# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 07:51:30 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-(piperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(CCN1)n2cnc3cnc4[nH]ccc4c23
#
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
 1RS  1RS  1-(piperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine  ligand  33  18  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1RS
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
 1RS  C2   C  CR15  0   0.082   0.5468   2.2188   0.0146
 1RS  N3   N  N     0  -0.459  -0.6323   2.7645   0.0090
 1RS  C4   C  CR56  0   0.005  -1.5066   1.7030  -0.0050
 1RS  C5   C  CR16  0  -0.136  -2.9088   1.6962  -0.0142
 1RS  N6   N  N     0  -0.433  -3.5989   0.5745  -0.0263
 1RS  C7   C  CR56  0   0.418  -2.8941  -0.5601  -0.0302
 1RS  C8   C  CR56  0   0.005  -1.4904  -0.7190  -0.0218
 1RS  C9   C  CR56  0   0.366  -0.7939   0.4965  -0.0078
 1RS  N10  N  NR5   0  -0.521   0.5211   0.8533   0.0064
 1RS  C11  C  CH1   0  -0.113   1.6788  -0.0306   0.0083
 1RS  C12  C  CH2   0  -0.439   2.5441   0.1656   1.2485
 1RS  C13  C  CH2   0  -0.323   3.7273  -0.8030   1.2026
 1RS  N14  N  NH1   0  -0.573   4.5187  -0.7132  -0.0118
 1RS  C15  C  CH2   0  -0.323   3.7012  -0.8422  -1.2052
 1RS  C16  C  CH2   0  -0.438   2.5166   0.1244  -1.2567
 1RS  C17  C  CR15  0  -0.458  -1.2278  -2.1198  -0.0315
 1RS  C18  C  CR15  0  -0.008  -2.4469  -2.7406  -0.0446
 1RS  N19  N  NR15  0  -0.655  -3.4402  -1.8086  -0.0437
 1RS  H1   H  HCR5  0   0.291   1.4783   2.7660   0.0250
 1RS  H2   H  HCR6  0   0.258  -3.4644   2.6279  -0.0110
 1RS  H4   H  HCH1  0   0.263   1.2779  -1.0460   0.0308
 1RS  H5   H  HCH2  0   0.231   2.9172   1.1941   1.2847
 1RS  H6   H  HCH2  0   0.248   1.9530   0.0018   2.1526
 1RS  H7   H  HCH2  0   0.247   4.3787  -0.6350   2.0617
 1RS  H8   H  HCH2  0   0.223   3.3525  -1.8283   1.2927
 1RS  H9   H  HNH1  0   0.343   5.0003   0.1783  -0.0313
 1RS  H11  H  HCH2  0   0.247   4.3333  -0.7037  -2.0837
 1RS  H12  H  HCH2  0   0.223   3.3238  -1.8695  -1.2519
 1RS  H13  H  HCH2  0   0.247   1.9060  -0.0698  -2.1417
 1RS  H14  H  HCH2  0   0.230   2.8857   1.1521  -1.3350
 1RS  H15  H  HCR5  0   0.251  -0.2740  -2.6210  -0.0316
 1RS  H16  H  HCR5  0   0.288  -2.6789  -3.7929  -0.0536
 1RS  H3   H  HNR5  0   0.411  -4.4278  -2.0061  -0.0501

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
 1RS  N3   C4   aromatic  1.375  0.020  1.375
 1RS  N3   C2   aromatic  1.299  0.020  1.299
 1RS  C5   C4   aromatic  1.402  0.020  1.402
 1RS  C5   N6   aromatic  1.317  0.020  1.317
 1RS  C4   C9   aromatic  1.401  0.020  1.401
 1RS  C2   N10  aromatic  1.366  0.020  1.366
 1RS  N6   C7   aromatic  1.336  0.020  1.336
 1RS  C9   N10  aromatic  1.363  0.020  1.363
 1RS  C9   C8   aromatic  1.401  0.020  1.401
 1RS  N10  C11  single    1.457  0.020  1.457
 1RS  C7   C8   aromatic  1.413  0.020  1.413
 1RS  C7   N19  aromatic  1.363  0.020  1.363
 1RS  C8   C17  aromatic  1.425  0.020  1.425
 1RS  C11  C12  single    1.525  0.020  1.525
