# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:14:16 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN(C[C@@H]1N2CCCCC2=O)c3cc(ncn3)c4ccccc4
#
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
 NXZ  NXZ  1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one  ligand  48  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXZ
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
 NXZ  N1    N  NR5   0  -0.510   0.2725  -0.1550  -0.0966
 NXZ  C2    C  CR15  0  -0.116   1.9498  -0.8952   1.3607
 NXZ  C3    C  CR15  0  -0.104   2.5406   0.0499   0.3149
 NXZ  C4    C  CH2   0  -0.245   1.5175   0.0427  -0.8226
 NXZ  C5    C  CH2   0  -0.272   0.4760  -0.5070   1.2985
 NXZ  C6    C  CR6   0   0.064  -4.6139   0.1443   0.1230
 NXZ  C7    C  CR16  0  -0.284  -5.7059   0.8344  -0.4056
 NXZ  C8    C  CR16  0  -0.240  -6.9323   0.8158   0.2410
 NXZ  C9    C  CR16  0  -0.259  -7.0914   0.0960   1.4183
 NXZ  C10   C  CR16  0  -0.239  -6.0144  -0.6048   1.9453
 NXZ  C11   C  CR16  0  -0.315  -4.7855  -0.5796   1.3037
 NXZ  C12   C  CR6   0   0.269  -3.3083   0.1918  -0.5691
 NXZ  C13   C  CR16  0  -0.448  -2.1223  -0.0213   0.1012
 NXZ  C14   C  CR6   0   0.575  -0.9299   0.0479  -0.6484
 NXZ  N15   N  N     0  -0.472  -0.9683   0.3341  -1.9574
 NXZ  C16   C  CR16  0   0.051  -2.1615   0.5347  -2.4849
 NXZ  N17   N  N     0  -0.464  -3.3328   0.4775  -1.8819
 NXZ  N18   N  NH2   0  -0.799   2.5216  -0.6653   2.6729
 NXZ  N19   N  NT    0  -0.496   3.9318  -0.1504  -0.0537
 NXZ  C20   C  CH2   0  -0.283   4.7877   1.0225   0.1483
 NXZ  C21   C  CH2   0  -0.469   6.2654   0.7137   0.0568
 NXZ  C22   C  CH2   0  -0.450   6.5424  -0.0999  -1.1913
 NXZ  C23   C  CH2   0  -0.552   5.7837  -1.4100  -1.0862
 NXZ  C24   C  C     0   0.549   4.3336  -1.2874  -0.6664
 NXZ  O25   O  O     0  -0.512   3.5697  -2.2257  -0.8643
 NXZ  H2    H  HCR5  0   0.244   2.0500  -1.9301   1.0184
 NXZ  H3    H  HCR5  0   0.270   2.5024   1.0441   0.7691
 NXZ  H4    H  HCH2  0   0.248   1.6881  -0.7583  -1.5420
 NXZ  H4A   H  HCH2  0   0.250   1.5151   0.9882  -1.3663
 NXZ  H5    H  HCH2  0   0.239   0.2821   0.3430   1.9630
 NXZ  H5A   H  HCH2  0   0.257  -0.1758  -1.3289   1.6022
 NXZ  H7    H  HCR6  0   0.255  -5.5883   1.3959  -1.3225
 NXZ  H8    H  HCR6  0   0.259  -7.7657   1.3668  -0.1749
 NXZ  H9    H  HCR6  0   0.261  -8.0505   0.0760   1.9193
 NXZ  H10   H  HCR6  0   0.261  -6.1315  -1.1785   2.8553
 NXZ  H11   H  HCR6  0   0.253  -3.9643  -1.1486   1.7202
 NXZ  H13   H  HCR6  0   0.276  -2.1032  -0.2010   1.1658
 NXZ  H16   H  HCR6  0   0.250  -2.1775   0.7709  -3.5448
 NXZ  HN18  H  HNH2  0   0.353   2.1013  -1.3015   3.3399
 NXZ  HN1A  H  HNH2  0   0.349   3.5024  -0.9184   2.6529
 NXZ  H20   H  HCH2  0   0.241   4.5252   1.7866  -0.5913
 NXZ  H20A  H  HCH2  0   0.255   4.5564   1.4380   1.1301
 NXZ  H21   H  HCH2  0   0.253   6.8134   1.6570   0.0532
 NXZ  H21A  H  HCH2  0   0.234   6.5912   0.1593   0.9417
 NXZ  H22   H  HCH2  0   0.231   6.2190   0.4548  -2.0765
