# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jun  5 15:00:10 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H]1CCC=C[C@H]1NC(=O)OCc2ccc(cc2)C(=O)NCCO[P](O)(O)=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
 XDA  XDA  '4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate'  ligand  60  32  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XDA
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
 XDA  O8    O  O     0  -0.504   3.8555  -2.5917  -0.2738
 XDA  C7    C  C     0   0.594   4.9130  -2.0610   0.0475
 XDA  N9    N  NT    0  -0.435   5.3659  -2.1279   1.3144
 XDA  C11   C  CH3   0  -0.539   6.6384  -1.6357   1.7946
 XDA  C10   C  CH3   0  -0.521   4.5217  -2.7485   2.3166
 XDA  C4    C  CH1   0  -0.418   5.7129  -1.2610  -0.9699
 XDA  C5    C  CH2   0  -0.430   5.3065  -1.5952  -2.4019
 XDA  C6    C  CH2   0  -0.486   6.2206  -0.8716  -3.3813
 XDA  C1    C  C1    0  -0.215   6.4034   0.5682  -3.0193
 XDA  C2    C  C1    0  -0.208   6.0885   1.0717  -1.8301
 XDA  C3    C  CH1   0  -0.138   5.5422   0.2491  -0.6968
 XDA  N12   N  NH1   0  -0.657   4.1579   0.6099  -0.4608
 XDA  C13   C  C     0   0.769   3.6474   0.8534   0.7609
 XDA  O14   O  O     0  -0.507   4.2744   0.9095   1.7976
 XDA  O15   O  O2    0  -0.482   2.3242   1.0534   0.6825
 XDA  C16   C  CH2   0  -0.231   1.6369   1.3059   1.9070
 XDA  C17   C  CR6   0   0.075   0.1688   1.3005   1.6032
 XDA  C22   C  CR16  0  -0.291  -0.6132   2.4229   1.8451
 XDA  C21   C  CR16  0  -0.249  -1.9742   2.4091   1.5810
 XDA  C18   C  CR16  0  -0.260  -0.4375   0.1594   1.0846
 XDA  C19   C  CR16  0  -0.308  -1.7967   0.1410   0.8250
 XDA  C20   C  CR6   0  -0.028  -2.5839   1.2657   1.0758
 XDA  C23   C  C     0   0.534  -4.0517   1.3179   0.7892
 XDA  O24   O  O     0  -0.482  -4.6369   2.3871   0.6854
 XDA  N25   N  NH1   0  -0.657  -4.6789   0.1384   0.6487
 XDA  C26   C  CH2   0  -0.318  -6.0782   0.0378   0.3074
 XDA  C27   C  CH2   0  -0.194  -6.3610   0.3672  -1.1449
 XDA  O28   O  O2    0  -0.583  -5.6149  -0.5227  -1.9868
 XDA  P29   P  P     0   1.444  -4.6403   0.0538  -3.1070
 XDA  O31   O  OH1   0  -0.739  -3.3886   0.7205  -2.3617
 XDA  O30   O  OH1   0  -0.731  -4.1634  -1.3537  -3.6813
 XDA  O32   O  O     0  -0.707  -5.2166   1.0316  -4.0483
 XDA  H11B  H  HCH3  0   0.245   6.5027  -0.7770   2.4536
 XDA  H11A  H  HCH3  0   0.253   7.1494  -2.4204   2.3546
 XDA  H11C  H  HCH3  0   0.255   7.2966  -1.3438   0.9832
 XDA  H10C  H  HCH3  0   0.237   4.6097  -3.8371   2.3079
 XDA  H10B  H  HCH3  0   0.244   4.8223  -2.3915   3.2991
 XDA  H10A  H  HCH3  0   0.244   3.4769  -2.4861   2.1671
 XDA  H4    H  HCH1  0   0.274   6.7797  -1.4864  -0.8747
