# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:05:59 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[[6-[(3~{R})-3-azanylpiperidin-1-yl]-3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]methyl]-4-fluoranyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C=C(N2CCC[C@@H](N)C2)N(Cc3cc(F)ccc3C#N)C1=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
 6RL  6RL  2-[[6-[(3~{R})-3-azanylpiperidin-1-yl]-3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]methyl]-4-fluoranyl-benzenecarbonitrile  ligand  46  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6RL
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
 6RL  C5   C  CR16  0  -0.567  -0.2013   1.9556   1.0084
 6RL  C6   C  CR6   0   0.668   0.1287   1.0074   0.0960
 6RL  C8   C  C     0  -0.334   1.9544   0.0154   1.3758
 6RL  C10  C  C     0  -0.449   4.0670   0.9973   0.4768
 6RL  C17  C  CR6   0   0.207  -0.4497  -1.7736  -0.6390
 6RL  C21  C  CR16  0  -0.423   0.0034  -3.9818   1.0450
 6RL  C22  C  CR16  0  -0.213  -1.0007  -3.0795   1.3374
 6RL  C24  C  CSP   0   0.019  -2.3134  -1.1106   0.8246
 6RL  C26  C  CR6   0   0.772  -1.9231   1.4225  -1.1150
 6RL  N2   N  NR6   0  -0.585  -2.2039   2.4096  -0.2076
 6RL  C3   C  CR6   0   0.588  -1.4362   2.6709   0.9310
 6RL  O4   O  O     0  -0.486  -1.7969   3.5071   1.7450
 6RL  N7   N  NR6   0  -0.490   1.2843   0.2859   0.1138
 6RL  C9   C  C     0  -0.448   3.1043   0.9724   1.6580
 6RL  C11  C  CR16  0  -0.083   3.3351   1.3040  -0.8282
 6RL  N13  N  NH2   0  -0.791   4.1690   1.2758  -2.0188
 6RL  C14  C  C     0  -0.323   2.1796   0.3217  -1.0362
 6RL  N15  N  NR6   0  -0.590  -0.7771   0.6718  -0.8969
 6RL  C16  C  CH2   0  -0.422  -0.6972  -0.6226  -1.5769
 6RL  C18  C  CR16  0  -0.481   0.5440  -2.6919  -0.9365
 6RL  C19  C  CR6   0   0.576   0.7546  -3.7689  -0.0960
 6RL  F20  F  F     0  -0.299   1.7282  -4.6306  -0.3997
 6RL  C23  C  CR6   0  -0.020  -1.2364  -1.9877   0.5010
 6RL  N25  N  NS    0  -0.247  -3.1994  -0.4252   1.0976
 6RL  O27  O  O     0  -0.482  -2.6591   1.1947  -2.0544
 6RL  H1   H  HCR6  0   0.280   0.5036   2.2543   1.7690
 6RL  H2   H  H     0   0.267   1.2160   0.0174   2.1765
 6RL  H3   H  H     0   0.253   2.3462  -1.0061   1.3114
 6RL  H4   H  H     0   0.241   4.8565   1.7358   0.6382
 6RL  H5   H  H     0   0.215   4.5597   0.0215   0.3843
 6RL  H6   H  HCR6  0   0.298   0.1934  -4.8302   1.6877
 6RL  H7   H  HCR6  0   0.296  -1.6133  -3.2241   2.2164
 6RL  H8   H  HCH3  0   0.252  -4.3022   2.4993  -0.3447
 6RL  H9   H  HCH3  0   0.265  -3.5094   3.9359   0.3121
 6RL  H10  H  HCH3  0   0.255  -3.4317   3.6055  -1.4204
 6RL  H11  H  H     0   0.230   2.7211   1.9791   1.8490
 6RL  H12  H  H     0   0.245   3.6166   0.6545   2.5682
