# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:23:41 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-O-methyl-D-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H](C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(O)=O)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
 M2W  M2W  N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-O-methyl-D-threonine  ligand  50  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M2W
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
 M2W  C8    C  C     0   0.563  11.9654  38.7617  5.0695
 M2W  O27   O  O     0  -0.499  11.6509  39.6266  5.8758
 M2W  O22   O  O     0  -0.455  17.6964  35.4368  6.3445
 M2W  C9    C  CH2   0  -0.563  13.3922  38.2873  4.9190
 M2W  C20   C  C     0   0.537  17.4653  36.3917  7.0469
 M2W  C16   C  CH1   0  -0.193  16.0554  36.8428  7.3766
 M2W  C13   C  CH2   0  -0.425  15.4321  37.3966  6.0878
 M2W  C10   C  CH2   0  -0.440  13.9653  37.7780  6.2403
 M2W  N19   N  NH2   0  -0.803  16.0330  37.8401  8.4275
 M2W  N7    N  NH1   0  -0.643  11.0708  38.1710  4.2569
 M2W  C3    C  CH1   0  -0.217   9.6694  38.4914  4.2724
 M2W  C1    C  C     0   0.572   8.8983  37.3185  3.6685
 M2W  O6    O  O     0  -0.471   9.4606  36.3900  3.1140
 M2W  C35   C  CH2   0  -0.547   9.3679  39.7921  3.5248
 M2W  S37   S  S2    0  -0.245   9.9012  39.6497  1.7858
 M2W  N2    N  NH1   0  -0.633   7.5662  37.4216  3.7851
 M2W  C4    C  CH1   0  -0.233   6.6469  36.4675  3.2319
 M2W  C23   C  C     0   0.560   6.1661  35.4282  4.2367
 M2W  O25   O  OH1   0  -0.575   6.6656  35.5918  5.4469
 M2W  C5    C  CH1   0   0.046   5.4334  37.1694  2.6163
 M2W  O41   O  O2    0  -0.495   4.7641  37.7769  3.6982
 M2W  C46   C  CH3   0  -0.687   5.8397  38.1487  1.5264
 M2W  C42   C  CH3   0  -0.401   3.4825  38.2745  3.3945
 M2W  O26   O  O     0  -0.444   5.4127  34.5392  3.9298
 M2W  H91C  H  HCH2  0   0.253  13.4742  37.5150  4.1517
 M2W  H92C  H  HCH2  0   0.267  13.9856  39.1397  4.5755
 M2W  H16   H  HCH1  0   0.249  15.5126  35.9207  7.6354
 M2W  H131  H  HCH2  0   0.235  16.0051  38.2691  5.7579
 M2W  H132  H  HCH2  0   0.240  15.5232  36.6375  5.3078
 M2W  H101  H  HCH2  0   0.235  13.8446  38.5577  6.9943
 M2W  H102  H  HCH2  0   0.238  13.3919  36.9104  6.5807
 M2W  H191  H  HNH2  0   0.358  15.0713  38.0647  8.6468
 M2W  H192  H  HNH2  0   0.353  16.4156  37.4572  9.2830
 M2W  H21   H  HOH1  0   0.480  19.2833  36.8007  7.3243
 M2W  H7    H  HNH1  0   0.405  11.3674  37.4249  3.6460
 M2W  H3    H  HCH1  0   0.310   9.3371  38.6313  5.3067
 M2W  H351  H  HCH2  0   0.284   8.3027  40.0149  3.5564
 M2W  H352  H  HCH2  0   0.295   9.8892  40.6145  4.0107
 M2W  H37   H  HSH1  0   0.230   8.9826  40.4684  1.2653
 M2W  H2    H  HNH1  0   0.409   7.1801  38.1692  4.3417
 M2W  H4    H  HCH1  0   0.319   7.1524  35.9165  2.4353
 M2W  H5    H  HCH1  0   0.236   4.7978  36.3940  2.1673
 M2W  H461  H  HCH3  0   0.249   4.9650  38.5623  1.0255
 M2W  H462  H  HCH3  0   0.230   6.4287  38.9774  1.9205
 M2W  H463  H  HCH3  0   0.243   6.4381  37.6401  0.7704
 M2W  H421  H  HCH3  0   0.241   3.0157  38.5731  4.3318
 M2W  H422  H  HCH3  0   0.215   3.5121  39.1472  2.7353
 M2W  H423  H  HCH3  0   0.209   2.8541  37.5108  2.9226
 M2W  H25   H  HOH1  0   0.487   6.3379  34.8955  6.0367
 M2W  O21   O  OH1   0  -0.578  18.4140  37.1438  7.5817

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
 M2W  C8   O27   double  1.224  0.020  1.224
