# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 08:13:38 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-{2-[(3,4-difluorophenoxy)methyl]-5-methoxypyridin-4-yl}-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cnc(COc2ccc(F)c(F)c2)cc1c3[nH]c4CCNC(=O)c4c3
#
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
 15G  15G  2-{2-[(3,4-difluorophenoxy)methyl]-5-methoxypyridin-4-yl}-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one  ligand  45  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_15G
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
 15G  C1   C  CR6   0   0.365  -6.1366   1.7291  -0.0175
 15G  C2   C  CR16  0  -0.391  -4.9715   2.4710  -0.0141
 15G  C3   C  CR16  0  -0.345  -3.7453   1.8310  -0.0049
 15G  C7   C  CH3   0  -0.440   3.3032  -4.5007  -0.0525
 15G  C8   C  CR15  0  -0.418   3.8860  -0.3878   0.3273
 15G  C9   C  CR5   0  -0.138   4.4304   0.8990   0.1147
 15G  C10  C  C     0   0.474   5.7865   1.4018   0.3148
 15G  C11  C  CH2   0  -0.284   4.7997   3.6467  -0.0343
 15G  C12  C  CH2   0  -0.527   3.6732   3.0814  -0.8934
 15G  C13  C  CR5   0   0.367   3.4477   1.6840  -0.4498
 15G  C14  C  CR5   0   0.363   2.5745  -0.3445  -0.0962
 15G  C15  C  CR6   0   0.062   1.4998  -1.3242  -0.0549
 15G  C16  C  CR16  0  -0.387   0.1650  -0.9198  -0.0411
 15G  C19  C  CR6   0   0.177  -0.8509  -1.8620  -0.0249
 15G  C20  C  CH2   0  -0.209  -2.3117  -1.5037  -0.0113
 15G  N2   N  NH1   0  -0.650   5.9232   2.7263   0.0550
 15G  N3   N  NR15  0  -0.709   2.3417   0.9337  -0.5673
 15G  C17  C  CR6   0   0.271   1.7457  -2.7080  -0.0375
 15G  C18  C  CR16  0  -0.204   0.6560  -3.5738  -0.0204
 15G  N1   N  N     0  -0.419  -0.6044  -3.1634  -0.0151
 15G  O2   O  O2    0  -0.464   3.0226  -3.1130  -0.0492
 15G  C4   C  CR6   0   0.420  -3.6796   0.4375   0.0014
 15G  C5   C  CR16  0  -0.540  -4.8538  -0.3113  -0.0013
 15G  C6   C  CR6   0   0.430  -6.0674   0.3511  -0.0114
 15G  F1   F  F     0  -0.311  -7.3335   2.3316  -0.0273
 15G  F2   F  F     0  -0.307  -7.2001  -0.3587  -0.0144
 15G  H1   H  HCR6  0   0.296  -5.0236   3.5518  -0.0195
 15G  H2   H  HCR6  0   0.281  -2.8333   2.4127  -0.0023
 15G  H3   H  HCH3  0   0.234   2.9208  -4.9958   0.8436
 15G  H4   H  HCH3  0   0.233   2.8941  -4.9968  -0.9361
 15G  H5   H  HCH3  0   0.264   4.3859  -4.5921  -0.0685
 15G  H6   H  HCR5  0   0.256   4.3864  -1.2281   0.7760
 15G  H7   H  HCH2  0   0.265   5.1621   4.5793  -0.4616
 15G  H8   H  HCH2  0   0.241   4.4087   3.8726   0.9635
 15G  H9   H  HCH2  0   0.274   2.7834   3.7012  -0.7776
 15G  H10  H  HCH2  0   0.269   3.9473   3.1025  -1.9528
 15G  H11  H  HCR6  0   0.261  -0.0808   0.1323  -0.0178
 15G  H12  H  HCH2  0   0.254  -2.7956  -1.9276  -0.8995
 15G  H13  H  HCH2  0   0.253  -2.7861  -1.9577   0.8669
 15G  H14  H  HNH1  0   0.396   6.8255   3.1289   0.2601
 15G  H15  H  HNR5  0   0.418   1.4865   1.2476  -0.9991
 15G  H16  H  HCR6  0   0.280   0.8016  -4.6474  -0.0136