 XDA  H5A   H  HCH2  0   0.248   5.3571  -2.6717  -2.5702
 XDA  H5B   H  HCH2  0   0.226   4.2692  -1.3020  -2.5823
 XDA  H6B   H  HCH2  0   0.243   7.2009  -1.3608  -3.4188
 XDA  H6A   H  HCH2  0   0.249   5.8213  -0.9449  -4.3959
 XDA  H1    H  H     0   0.247   6.8171   1.2244  -3.7777
 XDA  H2    H  H     0   0.251   6.2208   2.1295  -1.6305
 XDA  H3    H  HCH1  0   0.284   6.0881   0.5135   0.2103
 XDA  H12   H  HNH1  0   0.398   3.5230   0.5722  -1.2431
 XDA  H16A  H  HCH2  0   0.252   1.8710   0.5305   2.6406
 XDA  H16B  H  HCH2  0   0.254   1.9400   2.2673   2.3273
 XDA  H22   H  HCR6  0   0.265  -0.1580   3.3217   2.2421
 XDA  H21   H  HCR6  0   0.264  -2.5646   3.2951   1.7711
 XDA  H18   H  HCR6  0   0.261   0.1511  -0.7264   0.8801
 XDA  H19   H  HCR6  0   0.261  -2.2219  -0.7686   0.4181
 XDA  H25   H  HNH1  0   0.417  -4.1933  -0.7172   0.8560
 XDA  H26A  H  HCH2  0   0.271  -6.3955  -0.9805   0.5270
 XDA  H26B  H  HCH2  0   0.259  -6.6793   0.7034   0.9301
 XDA  H27A  H  HCH2  0   0.265  -7.4215   0.2225  -1.3529
 XDA  H27B  H  HCH2  0   0.244  -6.1224   1.4115  -1.3529
 XDA  H5    H  HOH1  0   0.487  -2.8463   0.1268  -1.8272
 XDA  H6    H  HOH1  0   0.505  -3.6399  -1.2921  -4.4917

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
 XDA  C11  N9    single    1.446  0.020  1.446
 XDA  O8   C7    double    1.226  0.020  1.226
 XDA  N9   C7    single    1.347  0.020  1.347
 XDA  N9   C10   single    1.450  0.020  1.450
 XDA  C7   C4    single    1.521  0.020  1.521
 XDA  O15  C16   single    1.427  0.020  1.427
 XDA  O15  C13   single    1.341  0.020  1.341
 XDA  C16  C17   single    1.499  0.020  1.499
 XDA  N12  C13   single    1.346  0.020  1.346
 XDA  N12  C3    single    1.450  0.020  1.450
 XDA  C2   C1    double    1.329  0.020  1.329
 XDA  C2   C3    single    1.503  0.020  1.503
 XDA  C22  C17   aromatic  1.389  0.020  1.389
 XDA  C22  C21   aromatic  1.386  0.020  1.386
 XDA  C1   C6    single    1.496  0.020  1.496
 XDA  C4   C3    single    1.544  0.020  1.544
 XDA  C4   C5    single    1.526  0.020  1.526
 XDA  C13  O14   double    1.213  0.020  1.213
 XDA  C17  C18   aromatic  1.392  0.020  1.392
 XDA  C5   C6    single    1.523  0.020  1.523
 XDA  C21  C20   aromatic  1.391  0.020  1.391
 XDA  O32  P29   double    1.475  0.020  1.475
 XDA  C18  C19   aromatic  1.384  0.020  1.384
 XDA  C20  C19   aromatic  1.396  0.020  1.396
 XDA  C20  C23   single    1.496  0.020  1.496
 XDA  P29  O31   single    1.602  0.020  1.602
 XDA  P29  O28   single    1.593  0.020  1.593
 XDA  P29  O30   single    1.593  0.020  1.593
 XDA  O24  C23   double    1.223  0.020  1.223
 XDA  C23  N25   single    1.343  0.020  1.343
