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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: XV221

Calculation Name: 4ID0-B-Xray13

Preferred Name:

Target Type:

Ligand Name: l-gamma-glutamyl-3-sulfino-l-alanylglycine

ligand 3-letter code: GSF

PDB ID: 4ID0

Chain ID: B

ChEMBL ID:

UniProt ID: Q4K4R5

Base Structure: X-ray

Registration Date: 2018-02-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181208
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge GSF=-2,ACT=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2431824.829782
FMO2-HF: Nuclear repulsion 2350361.075054
FMO2-HF: Total energy -81463.754728
FMO2-MP2: Total energy -81704.157669


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:-1:ACE)


Summations of interaction energy for fragment #1(B:-1:ACE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-1.109-1.2863.684-1.51-1.997-0.02
Interaction energy analysis for fragmet #1(B:-1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.002
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B1LEU00.0190.0183.8210.6961.415-0.012-0.336-0.3710.000
4B2THR0-0.027-0.0057.0850.2220.2220.0000.0000.0000.000
5B3LEU0-0.029-0.0049.3560.0490.0490.0000.0000.0000.000
6B4PHE0-0.016-0.00413.0580.0400.0400.0000.0000.0000.000
7B5HIS00.020-0.00315.8660.0040.0040.0000.0000.0000.000
8B6ASN00.0370.00018.2550.0190.0190.0000.0000.0000.000
9B7PRO00.0320.01121.608-0.008-0.0080.0000.0000.0000.000
10B8ALA0-0.005-0.00623.7480.0040.0040.0000.0000.0000.000
11B9SER0-0.0090.01123.2740.0030.0030.0000.0000.0000.000
12B10PRO00.0600.03224.554-0.013-0.0130.0000.0000.0000.000
13B11TYR0-0.009-0.05523.768-0.011-0.0110.0000.0000.0000.000
14B12VAL0-0.028-0.01319.022-0.020-0.0200.0000.0000.0000.000
15B13ARG10.9110.95920.6430.1020.1020.0000.0000.0000.000
16B14LYS10.8640.90422.6480.1400.1400.0000.0000.0000.000
17B15VAL00.0030.00516.552-0.010-0.0100.0000.0000.0000.000
18B16MET0-0.023-0.00516.689-0.035-0.0350.0000.0000.0000.000
19B17VAL00.0190.00319.372-0.010-0.0100.0000.0000.0000.000
20B18LEU00.0360.02318.078-0.001-0.0010.0000.0000.0000.000
21B19LEU0-0.019-0.00313.940-0.013-0.0130.0000.0000.0000.000
22B20HIS0-0.017-0.02217.379-0.007-0.0070.0000.0000.0000.000
23B21GLU-1-0.797-0.85619.768-0.157-0.1570.0000.0000.0000.000
24B22THR0-0.062-0.02717.844-0.010-0.0100.0000.0000.0000.000
25B23GLY00.0020.01217.576-0.016-0.0160.0000.0000.0000.000
26B24GLN0-0.049-0.05213.148-0.123-0.1230.0000.0000.0000.000
27B25LEU00.0240.01112.624-0.093-0.0930.0000.0000.0000.000
28B26ASN0-0.042-0.02311.143-0.077-0.0770.0000.0000.0000.000
29B27ARG10.8940.9408.0061.0781.0780.0000.0000.0000.000
30B28VAL0-0.028-0.0187.691-0.398-0.3980.0000.0000.0000.000
31B29ALA00.0300.0328.4750.1740.1740.0000.0000.0000.000
32B30LEU0-0.029-0.02310.155-0.001-0.0010.0000.0000.0000.000
33B31GLN00.0610.03012.7470.0260.0260.0000.0000.0000.000
34B32ALA0-0.018-0.01214.479-0.006-0.0060.0000.0000.0000.000
35B33SER0-0.024-0.02318.2380.0140.0140.0000.0000.0000.000
36B34GLN0-0.038-0.03520.522-0.011-0.0110.0000.0000.0000.000
37B35LEU00.0190.01722.7000.0050.0050.0000.0000.0000.000
38B36SER00.0070.00025.975-0.002-0.0020.0000.0000.0000.000
