# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:21:38 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-(morpholin-4-yl)-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(cc1NCc2cnc(N)nc2)N3CCOCC3)[N+]([O-])=O
#
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
 Z04  Z04  2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-(morpholin-4-yl)-5-nitrobenzamide  ligand  46  27  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z04
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
 Z04  N01   N  NH1    0  -0.685   1.5554  -0.3794   0.1590
 Z04  N02   N  NH2    0  -0.811   0.2075  -4.2288  -0.8295
 Z04  N03   N  N      0  -0.451   5.6646   0.7140  -0.9040
 Z04  N04   N  N      0  -0.452   5.7024   0.7329   1.4733
 Z04  N05   N  NT     0  -0.494  -2.9206   1.2985   0.0129
 Z04  N06   N  NH2    0  -0.817   7.6370   0.5560   0.2544
 Z04  N07   N  N      1   0.327  -3.8887  -1.5082   0.1492
 Z04  C08   C  CR16   0  -0.336  -1.6026  -2.1600  -0.1553
 Z04  C09   C  CR6    0  -0.148  -0.2379  -1.9657  -0.1306
 Z04  C11   C  CR6    0   0.453   0.2447  -0.6356   0.0688
 Z04  C12   C  CR16   0  -0.520  -0.6902   0.4144   0.1033
 Z04  C13   C  CR6    0   0.437  -2.0632   0.2228   0.0326
 Z04  C14   C  CR6    0   0.149  -2.5206  -1.1235  -0.0407
 Z04  C16   C  CH2    0  -0.352   2.1269   0.9393   0.3333
 Z04  C17   C  CR6    0  -0.094   3.6199   0.8588   0.3169
 Z04  C18   C  CR16   0  -0.018   4.3491   0.8025  -0.8649
 Z04  C19   C  CR6    0   0.553   6.2975   0.6788   0.2761
 Z04  C20   C  CR16   0  -0.024   4.3847   0.8192   1.4742
 Z04  C21   C  CH2    0  -0.337  -3.8318   1.4327  -1.1199
 Z04  C22   C  CH2    0  -0.184  -4.9738   2.3588  -0.7582
 Z04  C23   C  CH2    0  -0.345  -2.4371   2.5967   0.4463
 Z04  C24   C  CH2    0  -0.180  -3.6265   3.4901   0.7568
 Z04  O25   O  O      0  -0.504   1.8551  -3.0590   0.1462
 Z04  O26   O  O2     0  -0.483  -4.4964   3.6194  -0.3429
 Z04  O27   O  O      0  -0.408  -4.2334  -2.6136  -0.2263
 Z04  O28   O  O     -1  -0.395  -4.6483  -0.7450   0.7084
 Z04  HN01  H  HNH1   0   0.410   2.1651  -1.1846   0.2057
 Z04  HN02  H  HNH2   0   0.415  -0.6522  -4.2446  -1.3494
 Z04  HN0A  H  HNH2   0   0.408   0.8196  -5.0198  -0.9491
 Z04  HN06  H  HNH2   0   0.398   8.1230   0.7031  -0.6131
 Z04  HN0B  H  HNH2   0   0.398   8.1530   0.7208   1.1011
 Z04  H08   H  HCR6   0   0.288  -1.9898  -3.1675  -0.2067
 Z04  H12   H  HCR6   0   0.304  -0.3180   1.4266   0.1409
 Z04  H16   H  HCH2   0   0.260   1.7870   1.6008  -0.4693
 Z04  H16A  H  HCH2   0   0.261   1.7888   1.3869   1.2746
 Z04  H18   H  HCR6   0   0.270   3.8392   0.8381  -1.8240
 Z04  H20   H  HCR6   0   0.269   3.9047   0.8674   2.4479
 Z04  H21   H  HCH2   0   0.241  -3.2841   1.8434  -1.9798
 Z04  H21A  H  HCH2   0   0.263  -4.2329   0.4737  -1.4367
 Z04  H22   H  HCH2   0   0.242  -5.6068   2.5201  -1.6319
 Z04  H22A  H  HCH2   0   0.211  -5.5847   1.8956   0.0275
 Z04  H23   H  HCH2   0   0.267  -1.8505   2.4879   1.3597
 Z04  H23A  H  HCH2   0   0.230  -1.7961   3.0736  -0.3099
