# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 12:22:52 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2c3ccnc(N)n3c4nccc(O)c24
#
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
 VAR  VAR  9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol  ligand  33  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VAR
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
 VAR  O1    O  OH1   0  -0.635   1.4166   2.6747  -0.1252
 VAR  C1    C  CR6   0   0.379   0.1364   2.3615  -0.0761
 VAR  C2    C  CR16  0  -0.451  -0.8166   3.3814  -0.1104
 VAR  C3    C  CR16  0  -0.062  -2.1702   3.0857  -0.0755
 VAR  N1    N  N     0  -0.500  -2.6535   1.8503  -0.0191
 VAR  C4    C  CR56  0   0.505  -1.7382   0.8994   0.0123
 VAR  N2    N  N     0  -0.698  -2.0259  -0.4589   0.0649
 VAR  C5    C  CR6   0   0.704  -3.2582  -1.0762   0.0632
 VAR  N3    N  NH2   0  -0.838  -4.3398  -0.3078   0.0485
 VAR  N4    N  N     0  -0.495  -3.3614  -2.3809   0.0728
 VAR  C6    C  CR16  0  -0.046  -2.2260  -3.1039   0.0641
 VAR  C7    C  CR16  0  -0.459  -0.9654  -2.5843   0.0799
 VAR  C8    C  CR56  0   0.486  -0.8339  -1.1797   0.1010
 VAR  C9    C  CR5   0  -0.093   0.2336  -0.2831   0.0946
 VAR  C10   C  CR56  0  -0.102  -0.3464   1.0381   0.0044
 VAR  C11   C  CR6   0   0.337   1.6355  -0.6239   0.1727
 VAR  C14   C  CR16  0  -0.442   2.1139  -1.8615   0.6150
 VAR  C13   C  CR16  0  -0.021   3.4825  -2.0434   0.6127
 VAR  N7    N  N     0  -0.463   4.3540  -1.1273   0.2219
 VAR  C12   C  CR6   0   0.611   3.8270   0.0417  -0.1515
 VAR  N5    N  N     0  -0.648   2.5195   0.3223  -0.1808
 VAR  N6    N  NH2   0  -0.831   4.6782   0.9992  -0.5543
 VAR  HO1   H  HOH1  0   0.487   1.9537   1.8213  -0.1966
 VAR  H2    H  HCR6  0   0.273  -0.4935   4.4123  -0.1703
 VAR  H3    H  HCR6  0   0.268  -2.8975   3.8873  -0.1010
 VAR  HN3   H  HNH2  0   0.433  -4.2583   0.7013   0.0318
 VAR  HN3A  H  HNH2  0   0.414  -5.2422  -0.7514   0.0331
 VAR  H6    H  HCR6  0   0.274  -2.3595  -4.1789   0.0400
 VAR  H7    H  HCR6  0   0.267  -0.1126  -3.2388   0.0414
 VAR  H14   H  HCR6  0   0.262   1.4751  -2.6393   0.9960
 VAR  H13   H  HCR6  0   0.274   3.8968  -2.9857   0.9546
 VAR  HN6   H  HNH2  0   0.403   5.6625   0.8707  -0.3971
 VAR  HN6A  H  HNH2  0   0.404   4.3564   1.9377  -0.7124

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
 VAR  O1   C1    single    1.319  0.020  1.319
 VAR  C1   C2    aromatic  1.396  0.020  1.396
 VAR  C1   C10   aromatic  1.411  0.020  1.411
 VAR  C2   C3    aromatic  1.386  0.020  1.386
 VAR  C3   N1    aromatic  1.328  0.020  1.328
 VAR  N1   C4    aromatic  1.320  0.020  1.320
 VAR  C4   N2    aromatic  1.389  0.020  1.389
 VAR  C4   C10   aromatic  1.399  0.020  1.399
 VAR  N2   C5    aromatic  1.378  0.020  1.378
 VAR  N2   C8    aromatic  1.393  0.020  1.393
 VAR  C5   N3    single    1.327  0.020  1.327
 VAR  C5   N4    aromatic  1.309  0.020  1.309
 VAR  N4   C6    aromatic  1.346  0.020  1.346
 VAR  C6   C7    aromatic  1.364  0.020  1.364
 VAR  C7   C8    aromatic  1.411  0.020  1.411
 VAR  C8   C9    aromatic  1.394  0.020  1.394
 VAR  C9   C10   aromatic  1.446  0.020  1.446
 VAR  C9   C11   single    1.445  0.020  1.445
 VAR  C11  C14   aromatic  1.399  0.020  1.399
 VAR  C11  N5    aromatic  1.342  0.020  1.342
 VAR  C14  C13   aromatic  1.381  0.020  1.381
 VAR  C13  N7    aromatic  1.323  0.020  1.323
 VAR  N7   C12   aromatic  1.336  0.020  1.336
