# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 02:41:45 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (3S)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CC[C@@H](C1CCCC1)n2cc(cn2)c3ncnc4[nH]ccc34
#
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
 RG4  RG4  (3S)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile  ligand  41  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RG4
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
 RG4  C13  C  CR5   0  -0.193  21.5898  12.3502  54.6979
 RG4  C20  C  CR15  0  -0.500  24.3292  13.1655  56.3445
 RG4  C21  C  CR15  0   0.015  24.9920  13.8383  57.3273
 RG4  C03  C  CH2   0  -0.535  22.5151  11.1059  50.6382
 RG4  C04  C  CH1   0  -0.096  22.4499  10.2299  51.9004
 RG4  C05  C  CH1   0  -0.291  23.7728   9.5646  52.2499
 RG4  C06  C  CH2   0  -0.418  23.7012   8.6065  53.4394
 RG4  C07  C  CH2   0  -0.450  24.9927   7.7995  53.3148
 RG4  C08  C  CH2   0  -0.441  25.2455   7.6670  51.7990
 RG4  C09  C  CH2   0  -0.444  24.2865   8.6637  51.1193
 RG4  C12  C  CR15  0  -0.042  20.3716  11.9074  54.1364
 RG4  C14  C  CR6   0   0.235  21.7371  13.2423  55.8339
 RG4  C16  C  CR16  0   0.023  20.6800  14.6357  57.3265
 RG4  C18  C  CR56  0   0.487  22.8669  14.4280  57.5526
 RG4  C19  C  CR56  0  -0.004  22.9530  13.5299  56.4654
 RG4  C23  C  CR15  0   0.016  22.5530  11.7338  53.9195
 RG4  N01  N  NS    0  -0.263  24.2822  13.0081  50.8378
 RG4  N10  N  NR5   0  -0.289  21.9024  10.9970  53.0066
 RG4  N11  N  N     0  -0.267  20.5757  11.0991  53.1223
 RG4  N15  N  N     0  -0.456  20.6166  13.8069  56.2891
 RG4  N17  N  N     0  -0.423  21.7562  14.9946  58.0029
 RG4  N22  N  NR15  0  -0.660  24.1123  14.5984  58.0515
 RG4  H2   H  HCR5  0   0.294  26.0413  13.8351  57.5735
 RG4  H3   H  HCH2  0   0.331  21.5388  11.5534  50.4423
 RG4  H4   H  HCH2  0   0.327  22.7603  10.4890  49.7721
 RG4  H5   H  HCH1  0   0.301  21.7151   9.4491  51.6939
 RG4  H6   H  HCH1  0   0.254  24.5346  10.3264  52.4564
 RG4  H7   H  HCH2  0   0.242  23.6121   9.1103  54.4024
 RG4  H8   H  HCH2  0   0.225  22.8273   7.9566  53.3269
 RG4  H9   H  HCH2  0   0.234  24.9283   6.8336  53.8162
 RG4  H10  H  HCH2  0   0.227  25.8102   8.3484  53.7863
 RG4  H11  H  HCH2  0   0.232  25.0549   6.6525  51.4485
 RG4  H12  H  HCH2  0   0.232  26.2848   7.8890  51.5564
 RG4  H13  H  HCH2  0   0.246  24.7673   9.2286  50.3199
 RG4  H14  H  HCH2  0   0.233  23.4421   8.1310  50.6712
 RG4  H15  H  HCR5  0   0.265  19.3693  12.1477  54.4547
 RG4  H16  H  HCR6  0   0.249  19.7386  15.0652  57.6518
 RG4  H17  H  HCR5  0   0.307  23.6284  11.7745  53.9498
 RG4  H18  H  HNR5  0   0.416  24.3516  15.1840  58.8363
