# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:07:16 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NCC2(CCNCC2)c3[nH]c(cc13)c4ccnc(n4)c5ccc6OCOc6c5
#
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
 05B  05B  2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one  ligand  51  30  .  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_05B
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
 05B  C1    C  CT    0  -0.245  -4.6515   0.0080  -0.1501
 05B  C2    C  CH2   0  -0.254  -5.1730  -1.2640  -0.8402
 05B  N3    N  NH1   0  -0.652  -4.5566  -2.4742  -0.3280
 05B  C4    C  C     0   0.473  -3.2198  -2.6174  -0.1684
 05B  N5    N  NH1   0  -0.595  -6.9178   1.6381   0.6720
 05B  C6    C  CH2   0  -0.421  -5.1229   1.2495  -0.9201
 05B  C7    C  CH2   0  -0.398  -5.1352   0.1080   1.3119
 05B  C8    C  CH2   0  -0.305  -6.6217   0.4209   1.4042
 05B  C9    C  CH2   0  -0.305  -6.6138   1.4997  -0.7397
 05B  O10   O  O     0  -0.491  -2.6771  -3.7016   0.0116
 05B  C11   C  CR5   0   0.477  -3.1648  -0.1357  -0.1701
 05B  C12   C  CR5   0  -0.171  -2.4984  -1.3474  -0.1803
 05B  C13   C  CR15  0  -0.378  -1.1159  -1.0813  -0.1181
 05B  C14   C  CR5   0   0.307  -0.9768   0.2882  -0.0778
 05B  N15   N  NR15  0  -0.732  -2.2413   0.8366  -0.1051
 05B  C16   C  CR6   0   0.256   0.2313   1.0833  -0.0211
 05B  C17   C  CR16  0  -0.371   0.2286   2.4786   0.0185
 05B  C18   C  CR16  0  -0.015   1.4628   3.0946   0.0698
 05B  N19   N  N     0  -0.439   2.6049   2.4225   0.0836
 05B  C20   C  CR6   0   0.401   2.5140   1.0938   0.0458
 05B  N21   N  N     0  -0.467   1.3806   0.4098  -0.0059
 05B  C22   C  CR6   0  -0.043   3.7760   0.3268   0.0621
 05B  C23   C  CR16  0  -0.300   3.7555  -1.0648   0.0323
 05B  C24   C  CR16  0  -0.325   4.9304  -1.8198   0.0502
 05B  C25   C  CR16  0  -0.380   5.0030   1.0161   0.1098
 05B  C26   C  CR56  0   0.331   6.1439   0.2614   0.1266
 05B  C27   C  CR56  0   0.304   6.1147  -1.1256   0.0990
 05B  O28   O  O     0  -0.480   7.3776  -1.6028   0.1079
 05B  C29   C  CH2   0   0.067   8.2242  -0.4828   0.3443
 05B  O30   O  O     0  -0.487   7.4333   0.6801   0.1479
 05B  H2    H  HCH2  0   0.263  -6.2475  -1.3655  -0.7015
 05B  H2A   H  HCH2  0   0.247  -4.9975  -1.1687  -1.9190
 05B  HN3   H  HNH1  0   0.397  -5.0990  -3.3226  -0.3853
 05B  HN5   H  HNH1  0   0.355  -7.8948   1.8732   0.7866
 05B  H6    H  HCH2  0   0.235  -4.5919   2.1326  -0.5523
 05B  H6A   H  HCH2  0   0.248  -4.8836   1.1455  -1.9813
 05B  H7    H  HCH2  0   0.244  -4.9129  -0.8193   1.8440
 05B  H7A   H  HCH2  0   0.237  -4.5761   0.9035   1.8123
 05B  H8    H  HCH2  0   0.241  -6.8901   0.5633   2.4528
 05B  H8A   H  HCH2  0   0.198  -7.2067  -0.4424   1.0473
