# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 12:16:15 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: O-(cyclohexylmethyl)-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(OCC2CCCCC2)cc1)C(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
 U2X  U2X  O-(cyclohexylmethyl)-L-tyrosine  L-peptide  43  20  .  2022-03-23  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U2X
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
 U2X  N     N  NH2   0  -0.782   4.2547   0.6588   1.5562
 U2X  C     C  C     0   0.543   5.9676  -0.2943   0.1496
 U2X  O     O  O     0  -0.437   6.7819   0.5047   0.5374
 U2X  CA    C  CH1   0  -0.207   4.4818  -0.2193   0.4329
 U2X  CB    C  CH2   0  -0.536   3.7431   0.1695  -0.8740
 U2X  CG    C  CR6   0   0.101   2.2593   0.2465  -0.6593
 U2X  CD1   C  CR16  0  -0.298   1.6267   1.4601  -0.3906
 U2X  CD2   C  CR16  0  -0.284   1.4742  -0.9001  -0.6720
 U2X  CE1   C  CR16  0  -0.339   0.2661   1.5273  -0.1498
 U2X  CE2   C  CR16  0  -0.368   0.1062  -0.8557  -0.4310
 U2X  CZ    C  CR6   0   0.376  -0.5084   0.3665  -0.1658
 U2X  OH    O  O2    0  -0.478  -1.8232   0.5211   0.0803
 U2X  C7    C  CH2   0  -0.157  -2.6602  -0.6232   0.1068
 U2X  C1    C  CH2   0  -0.433  -6.0929   1.1232  -0.3786
 U2X  C2    C  CH2   0  -0.414  -4.6486   0.7320  -0.6769
 U2X  C3    C  CH1   0  -0.277  -4.0806  -0.1844   0.4070
 U2X  C4    C  CH2   0  -0.422  -4.9701  -1.4167   0.5822
 U2X  C5    C  CH2   0  -0.430  -6.4155  -1.0304   0.8801
 U2X  C6    C  CH2   0  -0.429  -6.9771  -0.1057  -0.1946
 U2X  H1    H  HNH2  0   0.345   4.5009   1.6117   1.3156
 U2X  H2    H  HNH2  0   0.358   3.2674   0.6684   1.7789
 U2X  HA    H  HCH1  0   0.278   4.1470  -1.2230   0.7139
 U2X  HB2   H  HCH2  0   0.256   4.1198   1.1365  -1.2201
 U2X  HB3   H  HCH2  0   0.259   3.9681  -0.5609  -1.6537
 U2X  HD11  H  HCR6  0   0.251   2.2083   2.3749  -0.3796
 U2X  HD21  H  HCR6  0   0.252   1.9320  -1.8605  -0.8804
 U2X  HE11  H  HCR6  0   0.258  -0.2063   2.4803   0.0544
 U2X  HE21  H  HCR6  0   0.277  -0.4604  -1.7768  -0.4576
 U2X  H72   H  HCH2  0   0.214  -2.6276  -1.1457  -0.8585
 U2X  H71   H  HCH2  0   0.228  -2.3129  -1.3259   0.8742
 U2X  H11   H  HCH2  0   0.209  -6.1223   1.7314   0.5321
 U2X  H12   H  HCH2  0   0.227  -6.4821   1.7531  -1.1821
 U2X  H21   H  HCH2  0   0.205  -4.6086   0.2077  -1.6399
 U2X  H22   H  HCH2  0   0.232  -4.0328   1.6276  -0.7817
 U2X  H31   H  HCH1  0   0.223  -4.0727   0.3627   1.3592
 U2X  H41   H  HCH2  0   0.211  -4.9363  -2.0187  -0.3338
 U2X  H42   H  HCH2  0   0.229  -4.5774  -2.0491   1.3831
 U2X  H51   H  HCH2  0   0.227  -7.0308  -1.9290   0.9668
 U2X  H52   H  HCH2  0   0.210  -6.4600  -0.5276   1.8521
 U2X  H61   H  HCH2  0   0.226  -7.9969   0.1942   0.0590
 U2X  H62   H  HCH2  0   0.208  -7.0387  -0.6504  -1.1433
 U2X  H3    H  HOH1  0   0.482   7.2179  -1.3257  -0.8287
 U2X  OXT   O  OH1   0  -0.594   6.2723  -1.3344  -0.6174

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
 U2X  O    C     double    1.231  0.020  1.231
 U2X  C    CA    single    1.525  0.021  1.525
 U2X  N    CA    single    1.458  0.019  1.458
 U2X  CA   CB    single    1.530  0.020  1.530
 U2X  CB   CG    single    1.501  0.020  1.501