39B37PRO00.011-0.00328.7230.0020.0020.0000.0000.0000.000
40B38VAL0-0.0090.00130.5360.0030.0030.0000.0000.0000.000
41B39ALA0-0.067-0.02429.3190.0050.0050.0000.0000.0000.000
42B40PRO00.0200.00826.288-0.006-0.0060.0000.0000.0000.000
43B41ASP-1-0.758-0.85820.560-0.055-0.0550.0000.0000.0000.000
44B42ALA0-0.007-0.02522.003-0.005-0.0050.0000.0000.0000.000
45B43ALA00.0400.02616.9750.0030.0030.0000.0000.0000.000
46B44LEU0-0.021-0.00917.484-0.008-0.0080.0000.0000.0000.000
47B45ASN0-0.016-0.01818.671-0.017-0.0170.0000.0000.0000.000
48B46GLN0-0.087-0.03617.4390.0030.0030.0000.0000.0000.000
49B47ASP-1-0.788-0.88213.422-0.115-0.1150.0000.0000.0000.000
50B48ASN0-0.017-0.02616.584-0.008-0.0080.0000.0000.0000.000
51B49PRO00.0080.01419.4170.0100.0100.0000.0000.0000.000
52B50LEU0-0.046-0.03422.7280.0080.0080.0000.0000.0000.000
53B51GLY00.0220.02722.8290.0030.0030.0000.0000.0000.000
54B52LYS10.8880.93622.4020.0870.0870.0000.0000.0000.000
55B53ILE00.0130.03919.405-0.012-0.0120.0000.0000.0000.000
56B54PRO0-0.054-0.04517.8790.0120.0120.0000.0000.0000.000
57B55ALA00.0320.00716.3330.0150.0150.0000.0000.0000.000
58B56LEU0-0.014-0.01011.255-0.004-0.0040.0000.0000.0000.000
59B57ARG10.8730.9548.2560.2130.2130.0000.0000.0000.000
60B58LEU0-0.016-0.0318.431-0.229-0.2290.0000.0000.0000.000
61B59ASP-1-0.862-0.9302.578-2.319-3.3573.697-1.169-1.490-0.020
62B60ASN0-0.005-0.0035.0300.4160.558-0.001-0.005-0.1360.000
63B61GLY0-0.016-0.0137.5850.1610.1610.0000.0000.0000.000
64B62GLN0-0.041-0.0129.2000.0270.0270.0000.0000.0000.000
65B63VAL00.0250.01111.321-0.094-0.0940.0000.0000.0000.000
66B64LEU0-0.035-0.00513.7250.0320.0320.0000.0000.0000.000
67B65TYR00.0300.00315.955-0.007-0.0070.0000.0000.0000.000
68B66ASP-1-0.829-0.91719.102-0.140-0.1400.0000.0000.0000.000
69B67SER00.025-0.00920.408-0.018-0.0180.0000.0000.0000.000
70B68ARG10.9220.95321.0420.1010.1010.0000.0000.0000.000
71B69VAL00.0310.03018.525-0.009-0.0090.0000.0000.0000.000
72B70ILE0-0.041-0.01515.562-0.025-0.0250.0000.0000.0000.000
73B71LEU0-0.007-0.00717.291-0.036-0.0360.0000.0000.0000.000
74B72ASP-1-0.918-0.95519.608-0.222-0.2220.0000.0000.0000.000
75B73TYR00.018-0.00310.778-0.068-0.0680.0000.0000.0000.000
76B74LEU0-0.001-0.01912.904-0.035-0.0350.0000.0000.0000.000
77B75ASP-1-0.746-0.86115.983-0.239-0.2390.0000.0000.0000.000
78B76GLN0-0.112-0.05717.9320.0230.0230.0000.0000.0000.000
79B77GLN0-0.0330.01411.405-0.139-0.1390.0000.0000.0000.000
80B78HIS0-0.0560.00314.811-0.025-0.0250.0000.0000.0000.000
81B79VAL00.000-0.01617.0340.0240.0240.0000.0000.0000.000
82B80GLY00.0130.01719.9540.0270.0270.0000.0000.0000.000
83B81ASN0-0.051-0.04322.3800.0020.0020.0000.0000.0000.000
84B82PRO0-0.0370.00323.261-0.010-0.0100.0000.0000.0000.000
85B83LEU00.025-0.00922.5880.0170.0170.0000.0000.0000.000
86B84ILE0-0.0090.00122.7210.0160.0160.0000.0000.0000.000
87B85PRO0-0.0070.00426.105-0.002-0.0020.0000.0000.0000.000
88B86ARG10.9920.98621.5990.1980.1980.0000.0000.0000.000
89B87ASP-1-0.909-0.95028.028-0.100-0.1000.0000.0000.0000.000
90B88GLY00.0420.01831.6200.0010.0010.0000.0000.0000.000
91B89SER0-0.002-0.02634.658-0.003-0.0030.0000.0000.0000.000
