# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 18:58:00 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cccc(c1)c2c[nH]c3ncnc(N4CCOCC4)c23
#
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
 3FE  3FE  3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile  ligand  38  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3FE
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
 3FE  N3   N  N     0  -0.438  -3.5088   2.3090   0.0919
 3FE  C4   C  CR16  0  -0.306   2.3745   1.1050  -0.4692
 3FE  N2   N  N     0  -0.472  -3.4069  -0.0497   0.3341
 3FE  C7   C  CR5   0  -0.034  -0.0092   1.5787   0.0384
 3FE  C6   C  CR16  0  -0.289   1.3127  -0.1038   1.3081
 3FE  C9   C  CR56  0   0.491  -2.1821   2.2717  -0.0071
 3FE  C13  C  CH2   0  -0.312  -2.2926  -2.4884   0.4028
 3FE  C8   C  CR15  0  -0.038  -0.0723   2.9374  -0.1212
 3FE  N5   N  NS    0  -0.250   5.6643   0.9522  -1.5986
 3FE  C16  C  CH2   0  -0.337  -0.6098  -1.5694  -1.0584
 3FE  C1   C  CR16  0  -0.227   2.4992  -0.7682   1.5791
 3FE  C2   C  CR16  0  -0.258   3.6379  -0.5028   0.8372
 3FE  C3   C  CR6   0   0.030   3.5663   0.4405  -0.1866
 3FE  C5   C  CR6   0   0.026   1.2324   0.8409   0.2813
 3FE  N1   N  NR15  0  -0.659  -1.3725   3.3456  -0.1612
 3FE  C10  C  CR56  0  -0.071  -1.3735   1.1244   0.0810
 3FE  C11  C  CR6   0   0.437  -2.0886  -0.0901   0.1645
 3FE  C12  C  CR16  0   0.038  -4.0367   1.1228   0.3074
 3FE  N4   N  NT    0  -0.498  -1.4862  -1.3194   0.0847
 3FE  C14  C  CH2   0  -0.192  -1.3788  -3.6816   0.6074
 3FE  O1   O  O2    0  -0.482  -0.5784  -3.9313  -0.5259
 3FE  C15  C  CH2   0  -0.186   0.2245  -2.8119  -0.8216
 3FE  H1   H  HCR6  0   0.277   2.3380   1.8188  -1.2819
 3FE  H2   H  HCR6  0   0.266   0.4365  -0.3187   1.9052
 3FE  H3   H  HCH2  0   0.258  -2.8531  -2.3116   1.3197
 3FE  H4   H  HCH2  0   0.226  -3.0194  -2.7013  -0.3915
 3FE  H5   H  HCR5  0   0.302   0.7311   3.6550  -0.1613
 3FE  H6   H  HCH2  0   0.244  -1.2155  -1.6959  -1.9662
 3FE  H7   H  HCH2  0   0.271   0.0567  -0.7279  -1.2321
 3FE  H8   H  HCR6  0   0.276   2.5360  -1.4961   2.3779
 3FE  H9   H  HCR6  0   0.282   4.5664  -1.0172   1.0436
 3FE  H10  H  HNR5  0   0.419  -1.6816   4.3030  -0.2212
 3FE  H11  H  HCR6  0   0.251  -5.1106   1.0869   0.4547
 3FE  H12  H  HCH2  0   0.205  -0.7498  -3.5114   1.4930
 3FE  H13  H  HCH2  0   0.244  -1.9793  -4.5740   0.7876
 3FE  H14  H  HCH2  0   0.244   0.7934  -3.0423  -1.7234
 3FE  H15  H  HCH2  0   0.211   0.9387  -2.6250  -0.0086
 3FE  C17  C  CSP   0   0.049   4.7275   0.7238  -0.9678

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
 3FE  N5   C17  triple    1.152  0.020  1.152
 3FE  C17  C3   single    1.428  0.020  1.428
 3FE  C3   C2   aromatic  1.394  0.020  1.394
 3FE  C3   C4   aromatic  1.393  0.020  1.393
 3FE  C2   C1   aromatic  1.385  0.020  1.385
 3FE  C4   C5   aromatic  1.392  0.020  1.392
 3FE  C1   C6   aromatic  1.387  0.020  1.387
 3FE  C14  O1   single    1.410  0.020  1.410
 3FE  C14  C13  single    1.517  0.020  1.517
 3FE  C5   C6   aromatic  1.398  0.020  1.398
 3FE  C5   C7   single    1.465  0.020  1.465
 3FE  O1   C15  single    1.409  0.020  1.409
 3FE  C13  N4   single    1.455  0.020  1.455
 3FE  C7   C8   aromatic  1.370  0.020  1.370
 3FE  C7   C10  aromatic  1.439  0.020  1.439
 3FE  C8   N1   aromatic  1.363  0.020  1.363
