# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:57:28 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-chloro-4-{[2-{[(1R)-1-(hydroxymethyl)-2-methylpropyl]amino}-9-(1-methylethyl)-9H-purin-6-yl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](CO)Nc1nc(Nc2ccc(C(O)=O)c(Cl)c2)c3ncn(C(C)C)c3n1
#
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
 PVB  PVB  '2-chloro-4-{[2-{[(1R)-1-(hydroxymethyl)-2-methylpropyl]amino}-9-(1-methylethyl)-9H-purin-6-yl]amino}benzoic acid'  ligand  54  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PVB
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
 PVB  N1    N   N      0  -0.554  -0.3321   0.0187   0.0584
 PVB  C9    C   CH1    0  -0.136  -5.1130   1.7852  -0.4855
 PVB  N9    N   NR5    0  -0.500  -3.7041   2.1193  -0.2942
 PVB  C4    C   CR56   0   0.512  -2.6680   1.2431  -0.1831
 PVB  N3    N   N      0  -0.513  -2.7144  -0.0835  -0.1941
 PVB  C2    C   CR6    0   0.610  -1.5109  -0.6340  -0.0628
 PVB  C6    C   CR6    0   0.524  -0.3190   1.3387   0.0639
 PVB  C5    C   CR56   0  -0.077  -1.5359   2.0337  -0.0566
 PVB  N7    N   N      0  -0.458  -1.8609   3.3657  -0.0913
 PVB  C8    C   CR15   0   0.092  -3.1540   3.3722  -0.2349
 PVB  N6    N   NH1    0  -0.773   0.8332   2.0442   0.1861
 PVB  C1A   C   CR6    0   0.355   2.1555   1.6306   0.2833
 PVB  C2A   C   CR16   0  -0.347   3.1202   2.6260   0.4720
 PVB  C3A   C   CR16   0  -0.287   4.4542   2.2924   0.5725
 PVB  C4A   C   CR6    0  -0.031   4.9150   0.9787   0.4574
 PVB  C5A   C   CR6    0  -0.077   3.9336   0.0113   0.2747
 PVB  CL1   CL  CL     0  -0.137   4.3304  -1.6812   0.1911
 PVB  C6A   C   CR16   0  -0.269   2.5774   0.3054   0.2030
 PVB  CX    C   C      0   0.377   6.4176   0.7242   0.5115
 PVB  OX1   O   OC    -1  -0.595   7.0658   1.4891   1.2505
 PVB  OX2   O   O      0  -0.586   6.8614  -0.1885  -0.2036
 PVB  N2    N   NH1    0  -0.665  -1.4079  -1.9776  -0.0493
 PVB  C12   C   CH1    0  -0.092  -2.5104  -2.9141  -0.0707
 PVB  C13   C   CH1    0  -0.226  -2.6102  -3.6691   1.2682
 PVB  C16   C   CH3    0  -0.656  -2.8432  -2.6955   2.4198
 PVB  C14   C   CH3    0  -0.672  -3.7112  -4.7255   1.2446
 PVB  C15   C   CH2    0  -0.160  -2.3893  -3.8203  -1.2871
 PVB  O1    O   OH1    0  -0.674  -1.2277  -4.6099  -1.1572
 PVB  C11   C   CH3    0  -0.654  -5.9675   2.4234   0.5997
 PVB  C10   C   CH3    0  -0.646  -5.5668   2.1746  -1.8853
 PVB  H9    H   HCH1   0   0.269  -5.1650   0.7000  -0.3836
 PVB  H111  H   HCH3   0   0.228  -5.9345   3.5129   0.5478
 PVB  H112  H   HCH3   0   0.245  -7.0067   2.1198   0.4768
 PVB  H113  H   HCH3   0   0.246  -5.6402   2.1158   1.5923
 PVB  H101  H   HCH3   0   0.243  -4.9511   1.6971  -2.6472
 PVB  H102  H   HCH3   0   0.242  -6.5991   1.8626  -2.0416
 PVB  H103  H   HCH3   0   0.229  -5.5198   3.2552  -2.0306
