# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 15:22:36 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-{4-[(morpholin-4-yl)methyl]phenyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(CN2CCOCC2)cc1
#
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
 RV4  RV4  N-{4-[(morpholin-4-yl)methyl]phenyl}acetamide  ligand  35  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RV4
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
 RV4  N1   N  NH1   0  -0.733   3.7435  -0.4800  -0.1736
 RV4  C4   C  CR16  0  -0.334   1.8216  -0.5161  -1.5755
 RV4  C5   C  CR16  0  -0.302   0.4943  -0.2293  -1.8475
 RV4  C6   C  CR6   0   0.074  -0.2993   0.4446  -0.9271
 RV4  C7   C  CR16  0  -0.272   0.2842   0.8154   0.2797
 RV4  C8   C  CR16  0  -0.302   1.6107   0.5354   0.5723
 RV4  C10  C  CH2   0  -0.298  -2.7155  -0.9505   0.1257
 RV4  C13  C  CH2   0  -0.302  -3.9444   1.0332  -0.3240
 RV4  C11  C  CH2   0  -0.186  -3.6192  -1.2062   1.3158
 RV4  C12  C  CH2   0  -0.188  -4.8177   0.7367   0.8798
 RV4  C2   C  C     0   0.510   4.5408  -0.2915   0.9088
 RV4  C3   C  CR6   0   0.355   2.3995  -0.1405  -0.3620
 RV4  N2   N  NT    0  -0.419  -2.6196   0.4757  -0.1258
 RV4  O1   O  O     0  -0.475   4.1715   0.2412   1.9413
 RV4  O2   O  O2    0  -0.486  -4.9019  -0.6493   1.1291
 RV4  H1   H  HNH1  0   0.414   4.1719  -0.9425  -0.9605
 RV4  H2   H  HCR6  0   0.267   2.4127  -1.0482  -2.3122
 RV4  H3   H  HCR6  0   0.252   0.0730  -0.5447  -2.7947
 RV4  H4   H  HCR6  0   0.246  -0.3147   1.3284   1.0221
 RV4  H5   H  HCR6  0   0.277   2.0165   0.8445   1.5210
 RV4  H7   H  HCH2  0   0.197  -3.0974  -1.4926  -0.7576
 RV4  H8   H  HCH2  0   0.196  -4.4261   0.6347  -1.2341
 RV4  H9   H  HCH2  0   0.241  -3.8672   2.1162  -0.4498
 RV4  H13  H  HCH2  0   0.235  -3.7480  -2.2792   1.4656
 RV4  H14  H  HCH2  0   0.199  -3.1492  -0.7934   2.2199
 RV4  H15  H  HCH2  0   0.200  -4.4174   1.2630   1.7583
 RV4  H16  H  HCH2  0   0.236  -5.8318   1.0996   0.7055
 RV4  C9   C  CH2   0  -0.322  -1.7348   0.7820  -1.2301
 RV4  C1   C  CH3   0  -0.782   5.9573  -0.7755   0.7254
 RV4  H6   H  HCH2  0   0.245  -1.7253  -1.3543   0.3480
 RV4  H10  H  HCH3  0   0.254   6.0792  -1.4720  -0.1021
 RV4  H11  H  HCH3  0   0.275   6.6063   0.0826   0.5433
 RV4  H12  H  HCH3  0   0.268   6.2991  -1.2560   1.6402
 RV4  H17  H  HCH2  0   0.250  -1.8173   1.8550  -1.4326
 RV4  H18  H  HCH2  0   0.211  -2.0413   0.2725  -2.1597

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
 RV4  C12  O2   single    1.411  0.020  1.411
 RV4  C12  C13  single    1.516  0.020  1.516
 RV4  O2   C11  single    1.411  0.020  1.411
 RV4  C13  N2   single    1.451  0.020  1.451
 RV4  C11  C10  single    1.516  0.020  1.516
 RV4  N2   C10  single    1.451  0.020  1.451
 RV4  N2   C9   single    1.448  0.020  1.448
