# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:40:43 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: [(2R)-4-benzylmorpholin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN(CCO1)Cc2ccccc2
#
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
 S7V  S7V  '[(2R)-4-benzylmorpholin-2-yl]methanol'  ligand  32  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S7V
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
 S7V  C4   C  CR6   0   0.080  49.0699  6.4300  63.0926
 S7V  C5   C  CR16  0  -0.313  47.7909  6.6728  63.5826
 S7V  C6   C  CR16  0  -0.241  46.7576  7.0369  62.7272
 S7V  C7   C  CR16  0  -0.271  46.9919  7.1543  61.3643
 S7V  C8   C  CR16  0  -0.241  48.2654  6.9066  60.8646
 S7V  C10  C  CH2   0  -0.351  50.4984  3.7757  63.3571
 S7V  N    N  NT    0  -0.418  51.0905  5.0883  63.4877
 S7V  C1   C  CH1   0   0.001  53.0988  3.7299  63.8404
 S7V  C11  C  CH2   0  -0.156  51.3931  2.9428  62.4395
 S7V  C2   C  CH2   0  -0.274  52.3332  5.0054  64.2358
 S7V  C3   C  CH2   0  -0.311  50.1985  6.0848  64.0307
 S7V  C9   C  CR16  0  -0.284  49.2956  6.5488  61.7223
 S7V  O1   O  O2    0  -0.495  52.7481  3.3337  62.5364
 S7V  H1   H  HCR6  0   0.247  47.5983  6.5742  64.6449
 S7V  H2   H  HCR6  0   0.253  45.7683  7.2224  63.1260
 S7V  H3   H  HCR6  0   0.253  46.1876  7.4323  60.6950
 S7V  H4   H  HCR6  0   0.252  48.4552  6.9917  59.8019
 S7V  H5   H  HCH2  0   0.258  49.5057  3.8530  62.9107
 S7V  H6   H  HCH2  0   0.212  50.3607  3.2875  64.3367
 S7V  H10  H  HOH1  0   0.460  55.9023  4.5561  65.1509
 S7V  H11  H  HCH1  0   0.216  52.8549  2.9284  64.5546
 S7V  H12  H  HCH2  0   0.224  51.1049  3.0926  61.3973
 S7V  H13  H  HCH2  0   0.203  51.2744  1.8767  62.6710
 S7V  H14  H  HCH2  0   0.231  52.9296  5.8997  64.0251
 S7V  H15  H  HCH2  0   0.201  52.1582  4.9853  65.3233
 S7V  H16  H  HCH2  0   0.253  50.7883  6.9891  64.2163
 S7V  H17  H  HCH2  0   0.211  49.7865  5.7895  65.0109
 S7V  H18  H  HCR6  0   0.245  50.2840  6.3463  61.3293
 S7V  C    C  CH2   0  -0.184  54.6025  3.9336  63.8563
 S7V  H8   H  HCH2  0   0.213  55.0977  2.9993  63.5612
 S7V  O    O  OH1   0  -0.673  54.9685  4.3301  65.1575
 S7V  H9   H  HCH2  0   0.201  54.8655  4.6937  63.1083

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
 S7V  C8   C7   aromatic  1.390  0.020  1.390
 S7V  C8   C9   aromatic  1.387  0.020  1.387
 S7V  C7   C6   aromatic  1.388  0.020  1.388
 S7V  C9   C4   aromatic  1.394  0.020  1.394
 S7V  C6   C5   aromatic  1.390  0.020  1.390
 S7V  C11  O1   single    1.414  0.020  1.414
 S7V  C11  C10  single    1.528  0.020  1.528
 S7V  O1   C1   single    1.407  0.020  1.407
 S7V  C4   C5   aromatic  1.391  0.020  1.391
 S7V  C4   C3   single    1.508  0.020  1.508
 S7V  N    C10  single    1.446  0.020  1.446
 S7V  N    C3   single    1.444  0.020  1.444
 S7V  N    C2   single    1.453  0.020  1.453
 S7V  C2   C1   single    1.539  0.020  1.539
 S7V  C1   C    single    1.518  0.020  1.518
 S7V  C    O    single    1.409  0.020  1.409
 S7V  C5   H1   single    0.930  0.020  1.080
 S7V  C6   H2   single    0.930  0.020  1.080
 S7V  C7   H3   single    0.930  0.020  1.080
 S7V  C8   H4   single    0.930  0.020  1.080
 S7V  C10  H5   single    0.970  0.020  1.090
 S7V  C10  H6   single    0.970  0.020  1.090
 S7V  C    H8   single    0.970  0.020  1.090
 S7V  C    H9   single    0.970  0.020  1.090
 S7V  O    H10  single    0.850  0.020  0.980
 S7V  C1   H11  single    0.970  0.020  1.090
 S7V  C11  H12  single    0.970  0.020  1.090
 S7V  C11  H13  single    0.970  0.020  1.090
 S7V  C2   H14  single    0.970  0.020  1.090
 S7V  C2   H15  single    0.970  0.020  1.090