 U2X  CG   CD1   aromatic  1.395  0.020  1.395
 U2X  CG   CD2   aromatic  1.390  0.020  1.390
 U2X  CD1  CE1   aromatic  1.383  0.020  1.383
 U2X  CD2  CE2   aromatic  1.390  0.020  1.390
 U2X  CE1  CZ    aromatic  1.396  0.020  1.396
 U2X  CE2  CZ    aromatic  1.394  0.020  1.394
 U2X  CZ   OH    single    1.346  0.020  1.346
 U2X  OH   C7    single    1.418  0.020  1.418
 U2X  C7   C3    single    1.517  0.020  1.517
 U2X  C3   C4    single    1.530  0.020  1.530
 U2X  C3   C2    single    1.529  0.020  1.529
 U2X  C4   C5    single    1.525  0.020  1.525
 U2X  C2   C1    single    1.526  0.020  1.526
 U2X  C5   C6    single    1.525  0.020  1.525
 U2X  C1   C6    single    1.525  0.020  1.525
 U2X  N    H1    single    0.890  0.020  1.040
 U2X  N    H2    single    0.890  0.020  1.040
 U2X  CA   HA    single    0.970  0.020  0.970
 U2X  CB   HB2   single    0.970  0.020  1.090
 U2X  CB   HB3   single    0.970  0.020  1.090
 U2X  CD1  HD11  single    0.930  0.020  1.080
 U2X  CD2  HD21  single    0.930  0.020  1.080
 U2X  CE1  HE11  single    0.930  0.020  1.080
 U2X  CE2  HE21  single    0.930  0.020  1.080
 U2X  C7   H72   single    0.970  0.020  1.090
 U2X  C7   H71   single    0.970  0.020  1.090
 U2X  C1   H11   single    0.970  0.020  1.090
 U2X  C1   H12   single    0.970  0.020  1.090
 U2X  C2   H21   single    0.970  0.020  1.090
 U2X  C2   H22   single    0.970  0.020  1.090
 U2X  C3   H31   single    0.970  0.020  1.090
 U2X  C4   H41   single    0.970  0.020  1.090
 U2X  C4   H42   single    0.970  0.020  1.090
 U2X  C5   H51   single    0.970  0.020  1.090
 U2X  C5   H52   single    0.970  0.020  1.090
 U2X  C6   H61   single    0.970  0.020  1.090
 U2X  C6   H62   single    0.970  0.020  1.090
 U2X  C    OXT   single    1.328  0.020  1.328
 U2X  OXT  H3    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
 U2X  H2    N    H1   106.28  3.000
 U2X  H2    N    CA   109.29  3.000
 U2X  H1    N    CA   110.43  3.000
 U2X  OXT   C    CA   111.84  3.000
 U2X  OXT   C    O    123.39  3.000
 U2X  CA    C    O    120.80  1.700
 U2X  HA    CA   CB   109.00  3.000
 U2X  HA    CA   C    109.00  3.000
 U2X  CB    CA   C    110.10  1.900
 U2X  HA    CA   N    110.00  3.000
 U2X  CB    CA   N    110.50  1.700
 U2X  C     CA   N    111.00  2.800
 U2X  HB3   CB   HB2  107.12  3.000
 U2X  HB3   CB   CG   109.89  3.000
 U2X  HB2   CB   CG   109.89  3.000
 U2X  HB3   CB   CA   109.64  3.000
 U2X  HB2   CB   CA   108.92  3.000
 U2X  CG    CB   CA   111.29  3.000
 U2X  CD2   CG   CD1  117.61  3.000
 U2X  CD2   CG   CB   120.98  3.000
 U2X  CD1   CG   CB   121.36  3.000
 U2X  HD11  CD1  CE1  119.01  3.000
 U2X  HD11  CD1  CG   119.53  3.000
 U2X  CE1   CD1  CG   121.46  3.000
 U2X  HD21  CD2  CE2  118.51  3.000
 U2X  HD21  CD2  CG   119.61  3.000
 U2X  CE2   CD2  CG   121.88  3.000
 U2X  HE11  CE1  CZ   119.47  3.000
 U2X  HE11  CE1  CD1  120.30  3.000
 U2X  CZ    CE1  CD1  120.23  3.000
 U2X  HE21  CE2  CZ   121.37  3.000
 U2X  HE21  CE2  CD2  118.95  3.000
 U2X  CZ    CE2  CD2  119.68  3.000
 U2X  OH    CZ   CE2  124.48  3.000
 U2X  OH    CZ   CE1  116.38  3.000
 U2X  CE2   CZ   CE1  119.14  3.000
 U2X  C7    OH   CZ   119.15  3.000
 U2X  H71   C7   H72  107.51  3.000
 U2X  H71   C7   C3   110.08  3.000
