# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 08:20:46 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: (2S)-[(2S,3S,4S,5S)-1,3,4,5-tetrahydroxy-4-(hydroxymethyl)piperidin-2-yl](L-tyrosylamino)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H]([C@H]2[C@H](O)[C@](O)(CO)[C@@H](O)CN2O)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
 629  629  '(2S)-[(2S,3S,4S,5S)-1,3,4,5-tetrahydroxy-4-(hydroxymethyl)piperidin-2-yl](L-tyrosylamino)ethanoic acid'  ligand  54  29  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_629
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
 629  C7    C  CR16  0  -0.325   -8.9954   9.3406  84.0168
 629  C8    C  CR16  0  -0.294   -9.0579  10.7161  83.8544
 629  C12   C  CR6   0   0.339   -9.4106   8.7645  85.2140
 629  C11   C  CR16  0  -0.369   -9.8800   9.5839  86.2381
 629  C10   C  CR16  0  -0.287   -9.9331  10.9577  86.0579
 629  C9    C  CR6   0   0.088   -9.5265  11.5514  84.8658
 629  C14   C  CH2   0  -0.504   -9.6308  13.0366  84.6637
 629  C15   C  CH1   0  -0.205  -11.0701  13.4763  84.3326
 629  C17   C  C     0   0.557  -11.0823  14.9925  84.1793
 629  N19   N  NH1   0  -0.646  -11.2072  15.6589  85.3430
 629  C20   C  CH1   0  -0.193  -11.1256  17.0865  85.4349
 629  C21   C  C     0   0.560   -9.7095  17.6398  85.3604
 629  O23   O  OH1   0  -0.580   -8.7755  16.7079  85.2881
 629  O18   O  O     0  -0.479  -10.9655  15.5577  83.1057
 629  N16   N  NH2   0  -0.795  -11.5085  12.8554  83.1044
 629  O22   O  O     0  -0.452   -9.4846  18.8239  85.3122
 629  C6    C  CH1   0  -0.134  -11.8582  17.5799  86.6943
 629  N5    N  NT    0  -0.220  -11.3547  16.8541  87.8515
 629  C4    C  CH2   0  -0.296  -12.0371  17.1808  89.0961
 629  C3    C  CH1   0   0.029  -13.5199  16.8835  89.0050
 629  C2    C  CT    0   0.120  -14.1758  17.6077  87.8155
 629  C1    C  CH1   0   0.046  -13.3646  17.3005  86.5495
 629  O28   O  OH1   0  -0.561  -10.0015  17.2105  88.0125
 629  O32   O  OH1   0  -0.670  -13.6732  15.4887  88.8931
 629  O29   O  OH1   0  -0.683  -15.4658  17.0327  87.6958
 629  C30   C  CH2   0  -0.158  -14.4186  19.0983  88.0849
 629  O31   O  OH1   0  -0.658  -13.2271  19.8370  88.1888
 629  O64   O  OH1   0  -0.673  -13.8985  18.0331  85.4700
 629  O13   O  OH1   0  -0.634   -9.3363   7.4225  85.3306
 629  H7    H  HCR6  0   0.261   -8.6260   8.7127  83.2152
 629  H8    H  HCR6  0   0.252   -8.7308  11.1482  82.9161
 629  H11   H  HCR6  0   0.269  -10.2043   9.1520  87.1784
 629  H10   H  HCR6  0   0.251  -10.2985  11.5747  86.8711
 629  H141  H  HCH2  0   0.254   -9.2965  13.5628  85.5603
 629  H142  H  HCH2  0   0.255   -8.9762  13.3486  83.8466
 629  H15   H  HCH1  0   0.238  -11.7013  13.2193  85.1980
 629  H19   H  HNH1  0   0.395  -11.2786  15.1470  86.2110
 629  H20   H  HCH1  0   0.300  -11.6347  17.5316  84.5752
 629  H23   H  HOH1  0   0.482   -7.9034  17.1241  85.2143
 629  H161  H  HNH2  0   0.350  -12.4701  13.1060  82.9117
 629  H162  H  HNH2  0   0.356  -11.5037  11.8500  83.2231