 S7V  C3   H16  single    0.970  0.020  1.090
 S7V  C3   H17  single    0.970  0.020  1.090
 S7V  C9   H18  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
 S7V  C9   C4   C3   120.67  3.000
 S7V  C3   C4   C5   120.60  3.000
 S7V  C9   C4   C5   118.70  3.000
 S7V  H1   C5   C6   119.66  3.000
 S7V  H1   C5   C4   119.51  3.000
 S7V  C6   C5   C4   120.83  3.000
 S7V  H2   C6   C7   120.09  3.000
 S7V  H2   C6   C5   119.83  3.000
 S7V  C7   C6   C5   120.07  3.000
 S7V  H3   C7   C8   120.26  3.000
 S7V  H3   C7   C6   120.23  3.000
 S7V  C8   C7   C6   119.50  3.000
 S7V  H4   C8   C9   119.79  3.000
 S7V  H4   C8   C7   119.95  3.000
 S7V  C9   C8   C7   120.26  3.000
 S7V  H6   C10  H5   106.32  3.000
 S7V  H6   C10  C11  111.41  3.000
 S7V  H5   C10  C11  109.00  3.000
 S7V  H6   C10  N    111.88  3.000
 S7V  H5   C10  N    110.19  3.000
 S7V  C11  C10  N    108.01  3.000
 S7V  C3   N    C2   111.98  3.000
 S7V  C2   N    C10  110.18  3.000
 S7V  C3   N    C10  114.05  3.000
 S7V  H11  C1   O1   109.94  3.000
 S7V  H11  C1   C2   109.05  3.000
 S7V  O1   C1   C2   110.33  3.000
 S7V  H11  C1   C    108.08  3.000
 S7V  C2   C1   C    112.27  3.000
 S7V  O1   C1   C    107.12  3.000
 S7V  H13  C11  H12  107.83  3.000
 S7V  H13  C11  O1   110.97  3.000
 S7V  H12  C11  O1   106.29  3.000
 S7V  H13  C11  C10  109.84  3.000
 S7V  H12  C11  C10  110.11  3.000
 S7V  O1   C11  C10  111.68  3.000
 S7V  H15  C2   H14  106.93  3.000
 S7V  H15  C2   C1   108.51  3.000
 S7V  H14  C2   C1   110.88  3.000
 S7V  H15  C2   N    111.93  3.000
 S7V  H14  C2   N    108.67  3.000
 S7V  C1   C2   N    109.90  3.000
 S7V  H17  C3   H16  105.75  3.000
 S7V  H17  C3   N    112.34  3.000
 S7V  H16  C3   N    107.51  3.000
 S7V  H17  C3   C4   109.54  3.000
 S7V  H16  C3   C4   108.63  3.000
 S7V  N    C3   C4   112.74  3.000
 S7V  H18  C9   C8   120.11  3.000
 S7V  H18  C9   C4   119.25  3.000
 S7V  C8   C9   C4   120.63  3.000
 S7V  C11  O1   C1   112.35  3.000
 S7V  H9   C    H8   107.33  3.000
 S7V  H9   C    C1   108.85  3.000
 S7V  H8   C    C1   109.26  3.000
 S7V  H9   C    O    111.84  3.000
 S7V  H8   C    O    111.75  3.000
 S7V  C1   C    O    107.75  3.000
 S7V  H10  O    C    108.20  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
 S7V  CONST_01  C7   C8   C9   C4     0.00   0.0  0
 S7V  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 S7V  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 S7V  CONST_04  C8   C9   C4   C5     0.00   0.0  0
 S7V  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 S7V  CONST_06  C9   C4   C5   C6     0.00   0.0  0
 S7V  CONST_07  C3   C4   C5   C6   180.00   0.0  0
 S7V  CONST_08  C3   C4   C9   C8   180.00   0.0  0
 S7V  CONST_09  H4   C8   C9   C4   180.00   0.0  0
 S7V  CONST_10  H2   C6   C5   C4   180.00   0.0  0
 S7V  CONST_11  H3   C7   C6   C5   180.00   0.0  0
 S7V  CONST_12  H18  C9   C4   C5   180.00   0.0  0
 S7V  CONST_13  H1   C5   C6   C7   180.00   0.0  0
 S7V  Var_01    C1   C2   N    C10   38.65  30.0  1
 S7V  Var_02    O1   C11  C10  N     30.19  30.0  1
 S7V  Var_03    C2   N    C10  C11  -68.35  30.0  1
 S7V  Var_04    C10  N    C3   C4   -68.22  30.0  1
 S7V  Var_05    N    C3   C4   C5   141.88  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
 S7V  chir_01  C1  O1  C2  C  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
 S7V  plan-1  C4   0.020
 S7V  plan-1  C5   0.020
 S7V  plan-1  C6   0.020
 S7V  plan-1  C7   0.020
 S7V  plan-1  C8   0.020
 S7V  plan-1  C3   0.020
 S7V  plan-1  C9   0.020
 S7V  plan-1  H1   0.020
 S7V  plan-1  H2   0.020
 S7V  plan-1  H3   0.020
 S7V  plan-1  H4   0.020
 S7V  plan-1  H18  0.020

