# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 10:46:45 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: tert-butyl [(1R,3R)-3-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)cyclopentyl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N[C@@H]1CC[C@H](C1)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
 0NL  0NL  'tert-butyl [(1R,3R)-3-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)cyclopentyl]carbamate'  ligand  48  25  .  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_0NL
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
 0NL  C1    C  CH3   0  -0.671   5.8555  -0.8931   1.3212
 0NL  C2    C  CT    0   0.189   5.4905  -1.0556  -0.1496
 0NL  C3    C  CH3   0  -0.669   6.4171  -0.2520  -1.0548
 0NL  C4    C  CH3   0  -0.659   5.5468  -2.5293  -0.5347
 0NL  O5    O  O2    0  -0.506   4.1000  -0.7073  -0.3823
 0NL  C6    C  C     0   0.764   3.6198   0.5167  -0.1573
 0NL  O7    O  O     0  -0.522   4.2637   1.4746   0.2249
 0NL  N8    N  NH1   0  -0.669   2.3004   0.5656  -0.4223
 0NL  C9    C  CR15  0  -0.067   1.5360   1.7824  -0.2287
 0NL  C11   C  CH2   0  -0.450   1.3168   2.1285   1.2720
 0NL  C12   C  CH2   0  -0.448  -0.1986   2.1385   1.4997
 0NL  C13   C  CR15  0  -0.110  -0.7214   1.2183   0.4014
 0NL  C15   C  CH2   0  -0.487   0.1262   1.6123  -0.8063
 0NL  N16   N  NR5   0  -0.526  -2.1512   1.2879   0.1736
 0NL  C17   C  CR15  0   0.082  -2.8969   2.4207   0.0021
 0NL  N18   N  N     0  -0.458  -4.1548   2.1888  -0.2213
 0NL  C19   C  CR56  0   0.004  -4.2653   0.8179  -0.2062
 0NL  C20   C  CR56  0   0.369  -3.0125   0.2404   0.0360
 0NL  C21   C  CR56  0   0.008  -2.8901  -1.1535   0.0850
 0NL  C22   C  CR15  0  -0.458  -1.8874  -2.1477   0.2781
 0NL  C23   C  CR15  0  -0.007  -2.5215  -3.3565   0.1871
 0NL  N24   N  NR15  0  -0.655  -3.8493  -3.1655  -0.0494
 0NL  C26   C  CR56  0   0.420  -4.1129  -1.8306  -0.1201
 0NL  N27   N  N     0  -0.432  -5.3204  -1.3074  -0.3477
 0NL  C28   C  CR16  0  -0.135  -5.3943   0.0066  -0.3903
 0NL  H1    H  HCH3  0   0.245   5.8752   0.1488   1.6329
 0NL  H1A   H  HCH3  0   0.234   5.1575  -1.4360   1.9607
 0NL  H1B   H  HCH3  0   0.233   6.8490  -1.3094   1.4914
 0NL  H3    H  HCH3  0   0.232   7.4287  -0.6522  -0.9778
 0NL  H3A   H  HCH3  0   0.234   6.1108  -0.3328  -2.0991
 0NL  H3B   H  HCH3  0   0.246   6.4543   0.7997  -0.7815
 0NL  H4    H  HCH3  0   0.237   4.8720  -3.1273   0.0796
 0NL  H4A   H  HCH3  0   0.237   5.2813  -2.6774  -1.5824
 0NL  H4B   H  HCH3  0   0.230   6.5577  -2.9099  -0.3889
 0NL  HN8   H  HNH1  0   0.394   1.8283  -0.2770  -0.7086
 0NL  H9    H  HCR5  0   0.265   2.0540   2.5956  -0.7376
 0NL  H11   H  HCH2  0   0.246   1.7888   1.3686   1.8953
 0NL  H11A  H  HCH2  0   0.250   1.7680   3.0839   1.5354
 0NL  H12   H  HCH2  0   0.261  -0.4853   1.8053   2.4966
 0NL  H12A  H  HCH2  0   0.241  -0.5956   3.1472   1.3636
 0NL  H13   H  HCR5  0   0.276  -0.5046   0.1861   0.6812
 0NL  H15   H  HCH2  0   0.264  -0.2227   2.5730  -1.1923
 0NL  H15A  H  HCH2  0   0.270   0.0783   0.8980  -1.6299