 1RS  C11  C16  single    1.525  0.020  1.525
 1RS  C12  C13  single    1.530  0.020  1.530
 1RS  N19  C18  aromatic  1.362  0.020  1.362
 1RS  C13  N14  single    1.452  0.020  1.452
 1RS  C17  C18  aromatic  1.368  0.020  1.368
 1RS  C16  C15  single    1.530  0.020  1.530
 1RS  N14  C15  single    1.452  0.020  1.452
 1RS  C2   H1   single    0.930  0.020  1.080
 1RS  C5   H2   single    0.930  0.020  1.080
 1RS  C11  H4   single    0.970  0.020  1.090
 1RS  C12  H5   single    0.970  0.020  1.090
 1RS  C12  H6   single    0.970  0.020  1.090
 1RS  C13  H7   single    0.970  0.020  1.090
 1RS  C13  H8   single    0.970  0.020  1.090
 1RS  N14  H9   single    0.890  0.020  1.040
 1RS  C15  H11  single    0.970  0.020  1.090
 1RS  C15  H12  single    0.970  0.020  1.090
 1RS  C16  H13  single    0.970  0.020  1.090
 1RS  C16  H14  single    0.970  0.020  1.090
 1RS  C17  H15  single    0.930  0.020  1.080
 1RS  C18  H16  single    0.930  0.020  1.080
 1RS  N19  H3   single    0.860  0.020  1.020

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
 1RS  H1   C2   N10  121.51  3.000
 1RS  H1   C2   N3   124.74  3.000
 1RS  N10  C2   N3   113.75  3.000
 1RS  C4   N3   C2   104.64  3.000
 1RS  C9   C4   C5   120.29  3.000
 1RS  C9   C4   N3   109.95  3.000
 1RS  C5   C4   N3   129.76  3.000
 1RS  H2   C5   N6   117.60  3.000
 1RS  H2   C5   C4   120.52  3.000
 1RS  N6   C5   C4   121.88  3.000
 1RS  C7   N6   C5   116.56  3.000
 1RS  N19  C7   C8   107.17  3.000
 1RS  N19  C7   N6   124.53  3.000
 1RS  C8   C7   N6   128.30  3.000
 1RS  C17  C8   C9   139.57  3.000
 1RS  C17  C8   C7   107.07  3.000
 1RS  C9   C8   C7   113.36  3.000
 1RS  N10  C9   C8   135.00  3.000
 1RS  C8   C9   C4   119.61  3.000
 1RS  N10  C9   C4   105.39  3.000
 1RS  C11  N10  C9   127.46  3.000
 1RS  C11  N10  C2   126.28  3.000
 1RS  C9   N10  C2   106.26  3.000
 1RS  H4   C11  C16  108.26  3.000
 1RS  H4   C11  C12  108.13  3.000
 1RS  C16  C11  C12  110.48  3.000
 1RS  H4   C11  N10  105.81  3.000
 1RS  C16  C11  N10  111.96  3.000
 1RS  C12  C11  N10  111.96  3.000
 1RS  H6   C12  H5   107.33  3.000
 1RS  H6   C12  C13  110.39  3.000
 1RS  H5   C12  C13  109.40  3.000
 1RS  H6   C12  C11  110.29  3.000
 1RS  H5   C12  C11  109.95  3.000
 1RS  C13  C12  C11  109.45  3.000
 1RS  H8   C13  H7   106.48  3.000
 1RS  H8   C13  N14  108.24  3.000
 1RS  H7   C13  N14  108.88  3.000
 1RS  H8   C13  C12  109.00  3.000
 1RS  H7   C13  C12  109.92  3.000
 1RS  N14  C13  C12  114.04  3.000
 1RS  H9   N14  C15  109.26  3.000
 1RS  H9   N14  C13  109.23  3.000
 1RS  C15  N14  C13  112.02  3.000
 1RS  H12  C15  H11  106.52  3.000
 1RS  H12  C15  C16  108.92  3.000
 1RS  H11  C15  C16  109.95  3.000
 1RS  H12  C15  N14  108.20  3.000
 1RS  H11  C15  N14  108.92  3.000
 1RS  C16  C15  N14  114.04  3.000
 1RS  H14  C16  H13  107.30  3.000
 1RS  H14  C16  C15  109.54  3.000
 1RS  H13  C16  C15  110.35  3.000
 1RS  H14  C16  C11  109.87  3.000
 1RS  H13  C16  C11  110.29  3.000
 1RS  C15  C16  C11  109.47  3.000
 1RS  H15  C17  C18  125.29  3.000
