# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:04:11 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (S)-1-phenyl-1-[4-(9H-purin-6-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](c1ccccc1)c2ccc(cc2)c3ncnc4[nH]cnc34
#
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
 GVJ  GVJ  (S)-1-phenyl-1-[4-(9H-purin-6-yl)phenyl]methanamine  ligand  38  23  .  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_GVJ
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
 GVJ  N1    N  NH2   0  -0.777  -5.3276   7.7717  -0.1462
 GVJ  C2    C  CH1   0  -0.241  -3.9768   7.2550  -0.0243
 GVJ  C3    C  CR6   0   0.162  -3.3193   7.2695  -1.3904
 GVJ  C4    C  CR16  0  -0.328  -3.2523   6.1101  -2.1554
 GVJ  C5    C  CR16  0  -0.242  -2.6848   6.1275  -3.4235
 GVJ  C6    C  CR16  0  -0.269  -2.1824   7.3118  -3.9449
 GVJ  C7    C  CR16  0  -0.241  -2.2473   8.4759  -3.1888
 GVJ  C8    C  CR16  0  -0.288  -2.8077   8.4523  -1.9195
 GVJ  C9    C  CR6   0   0.122  -3.0807   7.9320   1.0013
 GVJ  C10   C  CR16  0  -0.265  -1.8528   7.3553   1.3224
 GVJ  C11   C  CR16  0  -0.316  -1.0012   7.9429   2.2393
 GVJ  C12   C  CR6   0   0.028  -1.3550   9.1404   2.8724
 GVJ  C13   C  CR16  0  -0.253  -2.5865   9.7137   2.5546
 GVJ  C14   C  CR16  0  -0.319  -3.4346   9.1167   1.6354
 GVJ  C15   C  CR6   0   0.229  -0.4766   9.7975   3.8539
 GVJ  N16   N  N     0  -0.449  -0.9332  10.9078   4.4389
 GVJ  C17   C  CR16  0   0.034  -0.1942  11.5520   5.3321
 GVJ  N18   N  N     0  -0.412   1.0183  11.2296   5.7563
 GVJ  C19   C  CR56  0   0.484   1.4733  10.1336   5.1778
 GVJ  N20   N  NR15  0  -0.647   2.6680   9.5152   5.3613
 GVJ  C21   C  CR15  0   0.136   2.6775   8.4306   4.5440
 GVJ  N22   N  N     0  -0.461   1.5871   8.2950   3.8471
 GVJ  C23   C  CR56  0   0.062   0.7989   9.3558   4.2211
 GVJ  H1N1  H  HNH2  0   0.356  -5.7890   7.7619   0.7556
 GVJ  H1N2  H  HNH2  0   0.351  -5.3179   8.7367  -0.4551
 GVJ  H2    H  HCH1  0   0.266  -4.0691   6.2078   0.2822
 GVJ  H4    H  HCR6  0   0.252  -3.6415   5.1810  -1.7556
 GVJ  H8    H  HCR6  0   0.251  -2.8345   9.3642  -1.3335
 GVJ  H5    H  HCR6  0   0.255  -2.6319   5.2144  -4.0025
 GVJ  H6    H  HCR6  0   0.256  -1.7369   7.3273  -4.9313
 GVJ  H7    H  HCR6  0   0.256  -1.8550   9.4034  -3.5857
 GVJ  H10   H  HCR6  0   0.250  -1.5561   6.4285   0.8447
 GVJ  H14   H  HCR6  0   0.242  -4.3844   9.5877   1.4163
 GVJ  H11   H  HCR6  0   0.269  -0.0560   7.4701   2.4639
 GVJ  H13   H  HCR6  0   0.256  -2.8812  10.6374   3.0326
 GVJ  H17   H  HCR6  0   0.259  -0.6349  12.4437   5.7626
 GVJ  H20   H  HNR5  0   0.432   3.4104   9.8025   5.9813
 GVJ  H21   H  HCR5  0   0.300   3.5277   7.7674   4.5020

