# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jul 26 06:48:08 2021
#   Inital geometry file: a 154 line input string
#   Ligand name: N,N-bis{2-[(carboxymethyl){2-oxo-2-[(2-sulfanylethyl)amino]ethyl}amino]ethyl}glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN(CCN(CC(O)=O)CC(=O)NCCS)CCN(CC(O)=O)CC(=O)NCCS
#
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
 YMA  YMA  N,N-bis{2-[(carboxymethyl){2-oxo-2-[(2-sulfanylethyl)amino]ethyl}amino]ethyl}glycine  ligand  66  33  .  2022-04-11  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YMA
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
 YMA  O8    O  O     0  -0.456   6.3342  10.7533   4.2561
 YMA  C2    C  C     0   0.523   5.3521  11.1774   3.7006
 YMA  O7    O  OH1   0  -0.590   4.9588  12.4303   3.8078
 YMA  C1    C  CH2   0  -0.443   4.4129  10.3299   2.8531
 YMA  N1    N  NT    0  -0.502   3.5381  11.1947   2.0797
 YMA  C10   C  CH2   0  -0.295   4.1581  11.5392   0.7938
 YMA  C11   C  CH2   0  -0.311   3.7994  12.9134   0.2218
 YMA  N3    N  NT    0  -0.407   2.7045  12.9124  -0.7352
 YMA  C14   C  CH2   0  -0.429   2.0970  14.2117  -0.8676
 YMA  C15   C  C     0   0.558   0.7592  14.1766  -1.5852
 YMA  N5    N  NH1   0  -0.624   0.0691  15.3329  -1.6232
 YMA  C16   C  CH2   0  -0.325   0.3962  16.5830  -0.9766
 YMA  C18   C  CH2   0  -0.541   1.2751  17.5073  -1.8053
 YMA  S2    S  S2    0  -0.259   0.4542  17.8673  -3.3934
 YMA  O6    O  O     0  -0.477   0.3332  13.1646  -2.1222
 YMA  C12   C  CH2   0  -0.435   3.0274  12.2807  -1.9930
 YMA  C13   C  C     0   0.571   2.1143  11.1222  -2.3245
 YMA  O4    O  OH1   0  -0.603   1.9980  10.9584  -3.6404
 YMA  O3    O  O     0  -0.438   1.6238  10.3710  -1.5218
 YMA  C3    C  CH2   0  -0.261   2.1521  10.7339   2.0157
 YMA  C4    C  CH2   0  -0.310   1.1684  11.8833   1.8362
 YMA  N2    N  NT    0  -0.409  -0.1999  11.4106   1.9181
 YMA  C5    C  CH2   0  -0.403  -0.7780  11.2472   3.2288
 YMA  C6    C  C     0   0.537  -1.2749  12.5308   3.8787
 YMA  O2    O  O     0  -0.448  -2.4217  12.9067   3.8427
 YMA  O1    O  OH1   0  -0.585  -0.3112  13.2007   4.4991
 YMA  C7    C  CH2   0  -0.455  -1.0966  11.8426   0.8862
 YMA  C8    C  C     0   0.567  -1.4606  13.3262   0.9025
 YMA  O5    O  O     0  -0.490  -0.7522  14.1633   1.4414
 YMA  N4    N  NH1   0  -0.628  -2.5914  13.6350   0.2464
 YMA  C9    C  CH2   0  -0.293  -3.1364  14.9688   0.2017
 YMA  C17   C  CH2   0  -0.561  -3.8944  15.3511   1.4648
 YMA  S1    S  S2    0  -0.264  -5.3053  14.2574   1.8187
 YMA  HO7   H  HOH1  0   0.470   4.1473  12.4759   3.2376
 YMA  H11   H  HCH2  0   0.298   3.8267   9.7301   3.5536
 YMA  H12   H  HCH2  0   0.273   4.9952   9.6233   2.2527
 YMA  H101  H  HCH2  0   0.243   3.9724  10.7491   0.0552
 YMA  H102  H  HCH2  0   0.249   5.2376  11.5457   0.9549