 1RS  H15  C17  C8   128.34  3.000
 1RS  C18  C17  C8   106.37  3.000
 1RS  H16  C18  N19  120.74  3.000
 1RS  H16  C18  C17  129.42  3.000
 1RS  N19  C18  C17  109.84  3.000
 1RS  H3   N19  C18  125.51  3.000
 1RS  H3   N19  C7   124.94  3.000
 1RS  C18  N19  C7   109.55  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
 1RS  CONST_01  C5   C4   N3   C2   180.00   0.0  0
 1RS  CONST_02  C9   C4   N3   C2     0.00   0.0  0
 1RS  CONST_03  C4   C9   N10  C2     0.00   0.0  0
 1RS  CONST_04  C8   C9   N10  C2   180.00   0.0  0
 1RS  CONST_05  N6   C5   C4   N3   180.00   0.0  0
 1RS  CONST_06  N10  C9   C4   N3     0.00   0.0  0
 1RS  CONST_07  C8   C9   C4   N3   180.00   0.0  0
 1RS  CONST_08  C9   N10  C2   N3     0.00   0.0  0
 1RS  CONST_09  N10  C2   N3   C4     0.00   0.0  0
 1RS  CONST_10  C7   N6   C5   C4     0.00   0.0  0
 1RS  CONST_11  C7   C8   C9   C4     0.00   0.0  0
 1RS  CONST_12  C17  C8   C9   C4   180.00   0.0  0
 1RS  CONST_13  N10  C9   C4   C5   180.00   0.0  0
 1RS  CONST_14  C8   C9   C4   C5     0.00   0.0  0
 1RS  CONST_15  C8   C7   N6   C5     0.00   0.0  0
 1RS  CONST_16  N19  C7   N6   C5   180.00   0.0  0
 1RS  CONST_17  C9   C4   C5   N6     0.00   0.0  0
 1RS  CONST_18  C9   C8   C7   N6     0.00   0.0  0
 1RS  CONST_19  C17  C8   C7   N6   180.00   0.0  0
 1RS  CONST_20  C18  N19  C7   N6   180.00   0.0  0
 1RS  CONST_21  N10  C9   C8   C7   180.00   0.0  0
 1RS  CONST_22  C18  C17  C8   C7     0.00   0.0  0
 1RS  CONST_23  C17  C18  N19  C7     0.00   0.0  0
 1RS  CONST_24  C18  N19  C7   C8     0.00   0.0  0
 1RS  CONST_25  N19  C18  C17  C8     0.00   0.0  0
 1RS  CONST_26  N19  C7   C8   C9   180.00   0.0  0
 1RS  CONST_27  C18  C17  C8   C9   180.00   0.0  0
 1RS  CONST_28  C17  C8   C9   N10    0.00   0.0  0
 1RS  CONST_29  N19  C7   C8   C17    0.00   0.0  0
 1RS  CONST_30  C11  N10  C2   N3   180.00   0.0  0
 1RS  CONST_31  C11  N10  C9   C4   180.00   0.0  0
 1RS  CONST_32  C11  N10  C9   C8     0.00   0.0  0
 1RS  CONST_33  H2   C5   C4   N3     0.00   0.0  0
 1RS  CONST_34  H1   C2   N3   C4   180.00   0.0  0
 1RS  CONST_35  H3   N19  C7   N6     0.00   0.0  0
 1RS  CONST_36  H15  C17  C8   C7   180.00   0.0  0
 1RS  CONST_37  H16  C18  N19  C7   180.00   0.0  0
 1RS  Var_01    N14  C13  C12  C11   54.61  30.0  1
 1RS  Var_02    N14  C15  C16  C11  -54.57  30.0  1
 1RS  Var_03    C15  N14  C13  C12  -53.19  30.0  1
 1RS  Var_04    C16  C15  N14  C13   53.17  30.0  1

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
 1RS  chir_01  C11  N10  C12  C16  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
 1RS  plan-1  C2   0.020
 1RS  plan-1  N3   0.020
 1RS  plan-1  C4   0.020
 1RS  plan-1  C5   0.020
 1RS  plan-1  N6   0.020
 1RS  plan-1  C7   0.020
 1RS  plan-1  C8   0.020
 1RS  plan-1  C9   0.020
 1RS  plan-1  N10  0.020
 1RS  plan-1  C11  0.020
 1RS  plan-1  C17  0.020
 1RS  plan-1  C18  0.020
 1RS  plan-1  N19  0.020
 1RS  plan-1  H1   0.020
 1RS  plan-1  H2   0.020
 1RS  plan-1  H15  0.020
 1RS  plan-1  H16  0.020
 1RS  plan-1  H3   0.020

