# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:00:14 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: N-methyl-N-7H-pyrrolo[2,3-d]pyrimidin-4-yl-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCC(O)=O)c1ncnc2[nH]ccc12
#
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
 W5J  W5J  N-methyl-N-7H-pyrrolo[2,3-d]pyrimidin-4-yl-beta-alanine  ligand  27  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_W5J
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
 W5J  C10   C  CR16   0   0.035  -44.2962  -28.7035  6.3668
 W5J  C15   C  CR15   0  -0.433  -47.9199  -29.3851  4.6673
 W5J  C01   C  CH3    0  -0.549  -46.2853  -29.1398  2.0908
 W5J  C03   C  CH2    0  -0.309  -43.8376  -29.2601  2.3459
 W5J  C04   C  CH2    0  -0.568  -43.7087  -30.5179  1.4949
 W5J  C05   C  C      0   0.403  -43.9809  -31.8107  2.2885
 W5J  C08   C  CR6    0   0.510  -45.2915  -29.0454  4.3126
 W5J  C12   C  CR56   0   0.466  -46.4820  -28.9577  6.3752
 W5J  C14   C  CR15   0  -0.019  -48.6042  -29.3474  5.8443
 W5J  C16   C  CR56   0  -0.096  -46.5432  -29.1274  4.9805
 W5J  N02   N  NT     0  -0.471  -45.1450  -29.1472  2.9781
 W5J  N09   N  N      0  -0.495  -44.1927  -28.8407  5.0522
 W5J  N11   N  N      0  -0.456  -45.3854  -28.7374  7.1059
 W5J  N13   N  NR15   0  -0.657  -47.7340  -29.0842  6.8699
 W5J  O06   O  OC    -1  -0.611  -43.3349  -31.9539  3.3468
 W5J  O07   O  O      0  -0.610  -44.8119  -32.6076  1.8087
 W5J  H101  H  HCR6   0   0.236  -43.3614  -28.5375  6.8942
 W5J  H151  H  HCR5   0   0.255  -48.3655  -29.5822  3.7082
 W5J  H013  H  HCH3   0   0.252  -47.0120  -28.3844  2.3857
 W5J  H012  H  HCH3   0   0.266  -45.9468  -28.8820  1.0896
 W5J  H011  H  HCH3   0   0.239  -46.7869  -30.1084  2.0329
 W5J  H031  H  HCH2   0   0.255  -43.0830  -29.2586  3.1245
 W5J  H032  H  HCH2   0   0.229  -43.6686  -28.3739  1.7248
 W5J  H042  H  HCH2   0   0.208  -44.3573  -30.4626  0.6177
 W5J  H041  H  HCH2   0   0.233  -42.6820  -30.5396  1.1131
 W5J  H141  H  HCR5   0   0.282  -49.6550  -29.4893  6.0358
 W5J  H131  H  HNR5   0   0.408  -47.9785  -29.0163  7.8447

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
 W5J  C04  C03   single    1.524  0.020  1.524
 W5J  C04  C05   single    1.541  0.020  1.541
 W5J  C01  N02   single    1.445  0.020  1.445
 W5J  O07  C05   deloc     1.247  0.020  1.247
 W5J  C03  N02   single    1.457  0.020  1.457
 W5J  C05  O06   deloc     1.248  0.020  1.248
 W5J  N02  C08   single    1.346  0.020  1.346
 W5J  C08  C16   aromatic  1.421  0.020  1.421
 W5J  C08  N09   aromatic  1.340  0.020  1.340
 W5J  C15  C16   aromatic  1.435  0.020  1.435
 W5J  C15  C14   aromatic  1.362  0.020  1.362
 W5J  C16  C12   aromatic  1.406  0.020  1.406
 W5J  N09  C10   aromatic  1.326  0.020  1.326
 W5J  C14  N13   aromatic  1.371  0.020  1.371
 W5J  C10  N11   aromatic  1.317  0.020  1.317
 W5J  C12  N13   aromatic  1.352  0.020  1.352
 W5J  C12  N11   aromatic  1.336  0.020  1.336
 W5J  C10  H101  single    0.930  0.020  1.080
 W5J  C15  H151  single    0.930  0.020  1.080
 W5J  C01  H013  single    0.970  0.020  1.090
 W5J  C01  H012  single    0.970  0.020  1.090
 W5J  C01  H011  single    0.970  0.020  1.090
 W5J  C03  H031  single    0.970  0.020  1.090
 W5J  C03  H032  single    0.970  0.020  1.090
 W5J  C04  H042  single    0.970  0.020  1.090
 W5J  C04  H041  single    0.970  0.020  1.090
 W5J  C14  H141  single    0.930  0.020  1.080
 W5J  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
 W5J  H101  C10  N11   116.32  3.000
 W5J  H101  C10  N09   115.48  3.000
 W5J  N11   C10  N09   128.20  3.000
 W5J  H151  C15  C16   128.66  3.000
 W5J  H151  C15  C14   124.57  3.000
 W5J  C16   C15  C14   106.77  3.000
 W5J  H011  C01  H012  107.72  3.000
 W5J  H011  C01  H013  108.85  3.000