 YMA  H111  H  HCH2  0   0.234   4.7090  13.3407  -0.2258
 YMA  H112  H  HCH2  0   0.246   3.5344  13.5732   1.0513
 YMA  H141  H  HCH2  0   0.255   2.7496  14.9344  -1.3874
 YMA  H142  H  HCH2  0   0.278   1.9393  14.6168   0.1358
 YMA  HN5   H  HNH1  0   0.395  -0.8185  15.2821  -2.1009
 YMA  H161  H  HCH2  0   0.273   0.8823  16.4006  -0.0184
 YMA  H162  H  HCH2  0   0.278  -0.5434  17.0857  -0.7464
 YMA  H181  H  HCH2  0   0.271   2.2514  17.0608  -1.9916
 YMA  H182  H  HCH2  0   0.282   1.4256  18.4358  -1.2558
 YMA  HS2   H  HSH1  0   0.228   1.2727  18.8480  -3.7871
 YMA  H121  H  HCH2  0   0.281   4.0414  11.8631  -1.9606
 YMA  H122  H  HCH2  0   0.264   3.0456  12.9938  -2.8232
 YMA  HO4   H  HOH1  0   0.474   1.4677  10.1696  -3.8254
 YMA  H31   H  HCH2  0   0.229   1.9339  10.2213   2.9551
 YMA  H32   H  HCH2  0   0.220   2.0093  10.0068   1.2083
 YMA  H41   H  HCH2  0   0.288   1.3177  12.3008   0.8454
 YMA  H42   H  HCH2  0   0.208   1.3955  12.6725   2.5602
 YMA  H51   H  HCH2  0   0.265  -0.0463  10.7701   3.8839
 YMA  H52   H  HCH2  0   0.265  -1.6350  10.5730   3.1591
 YMA  HO1   H  HOH1  0   0.474  -0.6612  14.0342   4.8490
 YMA  H71   H  HCH2  0   0.256  -2.0076  11.2366   0.9265
 YMA  H72   H  HCH2  0   0.295  -0.6390  11.6368  -0.0863
 YMA  HN4   H  HNH1  0   0.396  -3.1539  12.8883  -0.1269
 YMA  H91   H  HCH2  0   0.258  -3.7972  15.0344  -0.6620
 YMA  H92   H  HCH2  0   0.256  -2.3298  15.6876   0.0502
 YMA  H171  H  HCH2  0   0.282  -4.3115  16.3520   1.3499
 YMA  H172  H  HCH2  0   0.280  -3.2333  15.3658   2.3300
 YMA  HS1   H  HSH1  0   0.221  -4.6106  13.2370   2.3331

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
 YMA  O8   C2    double  1.205  0.020  1.205
 YMA  C2   O7    single  1.318  0.020  1.318
 YMA  C2   C1    single  1.523  0.020  1.523
 YMA  O7   HO7   single  0.850  0.020  0.980
 YMA  C1   N1    single  1.453  0.020  1.453
 YMA  C1   H11   single  0.970  0.020  1.090
 YMA  C1   H12   single  0.970  0.020  1.090
 YMA  N1   C10   single  1.469  0.020  1.469
 YMA  N1   C3    single  1.462  0.020  1.462
 YMA  C10  C11   single  1.531  0.020  1.531
 YMA  C10  H101  single  0.970  0.020  1.090
 YMA  C10  H102  single  0.970  0.020  1.090
 YMA  C11  N3    single  1.454  0.020  1.454
 YMA  C11  H111  single  0.970  0.020  1.090
 YMA  C11  H112  single  0.970  0.020  1.090
 YMA  N3   C14   single  1.440  0.020  1.440
 YMA  N3   C12   single  1.444  0.020  1.444
 YMA  C14  C15   single  1.518  0.020  1.518
 YMA  C14  H141  single  0.970  0.020  1.090
 YMA  C14  H142  single  0.970  0.020  1.090
 YMA  C15  N5    single  1.347  0.020  1.347
 YMA  C15  O6    double  1.222  0.020  1.222
 YMA  N5   C16   single  1.445  0.020  1.445
 YMA  N5   HN5   single  0.860  0.020  1.020