 NXZ  H22A  H  HCH2  0   0.249   7.6091  -0.2939  -1.3108
 NXZ  H23   H  HCH2  0   0.268   5.7943  -1.9609  -2.0279
 NXZ  H23A  H  HCH2  0   0.266   6.2673  -2.0603  -0.3497

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
 NXZ  C4   N1    single    1.455  0.020  1.455
 NXZ  C5   N1    single    1.453  0.020  1.453
 NXZ  N1   C14   single    1.338  0.020  1.338
 NXZ  N18  C2    single    1.450  0.020  1.450
 NXZ  C2   C3    single    1.528  0.020  1.528
 NXZ  C2   C5    single    1.525  0.020  1.525
 NXZ  C2   H2    single    0.970  0.020  1.090
 NXZ  N19  C3    single    1.453  0.020  1.453
 NXZ  C3   C4    single    1.530  0.020  1.530
 NXZ  C3   H3    single    0.970  0.020  1.090
 NXZ  C4   H4    single    0.970  0.020  1.090
 NXZ  C4   H4A   single    0.970  0.020  1.090
 NXZ  C5   H5    single    0.970  0.020  1.090
 NXZ  C5   H5A   single    0.970  0.020  1.090
 NXZ  C12  C6    single    1.478  0.020  1.478
 NXZ  C11  C6    aromatic  1.396  0.020  1.396
 NXZ  C6   C7    aromatic  1.396  0.020  1.396
 NXZ  C7   C8    aromatic  1.387  0.020  1.387
 NXZ  C7   H7    single    0.930  0.020  1.080
 NXZ  C9   C8    aromatic  1.389  0.020  1.389
 NXZ  C8   H8    single    0.930  0.020  1.080
 NXZ  C10  C9    aromatic  1.389  0.020  1.389
 NXZ  C9   H9    single    0.930  0.020  1.080
 NXZ  C11  C10   aromatic  1.387  0.020  1.387
 NXZ  C10  H10   single    0.930  0.020  1.080
 NXZ  C11  H11   single    0.930  0.020  1.080
 NXZ  C13  C12   aromatic  1.379  0.020  1.379
 NXZ  C12  N17   aromatic  1.344  0.020  1.344
 NXZ  C14  C13   aromatic  1.410  0.020  1.410
 NXZ  C13  H13   single    0.930  0.020  1.080
 NXZ  C14  N15   aromatic  1.340  0.020  1.340
 NXZ  N15  C16   aromatic  1.320  0.020  1.320
 NXZ  C16  N17   aromatic  1.319  0.020  1.319
 NXZ  C16  H16   single    0.930  0.020  1.080
 NXZ  N18  HN18  single    0.890  0.020  1.040
 NXZ  N18  HN1A  single    0.890  0.020  1.040
 NXZ  C20  N19   single    1.466  0.020  1.466
 NXZ  C24  N19   single    1.353  0.020  1.353
 NXZ  C21  C20   single    1.512  0.020  1.512
 NXZ  C20  H20   single    0.970  0.020  1.090
 NXZ  C20  H20A  single    0.970  0.020  1.090
 NXZ  C22  C21   single    1.515  0.020  1.515
 NXZ  C21  H21   single    0.970  0.020  1.090
 NXZ  C21  H21A  single    0.970  0.020  1.090
 NXZ  C22  C23   single    1.518  0.020  1.518
 NXZ  C22  H22   single    0.970  0.020  1.090
 NXZ  C22  H22A  single    0.970  0.020  1.090
 NXZ  C23  C24   single    1.515  0.020  1.515
 NXZ  C23  H23   single    0.970  0.020  1.090
 NXZ  C23  H23A  single    0.970  0.020  1.090
 NXZ  C24  O25   double    1.226  0.020  1.226

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
 NXZ  C14   N1   C5    123.94  3.000
 NXZ  C14   N1   C4    122.85  3.000
 NXZ  C5    N1   C4    113.09  3.000
 NXZ  H2    C2   N18   113.39  3.000
 NXZ  H2    C2   C5    108.44  3.000
 NXZ  N18   C2   C5    112.19  3.000
 NXZ  H2    C2   C3    109.58  3.000
 NXZ  C5    C2   C3    100.85  3.000
