# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 17:15:19 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (3-fluorophenyl)methyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)OCc3cccc(F)c3
#
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
 XTJ  XTJ  '(3-fluorophenyl)methyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate'  ligand  58  30  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XTJ
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
 XTJ  C10   C  C     0   0.567  -11.6684  14.9721   4.4161
 XTJ  C15   C  CH2   0  -0.483  -16.7970  13.2103  -0.5871
 XTJ  C17   C  CH2   0  -0.485  -17.7073  11.4981   1.1417
 XTJ  C20   C  C     0   0.781  -15.4096  16.5110   0.3429
 XTJ  C22   C  CH2   0  -0.172  -14.8697  18.7889   0.1535
 XTJ  C24   C  CR16  0  -0.294  -14.3944  21.1355  -0.4953
 XTJ  C26   C  CR16  0  -0.422  -15.2652  22.1544  -2.4986
 XTJ  C02   C  C     0   0.538  -14.5448  13.6333   0.4260
 XTJ  C04   C  CH1   0  -0.135  -13.0485  12.3249   1.9061
 XTJ  C05   C  CH2   0  -0.424  -12.4686  12.8995   3.1973
 XTJ  C06   C  CH1   0  -0.419  -12.2079  14.3942   3.1168
 XTJ  C07   C  CH2   0  -0.467  -11.1721  14.8327   2.0815
 XTJ  C08   C  CH2   0  -0.259  -10.5857  16.1155   2.6736
 XTJ  C12   C  CH2   0  -0.130  -13.3160  10.8249   2.0010
 XTJ  C14   C  CH1   0  -0.155  -15.9773  14.1567   0.2951
 XTJ  C16   C  CH1   0  -0.257  -16.8545  11.8033  -0.0520
 XTJ  C18   C  CH2   0  -0.487  -18.1045  10.9960  -0.2143
 XTJ  C23   C  CR6   0   0.034  -15.0228  19.9317  -0.8105
 XTJ  C25   C  CR16  0  -0.225  -14.5170  22.2335  -1.3303
 XTJ  C27   C  CR6   0   0.551  -15.8761  20.9535  -2.7905
 XTJ  C29   C  CR16  0  -0.463  -15.7745  19.8399  -1.9750
 XTJ  F28   F  F     0  -0.317  -16.6041  20.8539  -3.9151
 XTJ  N03   N  NH1   0  -0.624  -14.2931  12.9856   1.5726
 XTJ  N09   N  NH1   0  -0.630  -10.7517  15.9012   4.0949
 XTJ  N19   N  NH1   0  -0.674  -15.9857  15.4743  -0.2895
 XTJ  O01   O  O     0  -0.483  -13.7391  13.7766  -0.4804
 XTJ  O11   O  O     0  -0.487  -12.0140  14.6616   5.5441
 XTJ  O13   O  OH1   0  -0.662  -12.1070  10.1586   2.2659
 XTJ  O21   O  O2    0  -0.488  -15.4396  17.6189  -0.4071
 XTJ  O30   O  O     0  -0.505  -14.9332  16.4608   1.4580
 XTJ  H151  H  HCH2  0   0.250  -16.3810  13.2074  -1.5991
 XTJ  H152  H  HCH2  0   0.257  -17.8094  13.6175  -0.6622
 XTJ  H171  H  HCH2  0   0.245  -18.2849  12.3093   1.5692
 XTJ  H172  H  HCH2  0   0.249  -17.3373  10.7857   1.8677
 XTJ  H222  H  HCH2  0   0.258  -15.3626  19.0408   1.0969
 XTJ  H221  H  HCH2  0   0.255  -13.8098  18.6327   0.3730
 XTJ  H261  H  HCR6  0   0.277  -15.3668  23.0033  -3.1617
 XTJ  H041  H  HCH1  0   0.261  -12.3567  12.5043   1.0811