 YMA  C16  C18   single  1.521  0.020  1.521
 YMA  C16  H161  single  0.970  0.020  1.090
 YMA  C16  H162  single  0.970  0.020  1.090
 YMA  C18  S2    single  1.824  0.020  1.824
 YMA  C18  H181  single  0.970  0.020  1.090
 YMA  C18  H182  single  0.970  0.020  1.090
 YMA  S2   HS2   single  1.200  0.020  1.300
 YMA  C12  C13   single  1.512  0.020  1.512
 YMA  C12  H121  single  0.970  0.020  1.090
 YMA  C12  H122  single  0.970  0.020  1.090
 YMA  C13  O4    single  1.331  0.020  1.331
 YMA  C13  O3    double  1.204  0.020  1.204
 YMA  O4   HO4   single  0.850  0.020  0.980
 YMA  C3   C4    single  1.523  0.020  1.523
 YMA  C3   H31   single  0.970  0.020  1.090
 YMA  C3   H32   single  0.970  0.020  1.090
 YMA  C4   N2    single  1.450  0.020  1.450
 YMA  C4   H41   single  0.970  0.020  1.090
 YMA  C4   H42   single  0.970  0.020  1.090
 YMA  N2   C5    single  1.442  0.020  1.442
 YMA  N2   C7    single  1.434  0.020  1.434
 YMA  C5   C6    single  1.522  0.020  1.522
 YMA  C5   H51   single  0.970  0.020  1.090
 YMA  C5   H52   single  0.970  0.020  1.090
 YMA  C6   O2    double  1.207  0.020  1.207
 YMA  C6   O1    single  1.328  0.020  1.328
 YMA  O1   HO1   single  0.850  0.020  0.980
 YMA  C7   C8    single  1.528  0.020  1.528
 YMA  C7   H71   single  0.970  0.020  1.090
 YMA  C7   H72   single  0.970  0.020  1.090
 YMA  C8   O5    double  1.222  0.020  1.222
 YMA  C8   N4    single  1.343  0.020  1.343
 YMA  N4   C9    single  1.442  0.020  1.442
 YMA  N4   HN4   single  0.860  0.020  1.020
 YMA  C9   C17   single  1.522  0.020  1.522
 YMA  C9   H91   single  0.970  0.020  1.090
 YMA  C9   H92   single  0.970  0.020  1.090
 YMA  C17  S1    single  1.820  0.020  1.820
 YMA  C17  H171  single  0.970  0.020  1.090
 YMA  C17  H172  single  0.970  0.020  1.090
 YMA  S1   HS1   single  1.200  0.020  1.300

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
 YMA  C1    C2   O7    112.98  3.000
 YMA  C1    C2   O8    124.28  3.000
 YMA  O7    C2   O8    122.70  3.000
 YMA  HO7   O7   C2    103.94  3.000
 YMA  H12   C1   H11   106.42  3.000
 YMA  H12   C1   N1    114.36  3.000
 YMA  H11   C1   N1    110.18  3.000
 YMA  H12   C1   C2    109.65  3.000
 YMA  H11   C1   C2    106.23  3.000
 YMA  N1    C1   C2    109.65  3.000
 YMA  C3    N1   C10   115.84  3.000
 YMA  C3    N1   C1    113.98  3.000
 YMA  C10   N1   C1    110.58  3.000
 YMA  H102  C10  H101  105.73  3.000
 YMA  H102  C10  C11   106.35  3.000
 YMA  H101  C10  C11   110.80  3.000
 YMA  H102  C10  N1    106.84  3.000
 YMA  H101  C10  N1    110.43  3.000
 YMA  C11   C10  N1    116.02  3.000
 YMA  H112  C11  H111  105.95  3.000
 YMA  H112  C11  N3    108.51  3.000
 YMA  H111  C11  N3    110.80  3.000
 YMA  H112  C11  C10   108.38  3.000
 YMA  H111  C11  C10   107.87  3.000
