# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:11:00 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: D-gamma-glutamyl-N-{[(R)-{4-[(4-aminobutyl)amino]butyl}(phosphonooxy)phosphoryl]methyl}-D-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)CC[C@@H](N)C(O)=O)C(=O)NC[P@@](=O)(CCCCNCCCCN)O[P](O)(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
 GGA  GGA  D-gamma-glutamyl-N-{[(R)-{4-[(4-aminobutyl)amino]butyl}(phosphonooxy)phosphoryl]methyl}-D-alaninamide  ligand  70  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GGA
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
 GGA  C1    C  C     0   0.533  -7.4583    2.8181  -3.0361
 GGA  O2    O  O     0  -0.435  -8.2971    2.8146  -3.9006
 GGA  O4    O  OH1   0  -0.591  -7.6795    2.3722  -1.8043
 GGA  C6    C  CH1   0  -0.173  -6.0299    3.2955  -3.2202
 GGA  N8    N  NH2   0  -0.798  -6.0246    4.4271  -4.1264
 GGA  C10   C  CH2   0  -0.441  -5.1918    2.1679  -3.8383
 GGA  C12   C  CH2   0  -0.603  -5.0520    0.9454  -2.9449
 GGA  C14   C  C     0   0.579  -4.0466   -0.0588  -3.4717
 GGA  O16   O  O     0  -0.497  -3.5721   -0.0004  -4.5966
 GGA  N18   N  NH1   0  -0.646  -3.7288   -1.0301  -2.5973
 GGA  C20   C  CH1   0  -0.201  -2.8525   -2.1268  -2.9197
 GGA  C22   C  CH3   0  -0.648  -3.5792   -3.2616  -3.6478
 GGA  C24   C  C     0   0.558  -2.2604   -2.6627  -1.6236
 GGA  O26   O  O     0  -0.469  -2.8503   -2.5894  -0.5605
 GGA  N30   N  NH1   0  -0.644  -1.0607   -3.2557  -1.7673
 GGA  C29   C  CH2   0  -0.548  -0.3829   -3.9205  -0.6862
 GGA  P34   P  P     0   1.254  -0.8347   -5.6877  -0.6690
 GGA  C33   C  CH2   0  -0.723  -0.1509   -6.4458  -2.1494
 GGA  C35   C  CH2   0  -0.435  -0.3577   -7.9589  -2.1966
 GGA  C37   C  CH2   0  -0.436   0.1376   -8.5485  -3.5111
 GGA  C39   C  CH2   0  -0.250  -0.0285  -10.0592  -3.5586
 GGA  N44   N  NH1   0  -0.602   0.4420  -10.6025  -4.8177
 GGA  C43   C  CH2   0  -0.246   0.3258  -12.0465  -4.8915
 GGA  C45   C  CH2   0  -0.445   0.8211  -12.5795  -6.2267
 GGA  C47   C  CH2   0  -0.428   0.7329  -14.0966  -6.3188
 GGA  C49   C  CH2   0  -0.270   1.2285  -14.6359  -7.6519
 GGA  N54   N  NH2   0  -0.801   1.1186  -16.0875  -7.6992
 GGA  O56   O  O     0  -0.703  -2.2802   -5.9611  -0.4100
 GGA  O58   O  O2    0  -0.701   0.1125   -6.3114   0.5238
 GGA  P60   P  P     0   1.452  -0.4306   -6.4400   2.0537
 GGA  O62   O  OH1   0  -0.715   0.7268   -7.2691   2.7442
 GGA  O64   O  OH1   0  -0.735  -1.5545   -7.5604   1.9864
 GGA  O66   O  O     0  -0.691  -0.7911   -5.1328   2.6309
 GGA  HO4   H  HOH1  0   0.479  -8.5802    2.0201  -1.7365
 GGA  H6    H  HCH1  0   0.242  -5.6153    3.5219  -2.2283
 GGA  HN81  H  HNH2  0   0.354  -5.0666    4.7219  -4.2684
 GGA  HN82  H  HNH2  0   0.353  -6.4944    5.2182  -3.7040
 GGA  H101  H  HCH2  0   0.244  -5.6240    1.8983  -4.8037
 GGA  H102  H  HCH2  0   0.252  -4.2016    2.5840  -4.0411