 6RL  H13  H  HCR6  0   0.229   2.9029   2.3090  -0.7566
 6RL  H14  H  HNH2  0   0.351   4.8607   2.0129  -1.9608
 6RL  H15  H  HNH2  0   0.339   4.6947   0.4086  -2.0427
 6RL  H17  H  H     0   0.235   2.5811  -0.6857  -1.2026
 6RL  H18  H  H     0   0.268   1.6404   0.6154  -1.9348
 6RL  H19  H  HCH2  0   0.296   0.0564  -0.6152  -2.3627
 6RL  H20  H  HCH2  0   0.324  -1.6501  -0.7708  -2.0823
 6RL  H21  H  HCR6  0   0.295   1.1633  -2.5663  -1.8156
 6RL  C1   C  CH3   0  -0.531  -3.4355   3.1525  -0.4319

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
 6RL  C1   N2   single    1.456  0.020  1.456
 6RL  O27  C26  double    1.215  0.020  1.215
 6RL  F20  C19  single    1.335  0.020  1.335
 6RL  N2   C26  single    1.370  0.020  1.370
 6RL  N2   C3   single    1.398  0.020  1.398
 6RL  C26  N15  single    1.387  0.020  1.387
 6RL  C18  C19  aromatic  1.382  0.020  1.382
 6RL  C18  C17  aromatic  1.385  0.020  1.385
 6RL  C19  C21  aromatic  1.383  0.020  1.383
 6RL  O4   C3   double    1.221  0.020  1.221
 6RL  C3   C5   single    1.429  0.020  1.429
 6RL  N15  C16  single    1.464  0.020  1.464
 6RL  N15  C6   single    1.385  0.020  1.385
 6RL  C16  C17  single    1.505  0.020  1.505
 6RL  C17  C23  aromatic  1.401  0.020  1.401
 6RL  C21  C22  aromatic  1.381  0.020  1.381
 6RL  C5   C6   double    1.357  0.020  1.357
 6RL  C6   N7   single    1.362  0.020  1.362
 6RL  C23  C22  aromatic  1.395  0.020  1.395
 6RL  C23  C24  single    1.426  0.020  1.426
 6RL  C8   N7   single    1.454  0.020  1.454
 6RL  C8   C9   single    1.522  0.020  1.522
 6RL  N7   C14  single    1.458  0.020  1.458
 6RL  C24  N25  triple    1.153  0.020  1.153
 6RL  C9   C10  single    1.524  0.020  1.524
 6RL  C14  C11  single    1.531  0.020  1.531
 6RL  C10  C11  single    1.527  0.020  1.527
 6RL  C11  N13  single    1.454  0.020  1.454
 6RL  C5   H1   single    0.930  0.020  1.080
 6RL  C8   H2   single    0.970  0.020  1.090
 6RL  C8   H3   single    0.970  0.020  1.090
 6RL  C10  H4   single    0.970  0.020  1.090
 6RL  C10  H5   single    0.970  0.020  1.090
 6RL  C21  H6   single    0.930  0.020  1.080
 6RL  C22  H7   single    0.930  0.020  1.080
 6RL  C1   H8   single    0.970  0.020  1.090
 6RL  C1   H9   single    0.970  0.020  1.090
 6RL  C1   H10  single    0.970  0.020  1.090
 6RL  C9   H11  single    0.970  0.020  1.090
 6RL  C9   H12  single    0.970  0.020  1.090
 6RL  C11  H13  single    0.970  0.020  1.090
 6RL  N13  H14  single    0.890  0.020  1.040
 6RL  N13  H15  single    0.890  0.020  1.040
 6RL  C14  H17  single    0.970  0.020  1.090
 6RL  C14  H18  single    0.970  0.020  1.090
 6RL  C16  H19  single    0.970  0.020  1.090
 6RL  C16  H20  single    0.970  0.020  1.090
