# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:42:33 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-(pyrido[1,2-e]purin-4-ylamino)ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCNc1ncnc2n3ccccc3nc12
#
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
 PPZ  PPZ  2-(pyrido[1,2-e]purin-4-ylamino)ethanol  ligand  28  17  .  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_PPZ
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
 PPZ  C4   C  CR56  0   0.470   0.9792   0.0227  -0.9997
 PPZ  C5   C  CR56  0   0.002   0.0298   0.0043   0.0077
 PPZ  N7   N  N     0  -0.494  -1.2404  -0.0279  -0.4776
 PPZ  C8   C  CR56  0   0.542  -1.0882  -0.0304  -1.7855
 PPZ  C13  C  CR16  0  -0.412  -2.0560  -0.0586  -2.8172
 PPZ  C12  C  CR16  0  -0.143  -1.6439  -0.0543  -4.1139
 PPZ  C11  C  CR16  0  -0.400  -0.2590  -0.0219  -4.4451
 PPZ  C10  C  CR16  0   0.046   0.6705   0.0048  -3.4632
 PPZ  N9   N  N     0  -0.594   0.2534   0.0001  -2.1631
 PPZ  C6   C  CR6   0   0.495   0.5425   0.0202   1.3286
 PPZ  N6   N  NH1   0  -0.651  -0.2675   0.0205   2.3890
 PPZ  N1   N  N     0  -0.488   1.8656   0.0460   1.4876
 PPZ  C2   C  CR16  0   0.037   2.6556   0.0660   0.4118
 PPZ  N3   N  N     0  -0.452   2.3024   0.0548  -0.8584
 PPZ  C61  C  CH2   0  -0.292   0.1878  -0.0562   3.7589
 PPZ  C7   C  CH2   0  -0.183  -0.8819   0.4457   4.7020
 PPZ  O8   O  OH1   0  -0.673  -2.0335  -0.3544   4.5446
 PPZ  H13  H  HCR6  0   0.283  -3.1026  -0.0829  -2.5481
 PPZ  H12  H  HCR6  0   0.282  -2.3746  -0.0758  -4.9104
 PPZ  H11  H  HCR6  0   0.285   0.0587  -0.0185  -5.4772
 PPZ  H10  H  HCR6  0   0.310   1.7374   0.0304  -3.6275
 PPZ  H6   H  HNH1  0   0.401  -1.2520  -0.1152   2.2181
 PPZ  H2   H  HCR6  0   0.250   3.7204   0.0906   0.6159
 PPZ  H61  H  HCH2  0   0.252   1.0759   0.5631   3.8802
 PPZ  H62  H  HCH2  0   0.240   0.4719  -1.0816   4.0201
 PPZ  H71  H  HCH2  0   0.210  -1.0905   1.4995   4.4823
 PPZ  H72  H  HCH2  0   0.216  -0.4852   0.3968   5.7231
 PPZ  H8   H  HOH1  0   0.461  -2.7504   0.0427   5.0470

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
 PPZ  C4   C5   aromatic  1.384  0.020  1.384
 PPZ  C4   N9   aromatic  1.371  0.020  1.371
 PPZ  C4   N3   aromatic  1.331  0.020  1.331
 PPZ  C5   N7   aromatic  1.360  0.020  1.360
 PPZ  C5   C6   aromatic  1.417  0.020  1.417
 PPZ  N7   C8   aromatic  1.317  0.020  1.317
 PPZ  C8   C13  aromatic  1.415  0.020  1.415
 PPZ  C8   N9   aromatic  1.394  0.020  1.394
 PPZ  C13  C12  aromatic  1.361  0.020  1.361
 PPZ  C13  H13  single    0.930  0.020  1.080
 PPZ  C12  C11  aromatic  1.424  0.020  1.424
 PPZ  C12  H12  single    0.930  0.020  1.080
 PPZ  C11  C10  aromatic  1.352  0.020  1.352
