# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 12:39:22 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-(cyclopropylmethoxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(OCC2CC2)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
 89Q  89Q  "4-(cyclopropylmethoxy)benzamide"
  ligand  27  14  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89Q
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
 89Q  C4   C  CR16  0  -0.338  14.8685  14.0565   8.8218
 89Q  C5   C  CR6   0   0.394  13.6918  14.6557   9.2835
 89Q  C6   C  CH2   0  -0.188  11.3236  14.8460   9.1098
 89Q  C11  C  CR16  0  -0.264  14.9818  15.8224  10.9462
 89Q  C7   C  CH1   0  -0.280  10.2291  14.2461   8.2878
 89Q  C8   C  CH2   0  -0.479   9.9261  14.8115   6.9347
 89Q  C9   C  CH2   0  -0.490   8.9800  15.0442   8.0717
 89Q  C10  C  CR16  0  -0.370  13.7592  15.5527  10.3486
 89Q  N1   N  NH2   0  -0.817  17.5060  15.9860  12.3542
 89Q  C3   C  CR16  0  -0.251  16.0768  14.3452   9.4189
 89Q  O1   O  O     0  -0.478  18.5211  15.2745  10.4752
 89Q  C2   C  CR6   0  -0.064  16.1550  15.2211  10.5042
 89Q  O2   O  O2    0  -0.462  12.5625  14.3208   8.6456
 89Q  H1   H  HCR6  0   0.263  14.8210  13.3641   7.9906
 89Q  H2   H  HCH2  0   0.226  11.3148  15.9384   9.0157
 89Q  H3   H  HCH2  0   0.236  11.1874  14.6018  10.1691
 89Q  H4   H  HCR6  0   0.258  14.9948  16.5393  11.7573
 89Q  H5   H  HCH1  0   0.264  10.1020  13.1754   8.4094
 89Q  H6   H  HCH2  0   0.248  10.5207  15.6488   6.5895
 89Q  H7   H  HCH2  0   0.253   9.6309  14.1242   6.1529
 89Q  H8   H  HCH2  0   0.249   8.9323  16.0388   8.4979
 89Q  H9   H  HCH2  0   0.255   8.0361  14.5155   8.0757
 89Q  H10  H  HCR6  0   0.284  12.8781  16.0547  10.7232
 89Q  H11  H  HNH2  0   0.400  18.3903  16.1531  12.8063
 89Q  H12  H  HNH2  0   0.408  16.6903  16.0054  12.9407
 89Q  H13  H  HCR6  0   0.260  16.9753  13.8733   9.0438
 89Q  C1   C  C     0   0.481  17.4931  15.4910  11.1034

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
 89Q  C8   C7   single    1.497  0.020  1.497
 89Q  C8   C9   single    1.497  0.020  1.497
 89Q  C7   C9   single    1.498  0.020  1.498
 89Q  C7   C6   single    1.494  0.020  1.494
 89Q  O2   C6   single    1.423  0.020  1.423
 89Q  O2   C5   single    1.340  0.020  1.340
 89Q  C4   C5   aromatic  1.399  0.020  1.399
 89Q  C4   C3   aromatic  1.378  0.020  1.378
 89Q  C5   C10  aromatic  1.394  0.020  1.394
 89Q  C3   C2   aromatic  1.397  0.020  1.397
 89Q  C10  C11  aromatic  1.387  0.020  1.387
 89Q  C2   C11  aromatic  1.391  0.020  1.391
 89Q  C2   C1   single    1.491  0.020  1.491
 89Q  O1   C1   double    1.224  0.020  1.224
 89Q  C1   N1   single    1.345  0.020  1.345
 89Q  C4   H1   single    0.930  0.020  1.080
