# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 09:21:37 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 7-(2,5-dihydro-1H-pyrrol-1-yl)-6-phenylpyrido[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc2cc(c3ccccc3)c(nc2n1)N4CC=CC4
#
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
 LZL  LZL  7-(2,5-dihydro-1H-pyrrol-1-yl)-6-phenylpyrido[2,3-d]pyrimidin-2-amine  ligand  37  22  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LZL
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
 LZL  N22   N  NH2   0  -0.816  2.0497  -27.6885  24.7774
 LZL  C21   C  CR6   0   0.541  2.4205  -26.3964  24.8211
 LZL  N20   N  N     0  -0.460  1.5310  -25.5547  25.4123
 LZL  C15   C  CR16  0  -0.043  1.8689  -24.2935  25.4464
 LZL  C9    C  CR66  0  -0.118  3.0654  -23.8100  24.9027
 LZL  C4    C  CR16  0  -0.211  3.5141  -22.4780  24.9625
 LZL  N18   N  N     0  -0.483  3.5776  -26.0634  24.2778
 LZL  C12   C  CR66  0   0.376  3.9153  -24.7644  24.3018
 LZL  N6    N  N     0  -0.509  5.0694  -24.4123  23.7302
 LZL  C2    C  CR6   0   0.499  5.4568  -23.1430  23.7271
 LZL  N5    N  NR5   0  -0.519  6.5820  -22.8920  23.0276
 LZL  C11   C  CH2   0  -0.292  7.0856  -21.5867  22.6029
 LZL  C17   C  CR15  0  -0.244  8.1415  -21.9521  21.6110
 LZL  C16   C  CR15  0  -0.256  8.2522  -23.2645  21.4795
 LZL  C10   C  CH2   0  -0.276  7.2650  -23.9847  22.3357
 LZL  C1    C  CR6   0  -0.053  4.7140  -22.1138  24.4238
 LZL  C3    C  CR6   0   0.013  5.1998  -20.7360  24.6734
 LZL  C8    C  CR16  0  -0.274  4.5576  -19.6367  24.1096
 LZL  C14   C  CR16  0  -0.244  4.9834  -18.3469  24.3982
 LZL  C19   C  CR16  0  -0.261  6.0542  -18.1412  25.2576
 LZL  C13   C  CR16  0  -0.241  6.6929  -19.2322  25.8336
 LZL  C7    C  CR16  0  -0.285  6.2655  -20.5204  25.5461
 LZL  H221  H  HNH2  0   0.396  2.7248  -28.3834  24.5101
 LZL  H222  H  HNH2  0   0.397  1.2626  -27.9915  25.3235
 LZL  H15   H  HCR6  0   0.272  1.1754  -23.6073  25.9256
 LZL  H4    H  HCR6  0   0.267  2.9179  -21.7396  25.4870
 LZL  H111  H  HCH2  0   0.257  6.2967  -20.9722  22.1590
 LZL  H112  H  HCH2  0   0.262  7.5095  -21.0124  23.4295
 LZL  H101  H  HCH2  0   0.248  7.7408  -24.6719  23.0429
 LZL  H102  H  HCH2  0   0.248  6.5674  -24.5825  21.7421
 LZL  H17   H  HCR5  0   0.260  8.7294  -21.2012  21.1027
 LZL  H16   H  HCR5  0   0.260  8.9460  -23.7886  20.8376
 LZL  H8    H  HCR6  0   0.253  3.7302  -19.7914  23.4280
 LZL  H7    H  HCR6  0   0.258  6.7636  -21.3678  26.0017
 LZL  H14   H  HCR6  0   0.258  4.4788  -17.5019  23.9476
 LZL  H19   H  HCR6  0   0.257  6.3886  -17.1361  25.4787
 LZL  H13   H  HCR6  0   0.258  7.5244  -19.0820  26.5099

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
 LZL  N22  C21   single    1.345  0.020  1.345
 LZL  C21  N20   aromatic  1.360  0.020  1.360
 LZL  C21  N18   aromatic  1.321  0.020  1.321
 LZL  N20  C15   aromatic  1.306  0.020  1.306
 LZL  C15  C9    aromatic  1.400  0.020  1.400
 LZL  C9   C4    aromatic  1.407  0.020  1.407
 LZL  C9   C12   aromatic  1.412  0.020  1.412
 LZL  C4   C1    aromatic  1.365  0.020  1.365
 LZL  N18  C12   aromatic  1.342  0.020  1.342
 LZL  C12  N6    aromatic  1.335  0.020  1.335
 LZL  N6   C2    aromatic  1.327  0.020  1.327
 LZL  C2   N5    single    1.349  0.020  1.349
 LZL  C2   C1    aromatic  1.448  0.020  1.448
 LZL  N5   C11   single    1.462  0.020  1.462
 LZL  N5   C10   single    1.463  0.020  1.463
 LZL  C11  C17   single    1.494  0.020  1.494
 LZL  C17  C16   double    1.324  0.020  1.324