 XTJ  H052  H  HCH2  0   0.233  -13.1590  12.6912   4.0209
 XTJ  H051  H  HCH2  0   0.245  -11.5361  12.3797   3.4281
 XTJ  H061  H  HCH1  0   0.282  -13.1517  14.9179   2.9202
 XTJ  H072  H  HCH2  0   0.253  -11.5939  14.9937   1.0913
 XTJ  H071  H  HCH2  0   0.243  -10.3906  14.0732   1.9917
 XTJ  H082  H  HCH2  0   0.248   -9.5362  16.2569   2.4165
 XTJ  H081  H  HCH2  0   0.233  -11.1353  17.0006   2.3388
 XTJ  H121  H  HCH2  0   0.191  -14.0613  10.6498   2.7902
 XTJ  H141  H  HCH1  0   0.270  -16.4516  14.1981   1.2802
 XTJ  H161  H  HCH1  0   0.267  -15.9277  11.2429  -0.1231
 XTJ  H181  H  HCH2  0   0.243  -18.9506  11.4659  -0.7006
 XTJ  H182  H  HCH2  0   0.250  -18.0057   9.9376  -0.4179
 XTJ  H251  H  HCR6  0   0.268  -14.0245  23.1623  -1.0751
 XTJ  H291  H  HCR6  0   0.274  -16.2787  18.9258  -2.2581
 XTJ  H031  H  HNH1  0   0.400  -15.0201  12.9608   2.2725
 XTJ  H091  H  HNH1  0   0.393  -10.3411  16.5072   4.7883
 XTJ  H191  H  HNH1  0   0.406  -16.2610  15.5776  -1.2541
 XTJ  H1    H  HCH2  0   0.211  -13.7657  10.4941   1.0557
 XTJ  H2    H  HOH1  0   0.456  -12.2926   9.2200   2.3595
 XTJ  H241  H  HCR6  0   0.259  -13.8046  21.2128   0.4104

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
 XTJ  F28  C27   single    1.343  0.020  1.343
 XTJ  C27  C29   aromatic  1.384  0.020  1.384
 XTJ  C27  C26   aromatic  1.379  0.020  1.379
 XTJ  C29  C23   aromatic  1.389  0.020  1.389
 XTJ  C26  C25   aromatic  1.390  0.020  1.390
 XTJ  C18  C16   single    1.497  0.020  1.497
 XTJ  C18  C17   single    1.500  0.020  1.500
 XTJ  C25  C24   aromatic  1.385  0.020  1.385
 XTJ  C15  C16   single    1.506  0.020  1.506
 XTJ  C15  C14   single    1.532  0.020  1.532
 XTJ  O21  C22   single    1.417  0.020  1.417
 XTJ  O21  C20   single    1.338  0.020  1.338
 XTJ  C23  C24   aromatic  1.394  0.020  1.394
 XTJ  C23  C22   single    1.503  0.020  1.503
 XTJ  N19  C20   single    1.344  0.020  1.344
 XTJ  N19  C14   single    1.441  0.020  1.441
 XTJ  O01  C02   double    1.221  0.020  1.221
 XTJ  C16  C17   single    1.499  0.020  1.499
 XTJ  C20  O30   double    1.214  0.020  1.214
 XTJ  C14  C02   single    1.531  0.020  1.531
 XTJ  C02  N03   single    1.341  0.020  1.341
 XTJ  N03  C04   single    1.448  0.020  1.448
 XTJ  C07  C08   single    1.530  0.020  1.530
 XTJ  C07  C06   single    1.529  0.020  1.529
 XTJ  C04  C12   single    1.527  0.020  1.527
 XTJ  C04  C05   single    1.528  0.020  1.528
 XTJ  C08  N09   single    1.447  0.020  1.447
 XTJ  C12  O13   single    1.406  0.020  1.406
 XTJ  C06  C05   single    1.519  0.020  1.519
 XTJ  C06  C10   single    1.521  0.020  1.521
 XTJ  N09  C10   single    1.344  0.020  1.344