 89Q  C6   H2   single    0.970  0.020  1.090
 89Q  C6   H3   single    0.970  0.020  1.090
 89Q  C11  H4   single    0.930  0.020  1.080
 89Q  C7   H5   single    0.970  0.020  1.090
 89Q  C8   H6   single    0.970  0.020  1.090
 89Q  C8   H7   single    0.970  0.020  1.090
 89Q  C9   H8   single    0.970  0.020  1.090
 89Q  C9   H9   single    0.970  0.020  1.090
 89Q  C10  H10  single    0.930  0.020  1.080
 89Q  N1   H11  single    0.860  0.020  1.020
 89Q  N1   H12  single    0.860  0.020  1.020
 89Q  C3   H13  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
 89Q  H1   C4   C3   120.33  3.000
 89Q  H1   C4   C5   119.37  3.000
 89Q  C3   C4   C5   120.31  3.000
 89Q  O2   C5   C10  124.43  3.000
 89Q  C10  C5   C4   119.15  3.000
 89Q  O2   C5   C4   116.41  3.000
 89Q  H3   C6   H2   107.70  3.000
 89Q  H3   C6   O2   109.96  3.000
 89Q  H2   C6   O2   110.28  3.000
 89Q  H3   C6   C7   110.57  3.000
 89Q  H2   C6   C7   110.29  3.000
 89Q  O2   C6   C7   108.06  3.000
 89Q  H4   C11  C2   120.96  3.000
 89Q  H4   C11  C10  117.52  3.000
 89Q  C2   C11  C10  121.51  3.000
 89Q  H5   C7   C9   116.37  3.000
 89Q  H5   C7   C8   116.75  3.000
 89Q  C9   C7   C8    59.98  3.000
 89Q  H5   C7   C6   114.85  3.000
 89Q  C9   C7   C6   118.44  3.000
 89Q  C8   C7   C6   119.58  3.000
 89Q  H7   C8   H6   114.23  3.000
 89Q  H7   C8   C9   118.35  3.000
 89Q  H6   C8   C9   117.95  3.000
 89Q  H7   C8   C7   117.92  3.000
 89Q  H6   C8   C7   117.95  3.000
 89Q  C9   C8   C7    60.03  3.000
 89Q  H9   C9   H8   114.13  3.000
 89Q  H9   C9   C8   118.57  3.000
 89Q  H8   C9   C8   117.99  3.000
 89Q  H9   C9   C7   117.82  3.000
 89Q  H8   C9   C7   117.98  3.000
 89Q  C8   C9   C7    59.99  3.000
 89Q  H10  C10  C11  118.60  3.000
 89Q  H10  C10  C5   121.61  3.000
 89Q  C11  C10  C5   119.79  3.000
 89Q  H12  N1   H11  116.58  3.000
 89Q  H12  N1   C1   122.82  3.000
 89Q  H11  N1   C1   119.14  3.000
 89Q  H13  C3   C2   119.76  3.000
 89Q  H13  C3   C4   119.10  3.000
 89Q  C2   C3   C4   121.13  3.000
 89Q  C1   C2   C3   118.43  3.000
 89Q  C1   C2   C11  123.45  3.000
 89Q  C3   C2   C11  118.09  3.000
 89Q  C6   O2   C5   119.09  3.000
 89Q  C2   C1   O1   121.03  3.000
 89Q  O1   C1   N1   122.29  3.000
 89Q  C2   C1   N1   116.68  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
 89Q  CONST_01  C11  C10  C5   C4      0.00   0.0  0
 89Q  CONST_02  C11  C2   C3   C4      0.00   0.0  0
 89Q  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 89Q  CONST_04  C2   C11  C10  C5      0.00   0.0  0
 89Q  CONST_05  C3   C4   C5   C10     0.00   0.0  0
 89Q  CONST_06  C3   C2   C11  C10     0.00   0.0  0
 89Q  CONST_07  C1   C2   C3   C4    180.00   0.0  0