 05B  H9    H  HCH2  0   0.201  -7.1890   0.6933  -1.2227
 05B  H9A   H  HCH2  0   0.242  -6.8853   2.4235  -1.2541
 05B  H13   H  HCR5  0   0.264  -0.3092  -1.7961  -0.1093
 05B  HN15  H  HNR5  0   0.423  -2.4480   1.8231  -0.0834
 05B  H17   H  HCR6  0   0.271  -0.6727   3.0737   0.0098
 05B  H18   H  HCR6  0   0.277   1.5327   4.1759   0.1007
 05B  H23   H  HCR6  0   0.264   2.8055  -1.5788  -0.0039
 05B  H24   H  HCR6  0   0.276   4.9018  -2.9003   0.0247
 05B  H25   H  HCR6  0   0.270   5.0355   2.0962   0.1283
 05B  H29   H  HCH2  0   0.236   8.5968  -0.5134   1.3736
 05B  H29A  H  HCH2  0   0.248   9.0525  -0.4918  -0.3633

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
 05B  C1   C2    single    1.538  0.020  1.538
 05B  C1   C6    single    1.535  0.020  1.535
 05B  C1   C7    single    1.543  0.020  1.543
 05B  C1   C11   single    1.494  0.020  1.494
 05B  C2   N3    single    1.451  0.020  1.451
 05B  N3   C4    single    1.354  0.020  1.354
 05B  C4   O10   double    1.226  0.020  1.226
 05B  C4   C12   single    1.461  0.020  1.461
 05B  N5   C8    single    1.451  0.020  1.451
 05B  N5   C9    single    1.451  0.020  1.451
 05B  C6   C9    single    1.522  0.020  1.522
 05B  C7   C8    single    1.522  0.020  1.522
 05B  C11  C12   aromatic  1.383  0.020  1.383
 05B  C11  N15   aromatic  1.343  0.020  1.343
 05B  C12  C13   aromatic  1.409  0.020  1.409
 05B  C13  C14   aromatic  1.377  0.020  1.377
 05B  C14  N15   aromatic  1.379  0.020  1.379
 05B  C14  C16   single    1.447  0.020  1.447
 05B  C16  C17   aromatic  1.396  0.020  1.396
 05B  C16  N21   aromatic  1.332  0.020  1.332
 05B  C17  C18   aromatic  1.380  0.020  1.380
 05B  C18  N19   aromatic  1.325  0.020  1.325
 05B  N19  C20   aromatic  1.332  0.020  1.332
 05B  C20  N21   aromatic  1.325  0.020  1.325
 05B  C20  C22   single    1.477  0.020  1.477
 05B  C22  C23   aromatic  1.392  0.020  1.392
 05B  C22  C25   aromatic  1.408  0.020  1.408
 05B  C23  C24   aromatic  1.397  0.020  1.397
 05B  C24  C27   aromatic  1.374  0.020  1.374
 05B  C25  C26   aromatic  1.368  0.020  1.368
 05B  C26  C27   aromatic  1.388  0.020  1.388
 05B  C26  O30   single    1.356  0.020  1.356
 05B  C27  O28   single    1.350  0.020  1.350
 05B  O28  C29   single    1.424  0.020  1.424
 05B  C29  O30   single    1.420  0.020  1.420
 05B  C2   H2    single    0.970  0.020  1.090
 05B  C2   H2A   single    0.970  0.020  1.090
 05B  N3   HN3   single    0.890  0.020  1.040
 05B  N5   HN5   single    0.890  0.020  1.040
 05B  C6   H6    single    0.970  0.020  1.090
 05B  C6   H6A   single    0.970  0.020  1.090
 05B  C7   H7    single    0.970  0.020  1.090
 05B  C7   H7A   single    0.970  0.020  1.090