 15G  H17  H  HCR6  0   0.314  -4.8587  -1.3929   0.0045
 15G  O3   O  O2    0  -0.478  -2.4474  -0.1019   0.0117
 15G  O1   O  O     0  -0.495   6.7285   0.6891   0.6452

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
 15G  F1   C1   single    1.340  0.020  1.340
 15G  C2   C1   aromatic  1.381  0.020  1.381
 15G  C2   C3   aromatic  1.383  0.020  1.383
 15G  C1   C6   aromatic  1.380  0.020  1.380
 15G  C3   C4   aromatic  1.395  0.020  1.395
 15G  C6   F2   single    1.337  0.020  1.337
 15G  C6   C5   aromatic  1.383  0.020  1.383
 15G  C4   C5   aromatic  1.393  0.020  1.393
 15G  C4   O3   single    1.345  0.020  1.345
 15G  C20  O3   single    1.408  0.020  1.408
 15G  C20  C19  single    1.504  0.020  1.504
 15G  N1   C19  aromatic  1.325  0.020  1.325
 15G  N1   C18  aromatic  1.326  0.020  1.326
 15G  C19  C16  aromatic  1.386  0.020  1.386
 15G  C18  C17  aromatic  1.392  0.020  1.392
 15G  C16  C15  aromatic  1.395  0.020  1.395
 15G  C17  C15  aromatic  1.406  0.020  1.406
 15G  C17  O2   single    1.340  0.020  1.340
 15G  C15  C14  single    1.455  0.020  1.455
 15G  C7   O2   single    1.416  0.020  1.416
 15G  C14  N3   aromatic  1.382  0.020  1.382
 15G  C14  C8   aromatic  1.379  0.020  1.379
 15G  N3   C13  aromatic  1.342  0.020  1.342
 15G  C8   C9   aromatic  1.413  0.020  1.413
 15G  C13  C9   aromatic  1.379  0.020  1.379
 15G  C13  C12  single    1.483  0.020  1.483
 15G  C9   C10  single    1.460  0.020  1.460
 15G  C12  C11  single    1.525  0.020  1.525
 15G  C10  O1   double    1.227  0.020  1.227
 15G  C10  N2   single    1.357  0.020  1.357
 15G  C11  N2   single    1.455  0.020  1.455
 15G  C2   H1   single    0.930  0.020  1.080
 15G  C3   H2   single    0.930  0.020  1.080
 15G  C7   H3   single    0.970  0.020  1.090
 15G  C7   H4   single    0.970  0.020  1.090
 15G  C7   H5   single    0.970  0.020  1.090
 15G  C8   H6   single    0.930  0.020  1.080
 15G  C11  H7   single    0.970  0.020  1.090
 15G  C11  H8   single    0.970  0.020  1.090
 15G  C12  H9   single    0.970  0.020  1.090
 15G  C12  H10  single    0.970  0.020  1.090
 15G  C16  H11  single    0.930  0.020  1.080
 15G  C20  H12  single    0.970  0.020  1.090
 15G  C20  H13  single    0.970  0.020  1.090
 15G  N2   H14  single    0.890  0.020  1.040
 15G  N3   H15  single    0.860  0.020  1.020
 15G  C18  H16  single    0.930  0.020  1.080
 15G  C5   H17  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
 15G  F1   C1   C6   119.60  3.000
 15G  C6   C1   C2   119.61  3.000
 15G  F1   C1   C2   120.79  3.000
 15G  H1   C2   C3   120.32  3.000
 15G  H1   C2   C1   119.73  3.000
 15G  C3   C2   C1   119.95  3.000
 15G  H2   C3   C4   119.83  3.000
 15G  H2   C3   C2   119.91  3.000
 15G  C4   C3   C2   120.26  3.000
 15G  H5   C7   H4   108.84  3.000
 15G  H5   C7   H3   108.82  3.000
 15G  H4   C7   H3   109.05  3.000
 15G  H5   C7   O2   106.25  3.000
 15G  H4   C7   O2   111.88  3.000
 15G  H3   C7   O2   111.89  3.000
 15G  H6   C8   C14  126.51  3.000
