# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:58:10 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-[4-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]phenoxy]ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-]C(=O)COc1ccc(cc1)N2C(=O)CCC2=O
#
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
 T9W  T9W  "2-[4-(2,5-Dioxopyrrolidin-1-yl)phenoxy]acetate"
  ligand  28  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T9W
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
 T9W  C10  C  CH2    0  -0.593  -1.5455  -6.7712  5.3069
 T9W  C15  C  CH2    0  -0.334   6.6849  -4.1362  5.9285
 T9W  C01  C  CR16   0  -0.249   1.9065  -4.0225  6.2096
 T9W  C02  C  CR16   0  -0.357   3.1370  -3.3972  6.2166
 T9W  C03  C  CR6    0   0.400   4.3131  -4.1390  6.0572
 T9W  C04  C  CR16   0  -0.388   4.2249  -5.5214  5.8867
 T9W  C05  C  CR16   0  -0.251   2.9815  -6.1394  5.8707
 T9W  C06  C  CR6    0   0.298   1.8240  -5.3991  6.0330
 T9W  C08  C  CR5    0   0.540  -0.3205  -5.9671  4.9555
 T9W  C11  C  CH2    0  -0.593  -1.2969  -7.2827  6.7200
 T9W  C12  C  CR5    0   0.540   0.0791  -6.7883  7.0839
 T9W  C16  C  C      0   0.382   7.8797  -3.1641  5.9827
 T9W  N07  N  NR5    0  -0.650   0.5588  -6.0390  6.0228
 T9W  O09  O  O      0  -0.415  -0.1016  -5.3594  3.9396
 T9W  O13  O  O      0  -0.414   0.6882  -6.9816  8.1041
 T9W  O17  O  OC    -1  -0.613   8.9749  -3.7354  5.8220
 T9W  O18  O  O      0  -0.586   7.6570  -1.9604  6.1757
 T9W  H1   H  HCH2   0   0.301  -2.4288  -6.1372  5.2284
 T9W  H2   H  HCH2   0   0.226   6.7049  -4.6738  4.9731
 T9W  H3   H  HCH2   0   0.226   6.8037  -4.8858  6.7206
 T9W  H4   H  HCR6   0   0.267   1.0051  -3.4383  6.3446
 T9W  H5   H  HCR6   0   0.264   3.2011  -2.3248  6.3507
 T9W  H6   H  HCR6   0   0.281   5.1082  -6.1316  5.7621
 T9W  H7   H  HCR6   0   0.268   2.9220  -7.2108  5.7269
 T9W  H8   H  HCH2   0   0.302  -2.0139  -6.8921  7.4431
 T9W  H10  H  HCH2   0   0.302  -1.6611  -7.5748  4.5786
 T9W  H11  H  HCH2   0   0.301  -1.3241  -8.3699  6.7964
 T9W  O14  O  O2     0  -0.455   5.4572  -3.4461  6.0821

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
 T9W  O09  C08  double    1.204  0.020  1.204
 T9W  C08  C10  single    1.507  0.020  1.507
 T9W  C08  N07  single    1.385  0.020  1.385
 T9W  O18  C16  deloc     1.239  0.020  1.239
 T9W  C10  C11  single    1.523  0.020  1.523
 T9W  C16  O17  deloc     1.246  0.020  1.246
 T9W  C16  C15  single    1.541  0.020  1.541
 T9W  C15  O14  single    1.417  0.020  1.417
 T9W  C01  C02  aromatic  1.380  0.020  1.380
 T9W  C01  C06  aromatic  1.390  0.020  1.390
 T9W  C02  C03  aromatic  1.400  0.020  1.400
 T9W  N07  C06  single    1.418  0.020  1.418
 T9W  N07  C12  single    1.385  0.020  1.385
 T9W  C06  C05  aromatic  1.384  0.020  1.384
 T9W  C03  O14  single    1.338  0.020  1.338
 T9W  C03  C04  aromatic  1.396  0.020  1.396
 T9W  C05  C04  aromatic  1.389  0.020  1.389
 T9W  C11  C12  single    1.507  0.020  1.507
 T9W  C12  O13  double    1.204  0.020  1.204
 T9W  C10  H1   single    0.970  0.020  1.090