 GGA  H121  H  HCH2  0   0.267  -4.7638    1.2434  -1.9326
 GGA  H122  H  HCH2  0   0.279  -6.0067    0.4211  -2.8402
 GGA  HN18  H  HNH1  0   0.400  -4.1805   -1.0507  -1.6951
 GGA  H20   H  HCH1  0   0.279  -2.0471   -1.7533  -3.5563
 GGA  H221  H  HCH3  0   0.239  -4.3991   -3.6459  -3.0411
 GGA  H222  H  HCH3  0   0.234  -2.9017   -4.0861  -3.8717
 GGA  H223  H  HCH3  0   0.254  -3.9871   -2.8980  -4.5897
 GGA  HN30  H  HNH1  0   0.422  -0.5933   -3.2105  -2.6587
 GGA  H291  H  HCH2  0   0.316   0.6953   -3.8159  -0.8082
 GGA  H292  H  HCH2  0   0.305  -0.6585   -3.4786   0.2722
 GGA  H331  H  HCH2  0   0.293   0.9095   -6.1882  -2.2174
 GGA  H332  H  HCH2  0   0.287  -0.6449   -5.9690  -3.0018
 GGA  H351  H  HCH2  0   0.240  -1.4179   -8.1906  -2.0669
 GGA  H352  H  HCH2  0   0.240   0.1714   -8.4309  -1.3649
 GGA  H371  H  HCH2  0   0.223  -0.4110   -8.0920  -4.3419
 GGA  H372  H  HCH2  0   0.224   1.1924   -8.2979  -3.6573
 GGA  H391  H  HCH2  0   0.186  -1.0807  -10.3171  -3.3521
 GGA  H392  H  HCH2  0   0.215   0.5572  -10.5105  -2.7510
 GGA  HN44  H  HNH1  0   0.334  -0.1031  -10.1947  -5.5695
 GGA  H431  H  HCH2  0   0.183  -0.7059  -12.3965  -4.7198
 GGA  H432  H  HCH2  0   0.211   0.9285  -12.4786  -4.0855
 GGA  H451  H  HCH2  0   0.215   1.8557  -12.2561  -6.3778
 GGA  H452  H  HCH2  0   0.213   0.2350  -12.1311  -7.0369
 GGA  H471  H  HCH2  0   0.213  -0.3014  -14.4212  -6.1666
 GGA  H472  H  HCH2  0   0.212   1.3195  -14.5435  -5.5080
 GGA  H491  H  HCH2  0   0.186   2.2503  -14.2683  -7.8271
 GGA  H492  H  HCH2  0   0.211   0.6139  -14.2195  -8.4552
 GGA  H541  H  HNH2  0   0.336   1.7670  -16.4902  -7.0330
 GGA  H542  H  HNH2  0   0.345   1.4221  -16.4205  -8.6054
 GGA  HO62  H  HOH1  0   0.511   1.3009   -6.7441   3.3186
 GGA  HO64  H  HOH1  0   0.494  -2.2958   -7.3182   1.4072

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
 GGA  C1   C6    single  1.517  0.020  1.517
 GGA  C1   O2    double  1.204  0.020  1.204
 GGA  C1   O4    single  1.329  0.020  1.329
 GGA  O4   HO4   single  0.850  0.020  0.980
 GGA  C6   N8    single  1.450  0.020  1.450
 GGA  C6   C10   single  1.535  0.020  1.535
 GGA  C6   H6    single  0.970  0.020  1.090
 GGA  N8   HN81  single  0.890  0.020  1.040
 GGA  N8   HN82  single  0.890  0.020  1.040
 GGA  C10  C12   single  1.521  0.020  1.521
 GGA  C10  H101  single  0.970  0.020  1.090
 GGA  C10  H102  single  0.970  0.020  1.090
 GGA  C12  C14   single  1.516  0.020  1.516
 GGA  C12  H121  single  0.970  0.020  1.090
 GGA  C12  H122  single  0.970  0.020  1.090
 GGA  C14  N18   single  1.345  0.020  1.345
 GGA  C14  O16   double  1.222  0.020  1.222
 GGA  N18  C20   single  1.440  0.020  1.440
 GGA  N18  HN18  single  0.860  0.020  1.020
 GGA  C20  C24   single  1.522  0.020  1.522
 GGA  C20  C22   single  1.532  0.020  1.532
 GGA  C20  H20   single  0.970  0.020  1.090