 PVB  H8    H   HCR5   0   0.288  -3.7644   4.2607  -0.3030
 PVB  H2    H   HNH1   0   0.382  -0.4784  -2.3464   0.0706
 PVB  H6    H   HNH1   0   0.418   0.7031   3.0452   0.2055
 PVB  H2A   H   HCR6   0   0.267   2.8189   3.6643   0.5489
 PVB  H6A   H   HCR6   0   0.303   1.8571  -0.4872   0.0871
 PVB  H3A   H   HCR6   0   0.257   5.1774   3.0802   0.7361
 PVB  H12   H   HCH1   0   0.256  -3.4237  -2.3299  -0.2025
 PVB  H13   H   HCH1   0   0.220  -1.6562  -4.1784   1.4441
 PVB  H151  H   HCH2   0   0.203  -3.2916  -4.4370  -1.3746
 PVB  H152  H   HCH2   0   0.212  -2.3485  -3.1878  -2.1825
 PVB  H161  H   HCH3   0   0.214  -3.7791  -2.1474   2.2884
 PVB  H162  H   HCH3   0   0.227  -2.9054  -3.2320   3.3680
 PVB  H163  H   HCH3   0   0.230  -2.0404  -1.9636   2.5111
 PVB  H141  H   HCH3   0   0.233  -3.5025  -5.5288   0.5385
 PVB  H142  H   HCH3   0   0.232  -3.8193  -5.1819   2.2299
 PVB  H143  H   HCH3   0   0.216  -4.6764  -4.2871   0.9787
 PVB  H1    H   HOH1   0   0.457  -1.1196  -5.1230  -1.9626

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
 PVB  N1   C2    aromatic  1.353  0.020  1.353
 PVB  N1   C6    aromatic  1.320  0.020  1.320
 PVB  C9   N9    single    1.460  0.020  1.460
 PVB  C9   C11   single    1.522  0.020  1.522
 PVB  C9   C10   single    1.522  0.020  1.522
 PVB  N9   C4    aromatic  1.361  0.020  1.361
 PVB  N9   C8    aromatic  1.370  0.020  1.370
 PVB  C4   N3    aromatic  1.327  0.020  1.327
 PVB  C4   C5    aromatic  1.387  0.020  1.387
 PVB  N3   C2    aromatic  1.330  0.020  1.330
 PVB  C2   N2    single    1.348  0.020  1.348
 PVB  C6   C5    aromatic  1.407  0.020  1.407
 PVB  C6   N6    single    1.357  0.020  1.357
 PVB  C5   N7    aromatic  1.371  0.020  1.371
 PVB  N7   C8    aromatic  1.301  0.020  1.301
 PVB  N6   C1A   single    1.389  0.020  1.389
 PVB  C1A  C2A   aromatic  1.399  0.020  1.399
 PVB  C1A  C6A   aromatic  1.393  0.020  1.393
 PVB  C2A  C3A   aromatic  1.379  0.020  1.379
 PVB  C3A  C4A   aromatic  1.397  0.020  1.397
 PVB  C4A  C5A   aromatic  1.390  0.020  1.390
 PVB  C4A  CX    single    1.525  0.020  1.525
 PVB  C5A  CL1   single    1.740  0.020  1.740
 PVB  C5A  C6A   aromatic  1.390  0.020  1.390
 PVB  CX   OX1   deloc     1.245  0.020  1.245
 PVB  CX   OX2   deloc     1.241  0.020  1.241
 PVB  N2   C12   single    1.447  0.020  1.447
 PVB  C12  C13   single    1.540  0.020  1.540
 PVB  C12  C15   single    1.522  0.020  1.522
 PVB  C13  C16   single    1.526  0.020  1.526
 PVB  C13  C14   single    1.526  0.020  1.526
 PVB  C15  O1    single    1.411  0.020  1.411
 PVB  C9   H9    single    0.970  0.020  1.090
 PVB  C11  H111  single    0.970  0.020  1.090
 PVB  C11  H112  single    0.970  0.020  1.090
 PVB  C11  H113  single    0.970  0.020  1.090