 VAR  C12  N5    aromatic  1.338  0.020  1.338
 VAR  C12  N6    single    1.343  0.020  1.343
 VAR  O1   HO1   single    0.850  0.020  0.980
 VAR  C2   H2    single    0.930  0.020  1.080
 VAR  C3   H3    single    0.930  0.020  1.080
 VAR  N3   HN3   single    0.860  0.020  1.020
 VAR  N3   HN3A  single    0.860  0.020  1.020
 VAR  C6   H6    single    0.930  0.020  1.080
 VAR  C7   H7    single    0.930  0.020  1.080
 VAR  C14  H14   single    0.930  0.020  1.080
 VAR  C13  H13   single    0.930  0.020  1.080
 VAR  N6   HN6   single    0.890  0.020  1.040
 VAR  N6   HN6A  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
 VAR  HO1   O1   C1   108.53  3.000
 VAR  C10   C1   C2   116.93  3.000
 VAR  C10   C1   O1   123.85  3.000
 VAR  C2    C1   O1   119.22  3.000
 VAR  H2    C2   C3   119.75  3.000
 VAR  H2    C2   C1   119.57  3.000
 VAR  C3    C2   C1   120.67  3.000
 VAR  H3    C3   N1   116.45  3.000
 VAR  H3    C3   C2   119.83  3.000
 VAR  N1    C3   C2   123.72  3.000
 VAR  C4    N1   C3   114.76  3.000
 VAR  C10   C4   N2   107.65  3.000
 VAR  C10   C4   N1   128.19  3.000
 VAR  N2    C4   N1   124.15  3.000
 VAR  C8    N2   C5   122.23  3.000
 VAR  C8    N2   C4   109.24  3.000
 VAR  C5    N2   C4   128.53  3.000
 VAR  N4    C5   N3   120.87  3.000
 VAR  N4    C5   N2   121.12  3.000
 VAR  N3    C5   N2   118.00  3.000
 VAR  HN3A  N3   HN3  120.77  3.000
 VAR  HN3A  N3   C5   118.44  3.000
 VAR  HN3   N3   C5   120.78  3.000
 VAR  C6    N4   C5   117.96  3.000
 VAR  H6    C6   C7   119.49  3.000
 VAR  H6    C6   N4   115.41  3.000
 VAR  C7    C6   N4   125.10  3.000
 VAR  H7    C7   C8   122.17  3.000
 VAR  H7    C7   C6   120.04  3.000
 VAR  C8    C7   C6   117.76  3.000
 VAR  C9    C8   C7   135.36  3.000
 VAR  C9    C8   N2   108.80  3.000
 VAR  C7    C8   N2   115.77  3.000
 VAR  C11   C9   C10  127.46  3.000
 VAR  C11   C9   C8   126.23  3.000
 VAR  C10   C9   C8   106.31  3.000
 VAR  C9    C10  C4   107.95  3.000
 VAR  C9    C10  C1   136.33  3.000
 VAR  C4    C10  C1   115.71  3.000
 VAR  N5    C11  C14  118.80  3.000
 VAR  N5    C11  C9   117.29  3.000
 VAR  C14   C11  C9   123.90  3.000
 VAR  H14   C14  C13  119.59  3.000
 VAR  H14   C14  C11  123.26  3.000
 VAR  C13   C14  C11  117.08  3.000
 VAR  H13   C13  N7   116.29  3.000
 VAR  H13   C13  C14  119.51  3.000
 VAR  N7    C13  C14  124.20  3.000
 VAR  C12   N7   C13  115.38  3.000
 VAR  N6    C12  N5   117.61  3.000
 VAR  N6    C12  N7   117.25  3.000
 VAR  N5    C12  N7   125.13  3.000
 VAR  C12   N5   C11  119.35  3.000
 VAR  HN6A  N6   HN6  117.25  3.000
 VAR  HN6A  N6   C12  120.67  3.000
 VAR  HN6   N6   C12  118.86  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
 VAR  CONST_01  N1    C3   C2   C1     0.00  0.0  0
 VAR  CONST_02  N1    C4   C10  C1     0.00  0.0  0
 VAR  CONST_03  N2    C4   C10  C1   180.00  0.0  0
 VAR  CONST_04  C8    C9   C10  C1   180.00  0.0  0
 VAR  CONST_05  C11   C9   C10  C1     0.00  0.0  0
 VAR  CONST_06  C4    C10  C1   C2     0.00  0.0  0
 VAR  CONST_07  C9    C10  C1   C2   180.00  0.0  0
 VAR  CONST_08  C4    N1   C3   C2     0.00  0.0  0
 VAR  CONST_09  C10   C1   C2   C3     0.00  0.0  0
 VAR  CONST_10  N2    C4   N1   C3   180.00  0.0  0
 VAR  CONST_11  C10   C4   N1   C3     0.00  0.0  0
 VAR  CONST_12  C5    N2   C4   N1     0.00  0.0  0
 VAR  CONST_13  C8    N2   C4   N1   180.00  0.0  0
 VAR  CONST_14  C9    C10  C4   N1   180.00  0.0  0
