# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:39:38 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc(n1)C(=O)NC[C@@H]2CCCO2
#
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
 JGY  JGY  1-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1H-pyrazole-3-carboxamide  ligand  30  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JGY
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
 JGY  C10   C  CH2   0  -0.312  -1.6616   0.8218   0.7046
 JGY  C13   C  CH2   0  -0.487  -4.7984  -0.5227  -0.6585
 JGY  C01   C  CH3   0  -0.508   4.1563  -2.0929   0.6296
 JGY  N02   N  NR5   0  -0.248   3.5146  -0.9065   0.1123
 JGY  C03   C  CR15  0   0.042   4.0632   0.0460  -0.6680
 JGY  C04   C  CR15  0  -0.507   3.0781   0.9690  -0.9232
 JGY  C05   C  CR5   0   0.162   1.9593   0.4687  -0.2395
 JGY  N06   N  N     0  -0.306   2.2456  -0.6678   0.3795
 JGY  C07   C  C     0   0.518   0.6138   1.0815  -0.1743
 JGY  O08   O  O     0  -0.494   0.3796   2.1362  -0.7516
 JGY  N09   N  NH1   0  -0.642  -0.2872   0.4095   0.5568
 JGY  C11   C  CR15  0   0.060  -2.5726   0.3003  -0.3965
 JGY  C12   C  CH2   0  -0.502  -4.0328   0.7100  -0.1910
 JGY  C14   C  CH2   0  -0.160  -3.8581  -1.6364  -0.2289
 JGY  O15   O  O     0  -0.508  -2.5500  -1.1232  -0.4245
 JGY  H101  H  HCH2  0   0.254  -2.0159   0.4659   1.6741
 JGY  H102  H  HCH2  0   0.249  -1.7141   1.9112   0.7245
 JGY  H131  H  HCH2  0   0.247  -5.7879  -0.6117  -0.2108
 JGY  H132  H  HCH2  0   0.237  -4.9183  -0.5161  -1.7441
 JGY  H013  H  HCH3  0   0.265   3.7089  -2.9855   0.1976
 JGY  H011  H  HCH3  0   0.263   5.2102  -2.0640   0.3705
 JGY  H012  H  HCH3  0   0.266   4.0578  -2.1280   1.7121
 JGY  H041  H  HCR5  0   0.270   3.1547   1.8674  -1.5113
 JGY  H091  H  HNH1  0   0.403  -0.0137  -0.4797   0.9442
 JGY  H111  H  HCR5  0   0.225  -2.2049   0.6671  -1.3626
 JGY  H122  H  HCH2  0   0.255  -4.2869   1.6148  -0.7420
 JGY  H121  H  HCH2  0   0.236  -4.2331   0.9020   0.8673
 JGY  H142  H  HCH2  0   0.200  -4.0228  -1.8942   0.8251
 JGY  H141  H  HCH2  0   0.226  -3.9710  -2.5494  -0.8172
 JGY  H031  H  HCR5  0   0.298   5.0945  -0.0013  -0.9772

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
 JGY  C04  C03   aromatic  1.374  0.020  1.374
 JGY  C04  C05   aromatic  1.403  0.020  1.403
 JGY  C03  N02   aromatic  1.348  0.020  1.348
 JGY  O08  C07   double    1.225  0.020  1.225
 JGY  C05  C07   single    1.480  0.020  1.480
 JGY  C05  N06   aromatic  1.325  0.020  1.325
 JGY  N02  C01   single    1.445  0.020  1.445
 JGY  N02  N06   aromatic  1.319  0.020  1.319
 JGY  C07  N09   single    1.341  0.020  1.341
 JGY  N09  C10   single    1.443  0.020  1.443
 JGY  C10  C11   single    1.521  0.020  1.521
 JGY  C11  C12   single    1.530  0.020  1.530
 JGY  C11  O15   single    1.424  0.020  1.424
 JGY  C12  C13   single    1.525  0.020  1.525
 JGY  O15  C14   single    1.419  0.020  1.419
 JGY  C13  C14   single    1.520  0.020  1.520
 JGY  C10  H101  single    0.970  0.020  1.090
 JGY  C10  H102  single    0.970  0.020  1.090
 JGY  C13  H131  single    0.970  0.020  1.090
 JGY  C13  H132  single    0.970  0.020  1.090
 JGY  C01  H013  single    0.970  0.020  1.090
 JGY  C01  H011  single    0.970  0.020  1.090
 JGY  C01  H012  single    0.970  0.020  1.090
 JGY  C03  H031  single    0.930  0.020  1.080
 JGY  C04  H041  single    0.930  0.020  1.080
 JGY  N09  H091  single    0.860  0.020  1.020
 JGY  C11  H111  single    0.970  0.020  1.090
 JGY  C12  H122  single    0.970  0.020  1.090
 JGY  C12  H121  single    0.970  0.020  1.090
 JGY  C14  H142  single    0.970  0.020  1.090
 JGY  C14  H141  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
 JGY  H102  C10  H101  107.08  3.000