 LZL  C16  C10   single    1.492  0.020  1.492
 LZL  C1   C3    single    1.482  0.020  1.482
 LZL  C3   C8    aromatic  1.392  0.020  1.392
 LZL  C3   C7    aromatic  1.394  0.020  1.394
 LZL  C8   C14   aromatic  1.389  0.020  1.389
 LZL  C14  C19   aromatic  1.388  0.020  1.388
 LZL  C19  C13   aromatic  1.389  0.020  1.389
 LZL  C13  C7    aromatic  1.387  0.020  1.387
 LZL  N22  H221  single    0.890  0.020  1.040
 LZL  N22  H222  single    0.890  0.020  1.040
 LZL  C15  H15   single    0.930  0.020  1.080
 LZL  C4   H4    single    0.930  0.020  1.080
 LZL  C11  H111  single    0.970  0.020  1.090
 LZL  C11  H112  single    0.970  0.020  1.090
 LZL  C10  H101  single    0.970  0.020  1.090
 LZL  C10  H102  single    0.970  0.020  1.090
 LZL  C17  H17   single    0.930  0.020  1.080
 LZL  C16  H16   single    0.930  0.020  1.080
 LZL  C8   H8    single    0.930  0.020  1.080
 LZL  C7   H7    single    0.930  0.020  1.080
 LZL  C14  H14   single    0.930  0.020  1.080
 LZL  C19  H19   single    0.930  0.020  1.080
 LZL  C13  H13   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
 LZL  H222  N22  H221  117.53  3.000
 LZL  H222  N22  C21   119.21  3.000
 LZL  H221  N22  C21   119.19  3.000
 LZL  N18   C21  N20   126.56  3.000
 LZL  N18   C21  N22   118.06  3.000
 LZL  N20   C21  N22   115.37  3.000
 LZL  C15   N20  C21   116.09  3.000
 LZL  H15   C15  C9    119.90  3.000
 LZL  H15   C15  N20   117.13  3.000
 LZL  C9    C15  N20   122.97  3.000
 LZL  C12   C9   C4    117.78  3.000
 LZL  C12   C9   C15   116.50  3.000
 LZL  C4    C9   C15   125.65  3.000
 LZL  H4    C4   C1    119.51  3.000
 LZL  H4    C4   C9    119.34  3.000
 LZL  C1    C4   C9    121.09  3.000
 LZL  C12   N18  C21   117.19  3.000
 LZL  N6    C12  N18   117.71  3.000
 LZL  N6    C12  C9    121.61  3.000
 LZL  N18   C12  C9    120.68  3.000
 LZL  C2    N6   C12   120.37  3.000
 LZL  C1    C2   N5    123.05  3.000
 LZL  C1    C2   N6    121.94  3.000
 LZL  N5    C2   N6    115.02  3.000
 LZL  C10   N5   C11   111.64  3.000
 LZL  C10   N5   C2    119.73  3.000
 LZL  C11   N5   C2    127.18  3.000
 LZL  H112  C11  H111  106.96  3.000
 LZL  H112  C11  C17   110.90  3.000
 LZL  H111  C11  C17   112.19  3.000
 LZL  H112  C11  N5    112.54  3.000
 LZL  H111  C11  N5    111.77  3.000
 LZL  C17   C11  N5    102.59  3.000
 LZL  H17   C17  C16   126.63  3.000
 LZL  H17   C17  C11   121.79  3.000
 LZL  C16   C17  C11   111.56  3.000
 LZL  H16   C16  C10   122.10  3.000
 LZL  H16   C16  C17   126.41  3.000
 LZL  C10   C16  C17   111.48  3.000
 LZL  H102  C10  H101  106.54  3.000
 LZL  H102  C10  C16   111.98  3.000
 LZL  H101  C10  C16   112.71  3.000
 LZL  H102  C10  N5    111.55  3.000
 LZL  H101  C10  N5    111.49  3.000
 LZL  C16   C10  N5    102.69  3.000
 LZL  C3    C1   C2    125.01  3.000
 LZL  C3    C1   C4    118.02  3.000
 LZL  C2    C1   C4    116.83  3.000
 LZL  C7    C3   C8    118.94  3.000
 LZL  C7    C3   C1    119.98  3.000
 LZL  C8    C3   C1    120.97  3.000
 LZL  H8    C8   C14   119.84  3.000
 LZL  H8    C8   C3    119.63  3.000
 LZL  C14   C8   C3    120.52  3.000
 LZL  H14   C14  C19   120.11  3.000
 LZL  H14   C14  C8    119.71  3.000
 LZL  C19   C14  C8    120.18  3.000
 LZL  H19   C19  C13   120.17  3.000
 LZL  H19   C19  C14   120.16  3.000
 LZL  C13   C19  C14   119.66  3.000
 LZL  H13   C13  C7    119.67  3.000
 LZL  H13   C13  C19   120.22  3.000
 LZL  C7    C13  C19   120.11  3.000
 LZL  H7    C7   C13   119.83  3.000
 LZL  H7    C7   C3    119.59  3.000
