# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 06:03:58 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 3,5-dimethyl-2-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](C[C@@H](C1)c2ccccc2)NC3=Nc4ccn(C)c4C(=O)N3C
#
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
 FN9  FN9  3,5-dimethyl-2-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one  ligand  51  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FN9
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
 FN9  C13   C  CR15  0  -0.024  28.5636  -2.7700  10.2618
 FN9  C15   C  CH3   0  -0.513  29.1912  -5.1207   9.7615
 FN9  C17   C  CR6   0   0.540  28.5012  -5.2779  12.8309
 FN9  C20   C  CH3   0  -0.586  28.1893  -6.0088  15.1456
 FN9  C21   C  CR6   0   0.190  26.8363  -0.7672  19.9080
 FN9  C22   C  CR16  0  -0.319  26.3198  -1.7209  20.7857
 FN9  C24   C  CR16  0  -0.273  27.2312  -0.5387  22.6759
 FN9  C26   C  CR16  0  -0.334  27.5507   0.3013  20.4439
 FN9  C01   C  CH3   0  -0.516  23.5919  -0.5826  16.2427
 FN9  C03   C  CH2   0  -0.243  25.1499  -0.7607  18.0504
 FN9  C04   C  CH1   0  -0.362  26.6288  -0.8754  18.4190
 FN9  C05   C  CH2   0  -0.426  27.2153  -2.1659  17.8454
 FN9  C06   C  CH1   0  -0.074  26.9449  -2.2434  16.3494
 FN9  C07   C  CH2   0  -0.264  25.4533  -2.0730  16.0706
 FN9  C09   C  CR6   0   0.740  27.7518  -3.6745  14.5251
 FN9  C11   C  CR56  0   0.193  28.0762  -2.8969  12.4337
 FN9  C12   C  CR15  0  -0.428  28.1450  -2.0122  11.3339
 FN9  C16   C  CR56  0   0.142  28.4573  -4.1509  11.9722
 FN9  C23   C  CR16  0  -0.235  26.5140  -1.6088  22.1554
 FN9  C25   C  CR16  0  -0.235  27.7490   0.4176  21.8140
 FN9  N02   N  NT    0  -0.415  24.9679  -0.8224  16.6141
 FN9  N08   N  NH1   0  -0.710  27.4454  -3.5003  15.8331
 FN9  N10   N  N     0  -0.531  27.7068  -2.6568  13.7172
 FN9  N14   N  NR5   0  -0.486  28.7523  -4.0558  10.6346
 FN9  N19   N  NR6   0  -0.591  28.1367  -4.9493  14.1487
 FN9  O18   O  O     0  -0.484  28.8166  -6.4205  12.5254
 FN9  H131  H  HCR5  0   0.285  28.7424  -2.4699   9.2407
 FN9  H151  H  HCH3  0   0.252  30.1281  -5.5521  10.1080
 FN9  H153  H  HCH3  0   0.251  28.4448  -5.9096   9.6965
 FN9  H152  H  HCH3  0   0.255  29.3453  -4.7077   8.7682
 FN9  H201  H  HCH3  0   0.261  27.1948  -6.2408  15.5288
 FN9  H203  H  HCH3  0   0.288  28.5881  -6.9041  14.6848
 FN9  H202  H  HCH3  0   0.263  28.8410  -5.7274  15.9721
 FN9  H221  H  HCR6  0   0.247  25.7581  -2.5645  20.4013
 FN9  H241  H  HCR6  0   0.251  27.3849  -0.4525  23.7440
 FN9  H261  H  HCR6  0   0.246  27.9611   1.0537  19.7800
 FN9  H013  H  HCH3  0   0.232  23.2690   0.3926  16.6101
 FN9  H012  H  HCH3  0   0.233  23.4929  -0.5809  15.1563
 FN9  H011  H  HCH3  0   0.192  22.8970  -1.3380  16.6410
 FN9  H032  H  HCH2  0   0.240  24.7587   0.1944  18.4109
 FN9  H031  H  HCH2  0   0.191  24.5779  -1.5541  18.5657
 FN9  H041  H  HCH1  0   0.247  27.1452  -0.0331  17.9461
 FN9  H051  H  HCH2  0   0.226  26.7613  -3.0308  18.3432
 FN9  H052  H  HCH2  0   0.252  28.2898  -2.2116  18.0371
 FN9  H061  H  HCH1  0   0.247  27.4844  -1.4374  15.8492
 FN9  H071  H  HCH2  0   0.241  25.2870  -2.0780  14.9912
 FN9  H072  H  HCH2  0   0.185  24.9122  -2.9431  16.4878