 3FE  C15  C16  single    1.515  0.020  1.515
 3FE  N4   C16  single    1.462  0.020  1.462
 3FE  N4   C11  single    1.371  0.020  1.371
 3FE  C10  C11  aromatic  1.412  0.020  1.412
 3FE  C10  C9   aromatic  1.406  0.020  1.406
 3FE  N1   C9   aromatic  1.354  0.020  1.354
 3FE  C11  N2   aromatic  1.330  0.020  1.330
 3FE  C9   N3   aromatic  1.331  0.020  1.331
 3FE  N2   C12  aromatic  1.331  0.020  1.331
 3FE  N3   C12  aromatic  1.316  0.020  1.316
 3FE  C4   H1   single    0.930  0.020  1.080
 3FE  C6   H2   single    0.930  0.020  1.080
 3FE  C13  H3   single    0.970  0.020  1.090
 3FE  C13  H4   single    0.970  0.020  1.090
 3FE  C8   H5   single    0.930  0.020  1.080
 3FE  C16  H6   single    0.970  0.020  1.090
 3FE  C16  H7   single    0.970  0.020  1.090
 3FE  C1   H8   single    0.930  0.020  1.080
 3FE  C2   H9   single    0.930  0.020  1.080
 3FE  N1   H10  single    0.860  0.020  1.020
 3FE  C12  H11  single    0.930  0.020  1.080
 3FE  C14  H12  single    0.970  0.020  1.090
 3FE  C14  H13  single    0.970  0.020  1.090
 3FE  C15  H14  single    0.970  0.020  1.090
 3FE  C15  H15  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
 3FE  C12  N3   C9   112.75  3.000
 3FE  H1   C4   C5   120.16  3.000
 3FE  H1   C4   C3   119.71  3.000
 3FE  C5   C4   C3   120.13  3.000
 3FE  C12  N2   C11  119.55  3.000
 3FE  C10  C7   C5   129.79  3.000
 3FE  C10  C7   C8   105.84  3.000
 3FE  C5   C7   C8   123.93  3.000
 3FE  H2   C6   C5   119.55  3.000
 3FE  H2   C6   C1   119.34  3.000
 3FE  C5   C6   C1   121.11  3.000
 3FE  C10  C9   N1   108.09  3.000
 3FE  N1   C9   N3   125.62  3.000
 3FE  C10  C9   N3   126.25  3.000
 3FE  H4   C13  H3   107.46  3.000
 3FE  H4   C13  C14  110.12  3.000
 3FE  H3   C13  C14  108.92  3.000
 3FE  H4   C13  N4   111.38  3.000
 3FE  H3   C13  N4   109.80  3.000
 3FE  C14  C13  N4   109.12  3.000
 3FE  H5   C8   N1   120.70  3.000
 3FE  H5   C8   C7   129.08  3.000
 3FE  N1   C8   C7   110.14  3.000
 3FE  H7   C16  H6   107.16  3.000
 3FE  H7   C16  C15  108.79  3.000
 3FE  H6   C16  C15  109.77  3.000
 3FE  H7   C16  N4   111.10  3.000
 3FE  H6   C16  N4   109.59  3.000
 3FE  C15  C16  N4   110.37  3.000
 3FE  H8   C1   C2   119.78  3.000
 3FE  H8   C1   C6   119.74  3.000
 3FE  C2   C1   C6   120.47  3.000
 3FE  H9   C2   C3   120.41  3.000
 3FE  H9   C2   C1   120.84  3.000
 3FE  C3   C2   C1   118.74  3.000
 3FE  C17  C3   C2   119.62  3.000
 3FE  C2   C3   C4   121.04  3.000
 3FE  C17  C3   C4   119.34  3.000
 3FE  C6   C5   C7   120.74  3.000
 3FE  C7   C5   C4   120.70  3.000
 3FE  C6   C5   C4   118.51  3.000
 3FE  H10  N1   C8   125.35  3.000
 3FE  H10  N1   C9   125.24  3.000
 3FE  C8   N1   C9   109.24  3.000
 3FE  C11  C10  C9   114.47  3.000
 3FE  C9   C10  C7   106.60  3.000
 3FE  C11  C10  C7   138.91  3.000
 3FE  N4   C11  C10  123.04  3.000
 3FE  C10  C11  N2   118.92  3.000
 3FE  N4   C11  N2   118.04  3.000
 3FE  H11  C12  N2   115.88  3.000
 3FE  H11  C12  N3   116.70  3.000
 3FE  N2   C12  N3   127.40  3.000
 3FE  C11  N4   C16  117.53  3.000
 3FE  C11  N4   C13  117.64  3.000
 3FE  C16  N4   C13  111.45  3.000
 3FE  H13  C14  H12  107.97  3.000
 3FE  H13  C14  O1   107.49  3.000
 3FE  H12  C14  O1   110.50  3.000
 3FE  H13  C14  C13  109.52  3.000
 3FE  H12  C14  C13  109.36  3.000
 3FE  O1   C14  C13  111.90  3.000
 3FE  C15  O1   C14  110.58  3.000