 89Q  CONST_08  O2   C5   C10  C11   180.00   0.0  0
 89Q  CONST_09  C1   C2   C11  C10   180.00   0.0  0
 89Q  CONST_10  O2   C5   C4   C3    180.00   0.0  0
 89Q  CONST_11  H10  C10  C5   C4    180.00   0.0  0
 89Q  CONST_12  H13  C3   C4   C5    180.00   0.0  0
 89Q  CONST_13  H4   C11  C10  C5    180.00   0.0  0
 89Q  CONST_14  H13  C3   C2   C11   180.00   0.0  0
 89Q  CONST_15  H1   C4   C5   C10   180.00   0.0  0
 89Q  CONST_16  H4   C11  C2   C3    180.00   0.0  0
 89Q  CONST_17  H1   C4   C3   C2    180.00   0.0  0
 89Q  CONST_18  H10  C10  C11  C2    180.00   0.0  0
 89Q  CONST_19  H11  N1   C1   C2    180.00   0.0  0
 89Q  CONST_20  H12  N1   C1   C2      0.00   0.0  0
 89Q  CONST_21  H11  N1   C1   O1      0.00   0.0  0
 89Q  CONST_22  H12  N1   C1   O1    180.00   0.0  0
 89Q  Var_01    C9   C8   C7   C6   -107.73  30.0  1
 89Q  Var_02    H8   C9   C8   C7    107.85  30.0  1
 89Q  Var_03    H9   C9   C8   C7   -107.40  30.0  1
 89Q  Var_04    H6   C8   C9   C7   -107.85  30.0  1
 89Q  Var_05    H7   C8   C9   C7    107.64  30.0  1
 89Q  Var_06    H5   C7   C9   C8   -107.09  30.0  1
 89Q  Var_07    C6   O2   C5   C4    176.95  30.0  2
 89Q  Var_08    C7   C6   O2   C5   -176.21  30.0  3
 89Q  Var_09    C10  C5   O2   C6     -3.52  30.0  2
 89Q  Var_10    O1   C1   C2   C11  -158.26  30.0  2
 89Q  Var_11    N1   C1   C2   C11    21.41  30.0  2
 89Q  Var_12    O2   C6   C7   C8    -80.79  30.0  3
 89Q  Var_13    O2   C6   C7   C9   -150.50  30.0  3
 89Q  Var_14    C3   C2   C1   N1   -160.33  30.0  2
 89Q  Var_15    O1   C1   C2   C3     20.00  30.0  2
 89Q  Var_16    H6   C8   C7   C6      0.12  30.0  1
 89Q  Var_17    H7   C8   C7   C6    143.92  30.0  1
 89Q  Var_18    H8   C9   C7   C6      1.73  30.0  1
 89Q  Var_19    H9   C9   C7   C6   -141.76  30.0  1
 89Q  Var_20    H2   C6   C7   C8     39.82  30.0  3
 89Q  Var_21    H3   C6   C7   C8    158.82  30.0  3
 89Q  Var_22    H2   C6   C7   C9    -29.89  30.0  3
 89Q  Var_23    H3   C6   C7   C9     89.11  30.0  3
 89Q  Var_24    H2   C6   O2   C5     63.17  30.0  3
 89Q  Var_25    H3   C6   O2   C5    -55.45  30.0  3
 89Q  Var_26    H5   C7   C6   O2     65.64  30.0  1

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
 89Q  chir_01  C7  C8  C9  C6  both

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
 89Q  plan-1  C4   0.020
 89Q  plan-1  C5   0.020
 89Q  plan-1  C11  0.020
 89Q  plan-1  C10  0.020
 89Q  plan-1  C3   0.020
 89Q  plan-1  C2   0.020
 89Q  plan-1  O2   0.020
 89Q  plan-1  H1   0.020
 89Q  plan-1  H4   0.020
 89Q  plan-1  H10  0.020
 89Q  plan-1  H13  0.020
 89Q  plan-1  C1   0.020
 89Q  plan-2  N1   0.020
 89Q  plan-2  O1   0.020
 89Q  plan-2  C2   0.020
 89Q  plan-2  H11  0.020
 89Q  plan-2  H12  0.020
 89Q  plan-2  C1   0.020

