# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:27:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 8-(2-chloro-3,4,5-trimethoxybenzyl)-9-pent-4-yn-1-yl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2nc3c(N)ncnc3n2CCCC#C)c(Cl)c(OC)c1OC
#
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
 PU9  PU9  8-(2-chloro-3,4,5-trimethoxybenzyl)-9-pent-4-yn-1-yl-9H-purin-6-amine  ligand  51  29  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PU9
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
 PU9  CL    CL  CL    0  -0.092  -2.2051  -0.5240  -1.5083
 PU9  C13   C   CR6   0  -0.254  -0.4865  -0.4389  -1.6762
 PU9  C15   C   CR6   0   0.391   0.0360   0.3377  -2.7116
 PU9  O3    O   O2    0  -0.472  -0.7877   1.0190  -3.5360
 PU9  C20   C   CH3   0  -0.411  -1.0986   0.3421  -4.7516
 PU9  C17   C   CR6   0   0.194   1.4132   0.4256  -2.8808
 PU9  O2    O   O2    0  -0.477   1.9251   1.1504  -3.9030
 PU9  C19   C   CH3   0  -0.411   2.1886   2.5118  -3.5804
 PU9  C16   C   CR6   0   0.346   2.2685  -0.2563  -2.0045
 PU9  O1    O   O2    0  -0.457   3.5804  -0.1128  -2.2372
 PU9  C18   C   CH3   0  -0.445   4.4934  -0.8172  -1.4166
 PU9  C14   C   CR16  0  -0.486   1.7239  -1.0155  -0.9762
 PU9  C12   C   CR6   0   0.188   0.3459  -1.1023  -0.7881
 PU9  C6    C   CH2   0  -0.631  -0.1932  -1.9117   0.3609
 PU9  C5    C   CR5   0   0.479  -1.0639  -1.1801   1.3323
 PU9  N3    N   N     0  -0.463  -2.1496  -1.7006   1.8337
 PU9  C2    C   CR56  0  -0.005  -2.6276  -0.7574   2.7000
 PU9  C3    C   CR6   0   0.443  -3.7579  -0.7061   3.5348
 PU9  N5    N   NH2   0  -0.819  -4.6428  -1.7029   3.6126
 PU9  C1    C   CR56  0   0.475  -1.8033   0.3543   2.7124
 PU9  N1    N   N     0  -0.462  -1.9760   1.4579   3.4370
 PU9  C4    C   CR16  0   0.037  -3.0662   1.3904   4.1809
 PU9  N2    N   N     0  -0.474  -3.9463   0.3962   4.2697
 PU9  N4    N   NR5   0  -0.541  -0.7998   0.0745   1.8306
 PU9  C7    C   CH2   0  -0.317   0.3179   0.9569   1.5553
 PU9  C8    C   CH2   0  -0.447   1.6215   0.4749   2.1759
 PU9  C9    C   CH2   0  -0.584   2.7782   1.3574   1.7051
 PU9  C10   C   CSP   0   0.290   4.0665   0.9067   2.2113
 PU9  C11   C   CSP1  0  -0.559   5.1220   0.5129   2.6317
 PU9  H201  H   HCH3  0   0.245  -1.7803   0.9836  -5.3053
 PU9  H202  H   HCH3  0   0.230  -0.2056   0.1698  -5.3544
 PU9  H203  H   HCH3  0   0.225  -1.5892  -0.6147  -4.5601
 PU9  H191  H   HCH3  0   0.243   2.5704   2.9856  -4.4822
 PU9  H192  H   HCH3  0   0.226   1.2808   3.0322  -3.2674
 PU9  H193  H   HCH3  0   0.225   2.9388   2.6019  -2.7912
 PU9  H181  H   HCH3  0   0.267   5.4864  -0.5835  -1.7914
