# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:43:57 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-[(3R)-3-fluoropiperidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: F[C@@H]1CCCN(C1)c2ncnc3[nH]ccc23
#
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
 W5P  W5P  4-[(3R)-3-fluoropiperidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine  ligand  29  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W5P
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
 W5P  C10   C  CR16  0   0.037  -44.4404  -29.9062   6.2969
 W5P  C15   C  CR15  0  -0.447  -47.6690  -28.7924   4.0923
 W5P  C02   C  CH1   0   0.194  -46.2234  -31.0568   1.2717
 W5P  C03   C  CH2   0  -0.501  -45.0642  -31.9712   0.9267
 W5P  C04   C  CH2   0  -0.446  -43.9930  -31.9815   2.0155
 W5P  C05   C  CH2   0  -0.330  -43.6051  -30.5602   2.4092
 W5P  C07   C  CH2   0  -0.395  -45.7267  -29.6883   1.7029
 W5P  C08   C  CR6   0   0.502  -45.1464  -29.7047   4.1048
 W5P  C12   C  CR56  0   0.463  -46.4771  -29.1343   5.9940
 W5P  C14   C  CR15  0  -0.015  -48.4264  -28.4617   5.1745
 W5P  C16   C  CR56  0  -0.068  -46.3939  -29.2257   4.5903
 W5P  F01   F  F     0  -0.380  -46.9447  -31.6105   2.3366
 W5P  N06   N  NT    0  -0.474  -44.7930  -29.8092   2.7998
 W5P  N09   N  N     0  -0.497  -44.2101  -30.0441   4.9980
 W5P  N11   N  N     0  -0.453  -45.5308  -29.4579   6.8784
 W5P  N13   N  NR15  0  -0.656  -47.7040  -28.6690   6.3175
 W5P  H101  H  HCR6  0   0.242  -43.6266  -30.2018   6.9519
 W5P  H151  H  HCR5  0   0.256  -48.0182  -28.7212   3.0777
 W5P  H021  H  HCH1  0   0.231  -46.9088  -30.9568   0.4267
 W5P  H032  H  HCH2  0   0.257  -45.4306  -32.9796   0.7239
 W5P  H031  H  HCH2  0   0.237  -44.6322  -31.6061  -0.0098
 W5P  H042  H  HCH2  0   0.233  -44.3502  -32.5144   2.9008
 W5P  H041  H  HCH2  0   0.245  -43.1097  -32.5170   1.6620
 W5P  H051  H  HCH2  0   0.275  -42.8840  -30.5566   3.2189
 W5P  H052  H  HCH2  0   0.241  -43.1529  -30.0438   1.5571
 W5P  H072  H  HCH2  0   0.269  -45.2061  -29.2333   0.8557
 W5P  H071  H  HCH2  0   0.281  -46.5434  -29.0198   1.9458
 W5P  H141  H  HCR5  0   0.287  -49.4376  -28.0926   5.2199
 W5P  H131  H  HNR5  0   0.412  -48.0329  -28.5149   7.2567

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
 W5P  C03  C02   single    1.516  0.020  1.516
 W5P  C03  C04   single    1.527  0.020  1.527
 W5P  C02  F01   single    1.400  0.020  1.400
 W5P  C02  C07   single    1.518  0.020  1.518
 W5P  C07  N06   single    1.446  0.020  1.446
 W5P  C04  C05   single    1.525  0.020  1.525
 W5P  C05  N06   single    1.459  0.020  1.459
 W5P  N06  C08   single    1.356  0.020  1.356
 W5P  C08  C16   aromatic  1.422  0.020  1.422
 W5P  C08  N09   aromatic  1.338  0.020  1.338
 W5P  C15  C16   aromatic  1.436  0.020  1.436
 W5P  C15  C14   aromatic  1.362  0.020  1.362
 W5P  C16  C12   aromatic  1.409  0.020  1.409
 W5P  N09  C10   aromatic  1.326  0.020  1.326
 W5P  C14  N13   aromatic  1.368  0.020  1.368
 W5P  C12  N13   aromatic  1.352  0.020  1.352
 W5P  C12  N11   aromatic  1.335  0.020  1.335
 W5P  C10  N11   aromatic  1.315  0.020  1.315
 W5P  C10  H101  single    0.930  0.020  1.080
 W5P  C15  H151  single    0.930  0.020  1.080
 W5P  C02  H021  single    0.970  0.020  1.090
 W5P  C03  H032  single    0.970  0.020  1.090
 W5P  C03  H031  single    0.970  0.020  1.090
 W5P  C04  H042  single    0.970  0.020  1.090
 W5P  C04  H041  single    0.970  0.020  1.090
 W5P  C05  H051  single    0.970  0.020  1.090
 W5P  C05  H052  single    0.970  0.020  1.090
 W5P  C07  H072  single    0.970  0.020  1.090
 W5P  C07  H071  single    0.970  0.020  1.090
 W5P  C14  H141  single    0.930  0.020  1.080
 W5P  N13  H131  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
 W5P  H101  C10  N11   116.59  3.000
 W5P  H101  C10  N09   115.62  3.000
 W5P  N11   C10  N09   127.79  3.000
 W5P  H151  C15  C16   129.46  3.000
 W5P  H151  C15  C14   123.59  3.000
 W5P  C16   C15  C14   106.95  3.000