 YMA  N3    C11  C10   114.94  3.000
 YMA  C12   N3   C14   114.13  3.000
 YMA  C12   N3   C11   113.90  3.000
 YMA  C14   N3   C11   112.17  3.000
 YMA  H142  C14  H141  105.95  3.000
 YMA  H142  C14  C15   108.37  3.000
 YMA  H141  C14  C15   108.27  3.000
 YMA  H142  C14  N3    108.10  3.000
 YMA  H141  C14  N3    112.62  3.000
 YMA  C15   C14  N3    113.21  3.000
 YMA  O6    C15  N5    121.31  3.000
 YMA  O6    C15  C14   122.27  3.000
 YMA  N5    C15  C14   116.41  3.000
 YMA  HN5   N5   C16   117.03  3.000
 YMA  HN5   N5   C15   114.88  3.000
 YMA  C16   N5   C15   127.88  3.000
 YMA  H162  C16  H161  106.01  3.000
 YMA  H162  C16  C18   109.44  3.000
 YMA  H161  C16  C18   108.84  3.000
 YMA  H162  C16  N5    107.36  3.000
 YMA  H161  C16  N5    110.47  3.000
 YMA  C18   C16  N5    114.38  3.000
 YMA  H182  C18  H181  108.17  3.000
 YMA  H182  C18  S2    109.46  3.000
 YMA  H181  C18  S2    109.59  3.000
 YMA  H182  C18  C16   108.84  3.000
 YMA  H181  C18  C16   111.21  3.000
 YMA  S2    C18  C16   109.53  3.000
 YMA  HS2   S2   C18    97.22  3.000
 YMA  H122  C12  H121  104.77  3.000
 YMA  H122  C12  C13   110.05  3.000
 YMA  H121  C12  C13   105.84  3.000
 YMA  H122  C12  N3    112.30  3.000
 YMA  H121  C12  N3    110.34  3.000
 YMA  C13   C12  N3    113.02  3.000
 YMA  O3    C13  O4    123.15  3.000
 YMA  O3    C13  C12   125.31  3.000
 YMA  O4    C13  C12   111.33  3.000
 YMA  HO4   O4   C13   109.69  3.000
 YMA  H32   C3   H31   107.23  3.000
 YMA  H32   C3   C4    109.25  3.000
 YMA  H31   C3   C4    109.05  3.000
 YMA  H32   C3   N1    111.40  3.000
 YMA  H31   C3   N1    107.44  3.000
 YMA  C4    C3   N1    112.30  3.000
 YMA  H42   C4   H41   107.33  3.000
 YMA  H42   C4   N2    113.17  3.000
 YMA  H41   C4   N2    107.86  3.000
 YMA  H42   C4   C3    109.39  3.000
 YMA  H41   C4   C3    107.99  3.000
 YMA  N2    C4   C3    110.90  3.000
 YMA  C7    N2   C5    115.95  3.000
 YMA  C7    N2   C4    116.83  3.000
 YMA  C5    N2   C4    117.82  3.000
 YMA  H52   C5   H51   107.11  3.000
 YMA  H52   C5   C6    106.95  3.000
 YMA  H51   C5   C6    109.33  3.000
 YMA  H52   C5   N2    109.06  3.000
 YMA  H51   C5   N2    109.04  3.000
 YMA  C6    C5   N2    115.05  3.000
 YMA  O1    C6   O2    123.11  3.000
 YMA  O1    C6   C5    112.84  3.000
 YMA  O2    C6   C5    124.05  3.000
 YMA  HO1   O1   C6    109.91  3.000
 YMA  H72   C7   H71   106.05  3.000
 YMA  H72   C7   C8    106.96  3.000
 YMA  H71   C7   C8    109.80  3.000
 YMA  H72   C7   N2    108.75  3.000
 YMA  H71   C7   N2    109.10  3.000
 YMA  C8    C7   N2    115.72  3.000
 YMA  N4    C8   O5    123.09  3.000
 YMA  N4    C8   C7    114.75  3.000
 YMA  O5    C8   C7    122.13  3.000
 YMA  HN4   N4   C9    117.62  3.000
 YMA  HN4   N4   C8    118.75  3.000
 YMA  C9    N4   C8    123.10  3.000
