# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:39:00 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-methyl-1-[4-(9H-purin-6-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccc(cc1)c2ncnc3[nH]cnc23
#
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
 GVI  GVI  N-methyl-1-[4-(9H-purin-6-yl)phenyl]methanamine  ligand  31  18  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GVI
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
 GVI  N1    N  N     0  -0.445  -2.2203   1.5438   1.2372
 GVI  C2    C  CR16  0   0.033  -1.7908   0.3027   1.4295
 GVI  N3    N  N     0  -0.412  -1.3820  -0.5594   0.5109
 GVI  C4    C  CR56  0   0.485  -1.4353  -0.0537  -0.7076
 GVI  C5    C  CR56  0   0.059  -1.8650   1.2388  -1.0522
 GVI  N7    N  N     0  -0.457  -1.7707   1.4139  -2.4106
 GVI  C8    C  CR15  0   0.131  -1.3131   0.2809  -2.8581
 GVI  N9    N  NR15  0  -0.646  -1.0922  -0.6393  -1.8836
 GVI  C10   C  CR6   0   0.104  -3.7146   6.0767  -0.3417
 GVI  C11   C  CR16  0  -0.288  -3.6330   5.2576  -1.4615
 GVI  C12   C  CR16  0  -0.303  -3.1629   3.9557  -1.3663
 GVI  C13   C  CR6   0   0.039  -2.7590   3.4380  -0.1353
 GVI  C14   C  CR16  0  -0.263  -2.8377   4.2632   0.9919
 GVI  C15   C  CR16  0  -0.277  -3.2993   5.5615   0.8856
 GVI  N10   N  NH1   0  -0.581  -3.1081   8.4312  -0.3714
 GVI  C16   C  CR6   0   0.219  -2.2765   2.0550   0.0055
 GVI  C1    C  CH3   0  -0.521  -3.5590   9.8071  -0.4564
 GVI  H2    H  HCR6  0   0.260  -1.7690  -0.0408   2.4574
 GVI  H9    H  HNR5  0   0.432  -0.7337  -1.5734  -2.0150
 GVI  H9C1  H  HCH2  0   0.212  -4.8047   7.6013  -1.3704
 GVI  H9C2  H  HCH2  0   0.238  -4.8934   7.6993   0.3808
 GVI  H10   H  HNH1  0   0.345  -2.4785   8.2508  -1.1442
 GVI  H8    H  HCR5  0   0.299  -1.1150   0.0574  -3.8955
 GVI  H11   H  HCR6  0   0.253  -3.9473   5.6372  -2.4266
 GVI  H15   H  HCR6  0   0.251  -3.3455   6.1845   1.7707
 GVI  H12   H  HCR6  0   0.265  -3.1203   3.3441  -2.2560
 GVI  H14   H  HCR6  0   0.256  -2.5291   3.8815   1.9551
 GVI  H1C1  H  HCH3  0   0.195  -4.1786  10.0234  -1.3378
 GVI  H1C2  H  HCH3  0   0.234  -2.6981  10.4747  -0.4801
 GVI  H1C3  H  HCH3  0   0.223  -4.1495  10.0597   0.4267
 GVI  C9    C  CH2   0  -0.341  -4.2120   7.4908  -0.4493

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
 GVI  N1   C2    aromatic  1.327  0.020  1.327
 GVI  C2   N3    aromatic  1.324  0.020  1.324
 GVI  N3   C4    aromatic  1.320  0.020  1.320
 GVI  C4   C5    aromatic  1.405  0.020  1.405
 GVI  C5   N7    single    1.373  0.020  1.373
 GVI  N7   C8    double    1.301  0.020  1.301
 GVI  C4   N9    single    1.358  0.020  1.358
 GVI  C8   N9    single    1.358  0.020  1.358
 GVI  C9   C10   single    1.503  0.020  1.503
 GVI  C10  C11   aromatic  1.390  0.020  1.390
 GVI  C11  C12   aromatic  1.387  0.020  1.387
