# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:38:42 2022
#   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  53  29  .  2022-03-10  2022-03-10
;
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  -0.372  -0.1164   0.2351  -6.7096
 629  C8    C  CR16   0  -0.308   0.5168   0.5630  -5.5182
 629  C12   C  CR6    0   0.338  -0.9478  -0.8784  -6.7701
 629  C11   C  CR16   0  -0.323  -1.1336  -1.6538  -5.6268
 629  C10   C  CR16   0  -0.290  -0.4922  -1.3107  -4.4485
 629  C9    C  CR6    0   0.111   0.3488  -0.2012  -4.3676
 629  C14   C  CH2    0  -0.529   1.0019   0.1787  -3.0717
 629  C15   C  CH1    0  -0.231   0.0635   1.0247  -2.1789
 629  C17   C  C      0   0.564   0.7949   1.2919  -0.8720
 629  N19   N  NH1    0  -0.610   0.5797   0.3841   0.0887
 629  C20   C  CH1    0  -0.232   1.4207   0.2462   1.2481
 629  C21   C  C      0   0.431   2.6691  -0.6433   0.9858
 629  O23   O  OC    -1  -0.580   2.9243  -0.9299  -0.1939
 629  O18   O  O      0  -0.509   1.5409   2.2550  -0.7472
 629  N16   N  NH2    0  -0.785  -0.3684   2.2801  -2.7553
 629  O22   O  O      0  -0.614   3.3413  -0.9290   1.9981
 629  C6    C  CH1    0  -0.155   0.5925  -0.1724   2.4641
 629  N5    N  NT     0  -0.175  -0.1646  -1.3867   2.1847
 629  C4    C  CH2    0  -0.354  -0.9360  -1.8465   3.3233
 629  C3    C  CH1    0   0.024  -1.9464  -0.7950   3.7595
 629  C2    C  CT     0   0.163  -1.2505   0.5435   4.0758
 629  C1    C  CH1    0   0.063  -0.4013   0.9377   2.8601
 629  O28   O  OH1    0  -0.566   0.6763  -2.4184   1.7624
 629  O32   O  OH1    0  -0.666  -2.9066  -0.5452   2.7592
 629  O29   O  OH1    0  -0.680  -2.2022   1.5644   4.2567
 629  C30   C  CH2    0  -0.181  -0.3957   0.4289   5.3432
 629  O31   O  OH1    0  -0.675  -1.2638   0.1715   6.4283
 629  O64   O  OH1    0  -0.670   0.2848   2.1325   3.1487
 629  O13   O  OH1    0  -0.635  -1.5884  -1.2528  -7.8982
 629  H7    H  HCR6   0   0.267   0.0415   0.8492  -7.5897
 629  H8    H  HCR6   0   0.254   1.1682   1.4289  -5.4956
 629  H11   H  HCR6   0   0.260  -1.7769  -2.5243  -5.6659
 629  H10   H  HCR6   0   0.246  -0.6471  -1.9283  -3.5709
 629  H141  H  HCH2   0   0.248   1.9108   0.7554  -3.2650
 629  H142  H  HCH2   0   0.256   1.3114  -0.7134  -2.5217
 629  H15   H  HCH1   0   0.252  -0.8315   0.4287  -1.9716
 629  H19   H  HNH1   0   0.385   0.0019  -0.4100  -0.1393
 629  H20   H  HCH1   0   0.257   1.8300   1.2325   1.4795
 629  H161  H  HNH2   0   0.340   0.4412   2.8480  -2.9753
 629  H162  H  HNH2   0   0.353  -0.8335   2.1009  -3.6369
 629  H6    H  HCH1   0   0.229   1.3059  -0.3283   3.2894
 629  H41   H  HCH2   0   0.215  -0.2960  -2.1211   4.1774
 629  H42   H  HCH2   0   0.260  -1.4659  -2.7577   3.0335
 629  H3    H  HCH1   0   0.230  -2.4300  -1.1725   4.6708
 629  H1    H  HCH1   0   0.240  -1.0898   1.0806   2.0192
 629  H28   H  HOH1   0   0.440   1.3702  -2.5321   2.4338
 629  H32   H  HOH1   0   0.449  -3.2781  -1.3887   2.4832
 629  H29   H  HOH1   0   0.440  -2.5980   1.4415   5.1276
 629  H301  H  HCH2   0   0.203   0.3526  -0.3625   5.2424
