# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 17:33:26 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-({2-[(3R)-3-aminopiperidin-1-yl]-5-bromo-6-oxopyrimidin-1(6H)-yl}methyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCN(C1)C2=NC=C(Br)C(=O)N2Cc3ccccc3C#N
#
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
 RUM  RUM  2-({2-[(3R)-3-aminopiperidin-1-yl]-5-bromo-6-oxopyrimidin-1(6H)-yl}methyl)benzonitrile  ligand  42  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RUM
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
 RUM  N17   N   NS    0  -0.245  -0.9449  -1.4515   2.4812
 RUM  C16   C   CSP   0   0.018  -0.2450  -2.0197   1.7628
 RUM  C15   C   CR6   0  -0.000   0.6196  -2.7495   0.8919
 RUM  C14   C   CR16  0  -0.234   1.5119  -3.6605   1.4591
 RUM  C13   C   CR16  0  -0.259   2.3379  -4.4105   0.6414
 RUM  C12   C   CR16  0  -0.225   2.2705  -4.2489  -0.7363
 RUM  C11   C   CR16  0  -0.294   1.3917  -3.3316  -1.2928
 RUM  C10   C   CR6   0   0.190   0.5548  -2.5670  -0.4941
 RUM  C9    C   CH2   0  -0.462  -0.4353  -1.6187  -1.1185
 RUM  N2    N   NR6   0  -0.562  -0.2778  -0.2434  -0.6354
 RUM  C3    C   CR6   0   0.753  -1.2972   0.4519  -0.0325
 RUM  N4    N   N     0  -0.474  -1.0646   1.4926   0.7224
 RUM  C5    C   CR16  0  -0.008   0.1950   1.9388   0.8330
 RUM  C6    C   CR6   0  -0.346   1.2245   1.4377   0.1011
 RUM  BR7   BR  BR    0  -0.025   2.9481   2.1623   0.1603
 RUM  C1    C   CR6   0   0.623   1.0158   0.2912  -0.7370
 RUM  O8    O   O     0  -0.444   1.8492  -0.2492  -1.4386
 RUM  N18   N   NT    0  -0.487  -2.5650   0.0036  -0.2031
 RUM  C23   C   CH2   0  -0.311  -3.5724   0.4027   0.7690
 RUM  C22   C   CH1   0  -0.090  -4.3189   1.6742   0.3727
 RUM  N24   N   NH2   0  -0.793  -5.2939   1.9772   1.4071
 RUM  C21   C   CH2   0  -0.448  -4.8978   1.5050  -1.0319
 RUM  C20   C   CH2   0  -0.438  -3.8265   1.0716  -2.0249
 RUM  C19   C   CH2   0  -0.356  -3.1086  -0.1871  -1.5525
 RUM  H14   H   HCR6  0   0.284   1.5463  -3.7814   2.5333
 RUM  H13   H   HCR6  0   0.276   3.0284  -5.1191   1.0779
 RUM  H12   H   HCR6  0   0.275   2.9137  -4.8323  -1.3815
 RUM  H11   H   HCR6  0   0.269   1.3586  -3.2025  -2.3669
 RUM  H9    H   HCH2  0   0.307  -0.3457  -1.6525  -2.2038
 RUM  H9A   H   HCH2  0   0.323  -1.4396  -1.9502  -0.8628
 RUM  H5    H   HCR6  0   0.290   0.3462   2.7712   1.5115
 RUM  H23   H   HCH2  0   0.245  -4.2873  -0.4259   0.8426
 RUM  H23A  H   HCH2  0   0.265  -3.1074   0.5157   1.7456
 RUM  H22   H   HCH1  0   0.231  -3.5927   2.4935   0.3568
 RUM  HN24  H   HNH2  0   0.348  -5.7410   2.8618   1.2000
 RUM  HN2A  H   HNH2  0   0.336  -6.0358   1.2860   1.3904
 RUM  H21   H   HCH2  0   0.214  -5.6915   0.7486  -0.9988
 RUM  H21A  H   HCH2  0   0.238  -5.3634   2.4379  -1.3597
 RUM  H20   H   HCH2  0   0.248  -4.2648   0.8772  -3.0060
 RUM  H20A  H   HCH2  0   0.229  -3.0911   1.8711  -2.1585
 RUM  H19   H   HCH2  0   0.284  -2.3165  -0.4385  -2.2543
 RUM  H19A  H   HCH2  0   0.257  -3.7989  -1.0344  -1.5240

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
 RUM  N17  C16   triple    1.153  0.020  1.153
 RUM  C16  C15   single    1.428  0.020  1.428
 RUM  C15  C10   aromatic  1.399  0.020  1.399
 RUM  C14  C15   aromatic  1.396  0.020  1.396
 RUM  C14  C13   aromatic  1.383  0.020  1.383
 RUM  C14  H14   single    0.930  0.020  1.080
