# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 02:11:09 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-[(2~{S})-2-methylmorpholin-4-yl]-2-pyrazol-1-yl-ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(CCO1)C(=O)Cn2cccn2
#
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
 S7D  S7D  1-[(2~{S})-2-methylmorpholin-4-yl]-2-pyrazol-1-yl-ethanone  ligand  30  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S7D
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
 S7D  N1   N  NR5   0  -0.252   2.5811   0.4876   0.1425
 S7D  C4   C  CH2   0  -0.176  -2.6697   1.5345   0.8461
 S7D  C5   C  C     0   0.549   0.2594  -0.0922  -0.3401
 S7D  C6   C  CH2   0  -0.441   1.2480   1.0047   0.0591
 S7D  C7   C  CR15  0   0.049   3.4693   0.3683  -0.8610
 S7D  C8   C  CR15  0  -0.512   4.5667  -0.2769  -0.3430
 S7D  N    N  NT    0  -0.473  -1.0337   0.2707  -0.4207
 S7D  C    C  CH3   0  -0.689  -4.3143  -1.5893  -0.1112
 S7D  O    O  O2    0  -0.488  -3.6742   0.6266   0.4599
 S7D  C1   C  CH1   0   0.037  -3.1676  -0.6844   0.2826
 S7D  C2   C  CH2   0  -0.298  -2.0664  -0.6892  -0.7715
 S7D  C3   C  CH2   0  -0.337  -1.5579   1.6049  -0.1865
 S7D  C9   C  CR15  0  -0.053   4.2213  -0.5172   0.9979
 S7D  N2   N  N     0  -0.286   3.0163  -0.0563   1.2756
 S7D  O1   O  O     0  -0.482   0.6578  -1.2213  -0.5715
 S7D  H2   H  HCH2  0   0.210  -2.2417   1.2511   1.8177
 S7D  H3   H  HCH2  0   0.306   0.9891   1.4297   1.0291
 S7D  H4   H  HCH2  0   0.305   1.2287   1.8197  -0.6663
 S7D  H5   H  HCR5  0   0.290   3.2661   0.7527  -1.8475
 S7D  H6   H  HCR5  0   0.262   5.4804  -0.5334  -0.8521
 S7D  H7   H  HCH3  0   0.230  -4.7575  -1.2780  -1.0587
 S7D  H8   H  HCH3  0   0.236  -3.9605  -2.6139  -0.2247
 S7D  H9   H  HCH3  0   0.245  -5.0934  -1.5884   0.6509
 S7D  H10  H  HCH1  0   0.213  -2.7310  -1.0351   1.2310
 S7D  H11  H  HCH2  0   0.244  -2.4871  -0.4243  -1.7485
 S7D  H12  H  HCH2  0   0.270  -1.6308  -1.6820  -0.8527
 S7D  H13  H  HCH2  0   0.257  -1.9422   2.0094  -1.1283
 S7D  H14  H  HCH2  0   0.279  -0.7869   2.2852   0.1660
 S7D  H15  H  HCR5  0   0.259   4.8103  -0.9965   1.7651
 S7D  H1   H  HCH2  0   0.247  -3.1362   2.5146   0.9543

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
 S7D  C   C1   single    1.513  0.020  1.513
 S7D  C1  O    single    1.417  0.020  1.417
 S7D  C1  C2   single    1.524  0.020  1.524
 S7D  O   C4   single    1.408  0.020  1.408
 S7D  C2  N    single    1.453  0.020  1.453
 S7D  C4  C3   single    1.519  0.020  1.519
 S7D  N   C3   single    1.453  0.020  1.453
 S7D  N   C5   single    1.346  0.020  1.346
 S7D  C6  C5   single    1.530  0.020  1.530
 S7D  C6  N1   single    1.432  0.020  1.432
 S7D  C5  O1   double    1.219  0.020  1.219
 S7D  N1  N2   aromatic  1.330  0.020  1.330
 S7D  N1  C7   aromatic  1.345  0.020  1.345
 S7D  N2  C9   aromatic  1.320  0.020  1.320
 S7D  C7  C8   aromatic  1.374  0.020  1.374
 S7D  C9  C8   aromatic  1.405  0.020  1.405
 S7D  C4  H1   single    0.970  0.020  1.090
 S7D  C4  H2   single    0.970  0.020  1.090
 S7D  C6  H3   single    0.970  0.020  1.090
 S7D  C6  H4   single    0.970  0.020  1.090
 S7D  C7  H5   single    0.930  0.020  1.080
 S7D  C8  H6   single    0.930  0.020  1.080
 S7D  C   H7   single    0.970  0.020  1.090
 S7D  C   H8   single    0.970  0.020  1.090
 S7D  C   H9   single    0.970  0.020  1.090
 S7D  C1  H10  single    0.970  0.020  1.090
 S7D  C2  H11  single    0.970  0.020  1.090
 S7D  C2  H12  single    0.970  0.020  1.090
 S7D  C3  H13  single    0.970  0.020  1.090