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
 GVJ  N1   C2    single    1.451  0.020  1.451
 GVJ  C2   C3    single    1.516  0.020  1.516
 GVJ  C3   C4    aromatic  1.391  0.020  1.391
 GVJ  C4   C5    aromatic  1.389  0.020  1.389
 GVJ  C5   C6    aromatic  1.388  0.020  1.388
 GVJ  C6   C7    aromatic  1.390  0.020  1.390
 GVJ  C3   C8    aromatic  1.393  0.020  1.393
 GVJ  C7   C8    aromatic  1.388  0.020  1.388
 GVJ  C2   C9    single    1.521  0.020  1.521
 GVJ  C9   C10   aromatic  1.394  0.020  1.394
 GVJ  C10  C11   aromatic  1.382  0.020  1.382
 GVJ  C11  C12   aromatic  1.400  0.020  1.400
 GVJ  C12  C13   aromatic  1.395  0.020  1.395
 GVJ  C9   C14   aromatic  1.390  0.020  1.390
 GVJ  C13  C14   aromatic  1.386  0.020  1.386
 GVJ  C12  C15   single    1.472  0.020  1.472
 GVJ  C15  N16   aromatic  1.335  0.020  1.335
 GVJ  N16  C17   aromatic  1.326  0.020  1.326
 GVJ  C17  N18   aromatic  1.324  0.020  1.324
 GVJ  N18  C19   aromatic  1.320  0.020  1.320
 GVJ  C19  N20   single    1.358  0.020  1.358
 GVJ  N20  C21   single    1.358  0.020  1.358
 GVJ  C21  N22   double    1.301  0.020  1.301
 GVJ  C15  C23   aromatic  1.399  0.020  1.399
 GVJ  C19  C23   aromatic  1.405  0.020  1.405
 GVJ  N22  C23   single    1.373  0.020  1.373
 GVJ  N1   H1N1  single    0.890  0.020  1.040
 GVJ  N1   H1N2  single    0.890  0.020  1.040
 GVJ  C2   H2    single    0.970  0.020  1.090
 GVJ  C4   H4    single    0.930  0.020  1.080
 GVJ  C8   H8    single    0.930  0.020  1.080
 GVJ  C5   H5    single    0.930  0.020  1.080
 GVJ  C6   H6    single    0.930  0.020  1.080
 GVJ  C7   H7    single    0.930  0.020  1.080
 GVJ  C10  H10   single    0.930  0.020  1.080
 GVJ  C14  H14   single    0.930  0.020  1.080
 GVJ  C11  H11   single    0.930  0.020  1.080
 GVJ  C13  H13   single    0.930  0.020  1.080
 GVJ  C17  H17   single    0.930  0.020  1.080
 GVJ  N20  H20   single    0.860  0.020  1.020
 GVJ  C21  H21   single    0.930  0.020  1.080

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
 GVJ  H1N2  N1   H1N1  106.56  3.000
 GVJ  H1N2  N1   C2    110.83  3.000
 GVJ  H1N1  N1   C2    110.22  3.000
 GVJ  H2    C2   C9    106.66  3.000
 GVJ  H2    C2   C3    107.33  3.000
 GVJ  C9    C2   C3    110.35  3.000
 GVJ  H2    C2   N1    106.59  3.000
 GVJ  C9    C2   N1    116.53  3.000
 GVJ  C3    C2   N1    108.94  3.000
 GVJ  C8    C3   C4    118.77  3.000
 GVJ  C8    C3   C2    120.64  3.000
 GVJ  C4    C3   C2    120.57  3.000
 GVJ  H4    C4   C5    119.62  3.000
 GVJ  H4    C4   C3    119.64  3.000
 GVJ  C5    C4   C3    120.75  3.000
 GVJ  H5    C5   C6    120.08  3.000
 GVJ  H5    C5   C4    119.83  3.000