 RG4  H1   H  HCR5  0   0.259  24.7906  12.4940  55.6408
 RG4  C02  C  CSP   0   0.121  23.5004  12.1695  50.7430

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
 RG4  C03  C02  single    1.454  0.020  1.454
 RG4  C03  C04  single    1.538  0.020  1.538
 RG4  C02  N01  triple    1.150  0.020  1.150
 RG4  C09  C08  single    1.541  0.020  1.541
 RG4  C09  C05  single    1.534  0.020  1.534
 RG4  C08  C07  single    1.542  0.020  1.542
 RG4  C04  C05  single    1.521  0.020  1.521
 RG4  C04  N10  single    1.453  0.020  1.453
 RG4  C05  C06  single    1.529  0.020  1.529
 RG4  N10  N11  aromatic  1.336  0.020  1.336
 RG4  N10  C23  aromatic  1.341  0.020  1.341
 RG4  C07  C06  single    1.528  0.020  1.528
 RG4  N11  C12  aromatic  1.313  0.020  1.313
 RG4  C23  C13  aromatic  1.383  0.020  1.383
 RG4  C12  C13  aromatic  1.413  0.020  1.413
 RG4  C13  C14  single    1.452  0.020  1.452
 RG4  C14  N15  aromatic  1.335  0.020  1.335
 RG4  C14  C19  aromatic  1.400  0.020  1.400
 RG4  C20  C19  aromatic  1.429  0.020  1.429
 RG4  C20  C21  aromatic  1.363  0.020  1.363
 RG4  N15  C16  aromatic  1.329  0.020  1.329
 RG4  C19  C18  aromatic  1.413  0.020  1.413
 RG4  C21  N22  aromatic  1.370  0.020  1.370
 RG4  C16  N17  aromatic  1.321  0.020  1.321
 RG4  C18  N17  aromatic  1.326  0.020  1.326
 RG4  C18  N22  aromatic  1.352  0.020  1.352
 RG4  C20  H1   single    0.930  0.020  1.080
 RG4  C21  H2   single    0.930  0.020  1.080
 RG4  C03  H3   single    0.970  0.020  1.090
 RG4  C03  H4   single    0.970  0.020  1.090
 RG4  C04  H5   single    0.970  0.020  1.090
 RG4  C05  H6   single    0.970  0.020  1.090
 RG4  C06  H7   single    0.970  0.020  1.090
 RG4  C06  H8   single    0.970  0.020  1.090
 RG4  C07  H9   single    0.970  0.020  1.090
 RG4  C07  H10  single    0.970  0.020  1.090
 RG4  C08  H11  single    0.970  0.020  1.090
 RG4  C08  H12  single    0.970  0.020  1.090
 RG4  C09  H13  single    0.970  0.020  1.090
 RG4  C09  H14  single    0.970  0.020  1.090
 RG4  C12  H15  single    0.930  0.020  1.080
 RG4  C16  H16  single    0.930  0.020  1.080
 RG4  C23  H17  single    0.930  0.020  1.080
 RG4  N22  H18  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
 RG4  C23  C13  C14  130.05  3.000
 RG4  C14  C13  C12  126.24  3.000
 RG4  C23  C13  C12  103.72  3.000
 RG4  H1   C20  C19  128.84  3.000
 RG4  H1   C20  C21  124.80  3.000
 RG4  C19  C20  C21  106.35  3.000
 RG4  H2   C21  N22  120.41  3.000
 RG4  H2   C21  C20  129.54  3.000
 RG4  N22  C21  C20  110.05  3.000
 RG4  H4   C03  H3   106.88  3.000
 RG4  H4   C03  C04  109.81  3.000
 RG4  H3   C03  C04  110.05  3.000
 RG4  H4   C03  C02  108.58  3.000