 XTJ  C10  O11   double    1.220  0.020  1.220
 XTJ  C15  H151  single    0.970  0.020  1.090
 XTJ  C15  H152  single    0.970  0.020  1.090
 XTJ  C17  H171  single    0.970  0.020  1.090
 XTJ  C17  H172  single    0.970  0.020  1.090
 XTJ  C22  H222  single    0.970  0.020  1.090
 XTJ  C22  H221  single    0.970  0.020  1.090
 XTJ  C24  H241  single    0.930  0.020  1.080
 XTJ  C26  H261  single    0.930  0.020  1.080
 XTJ  C04  H041  single    0.970  0.020  1.090
 XTJ  C05  H052  single    0.970  0.020  1.090
 XTJ  C05  H051  single    0.970  0.020  1.090
 XTJ  C06  H061  single    0.970  0.020  1.090
 XTJ  C07  H072  single    0.970  0.020  1.090
 XTJ  C07  H071  single    0.970  0.020  1.090
 XTJ  C08  H082  single    0.970  0.020  1.090
 XTJ  C08  H081  single    0.970  0.020  1.090
 XTJ  C12  H121  single    0.970  0.020  1.090
 XTJ  C14  H141  single    0.970  0.020  1.090
 XTJ  C16  H161  single    0.970  0.020  1.090
 XTJ  C18  H181  single    0.970  0.020  1.090
 XTJ  C18  H182  single    0.970  0.020  1.090
 XTJ  C25  H251  single    0.930  0.020  1.080
 XTJ  C29  H291  single    0.930  0.020  1.080
 XTJ  N03  H031  single    0.860  0.020  1.020
 XTJ  N09  H091  single    0.860  0.020  1.020
 XTJ  N19  H191  single    0.860  0.020  1.020
 XTJ  C12  H1    single    0.970  0.020  1.090
 XTJ  O13  H2    single    0.850  0.020  0.980

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
 XTJ  O11   C10  N09   126.16  3.000
 XTJ  O11   C10  C06   126.35  3.000
 XTJ  N09   C10  C06   107.48  3.000
 XTJ  H152  C15  H151  106.82  3.000
 XTJ  H152  C15  C16   109.68  3.000
 XTJ  H151  C15  C16   109.91  3.000
 XTJ  H152  C15  C14   107.75  3.000
 XTJ  H151  C15  C14   109.33  3.000
 XTJ  C16   C15  C14   113.14  3.000
 XTJ  H172  C17  H171  114.23  3.000
 XTJ  H172  C17  C18   118.47  3.000
 XTJ  H171  C17  C18   117.79  3.000
 XTJ  H172  C17  C16   118.28  3.000
 XTJ  H171  C17  C16   117.72  3.000
 XTJ  C18   C17  C16    59.91  3.000
 XTJ  O30   C20  O21   123.91  3.000
 XTJ  O30   C20  N19   124.66  3.000
 XTJ  O21   C20  N19   111.43  3.000
 XTJ  H221  C22  H222  107.25  3.000
 XTJ  H221  C22  O21   110.56  3.000
 XTJ  H222  C22  O21   110.50  3.000
 XTJ  H221  C22  C23   109.64  3.000
 XTJ  H222  C22  C23   109.40  3.000
 XTJ  O21   C22  C23   109.45  3.000
 XTJ  H241  C24  C25   119.71  3.000
 XTJ  H241  C24  C23   119.74  3.000
 XTJ  C25   C24  C23   120.55  3.000
 XTJ  H261  C26  C27   120.81  3.000
 XTJ  H261  C26  C25   121.41  3.000
 XTJ  C27   C26  C25   117.78  3.000
 XTJ  O01   C02  N03   124.58  3.000
 XTJ  N03   C02  C14   114.46  3.000
 XTJ  O01   C02  C14   120.92  3.000
 XTJ  H041  C04  N03   107.20  3.000