 T9W  C15  H2   single    0.970  0.020  1.090
 T9W  C15  H3   single    0.970  0.020  1.090
 T9W  C01  H4   single    0.930  0.020  1.080
 T9W  C02  H5   single    0.930  0.020  1.080
 T9W  C04  H6   single    0.930  0.020  1.080
 T9W  C05  H7   single    0.930  0.020  1.080
 T9W  C11  H8   single    0.970  0.020  1.090
 T9W  C10  H10  single    0.970  0.020  1.090
 T9W  C11  H11  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
 T9W  H10  C10  H1   107.13  3.000
 T9W  H10  C10  C11  112.91  3.000
 T9W  H1   C10  C11  113.22  3.000
 T9W  H10  C10  C08  108.89  3.000
 T9W  H1   C10  C08  109.37  3.000
 T9W  C11  C10  C08  105.24  3.000
 T9W  H3   C15  H2   106.99  3.000
 T9W  H3   C15  O14  110.39  3.000
 T9W  H2   C15  O14  110.43  3.000
 T9W  H3   C15  C16  108.76  3.000
 T9W  H2   C15  C16  109.01  3.000
 T9W  O14  C15  C16  111.15  3.000
 T9W  H4   C01  C06  120.04  3.000
 T9W  H4   C01  C02  119.82  3.000
 T9W  C06  C01  C02  120.14  3.000
 T9W  H5   C02  C03  119.30  3.000
 T9W  H5   C02  C01  120.14  3.000
 T9W  C03  C02  C01  120.56  3.000
 T9W  O14  C03  C04  124.70  3.000
 T9W  C04  C03  C02  119.06  3.000
 T9W  O14  C03  C02  116.23  3.000
 T9W  H6   C04  C05  118.63  3.000
 T9W  H6   C04  C03  121.44  3.000
 T9W  C05  C04  C03  119.92  3.000
 T9W  H7   C05  C06  119.94  3.000
 T9W  H7   C05  C04  119.42  3.000
 T9W  C06  C05  C04  120.64  3.000
 T9W  N07  C06  C05  120.28  3.000
 T9W  C05  C06  C01  119.67  3.000
 T9W  N07  C06  C01  120.05  3.000
 T9W  O09  C08  N07  124.14  3.000
 T9W  N07  C08  C10  107.99  3.000
 T9W  O09  C08  C10  127.87  3.000
 T9W  H11  C11  H8   107.12  3.000
 T9W  H11  C11  C12  109.45  3.000
 T9W  H8   C11  C12  108.82  3.000
 T9W  H11  C11  C10  113.32  3.000
 T9W  H8   C11  C10  112.80  3.000
 T9W  C12  C11  C10  105.24  3.000
 T9W  O13  C12  N07  124.12  3.000
 T9W  O13  C12  C11  127.89  3.000
 T9W  N07  C12  C11  107.99  3.000
 T9W  O18  C16  O17  128.58  3.000
 T9W  O17  C16  C15  112.82  3.000
 T9W  O18  C16  C15  118.60  3.000
 T9W  C12  N07  C08  113.50  3.000
 T9W  C12  N07  C06  123.22  3.000
 T9W  C08  N07  C06  123.28  3.000
 T9W  C03  O14  C15  119.13  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
 T9W  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 T9W  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 T9W  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 T9W  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 T9W  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 T9W  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 T9W  CONST_07  N07  C06  C01  C02   180.00   0.0  0
 T9W  CONST_08  N07  C06  C05  C04   180.00   0.0  0
 T9W  CONST_09  C06  N07  C08  C10   180.00   0.0  0
 T9W  CONST_10  C12  N07  C08  C10     0.00   0.0  0
 T9W  CONST_11  O14  C03  C02  C01   180.00   0.0  0
 T9W  CONST_12  O14  C03  C04  C05   180.00   0.0  0
 T9W  CONST_13  O09  C08  N07  C06     0.00   0.0  0
 T9W  CONST_14  O09  C08  N07  C12   180.00   0.0  0
 T9W  CONST_15  H7   C05  C06  C01   180.00   0.0  0