 FN9  H121  H  HCR5  0   0.246  27.9194  -0.9581  11.3224
 FN9  H231  H  HCR6  0   0.251  26.1046  -2.3604  22.8185
 FN9  H251  H  HCR6  0   0.251  28.3096   1.2565  22.2065
 FN9  H081  H  HNH1  0   0.411  27.2318  -4.3107  16.3915

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
 FN9  C15  N14   single    1.445  0.020  1.445
 FN9  C13  N14   aromatic  1.352  0.020  1.352
 FN9  C13  C12   aromatic  1.378  0.020  1.378
 FN9  N14  C16   aromatic  1.373  0.020  1.373
 FN9  C12  C11   aromatic  1.413  0.020  1.413
 FN9  C16  C11   aromatic  1.390  0.020  1.390
 FN9  C16  C17   single    1.418  0.020  1.418
 FN9  O18  C17   double    1.224  0.020  1.224
 FN9  C11  N10   single    1.357  0.020  1.357
 FN9  C17  N19   single    1.406  0.020  1.406
 FN9  N10  C09   double    1.300  0.020  1.300
 FN9  N19  C09   single    1.384  0.020  1.384
 FN9  N19  C20   single    1.456  0.020  1.456
 FN9  C09  N08   single    1.355  0.020  1.355
 FN9  C07  C06   single    1.527  0.020  1.527
 FN9  C07  N02   single    1.447  0.020  1.447
 FN9  N08  C06   single    1.448  0.020  1.448
 FN9  C01  N02   single    1.445  0.020  1.445
 FN9  C06  C05   single    1.522  0.020  1.522
 FN9  N02  C03   single    1.449  0.020  1.449
 FN9  C05  C04   single    1.529  0.020  1.529
 FN9  C03  C04   single    1.528  0.020  1.528
 FN9  C04  C21   single    1.507  0.020  1.507
 FN9  C21  C26   aromatic  1.393  0.020  1.393
 FN9  C21  C22   aromatic  1.395  0.020  1.395
 FN9  C26  C25   aromatic  1.389  0.020  1.389
 FN9  C22  C23   aromatic  1.388  0.020  1.388
 FN9  C25  C24   aromatic  1.388  0.020  1.388
 FN9  C23  C24   aromatic  1.389  0.020  1.389
 FN9  C13  H131  single    0.930  0.020  1.080
 FN9  C15  H151  single    0.970  0.020  1.090
 FN9  C15  H153  single    0.970  0.020  1.090
 FN9  C15  H152  single    0.970  0.020  1.090
 FN9  C20  H201  single    0.970  0.020  1.090
 FN9  C20  H203  single    0.970  0.020  1.090
 FN9  C20  H202  single    0.970  0.020  1.090
 FN9  C22  H221  single    0.930  0.020  1.080
 FN9  C24  H241  single    0.930  0.020  1.080
 FN9  C26  H261  single    0.930  0.020  1.080
 FN9  C01  H013  single    0.970  0.020  1.090
 FN9  C01  H012  single    0.970  0.020  1.090
 FN9  C01  H011  single    0.970  0.020  1.090
 FN9  C03  H032  single    0.970  0.020  1.090
 FN9  C03  H031  single    0.970  0.020  1.090
 FN9  C04  H041  single    0.970  0.020  1.090
 FN9  C05  H051  single    0.970  0.020  1.090
 FN9  C05  H052  single    0.970  0.020  1.090
 FN9  C06  H061  single    0.970  0.020  1.090
 FN9  C07  H071  single    0.970  0.020  1.090
 FN9  C07  H072  single    0.970  0.020  1.090
 FN9  C12  H121  single    0.930  0.020  1.080
 FN9  C23  H231  single    0.930  0.020  1.080
 FN9  C25  H251  single    0.930  0.020  1.080
 FN9  N08  H081  single    0.890  0.020  1.040

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
 FN9  H131  C13  N14   120.15  3.000
 FN9  H131  C13  C12   129.31  3.000
 FN9  N14   C13  C12   110.54  3.000
 FN9  H152  C15  H153  108.55  3.000
 FN9  H152  C15  H151  108.65  3.000
 FN9  H153  C15  H151  108.80  3.000
 FN9  H152  C15  N14   108.37  3.000
 FN9  H153  C15  N14   111.22  3.000
 FN9  H151  C15  N14   111.18  3.000