 6RL  C18  H21  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
 6RL  H1   C5   C3   117.65  3.000
 6RL  H1   C5   C6   120.57  3.000
 6RL  C3   C5   C6   121.58  3.000
 6RL  N15  C6   N7   115.83  3.000
 6RL  N7   C6   C5   124.59  3.000
 6RL  N15  C6   C5   119.49  3.000
 6RL  H3   C8   H2   106.70  3.000
 6RL  H3   C8   C9   109.08  3.000
 6RL  H2   C8   C9   112.00  3.000
 6RL  H3   C8   N7   106.68  3.000
 6RL  H2   C8   N7   108.98  3.000
 6RL  C9   C8   N7   113.08  3.000
 6RL  H5   C10  H4   106.80  3.000
 6RL  H5   C10  C11  108.77  3.000
 6RL  H4   C10  C11  109.67  3.000
 6RL  H5   C10  C9   109.54  3.000
 6RL  H4   C10  C9   110.66  3.000
 6RL  C11  C10  C9   111.27  3.000
 6RL  C23  C17  C18  118.43  3.000
 6RL  C23  C17  C16  122.10  3.000
 6RL  C18  C17  C16  119.40  3.000
 6RL  H6   C21  C19  121.06  3.000
 6RL  H6   C21  C22  120.97  3.000
 6RL  C19  C21  C22  117.98  3.000
 6RL  H7   C22  C23  119.75  3.000
 6RL  H7   C22  C21  119.78  3.000
 6RL  C23  C22  C21  120.47  3.000
 6RL  N25  C24  C23  180.00  3.000
 6RL  O27  C26  N15  121.37  3.000
 6RL  N15  C26  N2   117.07  3.000
 6RL  O27  C26  N2   121.54  3.000
 6RL  C3   N2   C1   119.65  3.000
 6RL  C3   N2   C26  124.17  3.000
 6RL  C1   N2   C26  116.05  3.000
 6RL  O4   C3   N2   120.57  3.000
 6RL  O4   C3   C5   124.17  3.000
 6RL  N2   C3   C5   115.15  3.000
 6RL  C14  N7   C8   113.96  3.000
 6RL  C14  N7   C6   119.84  3.000
 6RL  C8   N7   C6   120.04  3.000
 6RL  H12  C9   H11  106.66  3.000
 6RL  H12  C9   C10  110.77  3.000
 6RL  H11  C9   C10  109.97  3.000
 6RL  H12  C9   C8   109.02  3.000
 6RL  H11  C9   C8   110.26  3.000
 6RL  C10  C9   C8   110.10  3.000
 6RL  H13  C11  C14  107.43  3.000
 6RL  H13  C11  N13  107.30  3.000
 6RL  C14  C11  N13  108.01  3.000
 6RL  H13  C11  C10  108.49  3.000
 6RL  N13  C11  C10  114.89  3.000
 6RL  C14  C11  C10  110.42  3.000
 6RL  H15  N13  H14  105.65  3.000
 6RL  H15  N13  C11  109.46  3.000
 6RL  H14  N13  C11  109.32  3.000
 6RL  H18  C14  H17  107.70  3.000
 6RL  H18  C14  C11  108.23  3.000
 6RL  H17  C14  C11  109.48  3.000
 6RL  H18  C14  N7   110.71  3.000
 6RL  H17  C14  N7   108.77  3.000
 6RL  C11  C14  N7   111.85  3.000
 6RL  C16  N15  C26  116.77  3.000
 6RL  C16  N15  C6   120.75  3.000
 6RL  C26  N15  C6   121.45  3.000
 6RL  H20  C16  H19  105.76  3.000
 6RL  H20  C16  N15  106.74  3.000
 6RL  H19  C16  N15  111.53  3.000
 6RL  H20  C16  C17  109.21  3.000
 6RL  H19  C16  C17  109.95  3.000
 6RL  N15  C16  C17  113.30  3.000
 6RL  H21  C18  C19  119.80  3.000
 6RL  H21  C18  C17  120.52  3.000
 6RL  C19  C18  C17  119.68  3.000
 6RL  F20  C19  C18  118.40  3.000
 6RL  C18  C19  C21  122.61  3.000
 6RL  F20  C19  C21  118.99  3.000
 6RL  C24  C23  C22  118.21  3.000