 T9W  CONST_16  H6   C04  C03  C02   180.00   0.0  0
 T9W  CONST_17  H4   C01  C02  C03   180.00   0.0  0
 T9W  CONST_18  H7   C05  C04  C03   180.00   0.0  0
 T9W  CONST_19  H5   C02  C03  C04   180.00   0.0  0
 T9W  CONST_20  H4   C01  C06  C05   180.00   0.0  0
 T9W  CONST_21  H5   C02  C01  C06   180.00   0.0  0
 T9W  CONST_22  H6   C04  C05  C06   180.00   0.0  0
 T9W  CONST_23  H4   C01  C06  N07     0.00   0.0  0
 T9W  CONST_24  H7   C05  C06  N07     0.00   0.0  0
 T9W  Var_01    N07  C12  C11  C10     1.72  30.0  1
 T9W  Var_02    C08  N07  C06  C01    74.74  30.0  2
 T9W  Var_03    C12  N07  C06  C01  -104.78  30.0  2
 T9W  Var_04    C08  N07  C06  C05  -105.41  30.0  2
 T9W  Var_05    C12  N07  C06  C05    75.07  30.0  2
 T9W  Var_06    C11  C12  N07  C06   178.90  30.0  1
 T9W  Var_07    C12  C11  C10  C08    -2.07  30.0  1
 T9W  Var_08    C11  C12  N07  C08    -0.66  30.0  1
 T9W  Var_09    N07  C08  C10  C11     1.76  30.0  1
 T9W  Var_10    O13  C12  C11  C10  -178.54  30.0  1
 T9W  Var_11    O13  C12  N07  C06    -0.85  30.0  1
 T9W  Var_12    O13  C12  N07  C08   179.59  30.0  1
 T9W  Var_13    O09  C08  C10  C11  -178.47  30.0  1
 T9W  Var_14    H8   C11  C10  C08   116.44  30.0  1
 T9W  Var_15    H11  C11  C10  C08  -121.63  30.0  1
 T9W  Var_16    H1   C10  C11  C12  -121.47  30.0  1
 T9W  Var_17    H10  C10  C11  C12   116.57  30.0  1
 T9W  Var_18    H1   C10  C08  N07   123.69  30.0  1
 T9W  Var_19    H10  C10  C08  N07  -119.55  30.0  1
 T9W  Var_20    H8   C11  C12  N07  -119.42  30.0  1
 T9W  Var_21    H11  C11  C12  N07   123.82  30.0  1
 T9W  Var_22    C02  C03  O14  C15   179.90  30.0  3
 T9W  Var_23    C04  C03  O14  C15    -0.07  30.0  3
 T9W  Var_24    H1   C10  C08  O09   -56.54  30.0  1
 T9W  Var_25    H10  C10  C08  O09    60.22  30.0  1
 T9W  Var_26    H8   C11  C12  O13    60.32  30.0  1
 T9W  Var_27    H11  C11  C12  O13   -56.44  30.0  1
 T9W  Var_28    C16  C15  O14  C03   179.88  30.0  2
 T9W  Var_29    H2   C15  O14  C03    58.76  30.0  2
 T9W  Var_30    H3   C15  O14  C03   -59.35  30.0  2
 T9W  Var_31    O18  C16  C15  O14     1.64  30.0  3
 T9W  Var_32    O17  C16  C15  O14  -178.56  30.0  3
 T9W  Var_33    H2   C15  C16  O17   -56.61  30.0  3
 T9W  Var_34    H3   C15  C16  O17    59.71  30.0  3
 T9W  Var_35    H2   C15  C16  O18   123.60  30.0  3
 T9W  Var_36    H3   C15  C16  O18  -120.09  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
 T9W  plan-1  C01  0.020
 T9W  plan-1  C02  0.020
 T9W  plan-1  C03  0.020
 T9W  plan-1  C04  0.020
 T9W  plan-1  C05  0.020
 T9W  plan-1  C06  0.020
 T9W  plan-1  N07  0.020
 T9W  plan-1  H4   0.020
 T9W  plan-1  H5   0.020
 T9W  plan-1  H6   0.020
 T9W  plan-1  H7   0.020
 T9W  plan-1  O14  0.020
 T9W  plan-2  C10  0.020
 T9W  plan-2  C06  0.020
 T9W  plan-2  C08  0.020
 T9W  plan-2  C12  0.020
 T9W  plan-2  N07  0.020
 T9W  plan-2  O09  0.020
 T9W  plan-3  C15  0.020
 T9W  plan-3  C16  0.020
 T9W  plan-3  O17  0.020
 T9W  plan-3  O18  0.020
 T9W  plan-4  C11  0.020
 T9W  plan-4  C12  0.020
 T9W  plan-4  N07  0.020
 T9W  plan-4  O13  0.020