 PVB  C10  H101  single    0.970  0.020  1.090
 PVB  C10  H102  single    0.970  0.020  1.090
 PVB  C10  H103  single    0.970  0.020  1.090
 PVB  C8   H8    single    0.930  0.020  1.080
 PVB  N2   H2    single    0.860  0.020  1.020
 PVB  N6   H6    single    0.860  0.020  1.020
 PVB  C2A  H2A   single    0.930  0.020  1.080
 PVB  C6A  H6A   single    0.930  0.020  1.080
 PVB  C3A  H3A   single    0.930  0.020  1.080
 PVB  C12  H12   single    0.970  0.020  1.090
 PVB  C13  H13   single    0.970  0.020  1.090
 PVB  C15  H151  single    0.970  0.020  1.090
 PVB  C15  H152  single    0.970  0.020  1.090
 PVB  C16  H161  single    0.970  0.020  1.090
 PVB  C16  H162  single    0.970  0.020  1.090
 PVB  C16  H163  single    0.970  0.020  1.090
 PVB  C14  H141  single    0.970  0.020  1.090
 PVB  C14  H142  single    0.970  0.020  1.090
 PVB  C14  H143  single    0.970  0.020  1.090
 PVB  O1   H1    single    0.850  0.020  0.980

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
 PVB  C6    N1   C2    119.44  3.000
 PVB  H9    C9   C10   109.03  3.000
 PVB  H9    C9   C11   108.89  3.000
 PVB  C10   C9   C11   112.40  3.000
 PVB  H9    C9   N9    105.15  3.000
 PVB  C10   C9   N9    110.46  3.000
 PVB  C11   C9   N9    110.63  3.000
 PVB  C8    N9   C4    106.23  3.000
 PVB  C8    N9   C9    127.04  3.000
 PVB  C4    N9   C9    126.70  3.000
 PVB  C5    C4   N3    126.81  3.000
 PVB  C5    C4   N9    105.18  3.000
 PVB  N3    C4   N9    128.01  3.000
 PVB  C2    N3   C4    112.41  3.000
 PVB  N2    C2   N3    118.87  3.000
 PVB  N2    C2   N1    114.43  3.000
 PVB  N3    C2   N1    126.70  3.000
 PVB  N6    C6   C5    119.05  3.000
 PVB  N6    C6   N1    121.93  3.000
 PVB  C5    C6   N1    119.03  3.000
 PVB  N7    C5   C6    133.40  3.000
 PVB  N7    C5   C4    110.97  3.000
 PVB  C6    C5   C4    115.62  3.000
 PVB  C8    N7   C5    104.07  3.000
 PVB  H8    C8   N7    124.94  3.000
 PVB  H8    C8   N9    121.52  3.000
 PVB  N7    C8   N9    113.54  3.000
 PVB  H6    N6   C1A   114.62  3.000
 PVB  H6    N6   C6    114.08  3.000
 PVB  C1A   N6   C6    131.31  3.000
 PVB  C6A   C1A  C2A   118.41  3.000
 PVB  C6A   C1A  N6    124.58  3.000
 PVB  C2A   C1A  N6    117.01  3.000
 PVB  H2A   C2A  C3A   119.71  3.000
 PVB  H2A   C2A  C1A   119.96  3.000
 PVB  C3A   C2A  C1A   120.32  3.000
 PVB  H3A   C3A  C4A   118.48  3.000
 PVB  H3A   C3A  C2A   118.79  3.000
 PVB  C4A   C3A  C2A   122.73  3.000
 PVB  CX    C4A  C5A   125.75  3.000
 PVB  CX    C4A  C3A   118.62  3.000
 PVB  C5A   C4A  C3A   115.62  3.000
 PVB  C6A   C5A  CL1   115.21  3.000
 PVB  C6A   C5A  C4A   123.26  3.000
 PVB  CL1   C5A  C4A   121.47  3.000
 PVB  H6A   C6A  C5A   120.16  3.000
 PVB  H6A   C6A  C1A   120.24  3.000
 PVB  C5A   C6A  C1A   119.60  3.000
 PVB  OX2   CX   OX1   127.39  3.000
 PVB  OX2   CX   C4A   117.03  3.000