 0NL  H17   H  HCR5  0   0.291  -2.4521   3.4034   0.0556
 0NL  H22   H  HCR5  0   0.249  -0.8348  -2.0087   0.4616
 0NL  H23   H  HCR5  0   0.288  -2.1160  -4.3510   0.2751
 0NL  HN24  H  HNR5  0   0.411  -4.5326  -3.8957  -0.1669
 0NL  H28   H  HCR6  0   0.259  -6.3666   0.4504  -0.5754

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
 0NL  C1   C2    single    1.524  0.020  1.524
 0NL  C2   C3    single    1.524  0.020  1.524
 0NL  C2   C4    single    1.524  0.020  1.524
 0NL  C2   O5    single    1.452  0.020  1.452
 0NL  O5   C6    single    1.334  0.020  1.334
 0NL  C6   O7    double    1.216  0.020  1.216
 0NL  C6   N8    single    1.347  0.020  1.347
 0NL  N8   C9    single    1.450  0.020  1.450
 0NL  C9   C11   single    1.556  0.020  1.556
 0NL  C9   C15   single    1.533  0.020  1.533
 0NL  C11  C12   single    1.532  0.020  1.532
 0NL  C12  C13   single    1.525  0.020  1.525
 0NL  C13  C15   single    1.527  0.020  1.527
 0NL  C13  N16   single    1.449  0.020  1.449
 0NL  N16  C17   aromatic  1.367  0.020  1.367
 0NL  N16  C20   aromatic  1.363  0.020  1.363
 0NL  C17  N18   aromatic  1.298  0.020  1.298
 0NL  N18  C19   aromatic  1.375  0.020  1.375
 0NL  C19  C20   aromatic  1.401  0.020  1.401
 0NL  C19  C28   aromatic  1.402  0.020  1.402
 0NL  C20  C21   aromatic  1.400  0.020  1.400
 0NL  C21  C22   aromatic  1.425  0.020  1.425
 0NL  C21  C26   aromatic  1.413  0.020  1.413
 0NL  C22  C23   aromatic  1.368  0.020  1.368
 0NL  C23  N24   aromatic  1.362  0.020  1.362
 0NL  N24  C26   aromatic  1.363  0.020  1.363
 0NL  C26  N27   aromatic  1.336  0.020  1.336
 0NL  N27  C28   aromatic  1.317  0.020  1.317
 0NL  C1   H1    single    0.970  0.020  1.090
 0NL  C1   H1A   single    0.970  0.020  1.090
 0NL  C1   H1B   single    0.970  0.020  1.090
 0NL  C3   H3    single    0.970  0.020  1.090
 0NL  C3   H3A   single    0.970  0.020  1.090
 0NL  C3   H3B   single    0.970  0.020  1.090
 0NL  C4   H4    single    0.970  0.020  1.090
 0NL  C4   H4A   single    0.970  0.020  1.090
 0NL  C4   H4B   single    0.970  0.020  1.090
 0NL  N8   HN8   single    0.860  0.020  1.020
 0NL  C9   H9    single    0.970  0.020  1.090
 0NL  C11  H11   single    0.970  0.020  1.090
 0NL  C11  H11A  single    0.970  0.020  1.090
 0NL  C12  H12   single    0.970  0.020  1.090
 0NL  C12  H12A  single    0.970  0.020  1.090
 0NL  C13  H13   single    0.970  0.020  1.090
 0NL  C15  H15   single    0.970  0.020  1.090
 0NL  C15  H15A  single    0.970  0.020  1.090
 0NL  C17  H17   single    0.930  0.020  1.080
 0NL  C22  H22   single    0.930  0.020  1.080
 0NL  C23  H23   single    0.930  0.020  1.080
 0NL  N24  HN24  single    0.860  0.020  1.020
 0NL  C28  H28   single    0.930  0.020  1.080

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
 0NL  H1B   C1   H1A  107.54  3.000
 0NL  H1B   C1   H1   107.72  3.000
 0NL  H1A   C1   H1   108.68  3.000
 0NL  H1B   C1   C2   109.15  3.000
 0NL  H1A   C1   C2   111.06  3.000
 0NL  H1    C1   C2   112.52  3.000
 0NL  O5    C2   C4   103.11  3.000
 0NL  O5    C2   C3   111.13  3.000