 PPZ  C11  H11  single    0.930  0.020  1.080
 PPZ  C10  N9   aromatic  1.365  0.020  1.365
 PPZ  C10  H10  single    0.930  0.020  1.080
 PPZ  C6   N6   single    1.334  0.020  1.334
 PPZ  C6   N1   aromatic  1.333  0.020  1.333
 PPZ  N6   C61  single    1.446  0.020  1.446
 PPZ  N6   H6   single    0.860  0.020  1.020
 PPZ  N1   C2   aromatic  1.335  0.020  1.335
 PPZ  C2   N3   aromatic  1.318  0.020  1.318
 PPZ  C2   H2   single    0.930  0.020  1.080
 PPZ  C61  C7   single    1.512  0.020  1.512
 PPZ  C61  H61  single    0.970  0.020  1.090
 PPZ  C61  H62  single    0.970  0.020  1.090
 PPZ  C7   O8   single    1.411  0.020  1.411
 PPZ  C7   H71  single    0.970  0.020  1.090
 PPZ  C7   H72  single    0.970  0.020  1.090
 PPZ  O8   H8   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
 PPZ  N3   C4   N9   128.07  3.000
 PPZ  N3   C4   C5   127.21  3.000
 PPZ  N9   C4   C5   104.72  3.000
 PPZ  C6   C5   N7   132.13  3.000
 PPZ  C6   C5   C4   115.47  3.000
 PPZ  N7   C5   C4   112.40  3.000
 PPZ  C8   N7   C5   104.28  3.000
 PPZ  N9   C8   C13  117.47  3.000
 PPZ  N9   C8   N7   112.34  3.000
 PPZ  C13  C8   N7   130.19  3.000
 PPZ  H13  C13  C12  122.05  3.000
 PPZ  H13  C13  C8   118.76  3.000
 PPZ  C12  C13  C8   119.19  3.000
 PPZ  H12  C12  C11  119.10  3.000
 PPZ  H12  C12  C13  119.82  3.000
 PPZ  C11  C12  C13  121.08  3.000
 PPZ  H11  C11  C10  119.45  3.000
 PPZ  H11  C11  C12  120.55  3.000
 PPZ  C10  C11  C12  119.99  3.000
 PPZ  H10  C10  N9   116.55  3.000
 PPZ  H10  C10  C11  124.68  3.000
 PPZ  N9   C10  C11  118.77  3.000
 PPZ  C10  N9   C8   123.51  3.000
 PPZ  C10  N9   C4   130.24  3.000
 PPZ  C8   N9   C4   106.26  3.000
 PPZ  N1   C6   N6   120.51  3.000
 PPZ  N1   C6   C5   118.08  3.000
 PPZ  N6   C6   C5   121.41  3.000
 PPZ  H6   N6   C61  117.45  3.000
 PPZ  H6   N6   C6   117.25  3.000
 PPZ  C61  N6   C6   124.19  3.000
 PPZ  C2   N1   C6   119.45  3.000
 PPZ  H2   C2   N3   116.40  3.000
 PPZ  H2   C2   N1   115.45  3.000
 PPZ  N3   C2   N1   128.15  3.000
 PPZ  C2   N3   C4   111.64  3.000
 PPZ  H62  C61  H61  107.10  3.000
 PPZ  H62  C61  C7   110.21  3.000
 PPZ  H61  C61  C7   108.58  3.000
 PPZ  H62  C61  N6   110.93  3.000
 PPZ  H61  C61  N6   109.40  3.000
 PPZ  C7   C61  N6   110.53  3.000
 PPZ  H72  C7   H71  107.36  3.000
 PPZ  H72  C7   O8   111.95  3.000
 PPZ  H71  C7   O8   111.55  3.000
 PPZ  H72  C7   C61  108.07  3.000
 PPZ  H71  C7   C61  109.19  3.000
 PPZ  O8   C7   C61  108.64  3.000
 PPZ  H8   O8   C7   108.43  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
 PPZ  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 PPZ  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 PPZ  CONST_03  N7   C8   N9   C4     0.00   0.0  0