 YMA  H92   C9   H91   107.38  3.000
 YMA  H92   C9   C17   108.54  3.000
 YMA  H91   C9   C17   109.93  3.000
 YMA  H92   C9   N4    109.53  3.000
 YMA  H91   C9   N4    108.04  3.000
 YMA  C17   C9   N4    113.26  3.000
 YMA  H172  C17  H171  107.67  3.000
 YMA  H172  C17  S1    108.92  3.000
 YMA  H171  C17  S1    106.00  3.000
 YMA  H172  C17  C9    111.13  3.000
 YMA  H171  C17  C9    109.48  3.000
 YMA  S1    C17  C9    113.36  3.000
 YMA  HS1   S1   C17    97.51  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
 YMA  CONST_01  C16  N5   C15  C14     0.00   0.0  0
 YMA  CONST_02  O6   C15  N5   C16   180.00   0.0  0
 YMA  CONST_03  C9   N4   C8   C7    180.00   0.0  0
 YMA  CONST_04  C9   N4   C8   O5      0.00   0.0  0
 YMA  CONST_05  HN5  N5   C15  C14   180.00   0.0  0
 YMA  CONST_06  HN4  N4   C8   C7      0.00   0.0  0
 YMA  CONST_07  HO7  O7   C2   O8    180.00   0.0  0
 YMA  CONST_08  HO4  O4   C13  C12   180.00   0.0  0
 YMA  CONST_09  HO1  O1   C6   C5    180.00   0.0  0
 YMA  Var_01    N1   C1   C2   O8   -166.23  30.0  3
 YMA  Var_02    C10  N1   C1   C2     88.59  30.0  3
 YMA  Var_03    C11  C10  N1   C1   -148.84  30.0  3
 YMA  Var_04    C4   C3   N1   C1    151.98  30.0  3
 YMA  Var_05    N3   C11  C10  N1    -95.16  30.0  3
 YMA  Var_06    N2   C4   C3   N1   -173.96  30.0  3
 YMA  Var_07    C14  N3   C11  C10   158.94  30.0  3
 YMA  Var_08    C15  C14  N3   C11  -165.94  30.0  3
 YMA  Var_09    C13  C12  N3   C11   121.62  30.0  3
 YMA  Var_10    N5   C15  C14  N3    173.36  30.0  3
 YMA  Var_11    O4   C13  C12  N3    151.45  30.0  3
 YMA  Var_12    C18  C16  N5   C15    89.01  30.0  3
 YMA  Var_13    S2   C18  C16  N5     57.69  30.0  3
 YMA  Var_14    C5   N2   C4   C3     83.04  30.0  3
 YMA  Var_15    C6   C5   N2   C4     79.91  30.0  3
 YMA  Var_16    C8   C7   N2   C4    -69.09  30.0  3
 YMA  Var_17    O2   C6   C5   N2     96.23  30.0  3
 YMA  Var_18    O5   C8   C7   N2     22.59  30.0  3
 YMA  Var_19    C17  C9   N4   C8    -79.21  30.0  3
 YMA  Var_20    S1   C17  C9   N4    -59.69  30.0  3

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
 YMA  plan-1  C14  0.020
 YMA  plan-1  C15  0.020
 YMA  plan-1  N5   0.020
 YMA  plan-1  C16  0.020
 YMA  plan-1  O6   0.020
 YMA  plan-1  HN5  0.020
 YMA  plan-2  C7   0.020
 YMA  plan-2  C8   0.020
 YMA  plan-2  O5   0.020
 YMA  plan-2  N4   0.020
 YMA  plan-2  C9   0.020
 YMA  plan-2  HN4  0.020
 YMA  plan-3  O8   0.020
 YMA  plan-3  C2   0.020
 YMA  plan-3  O7   0.020
 YMA  plan-3  C1   0.020
 YMA  plan-3  HO7  0.020
 YMA  plan-4  C12  0.020
 YMA  plan-4  C13  0.020
 YMA  plan-4  O4   0.020
 YMA  plan-4  O3   0.020
 YMA  plan-4  HO4  0.020
 YMA  plan-5  C5   0.020
 YMA  plan-5  C6   0.020
 YMA  plan-5  O2   0.020
 YMA  plan-5  O1   0.020
 YMA  plan-5  HO1  0.020