 Z04  H24   H  HCH2   0   0.208  -4.1604   3.0834   1.6267
 Z04  H24A  H  HCH2   0   0.245  -3.2723   4.4888   1.0156
 Z04  C15   C  C      0   0.535   0.6928  -3.1154  -0.2580

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
 Z04  N01  C11   single    1.339  0.020  1.339
 Z04  N01  C16   single    1.448  0.020  1.448
 Z04  N01  HN01  single    0.860  0.020  1.020
 Z04  N02  C15   single    1.342  0.020  1.342
 Z04  N02  HN02  single    0.860  0.020  1.020
 Z04  N02  HN0A  single    0.860  0.020  1.020
 Z04  N03  C18   aromatic  1.319  0.020  1.319
 Z04  N03  C19   aromatic  1.340  0.020  1.340
 Z04  N04  C19   aromatic  1.338  0.020  1.338
 Z04  N04  C20   aromatic  1.321  0.020  1.321
 Z04  N05  C13   single    1.376  0.020  1.376
 Z04  N05  C21   single    1.460  0.020  1.460
 Z04  N05  C23   single    1.452  0.020  1.452
 Z04  N06  C19   single    1.345  0.020  1.345
 Z04  N06  HN06  single    0.890  0.020  1.040
 Z04  N06  HN0B  single    0.890  0.020  1.040
 Z04  N07  C14   single    1.434  0.020  1.434
 Z04  N07  O27   double    1.217  0.020  1.217
 Z04  N07  O28   single    1.213  0.020  1.213
 Z04  C08  C09   aromatic  1.379  0.020  1.379
 Z04  C08  C14   aromatic  1.389  0.020  1.389
 Z04  C08  H08   single    0.930  0.020  1.080
 Z04  C09  C11   aromatic  1.429  0.020  1.429
 Z04  C09  C15   single    1.485  0.020  1.485
 Z04  C11  C12   aromatic  1.406  0.020  1.406
 Z04  C12  C13   aromatic  1.388  0.020  1.388
 Z04  C12  H12   single    0.930  0.020  1.080
 Z04  C13  C14   aromatic  1.424  0.020  1.424
 Z04  C15  O25   double    1.232  0.020  1.232
 Z04  C16  C17   single    1.495  0.020  1.495
 Z04  C16  H16   single    0.970  0.020  1.090
 Z04  C16  H16A  single    0.970  0.020  1.090
 Z04  C17  C18   aromatic  1.390  0.020  1.390
 Z04  C17  C20   aromatic  1.388  0.020  1.388
 Z04  C18  H18   single    0.930  0.020  1.080
 Z04  C20  H20   single    0.930  0.020  1.080
 Z04  C21  C22   single    1.514  0.020  1.514
 Z04  C21  H21   single    0.970  0.020  1.090
 Z04  C21  H21A  single    0.970  0.020  1.090
 Z04  C22  O26   single    1.410  0.020  1.410
 Z04  C22  H22   single    0.970  0.020  1.090
 Z04  C22  H22A  single    0.970  0.020  1.090
 Z04  C23  C24   single    1.520  0.020  1.520
 Z04  C23  H23   single    0.970  0.020  1.090
 Z04  C23  H23A  single    0.970  0.020  1.090
 Z04  C24  O26   single    1.408  0.020  1.408
 Z04  C24  H24   single    0.970  0.020  1.090
 Z04  C24  H24A  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
 Z04  HN01  N01  C16   118.80  3.000
 Z04  HN01  N01  C11   116.18  3.000
 Z04  C16   N01  C11   124.68  3.000
 Z04  HN0A  N02  HN02  116.49  3.000
 Z04  HN0A  N02  C15   118.83  3.000
 Z04  HN02  N02  C15   122.86  3.000
 Z04  C19   N03  C18   116.55  3.000
 Z04  C20   N04  C19   116.56  3.000
 Z04  C23   N05  C21   110.94  3.000
 Z04  C23   N05  C13   119.18  3.000
 Z04  C21   N05  C13   118.16  3.000
 Z04  HN0B  N06  HN06  117.06  3.000
 Z04  HN0B  N06  C19   118.85  3.000
 Z04  HN06  N06  C19   118.82  3.000