 GVJ  C6    C5   C4    120.09  3.000
 GVJ  H6    C6   C7    120.20  3.000
 GVJ  H6    C6   C5    120.23  3.000
 GVJ  C7    C6   C5    119.57  3.000
 GVJ  H7    C7   C8    119.75  3.000
 GVJ  H7    C7   C6    120.09  3.000
 GVJ  C8    C7   C6    120.15  3.000
 GVJ  H8    C8   C7    119.34  3.000
 GVJ  H8    C8   C3    119.98  3.000
 GVJ  C7    C8   C3    120.67  3.000
 GVJ  C14   C9   C10   118.16  3.000
 GVJ  C14   C9   C2    122.49  3.000
 GVJ  C10   C9   C2    119.35  3.000
 GVJ  H10   C10  C11   119.14  3.000
 GVJ  H10   C10  C9    119.55  3.000
 GVJ  C11   C10  C9    121.30  3.000
 GVJ  H11   C11  C12   120.09  3.000
 GVJ  H11   C11  C10   119.40  3.000
 GVJ  C12   C11  C10   120.51  3.000
 GVJ  C15   C12  C13   119.68  3.000
 GVJ  C15   C12  C11   122.18  3.000
 GVJ  C13   C12  C11   118.14  3.000
 GVJ  H13   C13  C14   119.64  3.000
 GVJ  H13   C13  C12   119.41  3.000
 GVJ  C14   C13  C12   120.95  3.000
 GVJ  H14   C14  C13   118.93  3.000
 GVJ  H14   C14  C9    120.13  3.000
 GVJ  C13   C14  C9    120.94  3.000
 GVJ  C23   C15  N16   117.35  3.000
 GVJ  C23   C15  C12   125.32  3.000
 GVJ  N16   C15  C12   117.33  3.000
 GVJ  C17   N16  C15   120.55  3.000
 GVJ  H17   C17  N18   116.44  3.000
 GVJ  H17   C17  N16   116.14  3.000
 GVJ  N18   C17  N16   127.42  3.000
 GVJ  C19   N18  C17   112.16  3.000
 GVJ  C23   C19  N20   105.20  3.000
 GVJ  C23   C19  N18   126.33  3.000
 GVJ  N20   C19  N18   128.47  3.000
 GVJ  H20   N20  C21   126.30  3.000
 GVJ  H20   N20  C19   126.93  3.000
 GVJ  C21   N20  C19   106.77  3.000
 GVJ  H21   C21  N22   125.13  3.000
 GVJ  H21   C21  N20   121.31  3.000
 GVJ  N22   C21  N20   113.56  3.000
 GVJ  C23   N22  C21   104.75  3.000
 GVJ  N22   C23  C19   109.72  3.000
 GVJ  N22   C23  C15   134.09  3.000
 GVJ  C19   C23  C15   116.19  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
 GVJ  CONST_01  C6   C5   C4   C3     0.00  0.0  0
 GVJ  CONST_02  C6   C7   C8   C3     0.00  0.0  0
 GVJ  CONST_03  C7   C8   C3   C4     0.00  0.0  0
 GVJ  CONST_04  C7   C6   C5   C4     0.00  0.0  0
 GVJ  CONST_05  C8   C3   C4   C5     0.00  0.0  0
 GVJ  CONST_06  C8   C7   C6   C5     0.00  0.0  0
 GVJ  CONST_07  C12  C11  C10  C9     0.00  0.0  0
 GVJ  CONST_08  C12  C13  C14  C9     0.00  0.0  0
 GVJ  CONST_09  C13  C14  C9   C10    0.00  0.0  0
 GVJ  CONST_10  C13  C12  C11  C10    0.00  0.0  0
 GVJ  CONST_11  C15  C12  C11  C10  180.00  0.0  0
 GVJ  CONST_12  C14  C9   C10  C11    0.00  0.0  0
 GVJ  CONST_13  C14  C13  C12  C11    0.00  0.0  0
 GVJ  CONST_14  N16  C15  C12  C11  180.00  0.0  0
 GVJ  CONST_15  C23  C15  C12  C11    0.00  0.0  0
 GVJ  CONST_16  C17  N16  C15  C12  180.00  0.0  0