 XTJ  H041  C04  C12   108.63  3.000
 XTJ  N03   C04  C12   108.18  3.000
 XTJ  H041  C04  C05   109.66  3.000
 XTJ  C12   C04  C05   112.55  3.000
 XTJ  N03   C04  C05   110.45  3.000
 XTJ  H051  C05  H052  106.79  3.000
 XTJ  H051  C05  C06   109.44  3.000
 XTJ  H052  C05  C06   109.59  3.000
 XTJ  H051  C05  C04   108.89  3.000
 XTJ  H052  C05  C04   108.96  3.000
 XTJ  C06   C05  C04   112.98  3.000
 XTJ  H061  C06  C07   108.94  3.000
 XTJ  H061  C06  C05   109.36  3.000
 XTJ  C07   C06  C05   115.74  3.000
 XTJ  H061  C06  C10   106.07  3.000
 XTJ  C05   C06  C10   112.92  3.000
 XTJ  C07   C06  C10   103.25  3.000
 XTJ  H071  C07  H072  107.76  3.000
 XTJ  H071  C07  C08   109.89  3.000
 XTJ  H072  C07  C08   112.12  3.000
 XTJ  H071  C07  C06   109.91  3.000
 XTJ  H072  C07  C06   113.33  3.000
 XTJ  C08   C07  C06   103.78  3.000
 XTJ  H081  C08  H082  107.86  3.000
 XTJ  H081  C08  N09   111.26  3.000
 XTJ  H082  C08  N09   111.19  3.000
 XTJ  H081  C08  C07   111.55  3.000
 XTJ  H082  C08  C07   112.75  3.000
 XTJ  N09   C08  C07   102.23  3.000
 XTJ  H1    C12  H121  107.00  3.000
 XTJ  H1    C12  O13   111.82  3.000
 XTJ  H121  C12  O13   111.86  3.000
 XTJ  H1    C12  C04   108.32  3.000
 XTJ  H121  C12  C04   108.66  3.000
 XTJ  O13   C12  C04   109.07  3.000
 XTJ  H141  C14  N19   109.15  3.000
 XTJ  H141  C14  C02   109.97  3.000
 XTJ  N19   C14  C02   110.65  3.000
 XTJ  H141  C14  C15   108.05  3.000
 XTJ  C02   C14  C15   109.80  3.000
 XTJ  N19   C14  C15   109.15  3.000
 XTJ  H161  C16  C18   115.31  3.000
 XTJ  H161  C16  C17   115.66  3.000
 XTJ  C18   C16  C17    60.08  3.000
 XTJ  H161  C16  C15   115.24  3.000
 XTJ  C17   C16  C15   119.66  3.000
 XTJ  C18   C16  C15   119.81  3.000
 XTJ  H182  C18  H181  114.27  3.000
 XTJ  H182  C18  C16   118.14  3.000
 XTJ  H181  C18  C16   117.84  3.000
 XTJ  H182  C18  C17   118.25  3.000
 XTJ  H181  C18  C17   117.88  3.000
 XTJ  C16   C18  C17    60.01  3.000
 XTJ  C29   C23  C24   119.38  3.000
 XTJ  C24   C23  C22   117.75  3.000
 XTJ  C29   C23  C22   122.86  3.000
 XTJ  H251  C25  C26   119.49  3.000
 XTJ  H251  C25  C24   119.87  3.000
 XTJ  C26   C25  C24   120.63  3.000
 XTJ  F28   C27  C29   118.25  3.000
 XTJ  C29   C27  C26   122.93  3.000
 XTJ  F28   C27  C26   118.81  3.000
 XTJ  H291  C29  C27   119.45  3.000
 XTJ  H291  C29  C23   121.84  3.000
 XTJ  C27   C29  C23   118.72  3.000
 XTJ  H031  N03  C04   116.62  3.000
 XTJ  H031  N03  C02   118.01  3.000
 XTJ  C04   N03  C02   125.36  3.000
 XTJ  H091  N09  C08   122.67  3.000
 XTJ  H091  N09  C10   121.92  3.000
 XTJ  C08   N09  C10   114.55  3.000
 XTJ  H191  N19  C14   118.89  3.000
 XTJ  H191  N19  C20   119.21  3.000