 XDA  O28  C27   single    1.434  0.020  1.434
 XDA  N25  C26   single    1.444  0.020  1.444
 XDA  C26  C27   single    1.516  0.020  1.516
 XDA  C11  H11B  single    0.970  0.020  1.090
 XDA  C11  H11A  single    0.970  0.020  1.090
 XDA  C11  H11C  single    0.970  0.020  1.090
 XDA  C10  H10C  single    0.970  0.020  1.090
 XDA  C10  H10B  single    0.970  0.020  1.090
 XDA  C10  H10A  single    0.970  0.020  1.090
 XDA  C4   H4    single    0.970  0.020  1.090
 XDA  C5   H5A   single    0.970  0.020  1.090
 XDA  C5   H5B   single    0.970  0.020  1.090
 XDA  C6   H6B   single    0.970  0.020  1.090
 XDA  C6   H6A   single    0.970  0.020  1.090
 XDA  C1   H1    single    0.930  0.020  1.080
 XDA  C2   H2    single    0.930  0.020  1.080
 XDA  C3   H3    single    0.970  0.020  1.090
 XDA  N12  H12   single    0.860  0.020  1.020
 XDA  C16  H16A  single    0.970  0.020  1.090
 XDA  C16  H16B  single    0.970  0.020  1.090
 XDA  C22  H22   single    0.930  0.020  1.080
 XDA  C21  H21   single    0.930  0.020  1.080
 XDA  C18  H18   single    0.930  0.020  1.080
 XDA  C19  H19   single    0.930  0.020  1.080
 XDA  N25  H25   single    0.860  0.020  1.020
 XDA  C26  H26A  single    0.970  0.020  1.090
 XDA  C26  H26B  single    0.970  0.020  1.090
 XDA  C27  H27A  single    0.970  0.020  1.090
 XDA  C27  H27B  single    0.970  0.020  1.090
 XDA  O31  H5    single    0.850  0.020  0.980
 XDA  O30  H6    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
 XDA  C4    C7   N9    118.57  3.000
 XDA  C4    C7   O8    120.39  3.000
 XDA  N9    C7   O8    120.99  3.000
 XDA  C10   N9   C11   115.36  3.000
 XDA  C10   N9   C7    118.40  3.000
 XDA  C11   N9   C7    126.24  3.000
 XDA  H11C  C11  H11A  107.05  3.000
 XDA  H11C  C11  H11B  108.39  3.000
 XDA  H11A  C11  H11B  108.32  3.000
 XDA  H11C  C11  N9    112.15  3.000
 XDA  H11A  C11  N9    109.74  3.000
 XDA  H11B  C11  N9    111.03  3.000
 XDA  H10A  C10  H10B  108.09  3.000
 XDA  H10A  C10  H10C  108.46  3.000
 XDA  H10B  C10  H10C  108.18  3.000
 XDA  H10A  C10  N9    111.16  3.000
 XDA  H10B  C10  N9    108.85  3.000
 XDA  H10C  C10  N9    111.98  3.000
 XDA  H4    C4   C3    107.09  3.000
 XDA  H4    C4   C5    107.23  3.000
 XDA  C3    C4   C5    110.54  3.000
 XDA  H4    C4   C7    110.24  3.000
 XDA  C5    C4   C7    111.86  3.000
 XDA  C3    C4   C7    109.75  3.000
 XDA  H5B   C5   H5A   106.46  3.000
 XDA  H5B   C5   C6    109.64  3.000
 XDA  H5A   C5   C6    109.99  3.000
 XDA  H5B   C5   C4    110.43  3.000
 XDA  H5A   C5   C4    110.41  3.000
 XDA  C6    C5   C4    109.86  3.000
 XDA  H6A   C6   H6B   105.37  3.000
 XDA  H6A   C6   C1    109.51  3.000
 XDA  H6B   C6   C1    109.18  3.000
