# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 31 12:12:28 2022
#   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  63  33  .  2022-04-11  2022-04-11
;
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  -0.592   1.8274  15.1183   2.2461
 YMA  C2    C  C      0   0.430   2.7512  14.6830   2.9751
 YMA  O7    O  OC    -1  -0.592   3.2463  15.2564   3.9598
 YMA  C1    C  CH2    0  -0.408   3.3768  13.3194   2.6212
 YMA  N1    N  NT     0  -0.409   2.6283  12.5109   1.6936
 YMA  C10   C  CH2    0  -0.285   3.4512  11.5239   1.0167
 YMA  C11   C  CH2    0  -0.285   4.1920  12.0604  -0.2033
 YMA  N3    N  NT     0  -0.402   3.3382  12.2984  -1.3553
 YMA  C14   C  CH2    0  -0.447   2.5700  13.5147  -1.2465
 YMA  C15   C  C      0   0.522   1.2298  13.4336  -1.9618
 YMA  N5    N  NH1    0  -0.625   0.4124  14.5022  -1.8179
 YMA  C16   C  CH2    0  -0.339   0.6553  15.7176  -1.0739
 YMA  C18   C  CH2    0  -0.544   1.4308  16.7797  -1.8404
 YMA  S2    S  S2     0  -0.262   0.5809  17.1439  -3.4135
 YMA  O6    O  O      0  -0.488   0.8802  12.4632  -2.6171
 YMA  C12   C  CH2    0  -0.418   4.0834  12.2442  -2.5956
 YMA  C13   C  C      0   0.384   4.5827  10.8472  -3.0274
 YMA  O4    O  OC    -1  -0.619   5.4397  10.8623  -3.9350
 YMA  O3    O  O      0  -0.599   4.0838   9.8460  -2.4822
 YMA  C3    C  CH2    0  -0.283   1.3874  11.9832   2.2236
 YMA  C4    C  CH2    0  -0.275   0.3421  11.9123   1.1173
 YMA  N2    N  NT     0  -0.421  -0.9708  11.4857   1.5560
 YMA  C5    C  CH2    0  -0.428  -1.0863  10.0923   1.9138
 YMA  C6    C  C      0   0.404  -2.2442   9.7858   2.8904
 YMA  O2    O  O      0  -0.588  -2.8113  10.7462   3.4530
 YMA  O1    O  OC    -1  -0.608  -2.4861   8.5754   3.0556
 YMA  C7    C  CH2    0  -0.407  -1.9835  11.9307   0.6258
 YMA  C8    C  C      0   0.500  -2.4547  13.3480   0.9287
 YMA  O5    O  O      0  -0.507  -2.6936  14.1674   0.0476
 YMA  N4    N  NH1    0  -0.610  -2.6284  13.5746   2.2359
 YMA  C9    C  CH2    0  -0.281  -3.1419  14.8066   2.7712
 YMA  C17   C  CH2    0  -0.554  -2.0828  15.8775   2.9989
 YMA  S1    S  S2     0  -0.336  -0.8090  15.3689   4.2025
 YMA  H11   H  HCH2   0   0.194   3.6037  12.7845   3.5592
 YMA  H12   H  HCH2   0   0.236   4.3533  13.5371   2.1744
 YMA  H101  H  HCH2   0   0.226   2.8241  10.6971   0.6766
 YMA  H102  H  HCH2   0   0.197   4.1881  11.0798   1.7062
 YMA  H111  H  HCH2   0   0.229   4.9188  11.2973  -0.4822
 YMA  H112  H  HCH2   0   0.187   4.7821  12.9525   0.0684
 YMA  H141  H  HCH2   0   0.230   3.1207  14.3940  -1.6232
 YMA  H142  H  HCH2   0   0.303   2.3767  13.7106  -0.1887
 YMA  HN5   H  HNH1   0   0.387  -0.4792  14.4246  -2.2843
 YMA  H161  H  HCH2   0   0.283   1.1825  15.5015  -0.1437
 YMA  H162  H  HCH2   0   0.269  -0.3180  16.1175  -0.7879
 YMA  H181  H  HCH2   0   0.271   2.4497  16.4523  -2.0443
 YMA  H182  H  HCH2   0   0.276   1.4797  17.6853  -1.2366
 YMA  HS2   H  HSH1   0   0.223   1.2823  18.2364  -3.7330