 629  H6    H  HCH1  0   0.265  -11.6981  18.6602  86.7787
 629  H41   H  HCH2  0   0.253  -11.6065  16.5623  89.8868
 629  H42   H  HCH2  0   0.234  -11.8882  18.2260  89.3810
 629  H3    H  HCH1  0   0.227  -13.9869  17.2536  89.9305
 629  H1    H  HCH1  0   0.243  -13.4825  16.2252  86.3720
 629  H28   H  HOH1  0   0.467   -9.5369  16.3702  88.0960
 629  H32   H  HOH1  0   0.447  -14.6009  15.3135  88.6994
 629  H29   H  HOH1  0   0.453  -15.8445  17.2929  86.8479
 629  H301  H  HCH2  0   0.211  -15.0524  19.4869  87.2787
 629  H302  H  HCH2  0   0.211  -15.0099  19.1619  89.0085
 629  H31   H  HOH1  0   0.464  -13.4610  20.7621  88.3079
 629  H64   H  HOH1  0   0.464  -14.0421  17.4422  84.7265
 629  H13   H  HOH1  0   0.473   -9.6622   7.1418  86.1929

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
 629  C7   C8    aromatic  1.386  0.020  1.386
 629  C7   C12   aromatic  1.392  0.020  1.392
 629  C7   H7    single    0.930  0.020  1.080
 629  C8   C9    aromatic  1.393  0.020  1.393
 629  C8   H8    single    0.930  0.020  1.080
 629  C12  C11   aromatic  1.393  0.020  1.393
 629  C12  O13   single    1.349  0.020  1.349
 629  C11  C10   aromatic  1.386  0.020  1.386
 629  C11  H11   single    0.930  0.020  1.080
 629  C10  C9    aromatic  1.393  0.020  1.393
 629  C10  H10   single    0.930  0.020  1.080
 629  C9   C14   single    1.502  0.020  1.502
 629  C14  C15   single    1.541  0.020  1.541
 629  C14  H141  single    0.970  0.020  1.090
 629  C14  H142  single    0.970  0.020  1.090
 629  C15  C17   single    1.524  0.020  1.524
 629  C15  N16   single    1.444  0.020  1.444
 629  C15  H15   single    0.970  0.020  1.090
 629  C17  N19   single    1.347  0.020  1.347
 629  C17  O18   double    1.219  0.020  1.219
 629  N19  C20   single    1.433  0.020  1.433
 629  N19  H19   single    0.860  0.020  1.020
 629  C20  C21   single    1.522  0.020  1.522
 629  C20  C6    single    1.538  0.020  1.538
 629  C20  H20   single    0.970  0.020  1.090
 629  C21  O23   single    1.321  0.020  1.321
 629  C21  O22   double    1.206  0.020  1.206
 629  O23  H23   single    0.850  0.020  0.980
 629  N16  H161  single    0.890  0.020  1.040
 629  N16  H162  single    0.890  0.020  1.040
 629  C6   N5    single    1.456  0.020  1.456
 629  C6   C1    single    1.539  0.020  1.539
 629  C6   H6    single    0.970  0.020  1.090
 629  N5   C4    single    1.456  0.020  1.456
 629  N5   O28   single    1.409  0.020  1.409
 629  C4   C3    single    1.515  0.020  1.515
 629  C4   H41   single    0.970  0.020  1.090
 629  C4   H42   single    0.970  0.020  1.090
 629  C3   C2    single    1.539  0.020  1.539
 629  C3   O32   single    1.408  0.020  1.408
 629  C3   H3    single    0.970  0.020  1.090
 629  C2   C1    single    1.535  0.020  1.535
 629  C2   O29   single    1.417  0.020  1.417
 629  C2   C30   single    1.534  0.020  1.534
 629  C1   O64   single    1.410  0.020  1.410
 629  C1   H1    single    0.970  0.020  1.090