 GGA  C22  H221  single  0.970  0.020  1.090
 GGA  C22  H222  single  0.970  0.020  1.090
 GGA  C22  H223  single  0.970  0.020  1.090
 GGA  C24  O26   double  1.218  0.020  1.218
 GGA  C24  N30   single  1.346  0.020  1.346
 GGA  N30  C29   single  1.439  0.020  1.439
 GGA  N30  HN30  single  0.860  0.020  1.020
 GGA  C29  P34   single  1.824  0.020  1.824
 GGA  C29  H291  single  0.970  0.020  1.090
 GGA  C29  H292  single  0.970  0.020  1.090
 GGA  P34  C33   single  1.798  0.020  1.798
 GGA  P34  O58   single  1.646  0.020  1.646
 GGA  P34  O56   double  1.494  0.020  1.494
 GGA  C33  C35   single  1.528  0.020  1.528
 GGA  C33  H331  single  0.970  0.020  1.090
 GGA  C33  H332  single  0.970  0.020  1.090
 GGA  C35  C37   single  1.523  0.020  1.523
 GGA  C35  H351  single  0.970  0.020  1.090
 GGA  C35  H352  single  0.970  0.020  1.090
 GGA  C37  C39   single  1.521  0.020  1.521
 GGA  C37  H371  single  0.970  0.020  1.090
 GGA  C37  H372  single  0.970  0.020  1.090
 GGA  C39  N44   single  1.450  0.020  1.450
 GGA  C39  H391  single  0.970  0.020  1.090
 GGA  C39  H392  single  0.970  0.020  1.090
 GGA  N44  C43   single  1.451  0.020  1.451
 GGA  N44  HN44  single  0.890  0.020  1.040
 GGA  C43  C45   single  1.521  0.020  1.521
 GGA  C43  H431  single  0.970  0.020  1.090
 GGA  C43  H432  single  0.970  0.020  1.090
 GGA  C45  C47   single  1.523  0.020  1.523
 GGA  C45  H451  single  0.970  0.020  1.090
 GGA  C45  H452  single  0.970  0.020  1.090
 GGA  C47  C49   single  1.521  0.020  1.521
 GGA  C47  H471  single  0.970  0.020  1.090
 GGA  C47  H472  single  0.970  0.020  1.090
 GGA  C49  N54   single  1.456  0.020  1.456
 GGA  C49  H491  single  0.970  0.020  1.090
 GGA  C49  H492  single  0.970  0.020  1.090
 GGA  N54  H541  single  0.890  0.020  1.040
 GGA  N54  H542  single  0.890  0.020  1.040
 GGA  O58  P60   single  1.628  0.020  1.628
 GGA  P60  O66   double  1.474  0.020  1.474
 GGA  P60  O62   single  1.582  0.020  1.582
 GGA  P60  O64   single  1.588  0.020  1.588
 GGA  O62  HO62  single  0.850  0.020  0.980
 GGA  O64  HO64  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
 GGA  C6    C1   O4    112.01  3.000
 GGA  O4    C1   O2    123.27  3.000
 GGA  C6    C1   O2    124.71  3.000
 GGA  HO4   O4   C1    109.96  3.000
 GGA  H6    C6   C10   107.99  3.000
 GGA  H6    C6   N8    113.71  3.000
 GGA  C10   C6   N8    108.64  3.000
 GGA  H6    C6   C1    108.09  3.000
 GGA  C10   C6   C1    109.37  3.000
 GGA  N8    C6   C1    108.96  3.000
 GGA  HN82  N8   HN81  105.67  3.000
 GGA  HN82  N8   C6    110.33  3.000
 GGA  HN81  N8   C6    108.57  3.000
 GGA  H102  C10  H101  106.78  3.000
 GGA  H102  C10  C12   109.37  3.000
 GGA  H101  C10  C12   110.94  3.000
 GGA  H102  C10  C6    106.84  3.000
 GGA  H101  C10  C6    108.75  3.000
 GGA  C12   C10  C6    113.84  3.000
 GGA  H122  C12  H121  105.77  3.000