 629  H302  H  HCH2   0   0.230   0.1446   1.3694   5.4880
 629  H31   H  HOH1   0   0.464  -0.7984   0.3794   7.2430
 629  H64   H  HOH1   0   0.456   0.3049   2.6763   2.3573
 629  H13   H  HOH1   0   0.472  -1.3726  -0.6529  -8.6205

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  1.388  0.020  1.388
 629  C7   C12   aromatic  1.391  0.020  1.391
 629  C7   H7    single    0.930  0.020  1.080
 629  C8   C9    aromatic  1.392  0.020  1.392
 629  C8   H8    single    0.930  0.020  1.080
 629  C12  C11   aromatic  1.394  0.020  1.394
 629  C12  O13   single    1.350  0.020  1.350
 629  C11  C10   aromatic  1.385  0.020  1.385
 629  C11  H11   single    0.930  0.020  1.080
 629  C10  C9    aromatic  1.395  0.020  1.395
 629  C10  H10   single    0.930  0.020  1.080
 629  C9   C14   single    1.500  0.020  1.500
 629  C14  C15   single    1.547  0.020  1.547
 629  C14  H141  single    0.970  0.020  1.090
 629  C14  H142  single    0.970  0.020  1.090
 629  C15  C17   single    1.521  0.020  1.521
 629  C15  N16   single    1.447  0.020  1.447
 629  C15  H15   single    0.970  0.020  1.090
 629  C17  N19   single    1.339  0.020  1.339
 629  C17  O18   double    1.225  0.020  1.225
 629  N19  C20   single    1.439  0.020  1.439
 629  N19  H19   single    0.890  0.020  1.040
 629  C20  C21   single    1.555  0.020  1.555
 629  C20  C6    single    1.530  0.020  1.530
 629  C20  H20   single    0.970  0.020  1.090
 629  C21  O23   deloc     1.241  0.020  1.241
 629  C21  O22   deloc     1.248  0.020  1.248
 629  N16  H161  single    0.890  0.020  1.040
 629  N16  H162  single    0.890  0.020  1.040
 629  C6   N5    single    1.458  0.020  1.458
 629  C6   C1    single    1.542  0.020  1.542
 629  C6   H6    single    0.970  0.020  1.090
 629  N5   C4    single    1.450  0.020  1.450
 629  N5   O28   single    1.396  0.020  1.396
 629  C4   C3    single    1.522  0.020  1.522
 629  C4   H41   single    0.970  0.020  1.090
 629  C4   H42   single    0.970  0.020  1.090
 629  C3   C2    single    1.541  0.020  1.541
 629  C3   O32   single    1.409  0.020  1.409
 629  C3   H3    single    0.970  0.020  1.090
 629  C2   C1    single    1.534  0.020  1.534
 629  C2   O29   single    1.407  0.020  1.407
 629  C2   C30   single    1.533  0.020  1.533
 629  C1   O64   single    1.408  0.020  1.408
 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    1.413  0.020  1.413
 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   120.33  3.000
 629  H7    C7   C8    119.74  3.000
 629  C12   C7   C8    119.93  3.000
 629  H8    C8   C9    119.61  3.000
 629  H8    C8   C7    118.73  3.000
 629  C9    C8   C7    121.65  3.000
 629  O13   C12  C11   117.89  3.000
 629  O13   C12  C7    122.81  3.000
 629  C11   C12  C7    119.30  3.000
 629  H11   C11  C10   120.33  3.000
 629  H11   C11  C12   119.78  3.000
 629  C10   C11  C12   119.89  3.000
 629  H10   C10  C9    119.50  3.000
 629  H10   C10  C11   118.78  3.000
 629  C9    C10  C11   121.72  3.000
 629  C14   C9   C10   120.95  3.000
 629  C14   C9   C8    121.51  3.000