 M2W  C8   C9    single  1.511  0.020  1.511
 M2W  C8   N7    single  1.345  0.020  1.345
 M2W  O22  C20   double  1.208  0.020  1.208
 M2W  C9   C10   single  1.528  0.020  1.528
 M2W  C20  C16   single  1.517  0.020  1.517
 M2W  C20  O21   single  1.323  0.020  1.323
 M2W  C16  C13   single  1.535  0.020  1.535
 M2W  C16  N19   single  1.449  0.020  1.449
 M2W  C13  C10   single  1.523  0.020  1.523
 M2W  N7   C3    single  1.438  0.020  1.438
 M2W  C3   C1    single  1.528  0.020  1.528
 M2W  C3   C35   single  1.530  0.020  1.530
 M2W  C1   O6    double  1.219  0.020  1.219
 M2W  C1   N2    single  1.341  0.020  1.341
 M2W  C35  S37   single  1.825  0.020  1.825
 M2W  N2   C4    single  1.436  0.020  1.436
 M2W  C4   C23   single  1.523  0.020  1.523
 M2W  C4   C5    single  1.531  0.020  1.531
 M2W  C23  O25   single  1.319  0.020  1.319
 M2W  C23  O26   double  1.205  0.020  1.205
 M2W  C5   O41   single  1.410  0.020  1.410
 M2W  C5   C46   single  1.521  0.020  1.521
 M2W  O41  C42   single  1.408  0.020  1.408
 M2W  S37  H37   single  1.200  0.020  1.300
 M2W  C9   H91C  single  0.970  0.020  1.090
 M2W  C9   H92C  single  0.970  0.020  1.090
 M2W  N7   H7    single  0.860  0.020  1.020
 M2W  C10  H101  single  0.970  0.020  1.090
 M2W  C10  H102  single  0.970  0.020  1.090
 M2W  C16  H16   single  0.970  0.020  1.090
 M2W  O21  H21   single  0.850  0.020  0.980
 M2W  C13  H131  single  0.970  0.020  1.090
 M2W  C13  H132  single  0.970  0.020  1.090
 M2W  N19  H191  single  0.890  0.020  1.040
 M2W  N19  H192  single  0.890  0.020  1.040
 M2W  C3   H3    single  0.970  0.020  1.090
 M2W  C35  H351  single  0.970  0.020  1.090
 M2W  C35  H352  single  0.970  0.020  1.090
 M2W  N2   H2    single  0.860  0.020  1.020
 M2W  C4   H4    single  0.970  0.020  1.090
 M2W  C5   H5    single  0.970  0.020  1.090
 M2W  O25  H25   single  0.850  0.020  0.980
 M2W  C46  H461  single  0.970  0.020  1.090
 M2W  C46  H462  single  0.970  0.020  1.090
 M2W  C46  H463  single  0.970  0.020  1.090
 M2W  C42  H421  single  0.970  0.020  1.090
 M2W  C42  H422  single  0.970  0.020  1.090
 M2W  C42  H423  single  0.970  0.020  1.090

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
 M2W  N7    C8   C9    115.46  3.000
 M2W  N7    C8   O27   122.52  3.000
 M2W  C9    C8   O27   122.02  3.000
 M2W  H92C  C9   H91C  106.84  3.000
 M2W  H92C  C9   C10   109.14  3.000
 M2W  H91C  C9   C10   110.12  3.000
 M2W  H92C  C9   C8    107.39  3.000
 M2W  H91C  C9   C8    111.28  3.000
 M2W  C10   C9   C8    111.89  3.000
 M2W  O21   C20  C16   114.17  3.000
 M2W  O21   C20  O22   123.18  3.000
 M2W  C16   C20  O22   122.65  3.000
 M2W  H16   C16  N19   113.48  3.000
 M2W  H16   C16  C13   107.42  3.000
 M2W  N19   C16  C13   110.75  3.000
 M2W  H16   C16  C20   105.09  3.000
 M2W  N19   C16  C20   112.13  3.000
 M2W  C13   C16  C20   107.60  3.000
 M2W  H132  C13  H131  107.16  3.000
 M2W  H132  C13  C10   109.02  3.000
 M2W  H131  C13  C10   109.55  3.000
 M2W  H132  C13  C16   108.36  3.000
 M2W  H131  C13  C16   109.15  3.000
 M2W  C10   C13  C16   113.41  3.000
 M2W  H102  C10  H101  107.08  3.000
 M2W  H102  C10  C13   109.70  3.000
 M2W  H101  C10  C13   110.77  3.000
 M2W  H102  C10  C9    109.68  3.000
 M2W  H101  C10  C9    108.54  3.000
 M2W  C13   C10  C9    110.99  3.000
 M2W  H192  N19  H191  105.08  3.000
 M2W  H192  N19  C16   110.29  3.000
 M2W  H191  N19  C16   108.95  3.000