 FN9  O18   C17  N19   121.25  3.000
 FN9  N19   C17  C16   111.95  3.000
 FN9  O18   C17  C16   126.79  3.000
 FN9  H202  C20  H203  108.42  3.000
 FN9  H202  C20  H201  109.50  3.000
 FN9  H203  C20  H201  108.02  3.000
 FN9  H202  C20  N19   110.68  3.000
 FN9  H203  C20  N19   108.88  3.000
 FN9  H201  C20  N19   111.25  3.000
 FN9  C04   C21  C26   120.39  3.000
 FN9  C26   C21  C22   118.19  3.000
 FN9  C04   C21  C22   121.43  3.000
 FN9  H221  C22  C23   119.04  3.000
 FN9  H221  C22  C21   120.05  3.000
 FN9  C23   C22  C21   120.92  3.000
 FN9  H241  C24  C25   120.33  3.000
 FN9  H241  C24  C23   120.28  3.000
 FN9  C25   C24  C23   119.39  3.000
 FN9  H261  C26  C25   119.46  3.000
 FN9  H261  C26  C21   119.41  3.000
 FN9  C25   C26  C21   121.13  3.000
 FN9  H011  C01  H012  107.70  3.000
 FN9  H011  C01  H013  107.74  3.000
 FN9  H012  C01  H013  107.88  3.000
 FN9  H011  C01  N02   113.21  3.000
 FN9  H012  C01  N02   110.03  3.000
 FN9  H013  C01  N02   110.09  3.000
 FN9  H031  C03  H032  106.74  3.000
 FN9  H031  C03  N02   111.50  3.000
 FN9  H032  C03  N02   108.61  3.000
 FN9  H031  C03  C04   109.53  3.000
 FN9  H032  C03  C04   109.41  3.000
 FN9  N02   C03  C04   110.94  3.000
 FN9  H041  C04  C05   107.84  3.000
 FN9  H041  C04  C03   107.12  3.000
 FN9  C05   C04  C03   110.12  3.000
 FN9  H041  C04  C21   107.84  3.000
 FN9  C03   C04  C21   111.47  3.000
 FN9  C05   C04  C21   112.23  3.000
 FN9  H052  C05  H051  107.14  3.000
 FN9  H052  C05  C06   110.19  3.000
 FN9  H051  C05  C06   109.42  3.000
 FN9  H052  C05  C04   110.28  3.000
 FN9  H051  C05  C04   109.67  3.000
 FN9  C06   C05  C04   110.09  3.000
 FN9  H061  C06  N08   107.86  3.000
 FN9  H061  C06  C07   108.47  3.000
 FN9  N08   C06  C07   111.68  3.000
 FN9  H061  C06  C05   108.97  3.000
 FN9  N08   C06  C05   109.46  3.000
 FN9  C07   C06  C05   110.32  3.000
 FN9  H072  C07  H071  107.13  3.000
 FN9  H072  C07  N02   111.96  3.000
 FN9  H071  C07  N02   108.90  3.000
 FN9  H072  C07  C06   108.74  3.000
 FN9  H071  C07  C06   109.19  3.000
 FN9  N02   C07  C06   110.82  3.000
 FN9  N19   C09  N10   124.17  3.000
 FN9  N19   C09  N08   116.36  3.000
 FN9  N10   C09  N08   119.44  3.000
 FN9  N10   C11  C16   123.26  3.000
 FN9  N10   C11  C12   129.69  3.000
 FN9  C16   C11  C12   107.05  3.000
 FN9  H121  C12  C11   127.61  3.000
 FN9  H121  C12  C13   126.36  3.000
 FN9  C11   C12  C13   106.03  3.000
 FN9  N14   C16  C11   108.66  3.000
 FN9  C11   C16  C17   121.66  3.000
 FN9  N14   C16  C17   129.68  3.000
 FN9  H231  C23  C24   120.03  3.000
 FN9  H231  C23  C22   119.70  3.000
 FN9  C24   C23  C22   120.28  3.000
 FN9  H251  C25  C26   119.75  3.000
 FN9  H251  C25  C24   120.13  3.000
 FN9  C26   C25  C24   120.11  3.000
 FN9  C07   N02  C03   111.52  3.000
 FN9  C03   N02  C01   111.54  3.000
 FN9  C07   N02  C01   111.48  3.000
 FN9  H081  N08  C09   118.68  3.000
 FN9  H081  N08  C06   115.31  3.000
 FN9  C09   N08  C06   122.28  3.000
 FN9  C11   N10  C09   116.10  3.000
 FN9  C16   N14  C15   127.07  3.000
 FN9  C16   N14  C13   107.73  3.000
 FN9  C15   N14  C13   125.20  3.000
 FN9  C09   N19  C20   119.62  3.000
 FN9  C20   N19  C17   117.54  3.000