 RV4  C9   C6   single    1.505  0.020  1.505
 RV4  C5   C6   aromatic  1.390  0.020  1.390
 RV4  C5   C4   aromatic  1.385  0.020  1.385
 RV4  C6   C7   aromatic  1.391  0.020  1.391
 RV4  C4   C3   aromatic  1.396  0.020  1.396
 RV4  C7   C8   aromatic  1.387  0.020  1.387
 RV4  C3   C8   aromatic  1.397  0.020  1.397
 RV4  C3   N1   single    1.399  0.020  1.399
 RV4  N1   C2   single    1.357  0.020  1.357
 RV4  C2   O1   double    1.219  0.020  1.219
 RV4  C2   C1   single    1.508  0.020  1.508
 RV4  N1   H1   single    0.860  0.020  1.020
 RV4  C4   H2   single    0.930  0.020  1.080
 RV4  C5   H3   single    0.930  0.020  1.080
 RV4  C7   H4   single    0.930  0.020  1.080
 RV4  C8   H5   single    0.930  0.020  1.080
 RV4  C10  H6   single    0.970  0.020  1.090
 RV4  C10  H7   single    0.970  0.020  1.090
 RV4  C13  H8   single    0.970  0.020  1.090
 RV4  C13  H9   single    0.970  0.020  1.090
 RV4  C1   H10  single    0.970  0.020  1.090
 RV4  C1   H11  single    0.970  0.020  1.090
 RV4  C1   H12  single    0.970  0.020  1.090
 RV4  C11  H13  single    0.970  0.020  1.090
 RV4  C11  H14  single    0.970  0.020  1.090
 RV4  C12  H15  single    0.970  0.020  1.090
 RV4  C12  H16  single    0.970  0.020  1.090
 RV4  C9   H17  single    0.970  0.020  1.090
 RV4  C9   H18  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
 RV4  H1   N1   C3   114.48  3.000
 RV4  H1   N1   C2   115.88  3.000
 RV4  C3   N1   C2   129.64  3.000
 RV4  H2   C4   C3   119.82  3.000
 RV4  H2   C4   C5   119.39  3.000
 RV4  C3   C4   C5   120.80  3.000
 RV4  H3   C5   C6   119.87  3.000
 RV4  H3   C5   C4   118.95  3.000
 RV4  C6   C5   C4   121.17  3.000
 RV4  C9   C6   C7   120.99  3.000
 RV4  C7   C6   C5   117.67  3.000
 RV4  C9   C6   C5   121.33  3.000
 RV4  H4   C7   C8   118.68  3.000
 RV4  H4   C7   C6   119.28  3.000
 RV4  C8   C7   C6   122.04  3.000
 RV4  H5   C8   C3   121.00  3.000
 RV4  H5   C8   C7   119.23  3.000
 RV4  C3   C8   C7   119.77  3.000
 RV4  H7   C10  H6   107.14  3.000
 RV4  H7   C10  N2   111.50  3.000
 RV4  H6   C10  N2   109.80  3.000
 RV4  H7   C10  C11  109.81  3.000
 RV4  H6   C10  C11  108.56  3.000
 RV4  N2   C10  C11  109.95  3.000
 RV4  H9   C13  H8   107.07  3.000
 RV4  H9   C13  N2   109.39  3.000
 RV4  H8   C13  N2   111.86  3.000
 RV4  H9   C13  C12  109.01  3.000
 RV4  H8   C13  C12  109.42  3.000
 RV4  N2   C13  C12  110.01  3.000
 RV4  H14  C11  H13  107.87  3.000
 RV4  H14  C11  O2   110.45  3.000
 RV4  H13  C11  O2   107.40  3.000
 RV4  H14  C11  C10  109.11  3.000
 RV4  H13  C11  C10  110.12  3.000
 RV4  O2   C11  C10  111.81  3.000
 RV4  H16  C12  H15  107.86  3.000
 RV4  H16  C12  O2   107.43  3.000
 RV4  H15  C12  O2   110.54  3.000
 RV4  H16  C12  C13  110.09  3.000
 RV4  H15  C12  C13  109.33  3.000
 RV4  O2   C12  C13  111.52  3.000