 0NL  C4    C2   C3   109.71  3.000
 0NL  O5    C2   C1   110.99  3.000
 0NL  C4    C2   C1   109.76  3.000
 0NL  C3    C2   C1   111.80  3.000
 0NL  H3B   C3   H3A  108.77  3.000
 0NL  H3B   C3   H3   107.78  3.000
 0NL  H3A   C3   H3   107.50  3.000
 0NL  H3B   C3   C2   112.43  3.000
 0NL  H3A   C3   C2   111.01  3.000
 0NL  H3    C3   C2   109.18  3.000
 0NL  H4B   C4   H4A  107.87  3.000
 0NL  H4B   C4   H4   107.88  3.000
 0NL  H4A   C4   H4   108.41  3.000
 0NL  H4B   C4   C2   109.76  3.000
 0NL  H4A   C4   C2   111.40  3.000
 0NL  H4    C4   C2   111.40  3.000
 0NL  C6    O5   C2   122.53  3.000
 0NL  N8    C6   O7   123.51  3.000
 0NL  N8    C6   O5   110.66  3.000
 0NL  O7    C6   O5   125.83  3.000
 0NL  HN8   N8   C9   119.52  3.000
 0NL  HN8   N8   C6   118.99  3.000
 0NL  C9    N8   C6   121.39  3.000
 0NL  H9    C9   C15  110.10  3.000
 0NL  H9    C9   C11  110.57  3.000
 0NL  C15   C9   C11  104.99  3.000
 0NL  H9    C9   N8   108.25  3.000
 0NL  C15   C9   N8   109.97  3.000
 0NL  C11   C9   N8   112.94  3.000
 0NL  H11A  C11  H11  107.09  3.000
 0NL  H11A  C11  C12  111.59  3.000
 0NL  H11   C11  C12  110.34  3.000
 0NL  H11A  C11  C9   111.73  3.000
 0NL  H11   C11  C9   109.60  3.000
 0NL  C12   C11  C9   106.51  3.000
 0NL  H12A  C12  H12  107.50  3.000
 0NL  H12A  C12  C13  110.04  3.000
 0NL  H12   C12  C13  112.59  3.000
 0NL  H12A  C12  C11  110.30  3.000
 0NL  H12   C12  C11  113.22  3.000
 0NL  C13   C12  C11  103.18  3.000
 0NL  H13   C13  N16  106.36  3.000
 0NL  H13   C13  C15  109.67  3.000
 0NL  N16   C13  C15  114.26  3.000
 0NL  H13   C13  C12  108.54  3.000
 0NL  N16   C13  C12  114.98  3.000
 0NL  C15   C13  C12  102.92  3.000
 0NL  H15A  C15  H15  107.15  3.000
 0NL  H15A  C15  C13  113.80  3.000
 0NL  H15   C15  C13  109.21  3.000
 0NL  H15A  C15  C9   113.41  3.000
 0NL  H15   C15  C9   109.23  3.000
 0NL  C13   C15  C9   103.95  3.000
 0NL  C20   N16  C17  106.23  3.000
 0NL  C20   N16  C13  127.03  3.000
 0NL  C17   N16  C13  126.70  3.000
 0NL  H17   C17  N18  124.75  3.000
 0NL  H17   C17  N16  121.54  3.000
 0NL  N18   C17  N16  113.71  3.000
 0NL  C19   N18  C17  104.71  3.000
 0NL  C28   C19  C20  120.28  3.000
 0NL  C28   C19  N18  129.78  3.000
 0NL  C20   C19  N18  109.94  3.000
 0NL  C21   C20  C19  119.65  3.000
 0NL  C21   C20  N16  134.93  3.000
 0NL  C19   C20  N16  105.41  3.000
 0NL  C26   C21  C22  107.12  3.000
 0NL  C26   C21  C20  113.35  3.000
 0NL  C22   C21  C20  139.53  3.000
 0NL  H22   C22  C23  125.32  3.000
 0NL  H22   C22  C21  128.35  3.000
 0NL  C23   C22  C21  106.34  3.000
 0NL  H23   C23  N24  120.69  3.000
 0NL  H23   C23  C22  129.47  3.000
 0NL  N24   C23  C22  109.84  3.000
 0NL  HN24  N24  C26  124.97  3.000
 0NL  HN24  N24  C23  125.46  3.000
 0NL  C26   N24  C23  109.57  3.000
 0NL  N27   C26  N24  124.58  3.000
 0NL  N27   C26  C21  128.29  3.000
 0NL  N24   C26  C21  107.13  3.000
 0NL  C28   N27  C26  116.56  3.000
 0NL  H28   C28  N27  117.65  3.000
 0NL  H28   C28  C19  120.49  3.000
 0NL  N27   C28  C19  121.86  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