 YMA  H121  H  HCH2   0   0.181   4.9444  12.9354  -2.5847
 YMA  H122  H  HCH2   0   0.231   3.4380  12.6043  -3.4027
 YMA  H31   H  HCH2   0   0.220   1.0068  12.6530   2.9963
 YMA  H32   H  HCH2   0   0.197   1.5332  11.0055   2.7086
 YMA  H41   H  HCH2   0   0.190   0.7093  11.2977   0.2778
 YMA  H42   H  HCH2   0   0.226   0.2477  12.9277   0.7255
 YMA  H51   H  HCH2   0   0.238  -0.1670   9.7818   2.4189
 YMA  H52   H  HCH2   0   0.198  -1.1700   9.4329   1.0348
 YMA  H71   H  HCH2   0   0.266  -2.8633  11.2842   0.6925
 YMA  H72   H  HCH2   0   0.228  -1.6508  11.8905  -0.4207
 YMA  HN4   H  HNH1   0   0.403  -2.4403  12.7888   2.8508
 YMA  H91   H  HCH2   0   0.249  -3.6422  14.5806   3.7133
 YMA  H92   H  HCH2   0   0.243  -3.9020  15.2130   2.0998
 YMA  H171  H  HCH2   0   0.266  -2.5665  16.7799   3.3738
 YMA  H172  H  HCH2   0   0.274  -1.5885  16.1384   2.0637
 YMA  HS1   H  HSH1   0   0.248   0.2443  15.3019   3.3561

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    deloc   1.255  0.020  1.255
 YMA  C2   O7    deloc   1.242  0.020  1.242
 YMA  C2   C1    single  1.541  0.020  1.541
 YMA  C1   N1    single  1.440  0.020  1.440
 YMA  C1   H11   single  0.970  0.020  1.090
 YMA  C1   H12   single  0.970  0.020  1.090
 YMA  N1   C10   single  1.452  0.020  1.452
 YMA  N1   C3    single  1.449  0.020  1.449
 YMA  C10  C11   single  1.525  0.020  1.525
 YMA  C10  H101  single  0.970  0.020  1.090
 YMA  C10  H102  single  0.970  0.020  1.090
 YMA  C11  N3    single  1.453  0.020  1.453
 YMA  C11  H111  single  0.970  0.020  1.090
 YMA  C11  H112  single  0.970  0.020  1.090
 YMA  N3   C14   single  1.443  0.020  1.443
 YMA  N3   C12   single  1.448  0.020  1.448
 YMA  C14  C15   single  1.521  0.020  1.521
 YMA  C14  H141  single  0.970  0.020  1.090
 YMA  C14  H142  single  0.970  0.020  1.090
 YMA  C15  N5    single  1.353  0.020  1.353
 YMA  C15  O6    double  1.222  0.020  1.222
 YMA  N5   C16   single  1.446  0.020  1.446
 YMA  N5   HN5   single  0.860  0.020  1.020
 YMA  C16  C18   single  1.522  0.020  1.522
 YMA  C16  H161  single  0.970  0.020  1.090
 YMA  C16  H162  single  0.970  0.020  1.090
 YMA  C18  S2    single  1.825  0.020  1.825
 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  1.545  0.020  1.545
 YMA  C12  H121  single  0.970  0.020  1.090
 YMA  C12  H122  single  0.970  0.020  1.090
 YMA  C13  O4    deloc   1.248  0.020  1.248
 YMA  C13  O3    deloc   1.244  0.020  1.244
 YMA  C3   C4    single  1.524  0.020  1.524
 YMA  C3   H31   single  0.970  0.020  1.090
 YMA  C3   H32   single  0.970  0.020  1.090
 YMA  C4   N2    single  1.448  0.020  1.448
 YMA  C4   H41   single  0.970  0.020  1.090
 YMA  C4   H42   single  0.970  0.020  1.090
 YMA  N2   C5    single  1.443  0.020  1.443
 YMA  N2   C7    single  1.445  0.020  1.445
 YMA  C5   C6    single  1.545  0.020  1.545
 YMA  C5   H51   single  0.970  0.020  1.090
 YMA  C5   H52   single  0.970  0.020  1.090
 YMA  C6   O2    deloc   1.249  0.020  1.249