 GVJ  CONST_17  C19  C23  C15  C12  180.00  0.0  0
 GVJ  CONST_18  N16  C15  C12  C13    0.00  0.0  0
 GVJ  CONST_19  C23  C15  C12  C13  180.00  0.0  0
 GVJ  CONST_20  C15  C12  C13  C14  180.00  0.0  0
 GVJ  CONST_21  N18  C17  N16  C15    0.00  0.0  0
 GVJ  CONST_22  N18  C19  C23  C15    0.00  0.0  0
 GVJ  CONST_23  C19  C23  C15  N16    0.00  0.0  0
 GVJ  CONST_24  C19  N18  C17  N16    0.00  0.0  0
 GVJ  CONST_25  C23  C15  N16  C17    0.00  0.0  0
 GVJ  CONST_26  C23  C19  N18  C17    0.00  0.0  0
 GVJ  CONST_27  N22  C23  C15  C12    0.00  0.0  0
 GVJ  CONST_28  N22  C21  N20  C19    0.00  0.0  0
 GVJ  CONST_29  C21  N22  C23  C19    0.00  0.0  0
 GVJ  CONST_30  N22  C23  C19  N20    0.00  0.0  0
 GVJ  CONST_31  C23  N22  C21  N20    0.00  0.0  0
 GVJ  CONST_32  C23  C19  N20  C21    0.00  0.0  0
 GVJ  CONST_33  C5   C4   C3   C2   180.00  0.0  0
 GVJ  CONST_34  C7   C8   C3   C2   180.00  0.0  0
 GVJ  CONST_35  C11  C10  C9   C2   180.00  0.0  0
 GVJ  CONST_36  C13  C14  C9   C2   180.00  0.0  0
 GVJ  CONST_37  H5   C5   C4   C3   180.00  0.0  0
 GVJ  CONST_38  H7   C7   C8   C3   180.00  0.0  0
 GVJ  CONST_39  H8   C8   C3   C4   180.00  0.0  0
 GVJ  CONST_40  H6   C6   C5   C4   180.00  0.0  0
 GVJ  CONST_41  H4   C4   C5   C6   180.00  0.0  0
 GVJ  CONST_42  H11  C11  C10  C9   180.00  0.0  0
 GVJ  CONST_43  H13  C13  C14  C9   180.00  0.0  0
 GVJ  CONST_44  H14  C14  C9   C10  180.00  0.0  0
 GVJ  CONST_45  H10  C10  C11  C12  180.00  0.0  0
 GVJ  CONST_46  H17  C17  N16  C15  180.00  0.0  0
 GVJ  CONST_47  H21  C21  N20  C19  180.00  0.0  0
 GVJ  CONST_48  H20  N20  C21  N22  180.00  0.0  0

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
 GVJ  chir_01  C2  N1  C3  C9  negativ

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
 GVJ  plan-1  C2   0.020
 GVJ  plan-1  C3   0.020
 GVJ  plan-1  C4   0.020
 GVJ  plan-1  C5   0.020
 GVJ  plan-1  C6   0.020
 GVJ  plan-1  C7   0.020
 GVJ  plan-1  C8   0.020
 GVJ  plan-1  H4   0.020
 GVJ  plan-1  H8   0.020
 GVJ  plan-1  H5   0.020
 GVJ  plan-1  H6   0.020
 GVJ  plan-1  H7   0.020
 GVJ  plan-2  C2   0.020
 GVJ  plan-2  C9   0.020
 GVJ  plan-2  C10  0.020
 GVJ  plan-2  C11  0.020
 GVJ  plan-2  C12  0.020
 GVJ  plan-2  C13  0.020
 GVJ  plan-2  C14  0.020
 GVJ  plan-2  C15  0.020
 GVJ  plan-2  H10  0.020
 GVJ  plan-2  H14  0.020
 GVJ  plan-2  H11  0.020
 GVJ  plan-2  H13  0.020
 GVJ  plan-3  C12  0.020
 GVJ  plan-3  C15  0.020
 GVJ  plan-3  N16  0.020
 GVJ  plan-3  C17  0.020
 GVJ  plan-3  N18  0.020
 GVJ  plan-3  C19  0.020
 GVJ  plan-3  N20  0.020
 GVJ  plan-3  C21  0.020
 GVJ  plan-3  N22  0.020
 GVJ  plan-3  C23  0.020
 GVJ  plan-3  H17  0.020
 GVJ  plan-3  H20  0.020
 GVJ  plan-3  H21  0.020