 M2W  H7    N7   C3    117.25  3.000
 M2W  H7    N7   C8    119.67  3.000
 M2W  C3    N7   C8    122.95  3.000
 M2W  H3    C3   C35   107.03  3.000
 M2W  H3    C3   C1    108.55  3.000
 M2W  C35   C3   C1    111.10  3.000
 M2W  H3    C3   N7    109.53  3.000
 M2W  C35   C3   N7    112.10  3.000
 M2W  C1    C3   N7    108.46  3.000
 M2W  N2    C1   O6    123.80  3.000
 M2W  N2    C1   C3    114.07  3.000
 M2W  O6    C1   C3    122.12  3.000
 M2W  H352  C35  H351  107.52  3.000
 M2W  H352  C35  S37   110.16  3.000
 M2W  H351  C35  S37   109.24  3.000
 M2W  H352  C35  C3    109.26  3.000
 M2W  H351  C35  C3    110.64  3.000
 M2W  S37   C35  C3    109.98  3.000
 M2W  H37   S37  C35    97.04  3.000
 M2W  H2    N2   C4    117.38  3.000
 M2W  H2    N2   C1    119.01  3.000
 M2W  C4    N2   C1    123.46  3.000
 M2W  H4    C4   C5    107.74  3.000
 M2W  H4    C4   C23   106.43  3.000
 M2W  C5    C4   C23   109.13  3.000
 M2W  H4    C4   N2    108.65  3.000
 M2W  C5    C4   N2    110.97  3.000
 M2W  C23   C4   N2    113.66  3.000
 M2W  O26   C23  O25   124.18  3.000
 M2W  O26   C23  C4    122.18  3.000
 M2W  O25   C23  C4    113.63  3.000
 M2W  H25   O25  C23   109.93  3.000
 M2W  H5    C5   C46   108.43  3.000
 M2W  H5    C5   O41   110.07  3.000
 M2W  C46   C5   O41   113.54  3.000
 M2W  H5    C5   C4    107.42  3.000
 M2W  C46   C5   C4    111.82  3.000
 M2W  O41   C5   C4    105.38  3.000
 M2W  C42   O41  C5    114.77  3.000
 M2W  H463  C46  H462  107.98  3.000
 M2W  H463  C46  H461  107.40  3.000
 M2W  H462  C46  H461  108.14  3.000
 M2W  H463  C46  C5    110.08  3.000
 M2W  H462  C46  C5    112.01  3.000
 M2W  H461  C46  C5    111.07  3.000
 M2W  H423  C42  H422  108.18  3.000
 M2W  H423  C42  H421  108.42  3.000
 M2W  H422  C42  H421  108.15  3.000
 M2W  H423  C42  O41   111.63  3.000
 M2W  H422  C42  O41   112.78  3.000
 M2W  H421  C42  O41   107.54  3.000
 M2W  H21   O21  C20   109.53  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
 M2W  CONST_01  C3    N7   C8   O27     0.00   0.0  0
 M2W  CONST_02  C3    N7   C8   C9    180.00   0.0  0
 M2W  CONST_03  C4    N2   C1   C3    180.00   0.0  0
 M2W  CONST_04  C4    N2   C1   O6      0.00   0.0  0
 M2W  CONST_05  H7    N7   C8   O27   180.00   0.0  0
 M2W  CONST_06  H2    N2   C1   C3      0.00   0.0  0
 M2W  CONST_07  H21   O21  C20  O22     0.00   0.0  0
 M2W  CONST_08  H25   O25  C23  C4    180.00   0.0  0
 M2W  Var_01    C13   C10  C9   C8   -176.04  30.0  3
 M2W  Var_02    C10   C9   C8   O27    56.38  30.0  3
 M2W  Var_03    C16   C13  C10  C9   -178.53  30.0  1
 M2W  Var_04    H421  C42  O41  C5    171.38  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
 M2W  chir_01  C16  C20  C13  N19  positiv
 M2W  chir_02  C3   N7   C35  C1   negativ
 M2W  chir_03  C4   N2   C23  C5   negativ
 M2W  chir_04  C5   O41  C4   C46  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
 M2W  plan-1  C8   0.020
 M2W  plan-1  O27  0.020
 M2W  plan-1  C9   0.020
 M2W  plan-1  N7   0.020
 M2W  plan-1  C3   0.020
 M2W  plan-1  H7   0.020
 M2W  plan-2  C3   0.020
 M2W  plan-2  C1   0.020
 M2W  plan-2  O6   0.020
 M2W  plan-2  N2   0.020
 M2W  plan-2  C4   0.020
 M2W  plan-2  H2   0.020
 M2W  plan-3  O22  0.020
 M2W  plan-3  C20  0.020
 M2W  plan-3  C16  0.020
 M2W  plan-3  H21  0.020
 M2W  plan-3  O21  0.020
 M2W  plan-4  C4   0.020
 M2W  plan-4  C23  0.020
 M2W  plan-4  O25  0.020
 M2W  plan-4  O26  0.020
 M2W  plan-4  H25  0.020