 YMA  C6   O1    deloc   1.245  0.020  1.245
 YMA  C7   C8    single  1.524  0.020  1.524
 YMA  C7   H71   single  0.970  0.020  1.090
 YMA  C7   H72   single  0.970  0.020  1.090
 YMA  C8   O5    double  1.227  0.020  1.227
 YMA  C8   N4    single  1.338  0.020  1.338
 YMA  N4   C9    single  1.438  0.020  1.438
 YMA  N4   HN4   single  0.860  0.020  1.020
 YMA  C9   C17   single  1.523  0.020  1.523
 YMA  C9   H91   single  0.970  0.020  1.090
 YMA  C9   H92   single  0.970  0.020  1.090
 YMA  C17  S1    single  1.825  0.020  1.825
 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    115.37  3.000
 YMA  C1    C2   O8    118.19  3.000
 YMA  O7    C2   O8    126.42  3.000
 YMA  H12   C1   H11   105.06  3.000
 YMA  H12   C1   N1    108.18  3.000
 YMA  H11   C1   N1    112.47  3.000
 YMA  H12   C1   C2    106.24  3.000
 YMA  H11   C1   C2    108.49  3.000
 YMA  N1    C1   C2    115.69  3.000
 YMA  C3    N1   C10   114.09  3.000
 YMA  C3    N1   C1    114.45  3.000
 YMA  C10   N1   C1    112.78  3.000
 YMA  H102  C10  H101  105.88  3.000
 YMA  H102  C10  C11   108.50  3.000
 YMA  H101  C10  C11   107.23  3.000
 YMA  H102  C10  N1    111.16  3.000
 YMA  H101  C10  N1    109.53  3.000
 YMA  C11   C10  N1    114.14  3.000
 YMA  H112  C11  H111  105.80  3.000
 YMA  H112  C11  N3    112.15  3.000
 YMA  H111  C11  N3    107.66  3.000
 YMA  H112  C11  C10   110.32  3.000
 YMA  H111  C11  C10   106.40  3.000
 YMA  N3    C11  C10   113.98  3.000
 YMA  C12   N3   C14   111.73  3.000
 YMA  C12   N3   C11   111.75  3.000
 YMA  C14   N3   C11   113.01  3.000
 YMA  H142  C14  H141  106.01  3.000
 YMA  H142  C14  C15   107.98  3.000
 YMA  H141  C14  C15   108.76  3.000
 YMA  H142  C14  N3    108.56  3.000
 YMA  H141  C14  N3    112.35  3.000
 YMA  C15   C14  N3    112.87  3.000
 YMA  O6    C15  N5    120.75  3.000
 YMA  O6    C15  C14   123.13  3.000
 YMA  N5    C15  C14   116.11  3.000
 YMA  HN5   N5   C16   116.80  3.000
 YMA  HN5   N5   C15   115.08  3.000
 YMA  C16   N5   C15   128.11  3.000
 YMA  H162  C16  H161  106.28  3.000
 YMA  H162  C16  C18   109.33  3.000
 YMA  H161  C16  C18   108.75  3.000
 YMA  H162  C16  N5    107.06  3.000
 YMA  H161  C16  N5    110.70  3.000
 YMA  C18   C16  N5    114.40  3.000
 YMA  H182  C18  H181  108.16  3.000
 YMA  H182  C18  S2    109.44  3.000
 YMA  H181  C18  S2    109.53  3.000
 YMA  H182  C18  C16   108.89  3.000
 YMA  H181  C18  C16   111.16  3.000
 YMA  S2    C18  C16   109.64  3.000
 YMA  HS2   S2   C18    97.17  3.000
 YMA  H122  C12  H121  105.14  3.000
 YMA  H122  C12  C13   106.38  3.000
 YMA  H121  C12  C13   108.46  3.000
 YMA  H122  C12  N3    108.42  3.000
 YMA  H121  C12  N3    111.68  3.000
 YMA  C13   C12  N3    116.07  3.000
 YMA  O3    C13  O4    127.12  3.000
 YMA  O3    C13  C12   118.39  3.000
 YMA  O4    C13  C12   114.46  3.000
 YMA  H32   C3   H31   106.22  3.000
 YMA  H32   C3   C4    111.67  3.000
 YMA  H31   C3   C4    107.67  3.000