 W5P  H021  C02  F01   107.53  3.000
 W5P  H021  C02  C07   110.01  3.000
 W5P  F01   C02  C07   107.99  3.000
 W5P  H021  C02  C03   111.03  3.000
 W5P  C07   C02  C03   110.98  3.000
 W5P  F01   C02  C03   109.17  3.000
 W5P  H031  C03  H032  106.36  3.000
 W5P  H031  C03  C04   109.61  3.000
 W5P  H032  C03  C04   111.20  3.000
 W5P  H031  C03  C02   107.18  3.000
 W5P  H032  C03  C02   110.04  3.000
 W5P  C04   C03  C02   112.21  3.000
 W5P  H041  C04  H042  106.71  3.000
 W5P  H041  C04  C05   109.57  3.000
 W5P  H042  C04  C05   109.17  3.000
 W5P  H041  C04  C03   109.87  3.000
 W5P  H042  C04  C03   110.57  3.000
 W5P  C05   C04  C03   110.86  3.000
 W5P  H052  C05  H051  107.77  3.000
 W5P  H052  C05  N06   107.59  3.000
 W5P  H051  C05  N06   109.88  3.000
 W5P  H052  C05  C04   110.12  3.000
 W5P  H051  C05  C04   111.41  3.000
 W5P  N06   C05  C04   109.99  3.000
 W5P  H071  C07  H072  106.02  3.000
 W5P  H071  C07  N06   111.62  3.000
 W5P  H072  C07  N06   108.37  3.000
 W5P  H071  C07  C02   111.93  3.000
 W5P  H072  C07  C02   108.11  3.000
 W5P  N06   C07  C02   110.57  3.000
 W5P  N09   C08  N06   116.14  3.000
 W5P  N09   C08  C16   118.14  3.000
 W5P  N06   C08  C16   125.68  3.000
 W5P  N13   C12  N11   124.64  3.000
 W5P  N11   C12  C16   127.04  3.000
 W5P  N13   C12  C16   108.32  3.000
 W5P  H141  C14  N13   120.82  3.000
 W5P  H141  C14  C15   129.70  3.000
 W5P  N13   C14  C15   109.49  3.000
 W5P  C12   C16  C08   114.44  3.000
 W5P  C12   C16  C15   105.88  3.000
 W5P  C08   C16  C15   139.68  3.000
 W5P  C08   N06  C07   123.74  3.000
 W5P  C08   N06  C05   120.64  3.000
 W5P  C07   N06  C05   111.46  3.000
 W5P  C08   N09  C10   120.39  3.000
 W5P  C12   N11  C10   112.18  3.000
 W5P  H131  N13  C14   125.71  3.000
 W5P  H131  N13  C12   124.92  3.000
 W5P  C14   N13  C12   109.37  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
 W5P  CONST_01  C16   C08  N09  C10     0.00   0.0  0
 W5P  CONST_02  C16   C12  N11  C10     0.00   0.0  0
 W5P  CONST_03  N13   C12  N11  C10   180.00   0.0  0
 W5P  CONST_04  N09   C08  C16  C15   180.00   0.0  0
 W5P  CONST_05  N13   C12  C16  C15     0.00   0.0  0
 W5P  CONST_06  N11   C12  C16  C15   180.00   0.0  0
 W5P  CONST_07  C12   N13  C14  C15     0.00   0.0  0
 W5P  CONST_08  C14   C15  C16  C08   180.00   0.0  0
 W5P  CONST_09  N13   C12  C16  C08   180.00   0.0  0
 W5P  CONST_10  N11   C12  C16  C08     0.00   0.0  0
 W5P  CONST_11  N11   C10  N09  C08     0.00   0.0  0
 W5P  CONST_12  N09   C08  C16  C12     0.00   0.0  0
 W5P  CONST_13  C14   C15  C16  C12     0.00   0.0  0
 W5P  CONST_14  N09   C10  N11  C12     0.00   0.0  0
 W5P  CONST_15  C16   C12  N13  C14     0.00   0.0  0
 W5P  CONST_16  N11   C12  N13  C14   180.00   0.0  0
 W5P  CONST_17  N13   C14  C15  C16     0.00   0.0  0
 W5P  CONST_18  N06   C08  N09  C10   180.00   0.0  0
 W5P  CONST_19  N06   C08  C16  C15     0.00   0.0  0
 W5P  CONST_20  N06   C08  C16  C12   180.00   0.0  0
 W5P  CONST_21  H131  N13  C14  C15   180.00   0.0  0
 W5P  CONST_22  H151  C15  C16  C08     0.00   0.0  0
 W5P  CONST_23  H101  C10  N09  C08   180.00   0.0  0
 W5P  CONST_24  H141  C14  N13  C12   180.00   0.0  0
 W5P  Var_01    C05   C04  C03  C02   -49.58  30.0  1
 W5P  Var_02    C05   N06  C07  C02    62.50  30.0  1
 W5P  Var_03    N06   C05  C04  C03    54.86  30.0  1
 W5P  Var_04    C07   N06  C05  C04   -62.24  30.0  1
 W5P  Var_05    C16   C08  N06  C05  -167.46  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
 W5P  chir_01  C02  C03  F01  C07  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
 W5P  plan-1  C10   0.020
 W5P  plan-1  C15   0.020
 W5P  plan-1  C08   0.020
 W5P  plan-1  C12   0.020
 W5P  plan-1  C14   0.020
 W5P  plan-1  C16   0.020
 W5P  plan-1  N06   0.020
 W5P  plan-1  N09   0.020
 W5P  plan-1  N11   0.020
 W5P  plan-1  N13   0.020
 W5P  plan-1  H101  0.020
 W5P  plan-1  H151  0.020
 W5P  plan-1  H141  0.020
 W5P  plan-1  H131  0.020