 XTJ  C14   N19  C20   120.78  3.000
 XTJ  H2    O13  C12   108.37  3.000
 XTJ  C22   O21  C20   116.93  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
 XTJ  CONST_01  C27   C26  C25  C24     0.00   0.0  0
 XTJ  CONST_02  C27   C29  C23  C24     0.00   0.0  0
 XTJ  CONST_03  C23   C29  C27  C26     0.00   0.0  0
 XTJ  CONST_04  C23   C24  C25  C26     0.00   0.0  0
 XTJ  CONST_05  C29   C27  C26  C25     0.00   0.0  0
 XTJ  CONST_06  C29   C23  C24  C25     0.00   0.0  0
 XTJ  CONST_07  C08   N09  C10  C06     0.00   0.0  0
 XTJ  CONST_08  C27   C29  C23  C22   180.00   0.0  0
 XTJ  CONST_09  C25   C24  C23  C22   180.00   0.0  0
 XTJ  CONST_10  F28   C27  C29  C23   180.00   0.0  0
 XTJ  CONST_11  F28   C27  C26  C25   180.00   0.0  0
 XTJ  CONST_12  O11   C10  N09  C08   180.00   0.0  0
 XTJ  CONST_13  H261  C26  C25  C24   180.00   0.0  0
 XTJ  CONST_14  H291  C29  C23  C24   180.00   0.0  0
 XTJ  CONST_15  H241  C24  C25  C26   180.00   0.0  0
 XTJ  CONST_16  H251  C25  C24  C23   180.00   0.0  0
 XTJ  CONST_17  H091  N09  C10  C06   180.00   0.0  0
 XTJ  CONST_18  O01   C02  N03  C04     0.00   0.0  0
 XTJ  CONST_19  C14   C02  N03  C04   180.00   0.0  0
 XTJ  CONST_20  H031  N03  C02  C14     0.00   0.0  0
 XTJ  Var_01    C07   C08  N09  C10   -19.75  30.0  1
 XTJ  Var_02    N09   C08  C07  C06    28.27  30.0  1
 XTJ  Var_03    C17   C18  C16  C15  -109.17  30.0  1
 XTJ  Var_04    H171  C17  C18  C16   107.59  30.0  1
 XTJ  Var_05    C14   C15  C16  C17    73.80  30.0  1
 XTJ  Var_06    O21   C22  C23  C24  -173.24  30.0  2
 XTJ  Var_07    C23   C22  O21  C20  -178.65  30.0  3
 XTJ  Var_08    N19   C20  O21  C22   179.56  30.0  3
 XTJ  Var_09    O21   C20  N19  C14   175.42  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
 XTJ  chir_01  C04  N03  C12  C05  positiv
 XTJ  chir_02  C06  C10  C05  C07  positiv
 XTJ  chir_03  C14  N19  C15  C02  negativ
 XTJ  chir_04  C16  C18  C15  C17  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
 XTJ  plan-1  C02   0.020
 XTJ  plan-1  C04   0.020
 XTJ  plan-1  C14   0.020
 XTJ  plan-1  N03   0.020
 XTJ  plan-1  O01   0.020
 XTJ  plan-1  H031  0.020
 XTJ  plan-2  C22   0.020
 XTJ  plan-2  C24   0.020
 XTJ  plan-2  C26   0.020
 XTJ  plan-2  C23   0.020
 XTJ  plan-2  C25   0.020
 XTJ  plan-2  C27   0.020
 XTJ  plan-2  C29   0.020
 XTJ  plan-2  F28   0.020
 XTJ  plan-2  H261  0.020
 XTJ  plan-2  H251  0.020
 XTJ  plan-2  H291  0.020
 XTJ  plan-2  H241  0.020
 XTJ  plan-3  C10   0.020
 XTJ  plan-3  C06   0.020
 XTJ  plan-3  C08   0.020
 XTJ  plan-3  N09   0.020
 XTJ  plan-3  O11   0.020
 XTJ  plan-3  H091  0.020
 XTJ  plan-4  C20   0.020
 XTJ  plan-4  N19   0.020
 XTJ  plan-4  O21   0.020
 XTJ  plan-4  O30   0.020