 YMA  H32   C3   N1    111.78  3.000
 YMA  H31   C3   N1    109.53  3.000
 YMA  C4    C3   N1    109.81  3.000
 YMA  H42   C4   H41   105.88  3.000
 YMA  H42   C4   N2    107.70  3.000
 YMA  H41   C4   N2    111.60  3.000
 YMA  H42   C4   C3    106.05  3.000
 YMA  H41   C4   C3    110.49  3.000
 YMA  N2    C4   C3    114.55  3.000
 YMA  C7    N2   C5    113.62  3.000
 YMA  C7    N2   C4    110.45  3.000
 YMA  C5    N2   C4    115.60  3.000
 YMA  H52   C5   H51   105.20  3.000
 YMA  H52   C5   C6    109.17  3.000
 YMA  H51   C5   C6    106.35  3.000
 YMA  H52   C5   N2    112.71  3.000
 YMA  H51   C5   N2    108.74  3.000
 YMA  C6    C5   N2    114.09  3.000
 YMA  O1    C6   O2    126.81  3.000
 YMA  O1    C6   C5    114.97  3.000
 YMA  O2    C6   C5    118.18  3.000
 YMA  H72   C7   H71   106.26  3.000
 YMA  H72   C7   C8    108.48  3.000
 YMA  H71   C7   C8    106.79  3.000
 YMA  H72   C7   N2    112.92  3.000
 YMA  H71   C7   N2    110.02  3.000
 YMA  C8    C7   N2    112.03  3.000
 YMA  N4    C8   O5    124.29  3.000
 YMA  N4    C8   C7    113.07  3.000
 YMA  O5    C8   C7    122.59  3.000
 YMA  HN4   N4   C9    120.25  3.000
 YMA  HN4   N4   C8    115.88  3.000
 YMA  C9    N4   C8    123.72  3.000
 YMA  H92   C9   H91   106.79  3.000
 YMA  H92   C9   C17   108.30  3.000
 YMA  H91   C9   C17   109.61  3.000
 YMA  H92   C9   N4    109.78  3.000
 YMA  H91   C9   N4    107.93  3.000
 YMA  C17   C9   N4    114.18  3.000
 YMA  H172  C17  H171  107.35  3.000
 YMA  H172  C17  S1    108.43  3.000
 YMA  H171  C17  S1    108.27  3.000
 YMA  H172  C17  C9    110.83  3.000
 YMA  H171  C17  C9    108.96  3.000
 YMA  S1    C17  C9    112.83  3.000
 YMA  HS1   S1   C17    98.32  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  Var_01    N1   C1   C2   O8    -15.11  30.0  3
 YMA  Var_02    C10  N1   C1   C2    157.99  30.0  3
 YMA  Var_03    C11  C10  N1   C1    -83.65  30.0  3
 YMA  Var_04    C4   C3   N1   C1    146.00  30.0  3
 YMA  Var_05    N3   C11  C10  N1    -73.21  30.0  3
 YMA  Var_06    N2   C4   C3   N1   -175.87  30.0  3
 YMA  Var_07    C14  N3   C11  C10    77.55  30.0  3
 YMA  Var_08    C15  C14  N3   C11  -149.33  30.0  3
 YMA  Var_09    C13  C12  N3   C11    70.45  30.0  3
 YMA  Var_10    N5   C15  C14  N3    175.23  30.0  3
 YMA  Var_11    O4   C13  C12  N3   -166.08  30.0  3
 YMA  Var_12    C18  C16  N5   C15    84.78  30.0  3
 YMA  Var_13    S2   C18  C16  N5     54.92  30.0  3
 YMA  Var_14    C5   N2   C4   C3    -71.55  30.0  3
 YMA  Var_15    C6   C5   N2   C4    156.08  30.0  3
 YMA  Var_16    C8   C7   N2   C4    -85.74  30.0  3
 YMA  Var_17    O2   C6   C5   N2    -12.04  30.0  3
 YMA  Var_18    O5   C8   C7   N2    140.47  30.0  3
 YMA  Var_19    C17  C9   N4   C8    -86.03  30.0  3
 YMA  Var_20    S1   C17  C9   N4    -61.48  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-4  C12  0.020
 YMA  plan-4  C13  0.020
 YMA  plan-4  O4   0.020
 YMA  plan-4  O3   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