 629  C10   C9   C8    117.50  3.000
 629  H142  C14  H141  106.50  3.000
 629  H142  C14  C15   109.13  3.000
 629  H141  C14  C15   108.53  3.000
 629  H142  C14  C9    110.57  3.000
 629  H141  C14  C9    110.05  3.000
 629  C15   C14  C9    111.90  3.000
 629  H15   C15  N16   107.67  3.000
 629  H15   C15  C17   109.02  3.000
 629  N16   C15  C17   109.46  3.000
 629  H15   C15  C14   107.90  3.000
 629  N16   C15  C14   115.18  3.000
 629  C17   C15  C14   107.47  3.000
 629  O18   C17  N19   123.91  3.000
 629  O18   C17  C15   121.24  3.000
 629  N19   C17  C15   114.83  3.000
 629  H19   N19  C20   116.22  3.000
 629  H19   N19  C17   117.63  3.000
 629  C20   N19  C17   123.30  3.000
 629  H20   C20  C6    106.35  3.000
 629  H20   C20  C21   104.56  3.000
 629  C6    C20  C21   114.35  3.000
 629  H20   C20  N19   107.64  3.000
 629  C6    C20  N19   110.50  3.000
 629  C21   C20  N19   112.84  3.000
 629  O22   C21  O23   127.40  3.000
 629  O22   C21  C20   115.24  3.000
 629  O23   C21  C20   117.24  3.000
 629  H162  N16  H161  106.09  3.000
 629  H162  N16  C15   109.28  3.000
 629  H161  N16  C15   109.53  3.000
 629  H6    C6   C1    109.08  3.000
 629  H6    C6   N5    111.21  3.000
 629  C1    C6   N5    108.31  3.000
 629  H6    C6   C20   106.48  3.000
 629  C1    C6   C20   110.87  3.000
 629  N5    C6   C20   110.90  3.000
 629  O28   N5   C4    108.88  3.000
 629  O28   N5   C6    111.14  3.000
 629  C4    N5   C6    112.94  3.000
 629  H42   C4   H41   106.21  3.000
 629  H42   C4   C3    109.27  3.000
 629  H41   C4   C3    109.61  3.000
 629  H42   C4   N5    108.30  3.000
 629  H41   C4   N5    112.24  3.000
 629  C3    C4   N5    111.05  3.000
 629  H3    C3   O32   110.48  3.000
 629  H3    C3   C2    109.08  3.000
 629  O32   C3   C2    107.42  3.000
 629  H3    C3   C4    107.01  3.000
 629  O32   C3   C4    111.80  3.000
 629  C2    C3   C4    111.04  3.000
 629  C30   C2   O29   108.97  3.000
 629  C30   C2   C1    111.45  3.000
 629  O29   C2   C1    106.84  3.000
 629  C30   C2   C3    110.88  3.000
 629  O29   C2   C3    110.55  3.000
 629  C1    C2   C3    108.08  3.000
 629  H1    C1   O64   110.65  3.000
 629  H1    C1   C2    107.08  3.000
 629  O64   C1   C2    108.99  3.000
 629  H1    C1   C6    107.56  3.000
 629  O64   C1   C6    110.46  3.000
 629  C2    C1   C6    112.04  3.000
 629  H28   O28  N5    107.90  3.000
 629  H32   O32  C3    108.14  3.000
 629  H29   O29  C2    107.53  3.000
 629  H302  C30  H301  107.23  3.000
 629  H302  C30  O31   110.99  3.000
 629  H301  C30  O31   111.05  3.000
 629  H302  C30  C2    108.69  3.000
 629  H301  C30  C2    111.06  3.000
 629  O31   C30  C2    107.81  3.000
 629  H31   O31  C30   108.30  3.000
 629  H64   O64  C1    108.78  3.000
 629  H13   O13  C12   110.33  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_17  H19  N19  C17  C15    0.00   0.0  0
 629  Var_01    C3   C4   N5   C6    60.32  30.0  1
 629  Var_02    C15  C14  C9   C8    94.00  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