 W5J  H012  C01  H013  107.01  3.000
 W5J  H011  C01  N02   112.98  3.000
 W5J  H012  C01  N02   108.71  3.000
 W5J  H013  C01  N02   111.34  3.000
 W5J  H032  C03  H031  107.38  3.000
 W5J  H032  C03  N02   108.78  3.000
 W5J  H031  C03  N02   108.24  3.000
 W5J  H032  C03  C04   109.76  3.000
 W5J  H031  C03  C04   110.07  3.000
 W5J  N02   C03  C04   112.47  3.000
 W5J  H041  C04  H042  106.12  3.000
 W5J  H041  C04  C05   109.17  3.000
 W5J  H042  C04  C05   110.56  3.000
 W5J  H041  C04  C03   106.86  3.000
 W5J  H042  C04  C03   110.88  3.000
 W5J  C05   C04  C03   112.94  3.000
 W5J  O07   C05  O06   126.70  3.000
 W5J  O06   C05  C04   116.20  3.000
 W5J  O07   C05  C04   117.10  3.000
 W5J  N09   C08  N02   117.99  3.000
 W5J  N09   C08  C16   118.14  3.000
 W5J  N02   C08  C16   123.87  3.000
 W5J  N13   C12  N11   125.13  3.000
 W5J  N11   C12  C16   126.73  3.000
 W5J  N13   C12  C16   108.13  3.000
 W5J  H141  C14  N13   120.76  3.000
 W5J  H141  C14  C15   129.79  3.000
 W5J  N13   C14  C15   109.45  3.000
 W5J  C12   C16  C08   114.88  3.000
 W5J  C12   C16  C15   106.25  3.000
 W5J  C08   C16  C15   138.83  3.000
 W5J  C08   N02  C03   122.26  3.000
 W5J  C08   N02  C01   121.49  3.000
 W5J  C03   N02  C01   116.25  3.000
 W5J  C08   N09  C10   119.93  3.000
 W5J  C12   N11  C10   112.10  3.000
 W5J  H131  N13  C14   125.66  3.000
 W5J  H131  N13  C12   124.92  3.000
 W5J  C14   N13  C12   109.40  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
 W5J  CONST_01  C16   C08  N09  C10    0.00   0.0  0
 W5J  CONST_02  C16   C12  N11  C10    0.00   0.0  0
 W5J  CONST_03  N13   C12  N11  C10  180.00   0.0  0
 W5J  CONST_04  N09   C08  C16  C15  180.00   0.0  0
 W5J  CONST_05  N13   C12  C16  C15    0.00   0.0  0
 W5J  CONST_06  N11   C12  C16  C15  180.00   0.0  0
 W5J  CONST_07  C12   N13  C14  C15    0.00   0.0  0
 W5J  CONST_08  C14   C15  C16  C08  180.00   0.0  0
 W5J  CONST_09  N13   C12  C16  C08  180.00   0.0  0
 W5J  CONST_10  N11   C12  C16  C08    0.00   0.0  0
 W5J  CONST_11  N11   C10  N09  C08    0.00   0.0  0
 W5J  CONST_12  N09   C08  C16  C12    0.00   0.0  0
 W5J  CONST_13  C14   C15  C16  C12    0.00   0.0  0
 W5J  CONST_14  N09   C10  N11  C12    0.00   0.0  0
 W5J  CONST_15  C16   C12  N13  C14    0.00   0.0  0
 W5J  CONST_16  N11   C12  N13  C14  180.00   0.0  0
 W5J  CONST_17  N13   C14  C15  C16    0.00   0.0  0
 W5J  CONST_18  N02   C08  N09  C10  180.00   0.0  0
 W5J  CONST_19  N02   C08  C16  C15    0.00   0.0  0
 W5J  CONST_20  N02   C08  C16  C12  180.00   0.0  0
 W5J  CONST_21  H131  N13  C14  C15  180.00   0.0  0
 W5J  CONST_22  H151  C15  C16  C08    0.00   0.0  0
 W5J  CONST_23  H101  C10  N09  C08  180.00   0.0  0
 W5J  CONST_24  H141  C14  N13  C12  180.00   0.0  0
 W5J  CONST_25  C16   C08  N02  C01    0.00   0.0  0
 W5J  CONST_26  N09   C08  N02  C01  180.00   0.0  0
 W5J  CONST_27  C16   C08  N02  C03  180.00   0.0  0
 W5J  CONST_28  N09   C08  N02  C03    0.00   0.0  0
 W5J  Var_01    C08   N02  C03  C04  122.60  30.0  3
 W5J  Var_02    H013  C01  N02  C08   42.70  30.0  3
 W5J  Var_03    O07   C05  C04  C03  128.30  30.0  3
 W5J  Var_04    N02   C03  C04  C05  -56.80  30.0  3

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
 W5J  plan-1  C10   0.020
 W5J  plan-1  C15   0.020
 W5J  plan-1  C08   0.020
 W5J  plan-1  C12   0.020
 W5J  plan-1  C14   0.020
 W5J  plan-1  C16   0.020
 W5J  plan-1  N02   0.020
 W5J  plan-1  N09   0.020
 W5J  plan-1  N11   0.020
 W5J  plan-1  N13   0.020
 W5J  plan-1  H101  0.020
 W5J  plan-1  H151  0.020
 W5J  plan-1  H141  0.020
 W5J  plan-1  H131  0.020
 W5J  plan-2  C01   0.020
 W5J  plan-2  C03   0.020
 W5J  plan-2  C08   0.020
 W5J  plan-2  N02   0.020
 W5J  plan-3  C04   0.020
 W5J  plan-3  C05   0.020
 W5J  plan-3  O06   0.020
 W5J  plan-3  O07   0.020