 RG4  H3   C03  C02  108.61  3.000
 RG4  C04  C03  C02  112.73  3.000
 RG4  H5   C04  N10  105.54  3.000
 RG4  H5   C04  C05  108.42  3.000
 RG4  N10  C04  C05  112.55  3.000
 RG4  H5   C04  C03  106.30  3.000
 RG4  N10  C04  C03  109.88  3.000
 RG4  C05  C04  C03  113.63  3.000
 RG4  H6   C05  C09  108.31  3.000
 RG4  H6   C05  C06  108.74  3.000
 RG4  C09  C05  C06  102.77  3.000
 RG4  H6   C05  C04  110.08  3.000
 RG4  C06  C05  C04  114.33  3.000
 RG4  C09  C05  C04  112.25  3.000
 RG4  H8   C06  H7   107.44  3.000
 RG4  H8   C06  C07  110.66  3.000
 RG4  H7   C06  C07  112.64  3.000
 RG4  H8   C06  C05  109.24  3.000
 RG4  H7   C06  C05  113.66  3.000
 RG4  C07  C06  C05  103.17  3.000
 RG4  H10  C07  H9   106.92  3.000
 RG4  H10  C07  C08  110.18  3.000
 RG4  H9   C07  C08  112.68  3.000
 RG4  H10  C07  C06  109.40  3.000
 RG4  H9   C07  C06  112.36  3.000
 RG4  C08  C07  C06  105.31  3.000
 RG4  H12  C08  H11  106.54  3.000
 RG4  H12  C08  C09  111.31  3.000
 RG4  H11  C08  C09  110.56  3.000
 RG4  H12  C08  C07  110.95  3.000
 RG4  H11  C08  C07  111.55  3.000
 RG4  C09  C08  C07  106.02  3.000
 RG4  H14  C09  H13  106.99  3.000
 RG4  H14  C09  C08  110.24  3.000
 RG4  H13  C09  C08  112.58  3.000
 RG4  H14  C09  C05  109.22  3.000
 RG4  H13  C09  C05  112.56  3.000
 RG4  C08  C09  C05  105.25  3.000
 RG4  H15  C12  N11  120.63  3.000
 RG4  H15  C12  C13  127.89  3.000
 RG4  N11  C12  C13  111.47  3.000
 RG4  N15  C14  C19  119.23  3.000
 RG4  C19  C14  C13  124.56  3.000
 RG4  N15  C14  C13  116.21  3.000
 RG4  H16  C16  N17  116.48  3.000
 RG4  H16  C16  N15  116.07  3.000
 RG4  N17  C16  N15  127.45  3.000
 RG4  N22  C18  N17  126.32  3.000
 RG4  N22  C18  C19  107.93  3.000
 RG4  N17  C18  C19  125.74  3.000
 RG4  C18  C19  C14  115.14  3.000
 RG4  C18  C19  C20  106.61  3.000
 RG4  C14  C19  C20  138.25  3.000
 RG4  H17  C23  N10  121.63  3.000
 RG4  H17  C23  C13  131.51  3.000
 RG4  N10  C23  C13  106.85  3.000
 RG4  N11  N10  C23  112.39  3.000
 RG4  C23  N10  C04  128.70  3.000
 RG4  N11  N10  C04  118.72  3.000
 RG4  N10  N11  C12  105.57  3.000
 RG4  C16  N15  C14  119.33  3.000
 RG4  C18  N17  C16  113.11  3.000
 RG4  H18  N22  C18  125.38  3.000
 RG4  H18  N22  C21  125.56  3.000
 RG4  C18  N22  C21  109.05  3.000
 RG4  N01  C02  C03  180.00  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
 RG4  CONST_01  N11  N10  C23  C13    0.00   0.0  0
 RG4  CONST_02  N10  N11  C12  C13    0.00   0.0  0
 RG4  CONST_03  C16  N15  C14  C13  180.00   0.0  0
 RG4  CONST_04  C20  C19  C14  C13    0.00   0.0  0
 RG4  CONST_05  C18  C19  C14  C13  180.00   0.0  0
 RG4  CONST_06  N15  C14  C19  C20  180.00   0.0  0