 LZL  C13   C7   C3    120.58  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
 LZL  CONST_01  C9    C15  N20  C21     0.00   0.0  0
 LZL  CONST_02  C9    C12  N18  C21     0.00   0.0  0
 LZL  CONST_03  N6    C12  N18  C21   180.00   0.0  0
 LZL  CONST_04  C12   N18  C21  N20     0.00   0.0  0
 LZL  CONST_05  C4    C9   C15  N20   180.00   0.0  0
 LZL  CONST_06  C12   C9   C15  N20     0.00   0.0  0
 LZL  CONST_07  N18   C21  N20  C15     0.00   0.0  0
 LZL  CONST_08  C1    C4   C9   C15   180.00   0.0  0
 LZL  CONST_09  N18   C12  C9   C15     0.00   0.0  0
 LZL  CONST_10  N6    C12  C9   C15   180.00   0.0  0
 LZL  CONST_11  C2    C1   C4   C9      0.00   0.0  0
 LZL  CONST_12  C3    C1   C4   C9    180.00   0.0  0
 LZL  CONST_13  C2    N6   C12  C9      0.00   0.0  0
 LZL  CONST_14  N18   C12  C9   C4    180.00   0.0  0
 LZL  CONST_15  N6    C12  C9   C4      0.00   0.0  0
 LZL  CONST_16  N6    C2   C1   C4      0.00   0.0  0
 LZL  CONST_19  C2    N6   C12  N18   180.00   0.0  0
 LZL  CONST_20  C1    C4   C9   C12     0.00   0.0  0
 LZL  CONST_21  C1    C2   N6   C12     0.00   0.0  0
 LZL  CONST_22  C3    C1   C2   N6    180.00   0.0  0
 LZL  CONST_25  C14   C8   C3   C1    180.00   0.0  0
 LZL  CONST_26  C13   C7   C3   C1    180.00   0.0  0
 LZL  CONST_27  C19   C14  C8   C3      0.00   0.0  0
 LZL  CONST_28  C19   C13  C7   C3      0.00   0.0  0
 LZL  CONST_29  C13   C7   C3   C8      0.00   0.0  0
 LZL  CONST_30  C13   C19  C14  C8      0.00   0.0  0
 LZL  CONST_31  C7    C3   C8   C14     0.00   0.0  0
 LZL  CONST_32  C7    C13  C19  C14     0.00   0.0  0
 LZL  CONST_33  N5    C2   C1   C4    180.00   0.0  0
 LZL  CONST_34  N5    C2   N6   C12   180.00   0.0  0
 LZL  CONST_35  C3    C1   C2   N5      0.00   0.0  0
 LZL  CONST_36  C15   N20  C21  N22   180.00   0.0  0
 LZL  CONST_37  C12   N18  C21  N22   180.00   0.0  0
 LZL  CONST_38  H15   C15  N20  C21   180.00   0.0  0
 LZL  CONST_39  H4    C4   C9   C15     0.00   0.0  0
 LZL  CONST_40  H8    C8   C3   C1      0.00   0.0  0
 LZL  CONST_41  H7    C7   C3   C1      0.00   0.0  0
 LZL  CONST_42  H14   C14  C8   C3    180.00   0.0  0
 LZL  CONST_43  H13   C13  C7   C3    180.00   0.0  0
 LZL  CONST_44  H19   C19  C14  C8    180.00   0.0  0
 LZL  CONST_45  H221  N22  C21  N20   180.00   0.0  0
 LZL  CONST_46  H222  N22  C21  N20     0.00   0.0  0
 LZL  Var_01    C11   N5   C2   N6    165.67  30.0  2
 LZL  Var_02    C17   C11  N5   C2   -166.74  30.0  1
 LZL  Var_03    C16   C10  N5   C2    168.67  30.0  1
 LZL  Var_04    C16   C17  C11  N5     -0.48  30.0  1
 LZL  Var_05    C17   C16  C10  N5     -1.77  30.0  1
 LZL  Var_06    C10   C16  C17  C11     1.45  30.0  1

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
 LZL  plan-1  C1    0.020
 LZL  plan-1  C3    0.020
 LZL  plan-1  C8    0.020
 LZL  plan-1  C14   0.020
 LZL  plan-1  C19   0.020
 LZL  plan-1  C13   0.020
 LZL  plan-1  C7    0.020
 LZL  plan-1  H8    0.020
 LZL  plan-1  H7    0.020
 LZL  plan-1  H14   0.020
 LZL  plan-1  H19   0.020
 LZL  plan-1  H13   0.020
 LZL  plan-2  N22   0.020
 LZL  plan-2  C21   0.020
 LZL  plan-2  N20   0.020
 LZL  plan-2  C15   0.020
 LZL  plan-2  C9    0.020
 LZL  plan-2  C4    0.020
 LZL  plan-2  N18   0.020
 LZL  plan-2  C12   0.020
 LZL  plan-2  N6    0.020
 LZL  plan-2  C2    0.020
 LZL  plan-2  N5    0.020
 LZL  plan-2  C1    0.020
 LZL  plan-2  C3    0.020
 LZL  plan-2  H15   0.020
 LZL  plan-2  H4    0.020
 LZL  plan-3  N22   0.020
 LZL  plan-3  C21   0.020
 LZL  plan-3  H221  0.020
 LZL  plan-3  H222  0.020