 15G  H6   C8   C9   126.48  3.000
 15G  C14  C8   C9   106.95  3.000
 15G  C13  C9   C10  121.47  3.000
 15G  C10  C9   C8   130.59  3.000
 15G  C13  C9   C8   107.79  3.000
 15G  N2   C10  O1   122.79  3.000
 15G  N2   C10  C9   113.80  3.000
 15G  O1   C10  C9   123.37  3.000
 15G  H8   C11  H7   107.46  3.000
 15G  H8   C11  N2   110.50  3.000
 15G  H7   C11  N2   108.01  3.000
 15G  H8   C11  C12  109.02  3.000
 15G  H7   C11  C12  110.02  3.000
 15G  N2   C11  C12  111.73  3.000
 15G  H10  C12  H9   107.22  3.000
 15G  H10  C12  C13  110.22  3.000
 15G  H9   C12  C13  112.31  3.000
 15G  H10  C12  C11  110.68  3.000
 15G  H9   C12  C11  109.40  3.000
 15G  C13  C12  C11  107.04  3.000
 15G  N3   C13  C12  128.75  3.000
 15G  C12  C13  C9   123.40  3.000
 15G  N3   C13  C9   107.76  3.000
 15G  N3   C14  C15  120.53  3.000
 15G  N3   C14  C8   107.10  3.000
 15G  C15  C14  C8   132.29  3.000
 15G  C17  C15  C16  116.92  3.000
 15G  C17  C15  C14  122.28  3.000
 15G  C16  C15  C14  120.80  3.000
 15G  H11  C16  C19  119.67  3.000
 15G  H11  C16  C15  120.01  3.000
 15G  C19  C16  C15  120.30  3.000
 15G  N1   C19  C20  114.50  3.000
 15G  N1   C19  C16  122.12  3.000
 15G  C20  C19  C16  123.38  3.000
 15G  H13  C20  H12  107.32  3.000
 15G  H13  C20  O3   110.94  3.000
 15G  H12  C20  O3   110.82  3.000
 15G  H13  C20  C19  109.19  3.000
 15G  H12  C20  C19  109.21  3.000
 15G  O3   C20  C19  109.32  3.000
 15G  H14  N2   C11  116.77  3.000
 15G  H14  N2   C10  116.15  3.000
 15G  C11  N2   C10  123.47  3.000
 15G  H15  N3   C14  125.24  3.000
 15G  H15  N3   C13  124.24  3.000
 15G  C14  N3   C13  110.40  3.000
 15G  O2   C17  C18  123.94  3.000
 15G  O2   C17  C15  117.67  3.000
 15G  C18  C17  C15  118.39  3.000
 15G  H16  C18  N1   115.76  3.000
 15G  H16  C18  C17  120.74  3.000
 15G  N1   C18  C17  123.50  3.000
 15G  C18  N1   C19  118.76  3.000
 15G  C17  O2   C7   119.03  3.000
 15G  C5   C4   O3   123.84  3.000
 15G  O3   C4   C3   116.34  3.000
 15G  C5   C4   C3   119.82  3.000
 15G  H17  C5   C6   118.37  3.000
 15G  H17  C5   C4   122.78  3.000
 15G  C6   C5   C4   118.85  3.000
 15G  F2   C6   C5   119.30  3.000
 15G  C5   C6   C1   121.50  3.000
 15G  F2   C6   C1   119.20  3.000
 15G  C4   O3   C20  119.16  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
 15G  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 15G  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 15G  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 15G  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 15G  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 15G  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 15G  CONST_09  C13  N3   C14  C8      0.00   0.0  0
 15G  CONST_10  N3   C13  C9   C8      0.00   0.0  0
 15G  CONST_11  C15  C14  C8   C9    180.00   0.0  0
 15G  CONST_12  N3   C14  C8   C9      0.00   0.0  0
 15G  CONST_13  C14  N3   C13  C9      0.00   0.0  0
 15G  CONST_14  C15  C14  N3   C13   180.00   0.0  0