 FN9  C09   N19  C17   122.84  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
 FN9  CONST_01  C11   C16  N14  C13     0.00   0.0  0
 FN9  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 FN9  CONST_03  C24   C25  C26  C21     0.00   0.0  0
 FN9  CONST_04  C24   C23  C22  C21     0.00   0.0  0
 FN9  CONST_05  C25   C26  C21  C22     0.00   0.0  0
 FN9  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 FN9  CONST_07  C23   C22  C21  C26     0.00   0.0  0
 FN9  CONST_08  C23   C24  C25  C26     0.00   0.0  0
 FN9  CONST_09  N14   C13  C12  C11     0.00   0.0  0
 FN9  CONST_10  C16   N14  C13  C12     0.00   0.0  0
 FN9  CONST_11  N14   C16  C11  C12     0.00   0.0  0
 FN9  CONST_12  C25   C26  C21  C04   180.00   0.0  0
 FN9  CONST_13  C23   C22  C21  C04   180.00   0.0  0
 FN9  CONST_14  N10   C09  N19  C17     0.00   0.0  0
 FN9  CONST_15  C16   C17  N19  C09     0.00   0.0  0
 FN9  CONST_16  N19   C09  N10  C11     0.00   0.0  0
 FN9  CONST_17  C12   C13  N14  C15   180.00   0.0  0
 FN9  CONST_18  C11   C16  N14  C15   180.00   0.0  0
 FN9  CONST_19  C17   C16  N14  C15     0.00   0.0  0
 FN9  CONST_20  N08   C09  N19  C17   180.00   0.0  0
 FN9  CONST_21  C16   C17  N19  C20   180.00   0.0  0
 FN9  CONST_22  N10   C09  N19  C20   180.00   0.0  0
 FN9  CONST_23  N10   C09  N08  C06     0.00   0.0  0
 FN9  CONST_24  N19   C09  N08  C06   180.00   0.0  0
 FN9  CONST_25  O18   C17  N19  C09   180.00   0.0  0
 FN9  CONST_26  N08   C09  N10  C11   180.00   0.0  0
 FN9  CONST_27  H251  C25  C26  C21   180.00   0.0  0
 FN9  CONST_28  H231  C23  C22  C21   180.00   0.0  0
 FN9  CONST_29  H261  C26  C21  C22   180.00   0.0  0
 FN9  CONST_30  H241  C24  C23  C22   180.00   0.0  0
 FN9  CONST_31  H221  C22  C23  C24   180.00   0.0  0
 FN9  CONST_32  H131  C13  C12  C11   180.00   0.0  0
 FN9  CONST_33  H121  C12  C11  C16   180.00   0.0  0
 FN9  CONST_34  O18   C17  N19  C20     0.00   0.0  0
 FN9  CONST_35  N08   C09  N19  C20     0.00   0.0  0
 FN9  Var_01    C06   C07  N02  C03   -60.42  30.0  1
 FN9  Var_02    C07   N02  C03  C04    60.35  30.0  1
 FN9  Var_03    H151  C15  N14  C13   119.64  30.0  2
 FN9  Var_04    H201  C20  N19  C17  -114.93  30.0  3
 FN9  Var_05    H013  C01  N02  C03    58.16  30.0  3

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
 FN9  chir_01  C04  C05  C03  C21  negativ
 FN9  chir_02  C06  N08  C05  C07  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
 FN9  plan-1  C21   0.020
 FN9  plan-1  C22   0.020
 FN9  plan-1  C24   0.020
 FN9  plan-1  C26   0.020
 FN9  plan-1  C04   0.020
 FN9  plan-1  C23   0.020
 FN9  plan-1  C25   0.020
 FN9  plan-1  H221  0.020
 FN9  plan-1  H241  0.020
 FN9  plan-1  H261  0.020
 FN9  plan-1  H231  0.020
 FN9  plan-1  H251  0.020
 FN9  plan-2  C13   0.020
 FN9  plan-2  C15   0.020
 FN9  plan-2  C17   0.020
 FN9  plan-2  C20   0.020
 FN9  plan-2  C06   0.020
 FN9  plan-2  C09   0.020
 FN9  plan-2  C11   0.020
 FN9  plan-2  C12   0.020
 FN9  plan-2  C16   0.020
 FN9  plan-2  N08   0.020
 FN9  plan-2  N10   0.020
 FN9  plan-2  N14   0.020
 FN9  plan-2  N19   0.020
 FN9  plan-2  O18   0.020
 FN9  plan-2  H131  0.020
 FN9  plan-2  H121  0.020
 FN9  plan-2  H081  0.020