 Z04  O28   N07  O27   122.41  3.000
 Z04  O28   N07  C14   119.32  3.000
 Z04  O27   N07  C14   118.23  3.000
 Z04  H08   C08  C14   117.57  3.000
 Z04  H08   C08  C09   119.14  3.000
 Z04  C14   C08  C09   123.19  3.000
 Z04  C15   C09  C11   121.40  3.000
 Z04  C15   C09  C08   120.65  3.000
 Z04  C11   C09  C08   117.90  3.000
 Z04  C12   C11  C09   118.28  3.000
 Z04  C12   C11  N01   120.43  3.000
 Z04  C09   C11  N01   121.22  3.000
 Z04  H12   C12  C13   118.19  3.000
 Z04  H12   C12  C11   118.16  3.000
 Z04  C13   C12  C11   123.59  3.000
 Z04  C14   C13  C12   116.80  3.000
 Z04  C14   C13  N05   122.58  3.000
 Z04  C12   C13  N05   120.61  3.000
 Z04  C13   C14  C08   119.83  3.000
 Z04  C13   C14  N07   123.60  3.000
 Z04  C08   C14  N07   116.18  3.000
 Z04  H16A  C16  H16   106.70  3.000
 Z04  H16A  C16  C17   109.85  3.000
 Z04  H16   C16  C17   109.55  3.000
 Z04  H16A  C16  N01   110.71  3.000
 Z04  H16   C16  N01   109.86  3.000
 Z04  C17   C16  N01   110.11  3.000
 Z04  C20   C17  C18   114.76  3.000
 Z04  C20   C17  C16   122.86  3.000
 Z04  C18   C17  C16   122.37  3.000
 Z04  H18   C18  C17   120.19  3.000
 Z04  H18   C18  N03   116.36  3.000
 Z04  C17   C18  N03   123.45  3.000
 Z04  N06   C19  N04   117.45  3.000
 Z04  N06   C19  N03   117.30  3.000
 Z04  N04   C19  N03   125.24  3.000
 Z04  H20   C20  C17   120.17  3.000
 Z04  H20   C20  N04   116.38  3.000
 Z04  C17   C20  N04   123.45  3.000
 Z04  H21A  C21  H21   106.60  3.000
 Z04  H21A  C21  C22   109.33  3.000
 Z04  H21   C21  C22   109.52  3.000
 Z04  H21A  C21  N05   112.06  3.000
 Z04  H21   C21  N05   109.30  3.000
 Z04  C22   C21  N05   109.97  3.000
 Z04  H22A  C22  H22   108.22  3.000
 Z04  H22A  C22  O26   110.78  3.000
 Z04  H22   C22  O26   107.47  3.000
 Z04  H22A  C22  C21   109.43  3.000
 Z04  H22   C22  C21   109.68  3.000
 Z04  O26   C22  C21   111.21  3.000
 Z04  H23A  C23  H23   107.79  3.000
 Z04  H23A  C23  C24   109.98  3.000
 Z04  H23   C23  C24   107.97  3.000
 Z04  H23A  C23  N05   112.12  3.000
 Z04  H23   C23  N05   109.87  3.000
 Z04  C24   C23  N05   109.04  3.000
 Z04  H24A  C24  H24   107.99  3.000
 Z04  H24A  C24  O26   107.57  3.000
 Z04  H24   C24  O26   110.62  3.000
 Z04  H24A  C24  C23   109.43  3.000
 Z04  H24   C24  C23   108.93  3.000
 Z04  O26   C24  C23   112.21  3.000
 Z04  C24   O26  C22   110.92  3.000
 Z04  O25   C15  C09   121.86  3.000
 Z04  O25   C15  N02   121.25  3.000
 Z04  C09   C15  N02   116.89  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
 Z04  CONST_01  C20   C17  C18  N03     0.00   0.0  0
 Z04  CONST_02  C20   N04  C19  N03     0.00   0.0  0
 Z04  CONST_03  C18   N03  C19  N04     0.00   0.0  0
 Z04  CONST_04  C18   C17  C20  N04     0.00   0.0  0
 Z04  CONST_05  C12   C11  C09  C08     0.00   0.0  0
 Z04  CONST_06  C12   C13  C14  C08     0.00   0.0  0
 Z04  CONST_07  C13   C14  C08  C09     0.00   0.0  0
 Z04  CONST_08  C13   C12  C11  C09     0.00   0.0  0
 Z04  CONST_09  C14   C08  C09  C11     0.00   0.0  0