 05B  C8   H8    single    0.970  0.020  1.090
 05B  C8   H8A   single    0.970  0.020  1.090
 05B  C9   H9    single    0.970  0.020  1.090
 05B  C9   H9A   single    0.970  0.020  1.090
 05B  C13  H13   single    0.930  0.020  1.080
 05B  N15  HN15  single    0.860  0.020  1.020
 05B  C17  H17   single    0.930  0.020  1.080
 05B  C18  H18   single    0.930  0.020  1.080
 05B  C23  H23   single    0.930  0.020  1.080
 05B  C24  H24   single    0.930  0.020  1.080
 05B  C25  H25   single    0.930  0.020  1.080
 05B  C29  H29   single    0.970  0.020  1.090
 05B  C29  H29A  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
 05B  C11   C1   C7   109.32  3.000
 05B  C11   C1   C6   112.13  3.000
 05B  C7    C1   C6   109.06  3.000
 05B  C11   C1   C2   104.59  3.000
 05B  C7    C1   C2   111.86  3.000
 05B  C6    C1   C2   109.86  3.000
 05B  H2A   C2   H2   106.94  3.000
 05B  H2A   C2   N3   110.58  3.000
 05B  H2    C2   N3   107.25  3.000
 05B  H2A   C2   C1   108.36  3.000
 05B  H2    C2   C1   110.77  3.000
 05B  N3    C2   C1   112.78  3.000
 05B  HN3   N3   C4   116.66  3.000
 05B  HN3   N3   C2   116.93  3.000
 05B  C4    N3   C2   123.30  3.000
 05B  C12   C4   O10  123.48  3.000
 05B  C12   C4   N3   113.25  3.000
 05B  O10   C4   N3   123.23  3.000
 05B  HN5   N5   C9   109.57  3.000
 05B  HN5   N5   C8   109.57  3.000
 05B  C9    N5   C8   111.61  3.000
 05B  H6A   C6   H6   107.28  3.000
 05B  H6A   C6   C9   110.19  3.000
 05B  H6    C6   C9   107.63  3.000
 05B  H6A   C6   C1   110.05  3.000
 05B  H6    C6   C1   109.58  3.000
 05B  C9    C6   C1   111.98  3.000
 05B  H7A   C7   H7   106.90  3.000
 05B  H7A   C7   C8   108.79  3.000
 05B  H7    C7   C8   110.12  3.000
 05B  H7A   C7   C1   108.69  3.000
 05B  H7    C7   C1   110.05  3.000
 05B  C8    C7   C1   112.14  3.000
 05B  H8A   C8   H8   106.42  3.000
 05B  H8A   C8   C7   109.74  3.000
 05B  H8    C8   C7   108.97  3.000
 05B  H8A   C8   N5   112.67  3.000
 05B  H8    C8   N5   108.97  3.000
 05B  C7    C8   N5   109.95  3.000
 05B  H9A   C9   H9   106.44  3.000
 05B  H9A   C9   C6   109.07  3.000
 05B  H9    C9   C6   109.81  3.000
 05B  H9A   C9   N5   109.00  3.000
 05B  H9    C9   N5   112.76  3.000
 05B  C6    C9   N5   109.64  3.000
 05B  N15   C11  C12  107.66  3.000
 05B  N15   C11  C1   127.90  3.000
 05B  C12   C11  C1   124.33  3.000
 05B  C13   C12  C11  107.88  3.000
 05B  C13   C12  C4   130.41  3.000
 05B  C11   C12  C4   121.59  3.000
 05B  H13   C13  C14  125.71  3.000
 05B  H13   C13  C12  127.55  3.000
 05B  C14   C13  C12  106.75  3.000
 05B  C16   C14  N15  123.22  3.000
 05B  C16   C14  C13  129.18  3.000
 05B  N15   C14  C13  107.60  3.000
 05B  HN15  N15  C14  125.23  3.000