 GVI  C12  C13   aromatic  1.395  0.020  1.395
 GVI  C13  C14   aromatic  1.399  0.020  1.399
 GVI  C10  C15   aromatic  1.394  0.020  1.394
 GVI  C14  C15   aromatic  1.382  0.020  1.382
 GVI  C9   N10   single    1.452  0.020  1.452
 GVI  N1   C16   aromatic  1.335  0.020  1.335
 GVI  C5   C16   aromatic  1.398  0.020  1.398
 GVI  C13  C16   single    1.472  0.020  1.472
 GVI  N10  C1    single    1.450  0.020  1.450
 GVI  C2   H2    single    0.930  0.020  1.080
 GVI  N9   H9    single    0.860  0.020  1.020
 GVI  C9   H9C1  single    0.970  0.020  1.090
 GVI  C9   H9C2  single    0.970  0.020  1.090
 GVI  N10  H10   single    0.890  0.020  1.040
 GVI  C8   H8    single    0.930  0.020  1.080
 GVI  C11  H11   single    0.930  0.020  1.080
 GVI  C15  H15   single    0.930  0.020  1.080
 GVI  C12  H12   single    0.930  0.020  1.080
 GVI  C14  H14   single    0.930  0.020  1.080
 GVI  C1   H1C1  single    0.970  0.020  1.090
 GVI  C1   H1C2  single    0.970  0.020  1.090
 GVI  C1   H1C3  single    0.970  0.020  1.090

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
 GVI  C16   N1   C2    120.36  3.000
 GVI  H2    C2   N3    116.43  3.000
 GVI  H2    C2   N1    116.12  3.000
 GVI  N3    C2   N1    127.45  3.000
 GVI  C4    N3   C2    112.23  3.000
 GVI  N9    C4   C5    105.16  3.000
 GVI  N9    C4   N3    128.61  3.000
 GVI  C5    C4   N3    126.23  3.000
 GVI  C16   C5   N7    133.97  3.000
 GVI  C16   C5   C4    116.21  3.000
 GVI  N7    C5   C4    109.82  3.000
 GVI  C8    N7   C5    104.68  3.000
 GVI  H8    C8   N9    121.29  3.000
 GVI  H8    C8   N7    125.12  3.000
 GVI  N9    C8   N7    113.59  3.000
 GVI  H9    N9   C8    126.25  3.000
 GVI  H9    N9   C4    127.00  3.000
 GVI  C8    N9   C4    106.75  3.000
 GVI  C15   C10  C11   118.29  3.000
 GVI  C15   C10  C9    120.62  3.000
 GVI  C11   C10  C9    121.08  3.000
 GVI  H11   C11  C12   119.21  3.000
 GVI  H11   C11  C10   119.61  3.000
 GVI  C12   C11  C10   121.17  3.000
 GVI  H12   C12  C13   120.33  3.000
 GVI  H12   C12  C11   119.21  3.000
 GVI  C13   C12  C11   120.45  3.000
 GVI  C16   C13  C14   119.72  3.000
 GVI  C16   C13  C12   121.87  3.000
 GVI  C14   C13  C12   118.40  3.000
 GVI  H14   C14  C15   119.70  3.000
 GVI  H14   C14  C13   119.57  3.000
 GVI  C15   C14  C13   120.73  3.000
 GVI  H15   C15  C14   119.45  3.000
 GVI  H15   C15  C10   119.60  3.000
 GVI  C14   C15  C10   120.95  3.000
 GVI  H10   N10  C1    108.51  3.000
 GVI  H10   N10  C9    108.43  3.000
 GVI  C1    N10  C9    112.01  3.000
 GVI  C13   C16  C5    124.95  3.000
 GVI  C13   C16  N1    117.52  3.000
 GVI  C5    C16  N1    117.53  3.000
 GVI  H1C3  C1   H1C2  107.65  3.000
 GVI  H1C3  C1   H1C1  107.36  3.000
 GVI  H1C2  C1   H1C1  107.91  3.000
 GVI  H1C3  C1   N10   109.88  3.000
 GVI  H1C2  C1   N10   109.68  3.000
 GVI  H1C1  C1   N10   114.14  3.000