 RUM  C13  C12   aromatic  1.389  0.020  1.389
 RUM  C13  H13   single    0.930  0.020  1.080
 RUM  C12  C11   aromatic  1.387  0.020  1.387
 RUM  C12  H12   single    0.930  0.020  1.080
 RUM  C11  H11   single    0.930  0.020  1.080
 RUM  C10  C11   aromatic  1.387  0.020  1.387
 RUM  C10  C9    single    1.506  0.020  1.506
 RUM  C9   H9    single    0.970  0.020  1.090
 RUM  C9   H9A   single    0.970  0.020  1.090
 RUM  N2   C9    single    1.466  0.020  1.466
 RUM  N2   C1    single    1.403  0.020  1.403
 RUM  C3   N2    single    1.373  0.020  1.373
 RUM  N4   C3    double    1.307  0.020  1.307
 RUM  N4   C5    single    1.341  0.020  1.341
 RUM  C5   C6    double    1.359  0.020  1.359
 RUM  C5   H5    single    0.930  0.020  1.080
 RUM  C6   C1    single    1.435  0.020  1.435
 RUM  C6   BR7   single    1.871  0.020  1.871
 RUM  C1   O8    double    1.216  0.020  1.216
 RUM  N18  C3    single    1.356  0.020  1.356
 RUM  N18  C19   single    1.467  0.020  1.467
 RUM  C23  N18   single    1.456  0.020  1.456
 RUM  C23  H23   single    0.970  0.020  1.090
 RUM  C23  H23A  single    0.970  0.020  1.090
 RUM  C22  C23   single    1.527  0.020  1.527
 RUM  C22  C21   single    1.529  0.020  1.529
 RUM  C22  H22   single    0.970  0.020  1.090
 RUM  N24  C22   single    1.453  0.020  1.453
 RUM  N24  HN24  single    0.890  0.020  1.040
 RUM  N24  HN2A  single    0.890  0.020  1.040
 RUM  C21  C20   single    1.524  0.020  1.524
 RUM  C21  H21   single    0.970  0.020  1.090
 RUM  C21  H21A  single    0.970  0.020  1.090
 RUM  C20  C19   single    1.524  0.020  1.524
 RUM  C20  H20   single    0.970  0.020  1.090
 RUM  C20  H20A  single    0.970  0.020  1.090
 RUM  C19  H19   single    0.970  0.020  1.090
 RUM  C19  H19A  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
 RUM  C15   C16  N17   180.00  3.000
 RUM  C10   C15  C14   121.15  3.000
 RUM  C14   C15  C16   118.22  3.000
 RUM  C10   C15  C16   120.62  3.000
 RUM  H14   C14  C13   120.50  3.000
 RUM  H14   C14  C15   119.81  3.000
 RUM  C13   C14  C15   119.70  3.000
 RUM  H13   C13  C12   120.51  3.000
 RUM  H13   C13  C14   119.86  3.000
 RUM  C12   C13  C14   119.63  3.000
 RUM  H12   C12  C11   119.61  3.000
 RUM  H12   C12  C13   120.00  3.000
 RUM  C11   C12  C13   120.38  3.000
 RUM  H11   C11  C10   119.17  3.000
 RUM  C10   C11  C12   121.06  3.000
 RUM  H11   C11  C12   119.77  3.000
 RUM  C9    C10  C11   120.33  3.000
 RUM  C9    C10  C15   121.54  3.000
 RUM  C11   C10  C15   118.07  3.000
 RUM  H9A   C9   H9    107.49  3.000
 RUM  H9A   C9   N2    107.91  3.000
 RUM  H9    C9   N2    110.40  3.000
 RUM  N2    C9   C10   112.54  3.000
 RUM  H9A   C9   C10   108.51  3.000
 RUM  H9    C9   C10   109.83  3.000
 RUM  C1    N2   C3    121.54  3.000
 RUM  C3    N2   C9    122.68  3.000
 RUM  C1    N2   C9    115.62  3.000
 RUM  N18   C3   N4    120.17  3.000
 RUM  N18   C3   N2    118.13  3.000
 RUM  N4    C3   N2    121.66  3.000
 RUM  C5    N4   C3    118.68  3.000
 RUM  H5    C5   C6    120.96  3.000
 RUM  H5    C5   N4    115.97  3.000
 RUM  C6    C5   N4    122.99  3.000
 RUM  C1    C6   BR7   117.50  3.000
 RUM  BR7   C6   C5    122.55  3.000
 RUM  C1    C6   C5    119.93  3.000
 RUM  O8    C1   C6    126.31  3.000
 RUM  O8    C1   N2    120.28  3.000
 RUM  C6    C1   N2    113.33  3.000
 RUM  C19   N18  C23   113.17  3.000
 RUM  C23   N18  C3    118.20  3.000