 05B  HN15  N15  C11  124.66  3.000
 05B  C14   N15  C11  110.11  3.000
 05B  N21   C16  C17  120.44  3.000
 05B  N21   C16  C14  116.28  3.000
 05B  C17   C16  C14  123.28  3.000
 05B  H17   C17  C18  120.03  3.000
 05B  H17   C17  C16  123.51  3.000
 05B  C18   C17  C16  116.46  3.000
 05B  H18   C18  N19  116.75  3.000
 05B  H18   C18  C17  120.26  3.000
 05B  N19   C18  C17  122.99  3.000
 05B  C20   N19  C18  116.53  3.000
 05B  C22   C20  N21  117.60  3.000
 05B  C22   C20  N19  117.35  3.000
 05B  N21   C20  N19  125.05  3.000
 05B  C20   N21  C16  118.52  3.000
 05B  C25   C22  C23  120.19  3.000
 05B  C25   C22  C20  119.39  3.000
 05B  C23   C22  C20  120.42  3.000
 05B  H23   C23  C24  118.87  3.000
 05B  H23   C23  C22  119.28  3.000
 05B  C24   C23  C22  121.85  3.000
 05B  H24   C24  C27  121.91  3.000
 05B  H24   C24  C23  121.18  3.000
 05B  C27   C24  C23  116.91  3.000
 05B  H25   C25  C26  121.74  3.000
 05B  H25   C25  C22  121.06  3.000
 05B  C26   C25  C22  117.20  3.000
 05B  O30   C26  C27  109.21  3.000
 05B  O30   C26  C25  128.53  3.000
 05B  C27   C26  C25  122.25  3.000
 05B  O28   C27  C26  109.48  3.000
 05B  O28   C27  C24  128.91  3.000
 05B  C26   C27  C24  121.60  3.000
 05B  C29   O28  C27  106.22  3.000
 05B  H29A  C29  H29  110.58  3.000
 05B  H29A  C29  O30  109.90  3.000
 05B  H29   C29  O30  110.02  3.000
 05B  H29A  C29  O28  109.74  3.000
 05B  H29   C29  O28  109.65  3.000
 05B  O30   C29  O28  106.86  3.000
 05B  C29   O30  C26  106.20  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
 05B  CONST_01  C14   C13  C12  C11    0.00   0.0  0
 05B  CONST_02  C13   C14  N15  C11    0.00   0.0  0
 05B  CONST_03  C16   C14  N15  C11  180.00   0.0  0
 05B  CONST_04  C14   N15  C11  C12    0.00   0.0  0
 05B  CONST_05  N15   C14  C13  C12    0.00   0.0  0
 05B  CONST_06  C16   C14  C13  C12  180.00   0.0  0
 05B  CONST_07  N15   C11  C12  C13    0.00   0.0  0
 05B  CONST_08  C17   C16  C14  C13  180.00   0.0  0
 05B  CONST_09  N21   C16  C14  C13    0.00   0.0  0
 05B  CONST_10  C18   C17  C16  C14  180.00   0.0  0
 05B  CONST_11  C20   N21  C16  C14  180.00   0.0  0
 05B  CONST_12  C17   C16  C14  N15    0.00   0.0  0
 05B  CONST_13  N21   C16  C14  N15  180.00   0.0  0
 05B  CONST_14  N19   C18  C17  C16    0.00   0.0  0
 05B  CONST_15  N19   C20  N21  C16    0.00   0.0  0
 05B  CONST_16  C22   C20  N21  C16  180.00   0.0  0
 05B  CONST_17  C20   N21  C16  C17    0.00   0.0  0
 05B  CONST_18  C20   N19  C18  C17    0.00   0.0  0
 05B  CONST_19  N21   C16  C17  C18    0.00   0.0  0
 05B  CONST_20  N21   C20  N19  C18    0.00   0.0  0
 05B  CONST_21  C22   C20  N19  C18  180.00   0.0  0
 05B  CONST_22  C23   C22  C20  N19  180.00   0.0  0