 GVI  H9C2  C9   H9C1  106.28  3.000
 GVI  H9C2  C9   N10   108.02  3.000
 GVI  H9C1  C9   N10   112.90  3.000
 GVI  H9C2  C9   C10   109.34  3.000
 GVI  H9C1  C9   C10   109.42  3.000
 GVI  N10   C9   C10   110.72  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
 GVI  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 GVI  CONST_02  C4    C5   C16  N1      0.00   0.0  0
 GVI  CONST_04  C14   C13  C16  N1      0.00   0.0  0
 GVI  CONST_05  C5    C16  N1   C2      0.00   0.0  0
 GVI  CONST_06  C13   C16  N1   C2    180.00   0.0  0
 GVI  CONST_07  C5    C4   N3   C2      0.00   0.0  0
 GVI  CONST_08  C16   N1   C2   N3      0.00   0.0  0
 GVI  CONST_09  C16   C5   C4   N3      0.00   0.0  0
 GVI  CONST_10  C13   C16  C5   C4    180.00   0.0  0
 GVI  CONST_13  C13   C12  C11  C10     0.00   0.0  0
 GVI  CONST_14  C13   C14  C15  C10     0.00   0.0  0
 GVI  CONST_15  C14   C15  C10  C11     0.00   0.0  0
 GVI  CONST_16  C14   C13  C12  C11     0.00   0.0  0
 GVI  CONST_17  C16   C13  C12  C11   180.00   0.0  0
 GVI  CONST_18  C15   C10  C11  C12     0.00   0.0  0
 GVI  CONST_19  C15   C14  C13  C12     0.00   0.0  0
 GVI  CONST_20  C16   C13  C14  C15   180.00   0.0  0
 GVI  CONST_21  C13   C16  C5   N7      0.00   0.0  0
 GVI  CONST_22  C8    N7   C5   C4      0.00   0.0  0
 GVI  CONST_23  N7    C8   N9   C4      0.00   0.0  0
 GVI  CONST_24  C8    N9   C4   C5      0.00   0.0  0
 GVI  CONST_25  N9    C8   N7   C5      0.00   0.0  0
 GVI  CONST_26  N9    C4   C5   N7      0.00   0.0  0
 GVI  CONST_27  C12   C11  C10  C9    180.00   0.0  0
 GVI  CONST_28  C14   C15  C10  C9    180.00   0.0  0
 GVI  CONST_29  H2    C2   N3   C4    180.00   0.0  0
 GVI  CONST_30  H12   C12  C11  C10   180.00   0.0  0
 GVI  CONST_31  H14   C14  C15  C10   180.00   0.0  0
 GVI  CONST_32  H15   C15  C10  C11   180.00   0.0  0
 GVI  CONST_33  H11   C11  C12  C13   180.00   0.0  0
 GVI  CONST_34  H8    C8   N9   C4    180.00   0.0  0
 GVI  CONST_35  H9    N9   C4   C5    180.00   0.0  0
 GVI  Var_01    N10   C9   C10  C11  -104.28  30.0  2
 GVI  Var_02    C1    N10  C9   C10  -179.31  30.0  3
 GVI  Var_03    H1C1  C1   N10  C9    -53.98  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
 GVI  plan-1  C10  0.020
 GVI  plan-1  C11  0.020
 GVI  plan-1  C12  0.020
 GVI  plan-1  C13  0.020
 GVI  plan-1  C14  0.020
 GVI  plan-1  C15  0.020
 GVI  plan-1  C16  0.020
 GVI  plan-1  H11  0.020
 GVI  plan-1  H15  0.020
 GVI  plan-1  H12  0.020
 GVI  plan-1  H14  0.020
 GVI  plan-1  C9   0.020
 GVI  plan-2  N1   0.020
 GVI  plan-2  C2   0.020
 GVI  plan-2  N3   0.020
 GVI  plan-2  C4   0.020
 GVI  plan-2  C5   0.020
 GVI  plan-2  N7   0.020
 GVI  plan-2  C8   0.020
 GVI  plan-2  N9   0.020
 GVI  plan-2  C13  0.020
 GVI  plan-2  C16  0.020
 GVI  plan-2  H2   0.020
 GVI  plan-2  H9   0.020
 GVI  plan-2  H8   0.020