 15G  CONST_15  C14  C8   C9   C13     0.00   0.0  0
 15G  CONST_16  C19  C16  C15  C14   180.00   0.0  0
 15G  CONST_17  C18  C17  C15  C14   180.00   0.0  0
 15G  CONST_18  N1   C19  C16  C15     0.00   0.0  0
 15G  CONST_19  N1   C18  C17  C15     0.00   0.0  0
 15G  CONST_20  C18  N1   C19  C16     0.00   0.0  0
 15G  CONST_21  C18  C17  C15  C16     0.00   0.0  0
 15G  CONST_23  C17  C18  N1   C19     0.00   0.0  0
 15G  CONST_24  C17  C15  C16  C19     0.00   0.0  0
 15G  CONST_27  F2   C6   C1   C2    180.00   0.0  0
 15G  CONST_28  O3   C4   C3   C2    180.00   0.0  0
 15G  CONST_29  F1   C1   C2   C3    180.00   0.0  0
 15G  CONST_30  O2   C17  C15  C14     0.00   0.0  0
 15G  CONST_31  C20  C19  C16  C15   180.00   0.0  0
 15G  CONST_32  O2   C17  C15  C16   180.00   0.0  0
 15G  CONST_33  C18  N1   C19  C20   180.00   0.0  0
 15G  CONST_34  O2   C17  C18  N1    180.00   0.0  0
 15G  CONST_35  C6   C5   C4   O3    180.00   0.0  0
 15G  CONST_36  F2   C6   C5   C4    180.00   0.0  0
 15G  CONST_37  F1   C1   C6   C5    180.00   0.0  0
 15G  CONST_38  O1   C10  N2   C11   180.00   0.0  0
 15G  CONST_39  H2   C3   C2   C1    180.00   0.0  0
 15G  CONST_40  H17  C5   C6   C1    180.00   0.0  0
 15G  CONST_41  H15  N3   C14  C8    180.00   0.0  0
 15G  CONST_42  H6   C8   C9   C10     0.00   0.0  0
 15G  CONST_43  H11  C16  C15  C14     0.00   0.0  0
 15G  CONST_44  H16  C18  C17  C15   180.00   0.0  0
 15G  CONST_45  H1   C2   C3   C4    180.00   0.0  0
 15G  CONST_46  H14  N2   C10  C9    180.00   0.0  0
 15G  Var_01    N2   C10  C9   C8   -177.23  30.0  1
 15G  Var_02    C11  C12  C13  C9    -27.61  30.0  1
 15G  Var_03    C12  C11  N2   C10   -46.58  30.0  1
 15G  Var_04    N2   C11  C12  C13    47.03  30.0  1
 15G  Var_05    C18  C17  O2   C7      0.39  30.0  1
 15G  Var_06    O3   C20  C19  C16    -1.27  30.0  2
 15G  Var_07    C5   C4   O3   C20     1.47  30.0  2
 15G  Var_08    H3   C7   O2   C17   -61.70  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
 15G  plan-1  C1   0.020
 15G  plan-1  C2   0.020
 15G  plan-1  C3   0.020
 15G  plan-1  C4   0.020
 15G  plan-1  C5   0.020
 15G  plan-1  C6   0.020
 15G  plan-1  F1   0.020
 15G  plan-1  F2   0.020
 15G  plan-1  H1   0.020
 15G  plan-1  H2   0.020
 15G  plan-1  H17  0.020
 15G  plan-1  O3   0.020
 15G  plan-2  C14  0.020
 15G  plan-2  C15  0.020
 15G  plan-2  C16  0.020
 15G  plan-2  C19  0.020
 15G  plan-2  C20  0.020
 15G  plan-2  C17  0.020
 15G  plan-2  C18  0.020
 15G  plan-2  N1   0.020
 15G  plan-2  O2   0.020
 15G  plan-2  H11  0.020
 15G  plan-2  H16  0.020
 15G  plan-3  C8   0.020
 15G  plan-3  C9   0.020
 15G  plan-3  C10  0.020
 15G  plan-3  C12  0.020
 15G  plan-3  C13  0.020
 15G  plan-3  C14  0.020
 15G  plan-3  C15  0.020
 15G  plan-3  N3   0.020
 15G  plan-3  H6   0.020
 15G  plan-3  H15  0.020
 15G  plan-4  C9   0.020
 15G  plan-4  C10  0.020
 15G  plan-4  C11  0.020
 15G  plan-4  N2   0.020
 15G  plan-4  H14  0.020
 15G  plan-4  O1   0.020