 05B  CONST_23  C25   C22  C20  N19    0.00   0.0  0
 05B  CONST_24  C24   C23  C22  C20  180.00   0.0  0
 05B  CONST_25  C26   C25  C22  C20  180.00   0.0  0
 05B  CONST_26  C23   C22  C20  N21    0.00   0.0  0
 05B  CONST_27  C25   C22  C20  N21  180.00   0.0  0
 05B  CONST_28  C27   C24  C23  C22    0.00   0.0  0
 05B  CONST_29  C27   C26  C25  C22    0.00   0.0  0
 05B  CONST_30  C26   C25  C22  C23    0.00   0.0  0
 05B  CONST_31  C26   C27  C24  C23    0.00   0.0  0
 05B  CONST_32  C25   C22  C23  C24    0.00   0.0  0
 05B  CONST_33  C25   C26  C27  C24    0.00   0.0  0
 05B  CONST_35  O10   C4   N3   C2   180.00   0.0  0
 05B  CONST_36  HN15  N15  C11  C1     0.00   0.0  0
 05B  CONST_37  H13   C13  C12  C4     0.00   0.0  0
 05B  CONST_38  H17   C17  C16  C14    0.00   0.0  0
 05B  CONST_39  H18   C18  C17  C16  180.00   0.0  0
 05B  CONST_40  H23   C23  C22  C20    0.00   0.0  0
 05B  CONST_41  H25   C25  C22  C20    0.00   0.0  0
 05B  CONST_42  H24   C24  C23  C22  180.00   0.0  0
 05B  CONST_43  HN3   N3   C4   C12  180.00   0.0  0
 05B  Var_01    C4    N3   C2   C1   -48.29  30.0  1
 05B  Var_02    N5    C9   C6   C1    57.26  30.0  1
 05B  Var_03    N5    C8   C7   C1   -55.88  30.0  1
 05B  Var_04    C9    C6   C1   C2    71.96  30.0  3
 05B  Var_05    C8    C7   C1   C2   -71.39  30.0  3
 05B  Var_06    C12   C11  C1   C2   -27.86  30.0  1
 05B  Var_07    C6    C1   C2   N3   168.65  30.0  1
 05B  Var_08    C11   C12  C4   N3     8.36  30.0  1
 05B  Var_09    C8    N5   C9   C6   -62.69  30.0  1
 05B  Var_10    C9    N5   C8   C7    62.10  30.0  1
 05B  Var_11    O28   C29  O30  C26   13.94  30.0  1
 05B  Var_12    O30   C29  O28  C27  -13.80  30.0  1

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
 05B  plan-1  C14   0.020
 05B  plan-1  C16   0.020
 05B  plan-1  C17   0.020
 05B  plan-1  C18   0.020
 05B  plan-1  N19   0.020
 05B  plan-1  C20   0.020
 05B  plan-1  N21   0.020
 05B  plan-1  C22   0.020
 05B  plan-1  H17   0.020
 05B  plan-1  H18   0.020
 05B  plan-2  C1    0.020
 05B  plan-2  C4    0.020
 05B  plan-2  C11   0.020
 05B  plan-2  C12   0.020
 05B  plan-2  C13   0.020
 05B  plan-2  C14   0.020
 05B  plan-2  N15   0.020
 05B  plan-2  C16   0.020
 05B  plan-2  H13   0.020
 05B  plan-2  HN15  0.020
 05B  plan-3  C20   0.020
 05B  plan-3  C22   0.020
 05B  plan-3  C23   0.020
 05B  plan-3  C24   0.020
 05B  plan-3  C25   0.020
 05B  plan-3  C26   0.020
 05B  plan-3  C27   0.020
 05B  plan-3  O28   0.020
 05B  plan-3  O30   0.020
 05B  plan-3  H23   0.020
 05B  plan-3  H24   0.020
 05B  plan-3  H25   0.020
 05B  plan-4  C2    0.020
 05B  plan-4  N3    0.020
 05B  plan-4  C4    0.020
 05B  plan-4  O10   0.020
 05B  plan-4  C12   0.020
 05B  plan-4  HN3   0.020