 XDA  H6A   C6   C5    110.24  3.000
 XDA  H6B   C6   C5    110.29  3.000
 XDA  C1    C6   C5    112.03  3.000
 XDA  H1    C1   C2    119.12  3.000
 XDA  H1    C1   C6    117.36  3.000
 XDA  C2    C1   C6    123.52  3.000
 XDA  H2    C2   C3    116.06  3.000
 XDA  H2    C2   C1    120.34  3.000
 XDA  C3    C2   C1    123.59  3.000
 XDA  H3    C3   N12   106.38  3.000
 XDA  H3    C3   C2    108.20  3.000
 XDA  N12   C3   C2    109.49  3.000
 XDA  H3    C3   C4    109.19  3.000
 XDA  C2    C3   C4    111.21  3.000
 XDA  N12   C3   C4    112.19  3.000
 XDA  H12   N12  C13   118.17  3.000
 XDA  H12   N12  C3    117.75  3.000
 XDA  C13   N12  C3    123.69  3.000
 XDA  O15   C13  O14   123.60  3.000
 XDA  O14   C13  N12   126.01  3.000
 XDA  O15   C13  N12   110.38  3.000
 XDA  C16   O15  C13   116.85  3.000
 XDA  H16B  C16  H16A  107.87  3.000
 XDA  H16B  C16  C17   110.67  3.000
 XDA  H16A  C16  C17   110.07  3.000
 XDA  H16B  C16  O15   110.64  3.000
 XDA  H16A  C16  O15   110.33  3.000
 XDA  C17   C16  O15   107.29  3.000
 XDA  C18   C17  C22   118.81  3.000
 XDA  C18   C17  C16   120.32  3.000
 XDA  C22   C17  C16   120.87  3.000
 XDA  H22   C22  C21   119.39  3.000
 XDA  H22   C22  C17   119.85  3.000
 XDA  C21   C22  C17   120.76  3.000
 XDA  H21   C21  C20   119.87  3.000
 XDA  H21   C21  C22   119.62  3.000
 XDA  C20   C21  C22   120.51  3.000
 XDA  H18   C18  C19   119.18  3.000
 XDA  H18   C18  C17   120.26  3.000
 XDA  C19   C18  C17   120.56  3.000
 XDA  H19   C19  C20   121.52  3.000
 XDA  H19   C19  C18   117.84  3.000
 XDA  C20   C19  C18   120.64  3.000
 XDA  C23   C20  C19   123.16  3.000
 XDA  C23   C20  C21   118.09  3.000
 XDA  C19   C20  C21   118.72  3.000
 XDA  N25   C23  O24   122.36  3.000
 XDA  N25   C23  C20   116.58  3.000
 XDA  O24   C23  C20   121.06  3.000
 XDA  H25   N25  C26   117.23  3.000
 XDA  H25   N25  C23   120.01  3.000
 XDA  C26   N25  C23   122.58  3.000
 XDA  H26B  C26  H26A  107.14  3.000
 XDA  H26B  C26  C27   108.14  3.000
 XDA  H26A  C26  C27   110.00  3.000
 XDA  H26B  C26  N25   110.87  3.000
 XDA  H26A  C26  N25   107.45  3.000
 XDA  C27   C26  N25   113.08  3.000
 XDA  H27B  C27  H27A  107.65  3.000
 XDA  H27B  C27  O28   111.60  3.000
 XDA  H27A  C27  O28   108.16  3.000
 XDA  H27B  C27  C26   110.48  3.000
 XDA  H27A  C27  C26   109.59  3.000
 XDA  O28   C27  C26   109.30  3.000
 XDA  P29   O28  C27   120.43  3.000
 XDA  O32   P29  O30   118.21  3.000
 XDA  O30   P29  O31   107.55  3.000
 XDA  O32   P29  O31   109.05  3.000
 XDA  O30   P29  O28    96.71  3.000
 XDA  O31   P29  O28   107.55  3.000
 XDA  O32   P29  O28   116.73  3.000
 XDA  H5    O31  P29   116.13  3.000
 XDA  H6    O30  P29   114.08  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