 GGA  H122  C12  C14   107.13  3.000
 GGA  H121  C12  C14   109.11  3.000
 GGA  H122  C12  C10   111.18  3.000
 GGA  H121  C12  C10   110.42  3.000
 GGA  C14   C12  C10   112.92  3.000
 GGA  N18   C14  O16   122.76  3.000
 GGA  O16   C14  C12   123.08  3.000
 GGA  N18   C14  C12   114.16  3.000
 GGA  HN18  N18  C20   117.18  3.000
 GGA  HN18  N18  C14   119.36  3.000
 GGA  C20   N18  C14   123.24  3.000
 GGA  H20   C20  C24   109.25  3.000
 GGA  H20   C20  C22   109.03  3.000
 GGA  C24   C20  C22   109.18  3.000
 GGA  H20   C20  N18   108.58  3.000
 GGA  C22   C20  N18   112.45  3.000
 GGA  C24   C20  N18   108.31  3.000
 GGA  H223  C22  H222  107.92  3.000
 GGA  H223  C22  H221  108.50  3.000
 GGA  H222  C22  H221  108.37  3.000
 GGA  H223  C22  C20   109.97  3.000
 GGA  H222  C22  C20   111.29  3.000
 GGA  H221  C22  C20   110.70  3.000
 GGA  N30   C24  O26   123.46  3.000
 GGA  N30   C24  C20   114.26  3.000
 GGA  O26   C24  C20   122.24  3.000
 GGA  HN30  N30  C29   117.84  3.000
 GGA  HN30  N30  C24   119.22  3.000
 GGA  C29   N30  C24   122.90  3.000
 GGA  H292  C29  H291  108.02  3.000
 GGA  H292  C29  P34   108.76  3.000
 GGA  H291  C29  P34   109.82  3.000
 GGA  H292  C29  N30   110.73  3.000
 GGA  H291  C29  N30   109.72  3.000
 GGA  P34   C29  N30   109.76  3.000
 GGA  O58   P34  O56   111.22  3.000
 GGA  O56   P34  C33   115.69  3.000
 GGA  O58   P34  C33   102.60  3.000
 GGA  O56   P34  C29   114.75  3.000
 GGA  O58   P34  C29   103.38  3.000
 GGA  C33   P34  C29   107.85  3.000
 GGA  H332  C33  H331  106.66  3.000
 GGA  H332  C33  C35   110.26  3.000
 GGA  H331  C33  C35   111.26  3.000
 GGA  H332  C33  P34   106.61  3.000
 GGA  H331  C33  P34   108.70  3.000
 GGA  C35   C33  P34   113.04  3.000
 GGA  H352  C35  H351  106.72  3.000
 GGA  H352  C35  C37   109.39  3.000
 GGA  H351  C35  C37   109.62  3.000
 GGA  H352  C35  C33   109.80  3.000
 GGA  H351  C35  C33   109.73  3.000
 GGA  C37   C35  C33   111.46  3.000
 GGA  H372  C37  H371  106.63  3.000
 GGA  H372  C37  C39   109.20  3.000
 GGA  H371  C37  C39   109.62  3.000
 GGA  H372  C37  C35   109.88  3.000
 GGA  H371  C37  C35   109.29  3.000
 GGA  C39   C37  C35   112.08  3.000
 GGA  H392  C39  H391  106.01  3.000
 GGA  H392  C39  N44   108.21  3.000
 GGA  H391  C39  N44   112.62  3.000
 GGA  H392  C39  C37   109.15  3.000
 GGA  H391  C39  C37   109.31  3.000
 GGA  N44   C39  C37   111.34  3.000
 GGA  HN44  N44  C43   108.64  3.000
 GGA  HN44  N44  C39   108.58  3.000
 GGA  C43   N44  C39   113.03  3.000
 GGA  H432  C43  H431  105.97  3.000
 GGA  H432  C43  C45   109.19  3.000
 GGA  H431  C43  C45   109.28  3.000
 GGA  H432  C43  N44   108.13  3.000
 GGA  H431  C43  N44   112.51  3.000
 GGA  C45   C43  N44   111.56  3.000
 GGA  H452  C45  H451  106.42  3.000
 GGA  H452  C45  C47   109.39  3.000
 GGA  H451  C45  C47   109.93  3.000
 GGA  H452  C45  C43   109.37  3.000