 0NL  CONST_01  C19   N18  C17  N16    0.00   0.0  0
 0NL  CONST_02  N18   C19  C20  N16    0.00   0.0  0
 0NL  CONST_03  C28   C19  C20  N16  180.00   0.0  0
 0NL  CONST_04  C22   C21  C20  N16    0.00   0.0  0
 0NL  CONST_05  C26   C21  C20  N16  180.00   0.0  0
 0NL  CONST_06  C19   C20  N16  C17    0.00   0.0  0
 0NL  CONST_07  C21   C20  N16  C17  180.00   0.0  0
 0NL  CONST_08  C20   C19  N18  C17    0.00   0.0  0
 0NL  CONST_09  C28   C19  N18  C17  180.00   0.0  0
 0NL  CONST_10  C20   N16  C17  N18    0.00   0.0  0
 0NL  CONST_11  C21   C20  C19  N18  180.00   0.0  0
 0NL  CONST_12  N27   C28  C19  N18  180.00   0.0  0
 0NL  CONST_13  C22   C21  C20  C19  180.00   0.0  0
 0NL  CONST_14  C26   C21  C20  C19    0.00   0.0  0
 0NL  CONST_15  C26   N27  C28  C19    0.00   0.0  0
 0NL  CONST_16  N27   C28  C19  C20    0.00   0.0  0
 0NL  CONST_17  C23   C22  C21  C20  180.00   0.0  0
 0NL  CONST_18  N24   C26  C21  C20  180.00   0.0  0
 0NL  CONST_19  N27   C26  C21  C20    0.00   0.0  0
 0NL  CONST_20  C28   C19  C20  C21    0.00   0.0  0
 0NL  CONST_21  N24   C23  C22  C21    0.00   0.0  0
 0NL  CONST_22  C23   N24  C26  C21    0.00   0.0  0
 0NL  CONST_23  C28   N27  C26  C21    0.00   0.0  0
 0NL  CONST_24  N24   C26  C21  C22    0.00   0.0  0
 0NL  CONST_25  N27   C26  C21  C22  180.00   0.0  0
 0NL  CONST_26  C26   N24  C23  C22    0.00   0.0  0
 0NL  CONST_27  C26   C21  C22  C23    0.00   0.0  0
 0NL  CONST_28  N27   C26  N24  C23  180.00   0.0  0
 0NL  CONST_29  C28   N27  C26  N24  180.00   0.0  0
 0NL  CONST_30  N18   C17  N16  C13  180.00   0.0  0
 0NL  CONST_31  C19   C20  N16  C13  180.00   0.0  0
 0NL  CONST_32  C21   C20  N16  C13    0.00   0.0  0
 0NL  CONST_33  H17   C17  N16  C13    0.00   0.0  0
 0NL  CONST_34  H28   C28  C19  N18    0.00   0.0  0
 0NL  CONST_35  H22   C22  C21  C20    0.00   0.0  0
 0NL  CONST_36  H23   C23  C22  C21  180.00   0.0  0
 0NL  CONST_37  HN24  N24  C26  C21  180.00   0.0  0
 0NL  Var_01    C13   C12  C11  C9    25.09  30.0  1
 0NL  Var_02    C9    N8   C6   O5   178.66  30.0  2
 0NL  Var_03    O7    C6   O5   C2     1.91  30.0  3
 0NL  Var_04    H3    C3   C2   C1    64.83  30.0  3
 0NL  Var_05    H4    C4   C2   C1    58.32  30.0  3
 0NL  Var_06    H1    C1   C2   C3    55.32  30.0  3

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
 0NL  chir_01  C9   N8   C11  C15  positiv
 0NL  chir_02  C13  N16  C12  C15  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
 0NL  plan-1  C13   0.020
 0NL  plan-1  N16   0.020
 0NL  plan-1  C17   0.020
 0NL  plan-1  N18   0.020
 0NL  plan-1  C19   0.020
 0NL  plan-1  C20   0.020
 0NL  plan-1  C21   0.020
 0NL  plan-1  C22   0.020
 0NL  plan-1  C23   0.020
 0NL  plan-1  N24   0.020
 0NL  plan-1  C26   0.020
 0NL  plan-1  N27   0.020
 0NL  plan-1  C28   0.020
 0NL  plan-1  H17   0.020
 0NL  plan-1  H22   0.020
 0NL  plan-1  H23   0.020
 0NL  plan-1  HN24  0.020
 0NL  plan-1  H28   0.020
 0NL  plan-2  O5    0.020
 0NL  plan-2  C6    0.020
 0NL  plan-2  O7    0.020
 0NL  plan-2  N8    0.020