 RG4  CONST_07  N17  C18  C19  C20  180.00   0.0  0
 RG4  CONST_08  N22  C18  C19  C20    0.00   0.0  0
 RG4  CONST_09  C18  N22  C21  C20    0.00   0.0  0
 RG4  CONST_10  C14  C19  C20  C21  180.00   0.0  0
 RG4  CONST_11  C18  C19  C20  C21    0.00   0.0  0
 RG4  CONST_12  C19  C18  N22  C21    0.00   0.0  0
 RG4  CONST_13  N17  C18  N22  C21  180.00   0.0  0
 RG4  CONST_14  C23  N10  N11  C12    0.00   0.0  0
 RG4  CONST_15  N10  C23  C13  C12    0.00   0.0  0
 RG4  CONST_16  N15  C14  C13  C12    0.00   0.0  0
 RG4  CONST_17  C19  C14  C13  C12  180.00   0.0  0
 RG4  CONST_18  N10  C23  C13  C14  180.00   0.0  0
 RG4  CONST_19  N11  C12  C13  C14  180.00   0.0  0
 RG4  CONST_20  N17  C16  N15  C14    0.00   0.0  0
 RG4  CONST_21  N17  C18  C19  C14    0.00   0.0  0
 RG4  CONST_22  N22  C18  C19  C14  180.00   0.0  0
 RG4  CONST_23  C19  C14  N15  C16    0.00   0.0  0
 RG4  CONST_24  C19  C18  N17  C16    0.00   0.0  0
 RG4  CONST_25  N22  C18  N17  C16  180.00   0.0  0
 RG4  CONST_26  N15  C14  C19  C18    0.00   0.0  0
 RG4  CONST_27  N15  C16  N17  C18    0.00   0.0  0
 RG4  CONST_28  C23  C13  C14  C19    0.00   0.0  0
 RG4  CONST_29  N22  C21  C20  C19    0.00   0.0  0
 RG4  CONST_30  N11  C12  C13  C23    0.00   0.0  0
 RG4  CONST_31  N15  C14  C13  C23  180.00   0.0  0
 RG4  CONST_32  C04  N10  C23  C13  180.00   0.0  0
 RG4  CONST_33  C12  N11  N10  C04  180.00   0.0  0
 RG4  CONST_34  H18  N22  C21  C20  180.00   0.0  0
 RG4  CONST_35  H17  C23  C13  C12  180.00   0.0  0
 RG4  CONST_36  H15  C12  C13  C14    0.00   0.0  0
 RG4  CONST_37  H16  C16  N15  C14  180.00   0.0  0
 RG4  CONST_38  H1   C20  C19  C14    0.00   0.0  0
 RG4  CONST_39  H2   C21  N22  C18  180.00   0.0  0
 RG4  Var_01    C07  C08  C09  C05   13.40  30.0  1
 RG4  Var_02    C08  C07  C06  C05  -34.01  30.0  1
 RG4  Var_03    C09  C08  C07  C06   12.70  30.0  1
 RG4  Var_04    H3   C03  C02  N01  116.58  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
 RG4  chir_01  C04  C03  C05  N10  negativ
 RG4  chir_02  C05  C09  C04  C06  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
 RG4  plan-1  C13  0.020
 RG4  plan-1  C04  0.020
 RG4  plan-1  C12  0.020
 RG4  plan-1  C14  0.020
 RG4  plan-1  C23  0.020
 RG4  plan-1  N10  0.020
 RG4  plan-1  N11  0.020
 RG4  plan-1  H15  0.020
 RG4  plan-1  H17  0.020
 RG4  plan-2  C13  0.020
 RG4  plan-2  C20  0.020
 RG4  plan-2  C21  0.020
 RG4  plan-2  C14  0.020
 RG4  plan-2  C16  0.020
 RG4  plan-2  C18  0.020
 RG4  plan-2  C19  0.020
 RG4  plan-2  N15  0.020
 RG4  plan-2  N17  0.020
 RG4  plan-2  N22  0.020
 RG4  plan-2  H2   0.020
 RG4  plan-2  H16  0.020
 RG4  plan-2  H18  0.020
 RG4  plan-2  H1   0.020