 PU9  H182  H   HCH3  0   0.226   4.4335  -0.5036  -0.3707
 PU9  H183  H   HCH3  0   0.236   4.3389  -1.8974  -1.4710
 PU9  H14   H   HCR6  0   0.293   2.3664  -1.5501  -0.2892
 PU9  H6C1  H   HCH2  0   0.300  -0.7881  -2.7485  -0.0108
 PU9  H6C2  H   HCH2  0   0.299   0.6480  -2.3551   0.8998
 PU9  H5N1  H   HNH2  0   0.402  -5.4197  -1.6437   4.2474
 PU9  H5N2  H   HNH2  0   0.410  -4.5014  -2.5617   3.1110
 PU9  H4    H   HCR6  0   0.248  -3.2757   2.2549   4.8019
 PU9  H7C1  H   HCH2  0   0.269   0.4257   1.0780   0.4778
 PU9  H7C2  H   HCH2  0   0.283   0.0519   1.9347   1.9554
 PU9  H8C1  H   HCH2  0   0.263   1.5479   0.4996   3.2645
 PU9  H8C2  H   HCH2  0   0.246   1.8196  -0.5608   1.8943
 PU9  H9C1  H   HCH2  0   0.283   2.6099   2.3934   2.0114
 PU9  H9C2  H   HCH2  0   0.263   2.8085   1.3663   0.6110
 PU9  H11   H   H     0   0.280   6.0585   0.1711   3.0089

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
 PU9  CL   C13   single    1.729  0.020  1.729
 PU9  C13  C15   aromatic  1.396  0.020  1.396
 PU9  C13  C12   aromatic  1.386  0.020  1.386
 PU9  C15  O3    single    1.350  0.020  1.350
 PU9  C15  C17   aromatic  1.390  0.020  1.390
 PU9  O3   C20   single    1.426  0.020  1.426
 PU9  C20  H201  single    0.939  0.020  1.096
 PU9  C20  H202  single    0.939  0.020  1.096
 PU9  C20  H203  single    0.939  0.020  1.096
 PU9  C17  O2    single    1.354  0.020  1.354
 PU9  C17  C16   aromatic  1.402  0.020  1.402
 PU9  O2   C19   single    1.424  0.020  1.424
 PU9  C19  H191  single    0.939  0.020  1.096
 PU9  C19  H192  single    0.939  0.020  1.096
 PU9  C19  H193  single    0.939  0.020  1.096
 PU9  C16  O1    single    1.340  0.020  1.340
 PU9  C16  C14   aromatic  1.389  0.020  1.389
 PU9  O1   C18   single    1.415  0.020  1.415
 PU9  C18  H181  single    0.939  0.020  1.096
 PU9  C18  H182  single    0.939  0.020  1.096
 PU9  C18  H183  single    0.939  0.020  1.096
 PU9  C14  C12   aromatic  1.394  0.020  1.394
 PU9  C14  H14   single    0.929  0.020  1.085
 PU9  C12  C6    single    1.505  0.020  1.505
 PU9  C6   C5    single    1.496  0.020  1.496
 PU9  C6   H6C1  single    0.939  0.020  1.096
 PU9  C6   H6C2  single    0.939  0.020  1.096
 PU9  C5   N3    aromatic  1.304  0.020  1.304
 PU9  C5   N4    aromatic  1.376  0.020  1.376
 PU9  N3   C2    aromatic  1.367  0.020  1.367
 PU9  C2   C3    aromatic  1.406  0.020  1.406
 PU9  C2   C1    aromatic  1.384  0.020  1.384
 PU9  C3   N5    single    1.335  0.020  1.335
 PU9  C3   N2    aromatic  1.338  0.020  1.338
 PU9  N5   H5N1  single    0.868  0.020  1.013
 PU9  N5   H5N2  single    0.868  0.020  1.013
 PU9  C1   N1    aromatic  1.331  0.020  1.331