 PPZ  CONST_04  C13  C8   N9   C4   180.00   0.0  0
 PPZ  CONST_05  C11  C10  N9   C4   180.00   0.0  0
 PPZ  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 PPZ  CONST_07  C8   N9   C4   C5     0.00   0.0  0
 PPZ  CONST_08  C10  N9   C4   C5   180.00   0.0  0
 PPZ  CONST_09  C2   N3   C4   C5     0.00   0.0  0
 PPZ  CONST_10  C13  C8   N7   C5   180.00   0.0  0
 PPZ  CONST_11  N9   C8   N7   C5     0.00   0.0  0
 PPZ  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 PPZ  CONST_13  N9   C4   C5   N7     0.00   0.0  0
 PPZ  CONST_14  N3   C4   C5   N7   180.00   0.0  0
 PPZ  CONST_15  N1   C6   C5   N7   180.00   0.0  0
 PPZ  CONST_16  C12  C13  C8   N7   180.00   0.0  0
 PPZ  CONST_17  C10  N9   C8   N7   180.00   0.0  0
 PPZ  CONST_18  C6   C5   N7   C8   180.00   0.0  0
 PPZ  CONST_19  C11  C12  C13  C8     0.00   0.0  0
 PPZ  CONST_20  N3   C4   N9   C8   180.00   0.0  0
 PPZ  CONST_21  C11  C10  N9   C8     0.00   0.0  0
 PPZ  CONST_22  C10  N9   C8   C13    0.00   0.0  0
 PPZ  CONST_23  C10  C11  C12  C13    0.00   0.0  0
 PPZ  CONST_24  N9   C8   C13  C12    0.00   0.0  0
 PPZ  CONST_25  N9   C10  C11  C12    0.00   0.0  0
 PPZ  CONST_26  N3   C4   N9   C10    0.00   0.0  0
 PPZ  CONST_27  C6   C5   C4   N9   180.00   0.0  0
 PPZ  CONST_28  C2   N3   C4   N9   180.00   0.0  0
 PPZ  CONST_29  N3   C4   C5   C6     0.00   0.0  0
 PPZ  CONST_30  N3   C2   N1   C6     0.00   0.0  0
 PPZ  CONST_31  N6   C6   C5   C4   180.00   0.0  0
 PPZ  CONST_32  N6   C6   C5   N7     0.00   0.0  0
 PPZ  CONST_33  C2   N1   C6   N6   180.00   0.0  0
 PPZ  CONST_34  H10  C10  N9   C4     0.00   0.0  0
 PPZ  CONST_35  H2   C2   N3   C4   180.00   0.0  0
 PPZ  CONST_36  H13  C13  C8   N7     0.00   0.0  0
 PPZ  CONST_37  H12  C12  C13  C8   180.00   0.0  0
 PPZ  CONST_38  H11  C11  C12  C13  180.00   0.0  0
 PPZ  CONST_39  C61  N6   C6   C5   180.00   0.0  0
 PPZ  CONST_40  C61  N6   C6   N1     0.00   0.0  0
 PPZ  CONST_41  H6   N6   C6   C5     0.00   0.0  0
 PPZ  Var_01    C7   C61  N6   C6   160.06  30.0  3
 PPZ  Var_02    O8   C7   C61  N6    59.92  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
 PPZ  plan-1  C4   0.020
 PPZ  plan-1  C5   0.020
 PPZ  plan-1  N7   0.020
 PPZ  plan-1  C8   0.020
 PPZ  plan-1  C13  0.020
 PPZ  plan-1  C12  0.020
 PPZ  plan-1  C11  0.020
 PPZ  plan-1  C10  0.020
 PPZ  plan-1  N9   0.020
 PPZ  plan-1  C6   0.020
 PPZ  plan-1  N6   0.020
 PPZ  plan-1  N1   0.020
 PPZ  plan-1  C2   0.020
 PPZ  plan-1  N3   0.020
 PPZ  plan-1  H13  0.020
 PPZ  plan-1  H12  0.020
 PPZ  plan-1  H11  0.020
 PPZ  plan-1  H10  0.020
 PPZ  plan-1  H2   0.020
 PPZ  plan-2  C6   0.020
 PPZ  plan-2  N6   0.020
 PPZ  plan-2  C61  0.020
 PPZ  plan-2  H6   0.020