 629  O28  H28   single    0.850  0.020  0.980
 629  O32  H32   single    0.850  0.020  0.980
 629  O29  H29   single    0.850  0.020  0.980
 629  C30  O31   single    1.406  0.020  1.406
 629  C30  H301  single    0.970  0.020  1.090
 629  C30  H302  single    0.970  0.020  1.090
 629  O31  H31   single    0.850  0.020  0.980
 629  O64  H64   single    0.850  0.020  0.980
 629  O13  H13   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
 629  H7    C7   C12   119.88  3.000
 629  H7    C7   C8    120.26  3.000
 629  C12   C7   C8    119.86  3.000
 629  H8    C8   C9    119.42  3.000
 629  H8    C8   C7    118.91  3.000
 629  C9    C8   C7    121.67  3.000
 629  O13   C12  C11   122.69  3.000
 629  O13   C12  C7    118.01  3.000
 629  C11   C12  C7    119.30  3.000
 629  H11   C11  C10   119.72  3.000
 629  H11   C11  C12   120.26  3.000
 629  C10   C11  C12   120.01  3.000
 629  H10   C10  C9    119.85  3.000
 629  H10   C10  C11   118.64  3.000
 629  C9    C10  C11   121.50  3.000
 629  C14   C9   C10   121.09  3.000
 629  C14   C9   C8    121.22  3.000
 629  C10   C9   C8    117.65  3.000
 629  H142  C14  H141  107.04  3.000
 629  H142  C14  C15   108.51  3.000
 629  H141  C14  C15   108.95  3.000
 629  H142  C14  C9    109.96  3.000
 629  H141  C14  C9    110.16  3.000
 629  C15   C14  C9    112.07  3.000
 629  H15   C15  N16   113.19  3.000
 629  H15   C15  C17   107.85  3.000
 629  N16   C15  C17   109.86  3.000
 629  H15   C15  C14   107.45  3.000
 629  N16   C15  C14   110.09  3.000
 629  C17   C15  C14   108.24  3.000
 629  O18   C17  N19   122.72  3.000
 629  O18   C17  C15   123.31  3.000
 629  N19   C17  C15   113.96  3.000
 629  H19   N19  C20   116.98  3.000
 629  H19   N19  C17   119.88  3.000
 629  C20   N19  C17   122.90  3.000
 629  H20   C20  C6    106.93  3.000
 629  H20   C20  C21   104.27  3.000
 629  C6    C20  C21   111.50  3.000
 629  H20   C20  N19   109.18  3.000
 629  C6    C20  N19   110.18  3.000
 629  C21   C20  N19   114.33  3.000
 629  O22   C21  O23   123.94  3.000
 629  O22   C21  C20   122.16  3.000
 629  O23   C21  C20   113.82  3.000
 629  H23   O23  C21   109.72  3.000
 629  H162  N16  H161  105.82  3.000
 629  H162  N16  C15   109.02  3.000
 629  H161  N16  C15   110.11  3.000
 629  H6    C6   C1    109.23  3.000
 629  H6    C6   N5    112.32  3.000
 629  C1    C6   N5    108.84  3.000
 629  H6    C6   C20   108.05  3.000
 629  C1    C6   C20   109.32  3.000
 629  N5    C6   C20   109.04  3.000
 629  O28   N5   C4    107.20  3.000
 629  O28   N5   C6    107.28  3.000
 629  C4    N5   C6    113.92  3.000
 629  H42   C4   H41   107.39  3.000
 629  H42   C4   C3    109.66  3.000
 629  H41   C4   C3    108.56  3.000
 629  H42   C4   N5    111.91  3.000
 629  H41   C4   N5    107.87  3.000
 629  C3    C4   N5    111.30  3.000
 629  H3    C3   O32   110.72  3.000
 629  H3    C3   C2    108.10  3.000
 629  O32   C3   C2    111.00  3.000
 629  H3    C3   C4    107.38  3.000