 PU9  C1   N4    aromatic  1.365  0.020  1.365
 PU9  N1   C4    aromatic  1.322  0.020  1.322
 PU9  C4   N2    aromatic  1.331  0.020  1.331
 PU9  C4   H4    single    0.929  0.020  1.085
 PU9  N4   C7    single    1.450  0.020  1.450
 PU9  C7   C8    single    1.522  0.020  1.522
 PU9  C7   H7C1  single    0.939  0.020  1.096
 PU9  C7   H7C2  single    0.939  0.020  1.096
 PU9  C8   C9    single    1.529  0.020  1.529
 PU9  C8   H8C1  single    0.939  0.020  1.096
 PU9  C8   H8C2  single    0.939  0.020  1.096
 PU9  C9   C10   single    1.456  0.020  1.456
 PU9  C9   H9C1  single    0.939  0.020  1.096
 PU9  C9   H9C2  single    0.939  0.020  1.096
 PU9  C10  C11   triple    1.202  0.020  1.202
 PU9  C11  H11   single    0.913  0.020  1.066

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
 PU9  C12   C13  C15   121.11  3.000
 PU9  C12   C13  CL    120.74  3.000
 PU9  C15   C13  CL    118.13  3.000
 PU9  C17   C15  O3    119.89  3.000
 PU9  C17   C15  C13   119.75  3.000
 PU9  O3    C15  C13   120.36  3.000
 PU9  C20   O3   C15   114.47  3.000
 PU9  H203  C20  H202  109.03  3.000
 PU9  H203  C20  H201  108.93  3.000
 PU9  H202  C20  H201  108.95  3.000
 PU9  H203  C20  O3    111.37  3.000
 PU9  H202  C20  O3    111.57  3.000
 PU9  H201  C20  O3    106.91  3.000
 PU9  C16   C17  O2    120.12  3.000
 PU9  C16   C17  C15   119.85  3.000
 PU9  O2    C17  C15   120.02  3.000
 PU9  C19   O2   C17   114.26  3.000
 PU9  H193  C19  H192  108.93  3.000
 PU9  H193  C19  H191  108.77  3.000
 PU9  H192  C19  H191  108.76  3.000
 PU9  H193  C19  O2    111.70  3.000
 PU9  H192  C19  O2    111.51  3.000
 PU9  H191  C19  O2    107.07  3.000
 PU9  C14   C16  O1    124.80  3.000
 PU9  C14   C16  C17   119.30  3.000
 PU9  O1    C16  C17   115.90  3.000
 PU9  C18   O1   C16   118.52  3.000
 PU9  H183  C18  H182  108.87  3.000
 PU9  H183  C18  H181  108.94  3.000
 PU9  H182  C18  H181  108.56  3.000
 PU9  H183  C18  O1    111.84  3.000
 PU9  H182  C18  O1    112.12  3.000
 PU9  H181  C18  O1    106.40  3.000
 PU9  H14   C14  C12   118.08  3.000
 PU9  H14   C14  C16   120.48  3.000
 PU9  C12   C14  C16   121.44  3.000
 PU9  C6    C12  C14   119.39  3.000
 PU9  C6    C12  C13   122.09  3.000
 PU9  C14   C12  C13   118.52  3.000
 PU9  H6C2  C6   H6C1  106.04  3.000
 PU9  H6C2  C6   C5    109.04  3.000
 PU9  H6C1  C6   C5    106.19  3.000
 PU9  H6C2  C6   C12   108.60  3.000
 PU9  H6C1  C6   C12   110.32  3.000
 PU9  C5    C6   C12   116.18  3.000
 PU9  N4    C5   N3    112.62  3.000
 PU9  N4    C5   C6    124.73  3.000
 PU9  N3    C5   C6    122.62  3.000
 PU9  C2    N3   C5    105.03  3.000
 PU9  C1    C2   C3    116.37  3.000