 RV4  O1   C2   C1   121.85  3.000
 RV4  C1   C2   N1   114.21  3.000
 RV4  O1   C2   N1   123.92  3.000
 RV4  C8   C3   C4   118.55  3.000
 RV4  C8   C3   N1   124.73  3.000
 RV4  C4   C3   N1   116.72  3.000
 RV4  C9   N2   C13  111.87  3.000
 RV4  C9   N2   C10  112.36  3.000
 RV4  C13  N2   C10  109.93  3.000
 RV4  C12  O2   C11  110.91  3.000
 RV4  H18  C9   H17  106.01  3.000
 RV4  H18  C9   N2   112.04  3.000
 RV4  H17  C9   N2   107.60  3.000
 RV4  H18  C9   C6   109.32  3.000
 RV4  H17  C9   C6   109.19  3.000
 RV4  N2   C9   C6   112.44  3.000
 RV4  H12  C1   H11  107.49  3.000
 RV4  H12  C1   H10  108.74  3.000
 RV4  H11  C1   H10  108.04  3.000
 RV4  H12  C1   C2   109.54  3.000
 RV4  H11  C1   C2   109.06  3.000
 RV4  H10  C1   C2   113.76  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
 RV4  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 RV4  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 RV4  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 RV4  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 RV4  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 RV4  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 RV4  CONST_07  C5   C4   C3   N1    180.00   0.0  0
 RV4  CONST_08  C7   C8   C3   N1    180.00   0.0  0
 RV4  CONST_09  C9   C6   C5   C4    180.00   0.0  0
 RV4  CONST_10  C9   C6   C7   C8    180.00   0.0  0
 RV4  CONST_11  H5   C8   C3   C4    180.00   0.0  0
 RV4  CONST_12  H4   C7   C6   C5    180.00   0.0  0
 RV4  CONST_13  H2   C4   C5   C6    180.00   0.0  0
 RV4  CONST_14  H3   C5   C6   C7    180.00   0.0  0
 RV4  CONST_15  C2   N1   C3   C4    180.00   0.0  0
 RV4  CONST_16  C2   N1   C3   C8      0.00   0.0  0
 RV4  CONST_17  H1   N1   C3   C4      0.00   0.0  0
 RV4  CONST_18  C3   N1   C2   C1    180.00   0.0  0
 RV4  CONST_19  O1   C2   N1   C3      0.00   0.0  0
 RV4  Var_01    C12  C13  N2   C10    56.74  30.0  1
 RV4  Var_02    C11  C10  N2   C13   -56.44  30.0  1
 RV4  Var_03    O2   C12  C13  N2    -57.27  30.0  1
 RV4  Var_04    O2   C11  C10  N2     56.83  30.0  1
 RV4  Var_05    N2   C9   C6   C5    134.47  30.0  2
 RV4  Var_06    C13  N2   C9   C6    169.03  30.0  2
 RV4  Var_07    H15  C12  O2   C11   -64.76  30.0  1
 RV4  Var_08    H13  C11  O2   C12  -177.89  30.0  1
 RV4  Var_09    H10  C1   C2   N1    -17.84  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
 RV4  plan-1  N1  0.020
 RV4  plan-1  C4  0.020
 RV4  plan-1  C5  0.020
 RV4  plan-1  C6  0.020
 RV4  plan-1  C7  0.020
 RV4  plan-1  C8  0.020
 RV4  plan-1  C3  0.020
 RV4  plan-1  H2  0.020
 RV4  plan-1  H3  0.020
 RV4  plan-1  H4  0.020
 RV4  plan-1  H5  0.020
 RV4  plan-1  C9  0.020
 RV4  plan-2  N1  0.020
 RV4  plan-2  C2  0.020
 RV4  plan-2  C3  0.020
 RV4  plan-2  O1  0.020
 RV4  plan-2  H1  0.020
 RV4  plan-2  C1  0.020