 PVB  OX1   CX   C4A   115.56  3.000
 PVB  H2    N2   C12   117.91  3.000
 PVB  H2    N2   C2    115.90  3.000
 PVB  C12   N2   C2    125.94  3.000
 PVB  H12   C12  C15   106.78  3.000
 PVB  H12   C12  C13   108.23  3.000
 PVB  C15   C12  C13   114.08  3.000
 PVB  H12   C12  N2    107.03  3.000
 PVB  C15   C12  N2    109.67  3.000
 PVB  C13   C12  N2    110.72  3.000
 PVB  H13   C13  C14   107.99  3.000
 PVB  H13   C13  C16   107.96  3.000
 PVB  C14   C13  C16   110.07  3.000
 PVB  H13   C13  C12   108.12  3.000
 PVB  C14   C13  C12   111.88  3.000
 PVB  C16   C13  C12   110.68  3.000
 PVB  H163  C16  H162  107.41  3.000
 PVB  H163  C16  H161  107.70  3.000
 PVB  H162  C16  H161  107.59  3.000
 PVB  H163  C16  C13   112.28  3.000
 PVB  H162  C16  C13   110.53  3.000
 PVB  H161  C16  C13   111.11  3.000
 PVB  H143  C14  H142  107.45  3.000
 PVB  H143  C14  H141  107.88  3.000
 PVB  H142  C14  H141  107.20  3.000
 PVB  H143  C14  C13   111.30  3.000
 PVB  H142  C14  C13   110.31  3.000
 PVB  H141  C14  C13   112.47  3.000
 PVB  H152  C15  H151  106.84  3.000
 PVB  H152  C15  O1    111.55  3.000
 PVB  H151  C15  O1    111.73  3.000
 PVB  H152  C15  C12   108.18  3.000
 PVB  H151  C15  C12   109.47  3.000
 PVB  O1    C15  C12   108.99  3.000
 PVB  H1    O1   C15   108.32  3.000
 PVB  H113  C11  H112  108.10  3.000
 PVB  H113  C11  H111  108.43  3.000
 PVB  H112  C11  H111  107.55  3.000
 PVB  H113  C11  C9    111.27  3.000
 PVB  H112  C11  C9    109.77  3.000
 PVB  H111  C11  C9    111.59  3.000
 PVB  H103  C10  H102  107.78  3.000
 PVB  H103  C10  H101  108.45  3.000
 PVB  H102  C10  H101  108.02  3.000
 PVB  H103  C10  C9    111.28  3.000
 PVB  H102  C10  C9    109.95  3.000
 PVB  H101  C10  C9    111.24  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
 PVB  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 PVB  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PVB  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 PVB  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 PVB  CONST_05  C6    C5   C4   N9    180.00   0.0  0
 PVB  CONST_06  N7    C5   C4   N9      0.00   0.0  0
 PVB  CONST_07  C5    N7   C8   N9      0.00   0.0  0
 PVB  CONST_08  N7    C8   N9   C4      0.00   0.0  0
 PVB  CONST_09  C8    N7   C5   C4      0.00   0.0  0
 PVB  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 PVB  CONST_11  C6    C5   C4   N3      0.00   0.0  0
 PVB  CONST_12  N7    C5   C4   N3    180.00   0.0  0
 PVB  CONST_13  C6    N1   C2   N3      0.00   0.0  0
 PVB  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 PVB  CONST_15  C5    C4   N3   C2      0.00   0.0  0
 PVB  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 PVB  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 PVB  CONST_18  C4A   C3A  C2A  C1A     0.00   0.0  0