 PU9  C1    C2   N3    110.59  3.000
 PU9  C3    C2   N3    133.04  3.000
 PU9  N2    C3   N5    119.32  3.000
 PU9  N2    C3   C2    117.99  3.000
 PU9  N5    C3   C2    122.69  3.000
 PU9  H5N2  N5   H5N1  118.34  3.000
 PU9  H5N2  N5   C3    121.05  3.000
 PU9  H5N1  N5   C3    120.34  3.000
 PU9  N4    C1   N1    128.08  3.000
 PU9  N4    C1   C2    105.52  3.000
 PU9  N1    C1   C2    126.40  3.000
 PU9  C4    N1   C1    111.77  3.000
 PU9  H4    C4   N2    115.43  3.000
 PU9  H4    C4   N1    116.16  3.000
 PU9  N2    C4   N1    128.41  3.000
 PU9  C4    N2   C3    119.06  3.000
 PU9  C7    N4   C1    124.37  3.000
 PU9  C7    N4   C5    129.35  3.000
 PU9  C1    N4   C5    106.25  3.000
 PU9  H7C2  C7   H7C1  106.71  3.000
 PU9  H7C2  C7   C8    110.09  3.000
 PU9  H7C1  C7   C8    110.70  3.000
 PU9  H7C2  C7   N4    106.75  3.000
 PU9  H7C1  C7   N4    109.37  3.000
 PU9  C8    C7   N4    112.96  3.000
 PU9  H8C2  C8   H8C1  106.92  3.000
 PU9  H8C2  C8   C9    109.33  3.000
 PU9  H8C1  C8   C9    110.18  3.000
 PU9  H8C2  C8   C7    110.53  3.000
 PU9  H8C1  C8   C7    109.98  3.000
 PU9  C9    C8   C7    109.86  3.000
 PU9  H9C2  C9   H9C1  106.05  3.000
 PU9  H9C2  C9   C10   109.00  3.000
 PU9  H9C1  C9   C10   109.40  3.000
 PU9  H9C2  C9   C8    109.47  3.000
 PU9  H9C1  C9   C8    110.13  3.000
 PU9  C10   C9   C8    112.57  3.000
 PU9  C11   C10  C9    180.00  3.000
 PU9  H11   C11  C10   180.00  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
 PU9  CONST_01  C16   C17  C15  C13     0.00   0.0  0
 PU9  CONST_02  C16   C14  C12  C13     0.00   0.0  0
 PU9  CONST_03  C14   C12  C13  C15     0.00   0.0  0
 PU9  CONST_04  C14   C16  C17  C15     0.00   0.0  0
 PU9  CONST_05  C12   C13  C15  C17     0.00   0.0  0
 PU9  CONST_06  C12   C14  C16  C17     0.00   0.0  0
 PU9  CONST_07  C3    C2   N3   C5    180.00   0.0  0
 PU9  CONST_08  C1    C2   N3   C5      0.00   0.0  0
 PU9  CONST_09  C2    C1   N4   C5      0.00   0.0  0
 PU9  CONST_10  N1    C1   N4   C5    180.00   0.0  0
 PU9  CONST_11  C1    N4   C5   N3      0.00   0.0  0
 PU9  CONST_12  N2    C3   C2   N3    180.00   0.0  0
 PU9  CONST_13  N1    C1   C2   N3    180.00   0.0  0
 PU9  CONST_14  N4    C1   C2   N3      0.00   0.0  0
 PU9  CONST_15  N4    C5   N3   C2      0.00   0.0  0
 PU9  CONST_16  C4    N2   C3   C2      0.00   0.0  0
 PU9  CONST_17  C4    N1   C1   C2      0.00   0.0  0
 PU9  CONST_18  N1    C1   C2   C3      0.00   0.0  0
 PU9  CONST_19  N4    C1   C2   C3    180.00   0.0  0
 PU9  CONST_20  N1    C4   N2   C3      0.00   0.0  0
 PU9  CONST_21  N2    C3   C2   C1      0.00   0.0  0
 PU9  CONST_22  N2    C4   N1   C1      0.00   0.0  0