 JGY  H102  C10  C11   109.07  3.000
 JGY  H101  C10  C11   109.67  3.000
 JGY  H102  C10  N09   109.46  3.000
 JGY  H101  C10  N09   107.88  3.000
 JGY  C11   C10  N09   113.48  3.000
 JGY  H132  C13  H131  108.01  3.000
 JGY  H132  C13  C14   110.69  3.000
 JGY  H131  C13  C14   112.70  3.000
 JGY  H132  C13  C12   110.80  3.000
 JGY  H131  C13  C12   113.33  3.000
 JGY  C14   C13  C12   101.26  3.000
 JGY  H012  C01  H011  109.05  3.000
 JGY  H012  C01  H013  109.36  3.000
 JGY  H011  C01  H013  109.05  3.000
 JGY  H012  C01  N02   110.04  3.000
 JGY  H011  C01  N02   108.90  3.000
 JGY  H013  C01  N02   110.42  3.000
 JGY  N06   N02  C03   112.40  3.000
 JGY  N06   N02  C01   120.24  3.000
 JGY  C03   N02  C01   127.36  3.000
 JGY  H031  C03  C04   131.48  3.000
 JGY  H031  C03  N02   121.63  3.000
 JGY  C04   C03  N02   106.88  3.000
 JGY  H041  C04  C05   128.34  3.000
 JGY  H041  C04  C03   127.67  3.000
 JGY  C05   C04  C03   103.98  3.000
 JGY  C07   C05  N06   122.06  3.000
 JGY  N06   C05  C04   111.16  3.000
 JGY  C07   C05  C04   126.77  3.000
 JGY  C05   N06  N02   105.57  3.000
 JGY  N09   C07  O08   124.05  3.000
 JGY  N09   C07  C05   115.30  3.000
 JGY  O08   C07  C05   120.64  3.000
 JGY  H091  N09  C07   118.00  3.000
 JGY  H091  N09  C10   118.12  3.000
 JGY  C07   N09  C10   123.56  3.000
 JGY  H111  C11  O15   108.16  3.000
 JGY  H111  C11  C12   110.40  3.000
 JGY  O15   C11  C12   106.58  3.000
 JGY  H111  C11  C10   108.79  3.000
 JGY  O15   C11  C10   110.33  3.000
 JGY  C12   C11  C10   112.48  3.000
 JGY  H121  C12  H122  107.51  3.000
 JGY  H121  C12  C11   110.58  3.000
 JGY  H122  C12  C11   112.14  3.000
 JGY  H121  C12  C13   110.28  3.000
 JGY  H122  C12  C13   113.53  3.000
 JGY  C11   C12  C13   102.80  3.000
 JGY  H141  C14  H142  107.78  3.000
 JGY  H141  C14  O15   108.88  3.000
 JGY  H142  C14  O15   110.83  3.000
 JGY  H141  C14  C13   113.36  3.000
 JGY  H142  C14  C13   110.54  3.000
 JGY  O15   C14  C13   105.45  3.000
 JGY  C14   O15  C11   110.14  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
 JGY  CONST_01  C05   C04  C03  N02     0.00   0.0  0
 JGY  CONST_02  C04   C05  N06  N02     0.00   0.0  0
 JGY  CONST_03  N06   C05  C04  C03     0.00   0.0  0
 JGY  CONST_04  C05   N06  N02  C03     0.00   0.0  0
 JGY  CONST_05  N06   N02  C03  C04     0.00   0.0  0
 JGY  CONST_06  C04   C03  N02  C01   180.00   0.0  0
 JGY  CONST_07  C05   N06  N02  C01   180.00   0.0  0
 JGY  CONST_08  C07   C05  N06  N02   180.00   0.0  0
 JGY  CONST_09  C07   C05  C04  C03   180.00   0.0  0
 JGY  CONST_10  H041  C04  C03  N02   180.00   0.0  0
 JGY  CONST_11  H031  C03  C04  C05   180.00   0.0  0
 JGY  CONST_12  C05   C07  N09  C10   180.00   0.0  0
 JGY  CONST_13  H091  N09  C07  C05     0.00   0.0  0
 JGY  CONST_14  O08   C07  N09  C10     0.00   0.0  0
 JGY  Var_01    C14   C13  C12  C11    34.11  30.0  1
 JGY  Var_02    O15   C14  C13  C12   -35.95  30.0  1
 JGY  Var_03    H142  C14  O15  C11   -95.96  30.0  1
 JGY  Var_04    O08   C07  C05  C04    -0.10  30.0  2
 JGY  Var_05    H013  C01  N02  C03  -114.22  30.0  2
 JGY  Var_06    C11   C10  N09  C07    86.94  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
 JGY  chir_01  C11  C10  C12  O15  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
 JGY  plan-1  C01   0.020
 JGY  plan-1  N02   0.020
 JGY  plan-1  C03   0.020
 JGY  plan-1  C04   0.020
 JGY  plan-1  C05   0.020
 JGY  plan-1  N06   0.020
 JGY  plan-1  C07   0.020
 JGY  plan-1  H041  0.020
 JGY  plan-1  H031  0.020
 JGY  plan-2  C10   0.020
 JGY  plan-2  C05   0.020
 JGY  plan-2  C07   0.020
 JGY  plan-2  O08   0.020
 JGY  plan-2  N09   0.020
 JGY  plan-2  H091  0.020