 S7D  C3  H14  single    0.970  0.020  1.090
 S7D  C9  H15  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
 S7D  N2   N1  C7   112.53  3.000
 S7D  C7   N1  C6   127.09  3.000
 S7D  N2   N1  C6   120.12  3.000
 S7D  H2   C4  H1   108.09  3.000
 S7D  H2   C4  C3   109.14  3.000
 S7D  H1   C4  C3   109.80  3.000
 S7D  H2   C4  O    110.74  3.000
 S7D  H1   C4  O    107.55  3.000
 S7D  C3   C4  O    111.45  3.000
 S7D  O1   C5  N    123.52  3.000
 S7D  O1   C5  C6   120.15  3.000
 S7D  N    C5  C6   116.32  3.000
 S7D  H4   C6  H3   107.23  3.000
 S7D  H4   C6  C5   110.52  3.000
 S7D  H3   C6  C5   111.00  3.000
 S7D  H4   C6  N1   108.95  3.000
 S7D  H3   C6  N1   108.06  3.000
 S7D  C5   C6  N1   110.97  3.000
 S7D  H5   C7  C8   131.51  3.000
 S7D  H5   C7  N1   121.77  3.000
 S7D  C8   C7  N1   106.72  3.000
 S7D  H6   C8  C9   128.24  3.000
 S7D  H6   C8  C7   127.66  3.000
 S7D  C9   C8  C7   104.10  3.000
 S7D  C3   N   C2   112.91  3.000
 S7D  C3   N   C5   125.80  3.000
 S7D  C2   N   C5   121.29  3.000
 S7D  H9   C   H8   107.79  3.000
 S7D  H9   C   H7   108.45  3.000
 S7D  H8   C   H7   108.03  3.000
 S7D  H9   C   C1   111.06  3.000
 S7D  H8   C   C1   110.08  3.000
 S7D  H7   C   C1   111.30  3.000
 S7D  C1   O   C4   112.08  3.000
 S7D  H10  C1  C2   107.94  3.000
 S7D  H10  C1  O    109.19  3.000
 S7D  C2   C1  O    110.35  3.000
 S7D  H10  C1  C    109.53  3.000
 S7D  C2   C1  C    111.45  3.000
 S7D  O    C1  C    108.36  3.000
 S7D  H12  C2  H11  107.93  3.000
 S7D  H12  C2  C1   110.12  3.000
 S7D  H11  C2  C1   109.77  3.000
 S7D  H12  C2  N    109.67  3.000
 S7D  H11  C2  N    109.16  3.000
 S7D  C1   C2  N    110.15  3.000
 S7D  H14  C3  H13  107.26  3.000
 S7D  H14  C3  N    111.79  3.000
 S7D  H13  C3  N    109.10  3.000
 S7D  H14  C3  C4   109.13  3.000
 S7D  H13  C3  C4   110.19  3.000
 S7D  N    C3  C4   109.34  3.000
 S7D  H15  C9  N2   120.25  3.000
 S7D  H15  C9  C8   128.31  3.000
 S7D  N2   C9  C8   111.44  3.000
 S7D  C9   N2  N1   105.21  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
 S7D  CONST_01  C8   C9  N2  N1    0.00   0.0  0
 S7D  CONST_02  C9   C8  C7  N1    0.00   0.0  0
 S7D  CONST_03  C9   N2  N1  C7    0.00   0.0  0
 S7D  CONST_04  N2   C9  C8  C7    0.00   0.0  0
 S7D  CONST_05  N2   N1  C7  C8    0.00   0.0  0
 S7D  CONST_06  C9   N2  N1  C6  180.00   0.0  0
 S7D  CONST_07  C8   C7  N1  C6  180.00   0.0  0
 S7D  CONST_08  H15  C9  N2  N1  180.00   0.0  0
 S7D  CONST_09  H6   C8  C7  N1  180.00   0.0  0
 S7D  CONST_10  H5   C7  C8  C9  180.00   0.0  0
 S7D  CONST_11  C2   N   C5  C6  180.00   0.0  0
 S7D  CONST_12  C3   N   C5  C6    0.00   0.0  0
 S7D  CONST_13  O1   C5  N   C2    0.00   0.0  0
 S7D  CONST_14  O1   C5  N   C3  180.00   0.0  0
 S7D  Var_01    C2   N   C3  C4   53.60  30.0  1
 S7D  Var_02    O    C4  C3  N   -55.28  30.0  1
 S7D  Var_03    C3   C4  O   C1   59.22  30.0  1
 S7D  Var_04    C3   N   C2  C1  -53.92  30.0  1
 S7D  Var_05    N    C5  C6  N1  178.54  30.0  3
 S7D  Var_06    N2   N1  C6  C5  -87.24  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
 S7D  chir_01  C1  C  O  C2  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
 S7D  plan-1  N1   0.020
 S7D  plan-1  C6   0.020
 S7D  plan-1  C7   0.020
 S7D  plan-1  C8   0.020
 S7D  plan-1  C9   0.020
 S7D  plan-1  N2   0.020
 S7D  plan-1  H5   0.020
 S7D  plan-1  H6   0.020
 S7D  plan-1  H15  0.020
 S7D  plan-2  C5   0.020
 S7D  plan-2  C6   0.020
 S7D  plan-2  N    0.020
 S7D  plan-2  C2   0.020
 S7D  plan-2  C3   0.020
 S7D  plan-2  O1   0.020