 U2X  H72   C7   C3   109.84  3.000
 U2X  H71   C7   OH   110.07  3.000
 U2X  H72   C7   OH   110.49  3.000
 U2X  C3    C7   OH   108.84  3.000
 U2X  H12   C1   H11  106.36  3.000
 U2X  H12   C1   C6   110.29  3.000
 U2X  H11   C1   C6   109.36  3.000
 U2X  H12   C1   C2   109.95  3.000
 U2X  H11   C1   C2   109.29  3.000
 U2X  C6    C1   C2   111.46  3.000
 U2X  H22   C2   H21  106.69  3.000
 U2X  H22   C2   C3   110.49  3.000
 U2X  H21   C2   C3   108.80  3.000
 U2X  H22   C2   C1   110.02  3.000
 U2X  H21   C2   C1   109.19  3.000
 U2X  C3    C2   C1   111.51  3.000
 U2X  H31   C3   C4   107.83  3.000
 U2X  H31   C3   C2   108.59  3.000
 U2X  C4    C3   C2   110.36  3.000
 U2X  H31   C3   C7   108.00  3.000
 U2X  C2    C3   C7   112.40  3.000
 U2X  C4    C3   C7   109.52  3.000
 U2X  H42   C4   H41  106.45  3.000
 U2X  H42   C4   C5   110.10  3.000
 U2X  H41   C4   C5   109.35  3.000
 U2X  H42   C4   C3   109.93  3.000
 U2X  H41   C4   C3   109.18  3.000
 U2X  C5    C4   C3   111.67  3.000
 U2X  H52   C5   H51  106.52  3.000
 U2X  H52   C5   C6   109.39  3.000
 U2X  H51   C5   C6   110.32  3.000
 U2X  H52   C5   C4   109.15  3.000
 U2X  H51   C5   C4   109.93  3.000
 U2X  C6    C5   C4   111.40  3.000
 U2X  H62   C6   H61  106.55  3.000
 U2X  H62   C6   C5   109.23  3.000
 U2X  H61   C6   C5   110.27  3.000
 U2X  H62   C6   C1   109.19  3.000
 U2X  H61   C6   C1   110.36  3.000
 U2X  C5    C6   C1   111.11  3.000
 U2X  H3    OXT  C    110.05  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
 U2X  CONST_01  CZ    CE1  CD1  CG     0.00   0.0  0
 U2X  CONST_02  CZ    CE2  CD2  CG     0.00   0.0  0
 U2X  CONST_03  CE2   CD2  CG   CD1    0.00   0.0  0
 U2X  CONST_04  CE2   CZ   CE1  CD1    0.00   0.0  0
 U2X  CONST_05  CE1   CD1  CG   CD2    0.00   0.0  0
 U2X  CONST_06  CE1   CZ   CE2  CD2    0.00   0.0  0
 U2X  CONST_07  CE1   CD1  CG   CB   180.00   0.0  0
 U2X  CONST_08  CE2   CD2  CG   CB   180.00   0.0  0
 U2X  CONST_09  OH    CZ   CE1  CD1  180.00   0.0  0
 U2X  CONST_10  OH    CZ   CE2  CD2  180.00   0.0  0
 U2X  CONST_11  HE11  CE1  CD1  CG   180.00   0.0  0
 U2X  CONST_12  HE21  CE2  CD2  CG   180.00   0.0  0
 U2X  CONST_13  HD21  CD2  CG   CD1  180.00   0.0  0
 U2X  CONST_14  HD11  CD1  CG   CD2  180.00   0.0  0
 U2X  CONST_15  H3    OXT  C    O      0.00   0.0  0
 U2X  Var_01    C4    C5   C6   C1   -54.83  30.0  1
 U2X  Var_02    C5    C6   C1   C2    55.00  30.0  1
 U2X  Var_03    C6    C5   C4   C3    55.52  30.0  1
 U2X  Var_04    C6    C1   C2   C3   -55.75  30.0  1
 U2X  Var_05    CD1   CG   CB   CA    95.98  30.0  2
 U2X  Var_06    C3    C7   OH   CZ   179.77  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
 U2X  chir_01  CA  C   N   CB  negativ
 U2X  chir_02  C3  C7  C4  C2  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
 U2X  plan-1  CB    0.020
 U2X  plan-1  CG    0.020
 U2X  plan-1  CD1   0.020
 U2X  plan-1  CD2   0.020
 U2X  plan-1  CE1   0.020
 U2X  plan-1  CE2   0.020
 U2X  plan-1  CZ    0.020
 U2X  plan-1  OH    0.020
 U2X  plan-1  HD11  0.020
 U2X  plan-1  HD21  0.020
 U2X  plan-1  HE11  0.020
 U2X  plan-1  HE21  0.020
 U2X  plan-2  C     0.020
 U2X  plan-2  O     0.020
 U2X  plan-2  CA    0.020
 U2X  plan-2  H3    0.020
 U2X  plan-2  OXT   0.020