 PVB  CONST_19  C4A   C5A  C6A  C1A     0.00   0.0  0
 PVB  CONST_20  C5A   C6A  C1A  C2A     0.00   0.0  0
 PVB  CONST_21  C5A   C4A  C3A  C2A     0.00   0.0  0
 PVB  CONST_22  C6A   C1A  C2A  C3A     0.00   0.0  0
 PVB  CONST_23  C6A   C5A  C4A  C3A     0.00   0.0  0
 PVB  CONST_24  N3    C4   N9   C9      0.00   0.0  0
 PVB  CONST_25  C5    C4   N9   C9    180.00   0.0  0
 PVB  CONST_26  N7    C8   N9   C9    180.00   0.0  0
 PVB  CONST_27  N2    C2   N3   C4    180.00   0.0  0
 PVB  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 PVB  CONST_29  N6    C6   N1   C2    180.00   0.0  0
 PVB  CONST_30  N2    C2   N1   C6    180.00   0.0  0
 PVB  CONST_31  N6    C6   C5   N7      0.00   0.0  0
 PVB  CONST_32  C3A   C2A  C1A  N6    180.00   0.0  0
 PVB  CONST_33  C5A   C6A  C1A  N6    180.00   0.0  0
 PVB  CONST_34  CL1   C5A  C6A  C1A   180.00   0.0  0
 PVB  CONST_35  CX    C4A  C3A  C2A   180.00   0.0  0
 PVB  CONST_36  CL1   C5A  C4A  C3A   180.00   0.0  0
 PVB  CONST_37  CX    C4A  C5A  C6A   180.00   0.0  0
 PVB  CONST_38  H8    C8   N9   C4    180.00   0.0  0
 PVB  CONST_39  H3A   C3A  C2A  C1A   180.00   0.0  0
 PVB  CONST_40  H6A   C6A  C1A  C2A   180.00   0.0  0
 PVB  CONST_41  H2A   C2A  C3A  C4A   180.00   0.0  0
 PVB  CONST_42  C12   N2   C2   N1    180.00   0.0  0
 PVB  CONST_43  C12   N2   C2   N3      0.00   0.0  0
 PVB  CONST_44  H2    N2   C2   N1      0.00   0.0  0
 PVB  Var_01    C1A   N6   C6   N1      2.14  30.0  2
 PVB  Var_02    C2A   C1A  N6   C6   -176.69  30.0  2
 PVB  Var_03    C11   C9   N9   C4    124.83  30.0  2
 PVB  Var_04    OX1   CX   C4A  C3A    33.36  30.0  2
 PVB  Var_05    H111  C11  C9   N9     64.04  30.0  3
 PVB  Var_06    H101  C10  C9   N9     56.67  30.0  3
 PVB  Var_07    H161  C16  C13  C12    61.08  30.0  3
 PVB  Var_08    H141  C14  C13  C12    65.42  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PVB  chir_01  C12  N2  C13  C15  positiv

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
 PVB  plan-1  N6   0.020
 PVB  plan-1  C1A  0.020
 PVB  plan-1  C2A  0.020
 PVB  plan-1  C3A  0.020
 PVB  plan-1  C4A  0.020
 PVB  plan-1  C5A  0.020
 PVB  plan-1  CL1  0.020
 PVB  plan-1  C6A  0.020
 PVB  plan-1  CX   0.020
 PVB  plan-1  H2A  0.020
 PVB  plan-1  H6A  0.020
 PVB  plan-1  H3A  0.020
 PVB  plan-2  N1   0.020
 PVB  plan-2  C9   0.020
 PVB  plan-2  N9   0.020
 PVB  plan-2  C4   0.020
 PVB  plan-2  N3   0.020
 PVB  plan-2  C2   0.020
 PVB  plan-2  C6   0.020
 PVB  plan-2  C5   0.020
 PVB  plan-2  N7   0.020
 PVB  plan-2  C8   0.020
 PVB  plan-2  N6   0.020
 PVB  plan-2  N2   0.020
 PVB  plan-2  H8   0.020
 PVB  plan-3  C2   0.020
 PVB  plan-3  N2   0.020
 PVB  plan-3  C12  0.020
 PVB  plan-3  H2   0.020
 PVB  plan-4  C4A  0.020
 PVB  plan-4  CX   0.020
 PVB  plan-4  OX1  0.020
 PVB  plan-4  OX2  0.020