 RUM  C19   N18  C3    120.35  3.000
 RUM  H23A  C23  H23   107.27  3.000
 RUM  H23A  C23  C22   110.83  3.000
 RUM  H23   C23  C22   109.14  3.000
 RUM  C22   C23  N18   113.16  3.000
 RUM  H23A  C23  N18   109.41  3.000
 RUM  H23   C23  N18   106.78  3.000
 RUM  H22   C22  C21   108.71  3.000
 RUM  H22   C22  N24   107.42  3.000
 RUM  C21   C22  N24   115.02  3.000
 RUM  N24   C22  C23   108.47  3.000
 RUM  H22   C22  C23   107.62  3.000
 RUM  C21   C22  C23   109.36  3.000
 RUM  HN2A  N24  HN24  105.61  3.000
 RUM  HN2A  N24  C22   109.69  3.000
 RUM  HN24  N24  C22   109.44  3.000
 RUM  H21A  C21  H21   106.83  3.000
 RUM  H21A  C21  C20   110.29  3.000
 RUM  H21   C21  C20   109.41  3.000
 RUM  H21A  C21  C22   110.02  3.000
 RUM  H21   C21  C22   108.83  3.000
 RUM  C20   C21  C22   111.35  3.000
 RUM  H20A  C20  H20   106.86  3.000
 RUM  H20A  C20  C19   108.94  3.000
 RUM  H20   C20  C19   108.70  3.000
 RUM  H20A  C20  C21   110.13  3.000
 RUM  H20   C20  C21   110.72  3.000
 RUM  C19   C20  C21   111.35  3.000
 RUM  H19A  C19  H19   107.31  3.000
 RUM  H19A  C19  C20   110.53  3.000
 RUM  H19   C19  C20   109.50  3.000
 RUM  H19A  C19  N18   108.10  3.000
 RUM  H19   C19  N18   110.72  3.000
 RUM  C20   C19  N18   110.62  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
 RUM  CONST_01  C12  C11  C10  C15    0.00   0.0  0
 RUM  CONST_02  C12  C13  C14  C15    0.00   0.0  0
 RUM  CONST_03  C11  C10  C15  C14    0.00   0.0  0
 RUM  CONST_04  C11  C12  C13  C14    0.00   0.0  0
 RUM  CONST_05  C10  C15  C14  C13    0.00   0.0  0
 RUM  CONST_06  C10  C11  C12  C13    0.00   0.0  0
 RUM  CONST_07  C5   N4   C3   N2     0.00   0.0  0
 RUM  CONST_10  C6   C1   N2   C3     0.00   0.0  0
 RUM  CONST_14  N18  C3   N4   C5   180.00   0.0  0
 RUM  CONST_15  N18  C3   N2   C1   180.00   0.0  0
 RUM  CONST_16  C11  C10  C15  C16  180.00   0.0  0
 RUM  CONST_17  C13  C14  C15  C16  180.00   0.0  0
 RUM  CONST_18  C9   C10  C15  C14  180.00   0.0  0
 RUM  CONST_19  C9   C10  C11  C12  180.00   0.0  0
 RUM  CONST_23  O8   C1   N2   C3   180.00   0.0  0
 RUM  CONST_24  H11  C11  C10  C15  180.00   0.0  0
 RUM  CONST_25  H13  C13  C14  C15  180.00   0.0  0
 RUM  CONST_26  H12  C12  C13  C14  180.00   0.0  0
 RUM  CONST_27  H14  C14  C13  C12  180.00   0.0  0
 RUM  Var_01    C20  C19  N18  C3   -92.02  30.0  1
 RUM  Var_02    C22  C23  N18  C3    92.03  30.0  1
 RUM  Var_03    C21  C20  C19  N18  -54.67  30.0  1
 RUM  Var_04    C19  C20  C21  C22   54.46  30.0  1
 RUM  Var_05    N2   C9   C10  C15   58.66  30.0  2
 RUM  Var_06    C1   N2   C9   C10   52.95  30.0  2

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
 RUM  chir_01  C22  C23  C21  N24  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
 RUM  plan-1  N17  0.020
 RUM  plan-1  C16  0.020
 RUM  plan-1  C15  0.020
 RUM  plan-1  C14  0.020
 RUM  plan-1  C13  0.020
 RUM  plan-1  C12  0.020
 RUM  plan-1  C11  0.020
 RUM  plan-1  C10  0.020
 RUM  plan-1  C9   0.020
 RUM  plan-1  H14  0.020
 RUM  plan-1  H13  0.020
 RUM  plan-1  H12  0.020
 RUM  plan-1  H11  0.020
 RUM  plan-2  C9   0.020
 RUM  plan-2  N2   0.020
 RUM  plan-2  C3   0.020
 RUM  plan-2  N4   0.020
 RUM  plan-2  C5   0.020
 RUM  plan-2  C6   0.020
 RUM  plan-2  BR7  0.020
 RUM  plan-2  C1   0.020
 RUM  plan-2  O8   0.020
 RUM  plan-2  N18  0.020
 RUM  plan-2  C23  0.020
 RUM  plan-2  C19  0.020
 RUM  plan-2  H5   0.020