 GGA  H451  C45  C43   109.00  3.000
 GGA  C47   C45  C43   112.55  3.000
 GGA  H472  C47  H471  106.38  3.000
 GGA  H472  C47  C49   109.23  3.000
 GGA  H471  C47  C49   108.95  3.000
 GGA  H472  C47  C45   109.30  3.000
 GGA  H471  C47  C45   109.99  3.000
 GGA  C49   C47  C45   112.79  3.000
 GGA  H492  C49  H491  106.13  3.000
 GGA  H492  C49  N54   108.25  3.000
 GGA  H491  C49  N54   113.45  3.000
 GGA  H492  C49  C47   109.00  3.000
 GGA  H491  C49  C47   108.89  3.000
 GGA  N54   C49  C47   110.93  3.000
 GGA  H542  N54  H541  105.43  3.000
 GGA  H542  N54  C49   109.54  3.000
 GGA  H541  N54  C49   109.06  3.000
 GGA  P60   O58  P34   121.25  3.000
 GGA  O66   P60  O64   117.98  3.000
 GGA  O64   P60  O62    99.58  3.000
 GGA  O66   P60  O62   118.21  3.000
 GGA  O64   P60  O58   104.59  3.000
 GGA  O62   P60  O58   101.97  3.000
 GGA  O66   P60  O58   112.30  3.000
 GGA  HO62  O62  P60   114.14  3.000
 GGA  HO64  O64  P60   112.91  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
 GGA  CONST_01  C20   N18  C14  C12   180.00   0.0  0
 GGA  CONST_02  C20   N18  C14  O16     0.00   0.0  0
 GGA  CONST_03  C29   N30  C24  C20   180.00   0.0  0
 GGA  CONST_04  C29   N30  C24  O26     0.00   0.0  0
 GGA  CONST_05  HN18  N18  C14  C12     0.00   0.0  0
 GGA  CONST_06  HN30  N30  C24  C20     0.00   0.0  0
 GGA  CONST_07  HO4   O4   C1   O2      0.00   0.0  0
 GGA  Var_01    C14   C12  C10  C6   -170.79  30.0  3
 GGA  Var_02    N18   C14  C12  C10   168.98  30.0  3
 GGA  Var_03    P34   C29  N30  C24    91.56  30.0  3
 GGA  Var_04    C33   P34  C29  N30    67.12  30.0  3
 GGA  Var_05    C35   C33  P34  C29   175.07  30.0  3
 GGA  Var_06    C37   C35  C33  P34   175.61  30.0  3
 GGA  Var_07    O66   P60  O58  P34   -60.46  30.0  3
 GGA  Var_08    C39   C37  C35  C33   178.52  30.0  3
 GGA  Var_09    N44   C39  C37  C35   179.75  30.0  3
 GGA  Var_10    C43   N44  C39  C37   178.80  30.0  3
 GGA  Var_11    C45   C43  N44  C39   179.70  30.0  3
 GGA  Var_12    C47   C45  C43  N44   178.95  30.0  3
 GGA  Var_13    C49   C47  C45  C43  -179.93  30.0  3
 GGA  Var_14    N54   C49  C47  C45  -179.65  30.0  3
 GGA  Var_15    H541  N54  C49  C47   -67.10  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
 GGA  chir_01  C6   C1   N8   C10  positiv
 GGA  chir_02  C20  N18  C24  C22  negativ
 GGA  chir_03  P34  C33  O58  O56  both

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
 GGA  plan-1  C12   0.020
 GGA  plan-1  C14   0.020
 GGA  plan-1  O16   0.020
 GGA  plan-1  N18   0.020
 GGA  plan-1  C20   0.020
 GGA  plan-1  HN18  0.020
 GGA  plan-2  C20   0.020
 GGA  plan-2  C24   0.020
 GGA  plan-2  O26   0.020
 GGA  plan-2  N30   0.020
 GGA  plan-2  C29   0.020
 GGA  plan-2  HN30  0.020
 GGA  plan-3  C1    0.020
 GGA  plan-3  O2    0.020
 GGA  plan-3  O4    0.020
 GGA  plan-3  C6    0.020
 GGA  plan-3  HO4   0.020