 PU9  CONST_23  N4    C1   N1   C4    180.00   0.0  0
 PU9  CONST_24  C17   C15  C13  CL    180.00   0.0  0
 PU9  CONST_25  C14   C12  C13  CL    180.00   0.0  0
 PU9  CONST_26  O2    C17  C15  C13   180.00   0.0  0
 PU9  CONST_27  C6    C12  C13  C15   180.00   0.0  0
 PU9  CONST_28  O1    C16  C17  C15   180.00   0.0  0
 PU9  CONST_29  C12   C13  C15  O3    180.00   0.0  0
 PU9  CONST_30  C16   C17  C15  O3    180.00   0.0  0
 PU9  CONST_31  C14   C16  C17  O2    180.00   0.0  0
 PU9  CONST_32  C6    C12  C14  C16   180.00   0.0  0
 PU9  CONST_33  C12   C14  C16  O1    180.00   0.0  0
 PU9  CONST_34  C2    N3   C5   C6    180.00   0.0  0
 PU9  CONST_35  C1    N4   C5   C6    180.00   0.0  0
 PU9  CONST_36  C7    N4   C5   N3    180.00   0.0  0
 PU9  CONST_37  N5    C3   C2   N3      0.00   0.0  0
 PU9  CONST_38  C7    N4   C1   C2    180.00   0.0  0
 PU9  CONST_39  C1    C2   C3   N5    180.00   0.0  0
 PU9  CONST_40  C4    N2   C3   N5    180.00   0.0  0
 PU9  CONST_41  C7    N4   C1   N1      0.00   0.0  0
 PU9  CONST_42  H14   C14  C12  C13   180.00   0.0  0
 PU9  CONST_43  H4    C4   N2   C3    180.00   0.0  0
 PU9  CONST_44  H5N1  N5   C3   C2    180.00   0.0  0
 PU9  CONST_45  H5N2  N5   C3   C2      0.00   0.0  0
 PU9  Var_01    C5    C6   C12  C13   -58.08  30.0  2
 PU9  Var_02    N3    C5   C6   C12   138.75  30.0  2
 PU9  Var_03    C17   C15  O3   C20    85.34  30.0  2
 PU9  Var_04    C16   C17  O2   C19   -90.32  30.0  2
 PU9  Var_05    C14   C16  O1   C18     2.46  30.0  2
 PU9  Var_06    C8    C7   N4   C5    -71.67  30.0  2
 PU9  Var_07    C9    C8   C7   N4    173.20  30.0  3
 PU9  Var_08    H201  C20  O3   C15   178.71  30.0  3
 PU9  Var_09    H191  C19  O2   C17  -178.70  30.0  3
 PU9  Var_10    H181  C18  O1   C16   178.40  30.0  3
 PU9  Var_11    C10   C9   C8   C7   -177.10  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
 PU9  plan-1  CL    0.020
 PU9  plan-1  C13   0.020
 PU9  plan-1  C15   0.020
 PU9  plan-1  O3    0.020
 PU9  plan-1  C17   0.020
 PU9  plan-1  O2    0.020
 PU9  plan-1  C16   0.020
 PU9  plan-1  O1    0.020
 PU9  plan-1  C14   0.020
 PU9  plan-1  C12   0.020
 PU9  plan-1  C6    0.020
 PU9  plan-1  H14   0.020
 PU9  plan-2  C6    0.020
 PU9  plan-2  C5    0.020
 PU9  plan-2  N3    0.020
 PU9  plan-2  C2    0.020
 PU9  plan-2  C3    0.020
 PU9  plan-2  N5    0.020
 PU9  plan-2  C1    0.020
 PU9  plan-2  N1    0.020
 PU9  plan-2  C4    0.020
 PU9  plan-2  N2    0.020
 PU9  plan-2  N4    0.020
 PU9  plan-2  C7    0.020
 PU9  plan-2  H4    0.020
 PU9  plan-3  C3    0.020
 PU9  plan-3  N5    0.020
 PU9  plan-3  H5N1  0.020
 PU9  plan-3  H5N2  0.020