 NXZ  N18   C2   C3    111.64  3.000
 NXZ  H3    C3   N19   105.31  3.000
 NXZ  H3    C3   C4    106.84  3.000
 NXZ  N19   C3   C4    116.81  3.000
 NXZ  H3    C3   C2    105.34  3.000
 NXZ  C4    C3   C2    104.32  3.000
 NXZ  N19   C3   C2    117.29  3.000
 NXZ  H4A   C4   H4    107.96  3.000
 NXZ  H4A   C4   C3    111.60  3.000
 NXZ  H4    C4   C3    112.92  3.000
 NXZ  H4A   C4   N1    111.39  3.000
 NXZ  H4    C4   N1    111.31  3.000
 NXZ  C3    C4   N1    101.65  3.000
 NXZ  H5A   C5   H5    108.03  3.000
 NXZ  H5A   C5   C2    111.95  3.000
 NXZ  H5    C5   C2    110.10  3.000
 NXZ  H5A   C5   N1    111.45  3.000
 NXZ  H5    C5   N1    111.67  3.000
 NXZ  C2    C5   N1    103.66  3.000
 NXZ  C12   C6   C11   121.41  3.000
 NXZ  C11   C6   C7    118.73  3.000
 NXZ  C12   C6   C7    119.86  3.000
 NXZ  H7    C7   C8    119.90  3.000
 NXZ  H7    C7   C6    119.51  3.000
 NXZ  C8    C7   C6    120.59  3.000
 NXZ  H8    C8   C9    120.09  3.000
 NXZ  H8    C8   C7    119.68  3.000
 NXZ  C9    C8   C7    120.23  3.000
 NXZ  H9    C9   C10   120.15  3.000
 NXZ  H9    C9   C8    120.23  3.000
 NXZ  C10   C9   C8    119.62  3.000
 NXZ  H10   C10  C11   119.65  3.000
 NXZ  H10   C10  C9    120.18  3.000
 NXZ  C11   C10  C9    120.17  3.000
 NXZ  H11   C11  C10   119.00  3.000
 NXZ  H11   C11  C6    120.33  3.000
 NXZ  C10   C11  C6    120.66  3.000
 NXZ  N17   C12  C13   121.57  3.000
 NXZ  N17   C12  C6    116.61  3.000
 NXZ  C13   C12  C6    121.81  3.000
 NXZ  H13   C13  C14   121.15  3.000
 NXZ  H13   C13  C12   121.35  3.000
 NXZ  C14   C13  C12   117.47  3.000
 NXZ  N15   C14  C13   120.35  3.000
 NXZ  N15   C14  N1    117.43  3.000
 NXZ  C13   C14  N1    122.21  3.000
 NXZ  C16   N15  C14   116.66  3.000
 NXZ  H16   C16  N17   116.28  3.000
 NXZ  H16   C16  N15   115.87  3.000
 NXZ  N17   C16  N15   127.85  3.000
 NXZ  C16   N17  C12   116.09  3.000
 NXZ  HN1A  N18  HN18  104.93  3.000
 NXZ  HN1A  N18  C2    108.93  3.000
 NXZ  HN18  N18  C2    109.43  3.000
 NXZ  C24   N19  C20   124.16  3.000
 NXZ  C24   N19  C3    121.01  3.000
 NXZ  C20   N19  C3    114.44  3.000
 NXZ  H20A  C20  H20   106.94  3.000
 NXZ  H20A  C20  C21   109.83  3.000
 NXZ  H20   C20  C21   109.61  3.000
 NXZ  H20A  C20  N19   107.76  3.000
 NXZ  H20   C20  N19   108.97  3.000
 NXZ  C21   C20  N19   113.50  3.000
 NXZ  H21A  C21  H21   106.94  3.000
 NXZ  H21A  C21  C22   109.86  3.000
 NXZ  H21   C21  C22   111.70  3.000
 NXZ  H21A  C21  C20   110.21  3.000
 NXZ  H21   C21  C20   108.33  3.000
 NXZ  C22   C21  C20   109.76  3.000
 NXZ  H22A  C22  H22   106.90  3.000
 NXZ  H22A  C22  C23   110.06  3.000
 NXZ  H22   C22  C23   110.24  3.000
 NXZ  H22A  C22  C21   111.37  3.000
 NXZ  H22   C22  C21   109.90  3.000
 NXZ  C23   C22  C21   108.37  3.000
 NXZ  H23A  C23  H23   106.04  3.000
 NXZ  H23A  C23  C24   106.53  3.000
 NXZ  H23   C23  C24   106.83  3.000
 NXZ  H23A  C23  C22   109.78  3.000
 NXZ  H23   C23  C22   111.80  3.000
 NXZ  C24   C23  C22   115.34  3.000
 NXZ  O25   C24  C23   119.33  3.000