 3FE  H15  C15  H14  107.98  3.000
 3FE  H15  C15  O1   110.51  3.000
 3FE  H14  C15  O1   107.63  3.000
 3FE  H15  C15  C16  109.52  3.000
 3FE  H14  C15  C16  109.34  3.000
 3FE  O1   C15  C16  111.75  3.000
 3FE  C3   C17  N5   180.00  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
 3FE  CONST_01  C7   C10  C9   N3   180.00   0.0  0
 3FE  CONST_02  C11  C10  C9   N3     0.00   0.0  0
 3FE  CONST_03  C8   N1   C9   N3   180.00   0.0  0
 3FE  CONST_04  C11  N2   C12  N3     0.00   0.0  0
 3FE  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 3FE  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 3FE  CONST_09  C7   C10  C11  N2   180.00   0.0  0
 3FE  CONST_10  C9   C10  C11  N2     0.00   0.0  0
 3FE  CONST_11  C9   N3   C12  N2     0.00   0.0  0
 3FE  CONST_12  C3   C4   C5   C7   180.00   0.0  0
 3FE  CONST_13  C1   C6   C5   C7   180.00   0.0  0
 3FE  CONST_14  C9   N1   C8   C7     0.00   0.0  0
 3FE  CONST_15  N1   C9   C10  C7     0.00   0.0  0
 3FE  CONST_16  C3   C2   C1   C6     0.00   0.0  0
 3FE  CONST_17  C3   C4   C5   C6     0.00   0.0  0
 3FE  CONST_20  C5   C7   C10  C9   180.00   0.0  0
 3FE  CONST_21  C8   C7   C10  C9     0.00   0.0  0
 3FE  CONST_22  C11  C10  C7   C8   180.00   0.0  0
 3FE  CONST_23  C10  C9   N1   C8     0.00   0.0  0
 3FE  CONST_24  C5   C4   C3   C2     0.00   0.0  0
 3FE  CONST_25  C5   C6   C1   C2     0.00   0.0  0
 3FE  CONST_26  N1   C8   C7   C5   180.00   0.0  0
 3FE  CONST_27  C11  C10  C7   C5     0.00   0.0  0
 3FE  CONST_28  C10  C7   C8   N1     0.00   0.0  0
 3FE  CONST_29  C11  C10  C9   N1   180.00   0.0  0
 3FE  CONST_30  C12  N3   C9   N1   180.00   0.0  0
 3FE  CONST_31  C12  N2   C11  C10    0.00   0.0  0
 3FE  CONST_32  C12  N3   C9   C10    0.00   0.0  0
 3FE  CONST_33  N4   C11  C10  C7     0.00   0.0  0
 3FE  CONST_34  N4   C11  C10  C9   180.00   0.0  0
 3FE  CONST_35  N4   C11  N2   C12  180.00   0.0  0
 3FE  CONST_36  C17  C3   C2   C1   180.00   0.0  0
 3FE  CONST_37  C17  C3   C4   C5   180.00   0.0  0
 3FE  CONST_38  H10  N1   C9   N3     0.00   0.0  0
 3FE  CONST_39  H9   C2   C3   C4   180.00   0.0  0
 3FE  CONST_40  H2   C6   C5   C4   180.00   0.0  0
 3FE  CONST_41  H1   C4   C5   C7     0.00   0.0  0
 3FE  CONST_42  H5   C8   N1   C9   180.00   0.0  0
 3FE  CONST_43  H11  C12  N3   C9   180.00   0.0  0
 3FE  CONST_44  H8   C1   C2   C3   180.00   0.0  0
 3FE  Var_01    C13  N4   C11  N2    -9.59  30.0  2
 3FE  Var_02    C15  C16  N4   C13  -53.82  30.0  1
 3FE  Var_03    C14  C13  N4   C16   54.55  30.0  1
 3FE  Var_04    O1   C14  C13  N4   -57.56  30.0  1
 3FE  Var_05    O1   C15  C16  N4    55.05  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
 3FE  plan-1  C4   0.020
 3FE  plan-1  C7   0.020
 3FE  plan-1  C6   0.020
 3FE  plan-1  N5   0.020
 3FE  plan-1  C1   0.020
 3FE  plan-1  C2   0.020
 3FE  plan-1  C3   0.020
 3FE  plan-1  C5   0.020
 3FE  plan-1  H1   0.020
 3FE  plan-1  H2   0.020
 3FE  plan-1  H8   0.020
 3FE  plan-1  H9   0.020
 3FE  plan-1  C17  0.020
 3FE  plan-2  N3   0.020
 3FE  plan-2  N2   0.020
 3FE  plan-2  C7   0.020
 3FE  plan-2  C9   0.020
 3FE  plan-2  C8   0.020
 3FE  plan-2  C5   0.020
 3FE  plan-2  N1   0.020
 3FE  plan-2  C10  0.020
 3FE  plan-2  C11  0.020
 3FE  plan-2  C12  0.020
 3FE  plan-2  N4   0.020
 3FE  plan-2  H5   0.020
 3FE  plan-2  H10  0.020
 3FE  plan-2  H11  0.020