 6RL  C24  C23  C17  120.97  3.000
 6RL  C22  C23  C17  120.81  3.000
 6RL  H10  C1   H9   108.88  3.000
 6RL  H10  C1   H8   109.00  3.000
 6RL  H9   C1   H8   108.95  3.000
 6RL  H10  C1   N2   110.47  3.000
 6RL  H9   C1   N2   108.72  3.000
 6RL  H8   C1   N2   110.79  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
 6RL  CONST_01  C21  C19  C18  C17     0.00   0.0  0
 6RL  CONST_02  C21  C22  C23  C17     0.00   0.0  0
 6RL  CONST_03  C18  C19  C21  C22     0.00   0.0  0
 6RL  CONST_04  C18  C17  C23  C22     0.00   0.0  0
 6RL  CONST_05  C23  C17  C18  C19     0.00   0.0  0
 6RL  CONST_06  C23  C22  C21  C19     0.00   0.0  0
 6RL  CONST_07  C26  N15  C6   C5      0.00   0.0  0
 6RL  CONST_10  N2   C26  N15  C6      0.00   0.0  0
 6RL  CONST_12  N7   C6   N15  C26   180.00   0.0  0
 6RL  CONST_13  N15  C26  N2   C3      0.00   0.0  0
 6RL  CONST_15  F20  C19  C18  C17   180.00   0.0  0
 6RL  CONST_16  C24  C23  C22  C21   180.00   0.0  0
 6RL  CONST_17  F20  C19  C21  C22   180.00   0.0  0
 6RL  CONST_18  C16  C17  C23  C22   180.00   0.0  0
 6RL  CONST_19  C18  C17  C23  C24   180.00   0.0  0
 6RL  CONST_20  C19  C18  C17  C16   180.00   0.0  0
 6RL  CONST_22  O27  C26  N15  C6    180.00   0.0  0
 6RL  CONST_23  N15  C26  N2   C1    180.00   0.0  0
 6RL  CONST_25  O27  C26  N2   C3    180.00   0.0  0
 6RL  CONST_27  H7   C22  C23  C17   180.00   0.0  0
 6RL  CONST_28  H21  C18  C19  C21   180.00   0.0  0
 6RL  CONST_29  H6   C21  C19  C18   180.00   0.0  0
 6RL  CONST_30  O27  C26  N2   C1      0.00   0.0  0
 6RL  Var_01    C9   C8   N7   C6    -98.22  30.0  1
 6RL  Var_02    C11  C14  N7   C6     98.36  30.0  1
 6RL  Var_03    C11  C10  C9   C8     53.64  30.0  1
 6RL  Var_04    N7   C8   C9   C10   -53.05  30.0  1
 6RL  Var_05    C17  C16  N15  C6     43.65  30.0  3
 6RL  Var_06    C18  C17  C16  N15  -131.54  30.0  2
 6RL  Var_07    H8   C1   N2   C26    63.71  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
 6RL  chir_01  C11  C14  C10  N13  negativ

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
 6RL  plan-1  C5   0.020
 6RL  plan-1  C6   0.020
 6RL  plan-1  C8   0.020
 6RL  plan-1  C26  0.020
 6RL  plan-1  N2   0.020
 6RL  plan-1  C3   0.020
 6RL  plan-1  O4   0.020
 6RL  plan-1  N7   0.020
 6RL  plan-1  C14  0.020
 6RL  plan-1  N15  0.020
 6RL  plan-1  C16  0.020
 6RL  plan-1  O27  0.020
 6RL  plan-1  H1   0.020
 6RL  plan-1  C1   0.020
 6RL  plan-2  C17  0.020
 6RL  plan-2  C21  0.020
 6RL  plan-2  C22  0.020
 6RL  plan-2  C24  0.020
 6RL  plan-2  C16  0.020
 6RL  plan-2  C18  0.020
 6RL  plan-2  C19  0.020
 6RL  plan-2  F20  0.020
 6RL  plan-2  C23  0.020
 6RL  plan-2  N25  0.020
 6RL  plan-2  H6   0.020
 6RL  plan-2  H7   0.020
 6RL  plan-2  H21  0.020