 NXZ  O25   C24  N19   122.10  3.000
 NXZ  C23   C24  N19   118.56  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
 NXZ  CONST_01  C14  C13  C12  C6    180.00   0.0  0
 NXZ  CONST_02  C16  N17  C12  C6    180.00   0.0  0
 NXZ  CONST_03  C9   C10  C11  C6      0.00   0.0  0
 NXZ  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 NXZ  CONST_07  C10  C11  C6   C7      0.00   0.0  0
 NXZ  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 NXZ  CONST_09  C12  C6   C7   C8    180.00   0.0  0
 NXZ  CONST_10  C11  C6   C7   C8      0.00   0.0  0
 NXZ  CONST_11  C11  C10  C9   C8      0.00   0.0  0
 NXZ  CONST_12  C12  C6   C11  C10   180.00   0.0  0
 NXZ  CONST_15  N15  C14  C13  C12     0.00   0.0  0
 NXZ  CONST_16  N15  C16  N17  C12     0.00   0.0  0
 NXZ  CONST_17  C16  N17  C12  C13     0.00   0.0  0
 NXZ  CONST_18  C16  N15  C14  C13     0.00   0.0  0
 NXZ  CONST_19  N17  C12  C13  C14     0.00   0.0  0
 NXZ  CONST_20  N17  C16  N15  C14     0.00   0.0  0
 NXZ  CONST_21  C12  C13  C14  N1    180.00   0.0  0
 NXZ  CONST_22  C16  N15  C14  N1    180.00   0.0  0
 NXZ  CONST_23  C23  C24  N19  C3    180.00   0.0  0
 NXZ  CONST_24  C23  C24  N19  C20     0.00   0.0  0
 NXZ  CONST_25  O25  C24  N19  C3      0.00   0.0  0
 NXZ  CONST_26  O25  C24  N19  C20   180.00   0.0  0
 NXZ  CONST_27  H13  C13  C14  N1      0.00   0.0  0
 NXZ  CONST_28  H10  C10  C11  C6    180.00   0.0  0
 NXZ  CONST_29  H8   C8   C7   C6    180.00   0.0  0
 NXZ  CONST_30  H11  C11  C6   C7    180.00   0.0  0
 NXZ  CONST_31  H9   C9   C8   C7    180.00   0.0  0
 NXZ  CONST_32  H7   C7   C8   C9    180.00   0.0  0
 NXZ  CONST_33  H16  C16  N17  C12   180.00   0.0  0
 NXZ  Var_01    C4   N1   C5   C2    -14.71  30.0  1
 NXZ  Var_02    C21  C20  N19  C3    167.15  30.0  1
 NXZ  Var_03    C5   N1   C4   C3    -10.62  30.0  1
 NXZ  Var_04    C13  C14  N1   C4   -173.70  30.0  2
 NXZ  Var_05    C22  C21  C20  N19    48.56  30.0  1
 NXZ  Var_06    C22  C23  C24  N19   -19.05  30.0  1
 NXZ  Var_07    C23  C22  C21  C20   -61.74  30.0  1
 NXZ  Var_08    C24  C23  C22  C21    47.30  30.0  1

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
 NXZ  chir_01  C2  N18  C3  C5  positiv
 NXZ  chir_02  C3  N19  C2  C4  positiv

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
 NXZ  plan-1  C6   0.020
 NXZ  plan-1  C7   0.020
 NXZ  plan-1  C8   0.020
 NXZ  plan-1  C9   0.020
 NXZ  plan-1  C10  0.020
 NXZ  plan-1  C11  0.020
 NXZ  plan-1  C12  0.020
 NXZ  plan-1  H7   0.020
 NXZ  plan-1  H8   0.020
 NXZ  plan-1  H9   0.020
 NXZ  plan-1  H10  0.020
 NXZ  plan-1  H11  0.020
 NXZ  plan-2  N1   0.020
 NXZ  plan-2  C6   0.020
 NXZ  plan-2  C12  0.020
 NXZ  plan-2  C13  0.020
 NXZ  plan-2  C14  0.020
 NXZ  plan-2  N15  0.020
 NXZ  plan-2  C16  0.020
 NXZ  plan-2  N17  0.020
 NXZ  plan-2  H13  0.020
 NXZ  plan-2  H16  0.020
 NXZ  plan-3  C3   0.020
 NXZ  plan-3  N19  0.020
 NXZ  plan-3  C20  0.020
 NXZ  plan-3  C23  0.020
 NXZ  plan-3  C24  0.020
 NXZ  plan-3  O25  0.020