 629  O32   C3   C4    107.80  3.000
 629  C2    C3   C4    111.79  3.000
 629  C30   C2   O29   105.37  3.000
 629  C30   C2   C1    115.03  3.000
 629  O29   C2   C1    109.28  3.000
 629  C30   C2   C3    112.88  3.000
 629  O29   C2   C3    105.20  3.000
 629  C1    C2   C3    108.54  3.000
 629  H1    C1   O64   110.19  3.000
 629  H1    C1   C2    105.85  3.000
 629  O64   C1   C2    109.12  3.000
 629  H1    C1   C6    107.37  3.000
 629  O64   C1   C6    110.39  3.000
 629  C2    C1   C6    113.79  3.000
 629  H28   O28  N5    104.62  3.000
 629  H32   O32  C3    107.51  3.000
 629  H29   O29  C2    108.80  3.000
 629  H302  C30  H301  106.64  3.000
 629  H302  C30  O31   111.33  3.000
 629  H301  C30  O31   110.97  3.000
 629  H302  C30  C2    106.81  3.000
 629  H301  C30  C2    107.86  3.000
 629  O31   C30  C2    112.92  3.000
 629  H31   O31  C30   107.97  3.000
 629  H64   O64  C1    109.25  3.000
 629  H13   O13  C12   110.40  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
 629  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 629  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 629  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 629  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 629  CONST_05  C9   C8   C7   C12    0.00   0.0  0
 629  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 629  CONST_07  C14  C9   C8   C7   180.00   0.0  0
 629  CONST_08  O13  C12  C7   C8   180.00   0.0  0
 629  CONST_09  C14  C9   C10  C11  180.00   0.0  0
 629  CONST_10  O13  C12  C11  C10  180.00   0.0  0
 629  CONST_11  H11  C11  C12  C7   180.00   0.0  0
 629  CONST_12  H10  C10  C9   C8   180.00   0.0  0
 629  CONST_13  H8   C8   C7   C12  180.00   0.0  0
 629  CONST_14  H7   C7   C12  C11  180.00   0.0  0
 629  CONST_15  C20  N19  C17  C15  180.00   0.0  0
 629  CONST_16  O18  C17  N19  C20    0.00   0.0  0
 629  CONST_17  H19  N19  C17  C15    0.00   0.0  0
 629  CONST_18  H23  O23  C21  C20  180.00   0.0  0
 629  Var_01    C3   C4   N5   C6    59.23  30.0  1
 629  Var_02    C15  C14  C9   C8    99.78  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
 629  chir_01  C15  C14  C17  N16  negativ
 629  chir_02  C20  N19  C21  C6   positiv
 629  chir_03  C6   N5   C1   C20  positiv
 629  chir_04  C3   O32  C2   C4   positiv
 629  chir_05  C2   C30  C1   C3   negativ
 629  chir_06  C1   O64  C2   C6   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
 629  plan-1  C7   0.020
 629  plan-1  C8   0.020
 629  plan-1  C12  0.020
 629  plan-1  C11  0.020
 629  plan-1  C10  0.020
 629  plan-1  C9   0.020
 629  plan-1  C14  0.020
 629  plan-1  O13  0.020
 629  plan-1  H7   0.020
 629  plan-1  H8   0.020
 629  plan-1  H11  0.020
 629  plan-1  H10  0.020
 629  plan-2  C15  0.020
 629  plan-2  C17  0.020
 629  plan-2  N19  0.020
 629  plan-2  C20  0.020
 629  plan-2  O18  0.020
 629  plan-2  H19  0.020
 629  plan-3  C20  0.020
 629  plan-3  C21  0.020
 629  plan-3  O23  0.020
 629  plan-3  O22  0.020
 629  plan-3  H23  0.020