 VAR  CONST_15  N4    C5   N2   C4   180.00  0.0  0
 VAR  CONST_16  C7    C8   N2   C4   180.00  0.0  0
 VAR  CONST_17  C9    C8   N2   C4     0.00  0.0  0
 VAR  CONST_18  C8    C9   C10  C4     0.00  0.0  0
 VAR  CONST_19  C11   C9   C10  C4   180.00  0.0  0
 VAR  CONST_20  C9    C10  C4   N2     0.00  0.0  0
 VAR  CONST_21  C6    N4   C5   N2     0.00  0.0  0
 VAR  CONST_22  C6    C7   C8   N2     0.00  0.0  0
 VAR  CONST_23  C10   C9   C8   N2     0.00  0.0  0
 VAR  CONST_24  C11   C9   C8   N2   180.00  0.0  0
 VAR  CONST_25  C10   C4   N2   C5   180.00  0.0  0
 VAR  CONST_26  C7    C8   N2   C5     0.00  0.0  0
 VAR  CONST_27  C9    C8   N2   C5   180.00  0.0  0
 VAR  CONST_28  C7    C6   N4   C5     0.00  0.0  0
 VAR  CONST_29  C8    N2   C5   N4     0.00  0.0  0
 VAR  CONST_30  C8    C7   C6   N4     0.00  0.0  0
 VAR  CONST_31  C9    C8   C7   C6   180.00  0.0  0
 VAR  CONST_32  C10   C9   C8   C7   180.00  0.0  0
 VAR  CONST_33  C11   C9   C8   C7     0.00  0.0  0
 VAR  CONST_34  C10   C4   N2   C8     0.00  0.0  0
 VAR  CONST_37  C13   C14  C11  C9   180.00  0.0  0
 VAR  CONST_38  C12   N5   C11  C9   180.00  0.0  0
 VAR  CONST_41  N7    C13  C14  C11    0.00  0.0  0
 VAR  CONST_42  N7    C12  N5   C11    0.00  0.0  0
 VAR  CONST_43  C12   N5   C11  C14    0.00  0.0  0
 VAR  CONST_44  C12   N7   C13  C14    0.00  0.0  0
 VAR  CONST_45  N5    C11  C14  C13    0.00  0.0  0
 VAR  CONST_46  N5    C12  N7   C13    0.00  0.0  0
 VAR  CONST_47  C3    C2   C1   O1   180.00  0.0  0
 VAR  CONST_48  C4    C10  C1   O1   180.00  0.0  0
 VAR  CONST_49  C9    C10  C1   O1     0.00  0.0  0
 VAR  CONST_50  N3    C5   N2   C4     0.00  0.0  0
 VAR  CONST_51  C8    N2   C5   N3   180.00  0.0  0
 VAR  CONST_52  C6    N4   C5   N3   180.00  0.0  0
 VAR  CONST_53  N6    C12  N5   C11  180.00  0.0  0
 VAR  CONST_54  N6    C12  N7   C13  180.00  0.0  0
 VAR  CONST_55  H3    C3   C2   C1   180.00  0.0  0
 VAR  CONST_56  H2    C2   C3   N1   180.00  0.0  0
 VAR  CONST_57  H7    C7   C8   N2   180.00  0.0  0
 VAR  CONST_58  H6    C6   N4   C5   180.00  0.0  0
 VAR  CONST_59  H14   C14  C11  C9     0.00  0.0  0
 VAR  CONST_60  H13   C13  C14  C11  180.00  0.0  0
 VAR  CONST_61  HN3   N3   C5   N2     0.00  0.0  0
 VAR  CONST_62  HN3A  N3   C5   N2   180.00  0.0  0
 VAR  CONST_63  HN6   N6   C12  N7     0.00  0.0  0
 VAR  CONST_64  HN6A  N6   C12  N7   180.00  0.0  0

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
 VAR  plan-1  C9    0.020
 VAR  plan-1  C11   0.020
 VAR  plan-1  C14   0.020
 VAR  plan-1  C13   0.020
 VAR  plan-1  N7    0.020
 VAR  plan-1  C12   0.020
 VAR  plan-1  N5    0.020
 VAR  plan-1  N6    0.020
 VAR  plan-1  H14   0.020
 VAR  plan-1  H13   0.020
 VAR  plan-2  O1    0.020
 VAR  plan-2  C1    0.020
 VAR  plan-2  C2    0.020
 VAR  plan-2  C3    0.020
 VAR  plan-2  N1    0.020
 VAR  plan-2  C4    0.020
 VAR  plan-2  N2    0.020
 VAR  plan-2  C5    0.020
 VAR  plan-2  N3    0.020
 VAR  plan-2  N4    0.020
 VAR  plan-2  C6    0.020
 VAR  plan-2  C7    0.020
 VAR  plan-2  C8    0.020
 VAR  plan-2  C9    0.020
 VAR  plan-2  C10   0.020
 VAR  plan-2  C11   0.020
 VAR  plan-2  H2    0.020
 VAR  plan-2  H3    0.020
 VAR  plan-2  H6    0.020
 VAR  plan-2  H7    0.020
 VAR  plan-3  C5    0.020
 VAR  plan-3  N3    0.020
 VAR  plan-3  HN3   0.020
 VAR  plan-3  HN3A  0.020
 VAR  plan-4  C12   0.020
 VAR  plan-4  N6    0.020
 VAR  plan-4  HN6   0.020
 VAR  plan-4  HN6A  0.020