 Z04  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 Z04  CONST_11  C19   N03  C18  C17     0.00   0.0  0
 Z04  CONST_12  C19   N04  C20  C17     0.00   0.0  0
 Z04  CONST_13  C11   C12  C13  N05   180.00   0.0  0
 Z04  CONST_14  C08   C14  C13  N05   180.00   0.0  0
 Z04  CONST_15  C08   C09  C11  N01   180.00   0.0  0
 Z04  CONST_16  C13   C12  C11  N01   180.00   0.0  0
 Z04  CONST_17  C16   C17  C18  N03   180.00   0.0  0
 Z04  CONST_18  C16   C17  C20  N04   180.00   0.0  0
 Z04  CONST_19  N07   C14  C13  N05     0.00   0.0  0
 Z04  CONST_20  C18   N03  C19  N06   180.00   0.0  0
 Z04  CONST_21  C20   N04  C19  N06   180.00   0.0  0
 Z04  CONST_22  C09   C08  C14  N07   180.00   0.0  0
 Z04  CONST_23  C12   C13  C14  N07   180.00   0.0  0
 Z04  CONST_24  C15   C09  C11  C12   180.00   0.0  0
 Z04  CONST_25  C15   C09  C08  C14   180.00   0.0  0
 Z04  CONST_26  H12   C12  C13  N05     0.00   0.0  0
 Z04  CONST_27  H08   C08  C09  C11   180.00   0.0  0
 Z04  CONST_28  H20   C20  C17  C18   180.00   0.0  0
 Z04  CONST_29  H18   C18  N03  C19   180.00   0.0  0
 Z04  CONST_32  C16   N01  C11  C09   180.00   0.0  0
 Z04  CONST_33  C16   N01  C11  C12     0.00   0.0  0
 Z04  CONST_36  HN06  N06  C19  N03     0.00   0.0  0
 Z04  CONST_37  HN0B  N06  C19  N03   180.00   0.0  0
 Z04  CONST_38  HN01  N01  C11  C09     0.00   0.0  0
 Z04  CONST_39  HN02  N02  C15  C09     0.00   0.0  0
 Z04  CONST_40  HN0A  N02  C15  C09   180.00   0.0  0
 Z04  Var_01    O26   C22  C21  N05    56.70  30.0  1
 Z04  Var_02    O26   C24  C23  N05   -56.73  30.0  1
 Z04  Var_03    C21   N05  C13  C12   122.16  30.0  2
 Z04  Var_04    C22   C21  N05  C13   161.05  30.0  1
 Z04  Var_05    C24   C23  N05  C13  -162.14  30.0  1
 Z04  Var_06    C23   C24  O26  C22    58.21  30.0  1
 Z04  Var_07    C18   C17  C16  N01    81.57  30.0  2
 Z04  Var_08    C08   C09  C15  N02    21.69  30.0  2
 Z04  Var_09    C17   C16  N01  C11  -176.86  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
 Z04  plan-1  N03   0.020
 Z04  plan-1  N04   0.020
 Z04  plan-1  N06   0.020
 Z04  plan-1  C16   0.020
 Z04  plan-1  C17   0.020
 Z04  plan-1  C18   0.020
 Z04  plan-1  C19   0.020
 Z04  plan-1  C20   0.020
 Z04  plan-1  H18   0.020
 Z04  plan-1  H20   0.020
 Z04  plan-2  N01   0.020
 Z04  plan-2  N05   0.020
 Z04  plan-2  N07   0.020
 Z04  plan-2  C08   0.020
 Z04  plan-2  C09   0.020
 Z04  plan-2  C11   0.020
 Z04  plan-2  C12   0.020
 Z04  plan-2  C13   0.020
 Z04  plan-2  C14   0.020
 Z04  plan-2  H08   0.020
 Z04  plan-2  H12   0.020
 Z04  plan-2  C15   0.020
 Z04  plan-3  N01   0.020
 Z04  plan-3  C11   0.020
 Z04  plan-3  C16   0.020
 Z04  plan-3  HN01  0.020
 Z04  plan-4  N06   0.020
 Z04  plan-4  C19   0.020
 Z04  plan-4  HN06  0.020
 Z04  plan-4  HN0B  0.020
 Z04  plan-5  N07   0.020
 Z04  plan-5  C14   0.020
 Z04  plan-5  O27   0.020
 Z04  plan-5  O28   0.020
 Z04  plan-6  N02   0.020
 Z04  plan-6  C09   0.020
 Z04  plan-6  O25   0.020
 Z04  plan-6  HN02  0.020
 Z04  plan-6  HN0A  0.020
 Z04  plan-6  C15   0.020

