  C5   0.020
 9JR  plan-2  N4   0.020
 9JR  plan-2  H29  0.020
 9JR  plan-2  H30  0.020
 9JR  plan-3  N    0.020
 9JR  plan-3  C    0.020
 9JR  plan-3  C1   0.020
 9JR  plan-3  C4   0.020
 9JR  plan-3  C5   0.020
 9JR  plan-3  N1   0.020
 9JR  plan-3  N2   0.020
 9JR  plan-3  N3   0.020
 9JR  plan-3  N4   0.020
 9JR  plan-3  O1   0.020
 9JR  plan-4  O    0.020
 9JR  plan-4  C1   0.020
 9JR  plan-4  C2   0.020
 9JR  plan-4  C3   0.020
 9JR  plan-4  N1   0.020
 9JR  plan-4  H28  0.020