 XDA  CONST_01  C20   C21  C22  C17     0.00   0.0  0
 XDA  CONST_02  C20   C19  C18  C17     0.00   0.0  0
 XDA  CONST_03  C19   C18  C17  C22     0.00   0.0  0
 XDA  CONST_04  C19   C20  C21  C22     0.00   0.0  0
 XDA  CONST_05  C18   C17  C22  C21     0.00   0.0  0
 XDA  CONST_06  C18   C19  C20  C21     0.00   0.0  0
 XDA  CONST_07  C21   C22  C17  C16   180.00   0.0  0
 XDA  CONST_08  C19   C18  C17  C16   180.00   0.0  0
 XDA  CONST_09  C23   C20  C21  C22   180.00   0.0  0
 XDA  CONST_10  C23   C20  C19  C18   180.00   0.0  0
 XDA  CONST_11  H21   C21  C22  C17   180.00   0.0  0
 XDA  CONST_12  H19   C19  C18  C17   180.00   0.0  0
 XDA  CONST_13  H18   C18  C17  C22   180.00   0.0  0
 XDA  CONST_14  H22   C22  C17  C18   180.00   0.0  0
 XDA  CONST_15  C4    C7   N9   C11     0.00   0.0  0
 XDA  CONST_16  C4    C7   N9   C10   180.00   0.0  0
 XDA  CONST_17  C26   N25  C23  C20   180.00   0.0  0
 XDA  CONST_18  H25   N25  C23  C20     0.00   0.0  0
 XDA  CONST_19  C11   N9   C7   O8    180.00   0.0  0
 XDA  CONST_20  C10   N9   C7   O8      0.00   0.0  0
 XDA  CONST_21  C26   N25  C23  O24     0.00   0.0  0
 XDA  Var_01    C1    C6   C5   C4    -46.69  30.0  1
 XDA  Var_02    C2    C1   C6   C5     15.49  30.0  1
 XDA  Var_03    C3    C2   C1   C6      1.51  30.0  1
 XDA  Var_04    C22   C17  C16  O15  -120.11  30.0  2
 XDA  Var_05    O24   C23  C20  C21    17.42  30.0  2
 XDA  Var_06    O15   C13  N12  C3   -174.91  30.0  2
 XDA  Var_07    C17   C16  O15  C13  -172.05  30.0  3
 XDA  Var_08    C27   C26  N25  C23    73.93  30.0  3
 XDA  Var_09    O28   C27  C26  N25    58.64  30.0  3
 XDA  Var_10    O32   P29  O28  C27   -52.58  30.0  2
 XDA  Var_11    H11B  C11  N9   C7    111.43  30.0  3
 XDA  Var_12    H10C  C10  N9   C7     82.32  30.0  3

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
 XDA  chir_01  C4  C7   C3  C5  positiv
 XDA  chir_02  C3  N12  C2  C4  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
 XDA  plan-1  C16  0.020
 XDA  plan-1  C17  0.020
 XDA  plan-1  C22  0.020
 XDA  plan-1  C21  0.020
 XDA  plan-1  C18  0.020
 XDA  plan-1  C19  0.020
 XDA  plan-1  C20  0.020
 XDA  plan-1  C23  0.020
 XDA  plan-1  H22  0.020
 XDA  plan-1  H21  0.020
 XDA  plan-1  H18  0.020
 XDA  plan-1  H19  0.020
 XDA  plan-2  C20  0.020
 XDA  plan-2  C23  0.020
 XDA  plan-2  O24  0.020
 XDA  plan-2  N25  0.020
 XDA  plan-2  C26  0.020
 XDA  plan-2  H25  0.020
 XDA  plan-3  O8   0.020
 XDA  plan-3  C7   0.020
 XDA  plan-3  N9   0.020
 XDA  plan-3  C11  0.020
 XDA  plan-3  C10  0.020
 XDA  plan-3  C4   0.020
 XDA  plan-4  N12  0.020
 XDA  plan-4  C13  0.020
 XDA  plan-4  O14  0.020
 XDA  plan-4  O15  0.020