92B90ALA00.0220.01633.5760.0000.0000.0000.0000.0000.000
93B91ARG10.9260.98726.0770.1330.1330.0000.0000.0000.000
94B92TRP00.0460.00531.482-0.005-0.0050.0000.0000.0000.000
95B93ARG10.9000.93734.4160.0790.0790.0000.0000.0000.000
96B94ARG10.7570.83731.3000.1020.1020.0000.0000.0000.000
97B95LEU00.0180.00427.277-0.004-0.0040.0000.0000.0000.000
98B96THR0-0.036-0.01031.1540.0010.0010.0000.0000.0000.000
99B97LEU00.0160.00633.9250.0010.0010.0000.0000.0000.000
100B98ALA0-0.003-0.00428.8690.0000.0000.0000.0000.0000.000
101B99ALA0-0.0100.00130.932-0.001-0.0010.0000.0000.0000.000
102B100LEU0-0.021-0.00332.1580.0030.0030.0000.0000.0000.000
103B101ALA00.0110.00631.3070.0030.0030.0000.0000.0000.000
104B102ASP-1-0.782-0.88228.207-0.127-0.1270.0000.0000.0000.000
105B103GLY00.0290.03530.9020.0030.0030.0000.0000.0000.000
106B104ILE00.0140.00234.2750.0050.0050.0000.0000.0000.000
107B105MET0-0.063-0.00728.6380.0010.0010.0000.0000.0000.000
108B106ASP-1-0.830-0.89130.550-0.088-0.0880.0000.0000.0000.000
109B107ALA00.0080.00832.6680.0040.0040.0000.0000.0000.000
110B108SER0-0.020-0.02433.7310.0050.0050.0000.0000.0000.000
111B109VAL0-0.029-0.00829.6530.0030.0030.0000.0000.0000.000
112B110LEU0-0.019-0.00132.9810.0040.0040.0000.0000.0000.000
113B111VAL00.0390.02635.5290.0040.0040.0000.0000.0000.000
114B112ARG10.9200.97233.1310.0540.0540.0000.0000.0000.000
115B113TYR0-0.020-0.03328.6890.0020.0020.0000.0000.0000.000
116B114GLU-1-0.874-0.93635.533-0.032-0.0320.0000.0000.0000.000
117B115LEU00.024-0.00739.1860.0030.0030.0000.0000.0000.000
118B116ALA0-0.081-0.03436.0150.0020.0020.0000.0000.0000.000
119B117LEU0-0.063-0.03832.9400.0010.0010.0000.0000.0000.000
120B118ARG10.8830.97637.5870.0360.0360.0000.0000.0000.000
121B119ALA00.0210.00840.5490.0000.0000.0000.0000.0000.000
122B120PRO00.0850.02443.8060.0000.0000.0000.0000.0000.000
123B121GLU-1-0.906-0.94946.194-0.020-0.0200.0000.0000.0000.000
124B122LYS10.8450.91144.6030.0210.0210.0000.0000.0000.000
125B123HIS0-0.0240.01542.531-0.001-0.0010.0000.0000.0000.000
126B124TRP0-0.0050.00345.3200.0010.0010.0000.0000.0000.000
127B125GLU-1-0.860-0.94946.341-0.032-0.0320.0000.0000.0000.000
128B126GLN00.0280.01047.876-0.002-0.0020.0000.0000.0000.000
129B127TRP0-0.0150.00238.815-0.002-0.0020.0000.0000.0000.000
130B128LEU00.003-0.00841.919-0.003-0.0030.0000.0000.0000.000
131B129ASP-1-0.849-0.93343.898-0.037-0.0370.0000.0000.0000.000
132B130GLY00.0030.01345.552-0.001-0.0010.0000.0000.0000.000
133B131GLN0-0.036-0.02638.934-0.006-0.0060.0000.0000.0000.000
134B132ARG10.9430.97241.3580.0360.0360.0000.0000.0000.000
135B133ASP-1-0.874-0.93543.007-0.041-0.0410.0000.0000.0000.000
136B134LYS10.7660.87440.7090.0470.0470.0000.0000.0000.000
137B135ILE00.0040.01238.054-0.003-0.0030.0000.0000.0000.000
138B136ARG10.9370.95840.5150.0400.0400.0000.0000.0000.000
139B137ARG10.9270.95643.7250.0410.0410.0000.0000.0000.000
140B138ALA00.0110.00938.8150.0000.0000.0000.0000.0000.000
141B139LEU00.001-0.01138.914-0.002-0.0020.0000.0000.0000.000
142B140ALA0-0.0080.00941.4740.0000.0000.0000.0000.0000.000
143B141VAL00.0030.00840.7750.0000.0000.0000.0000.0000.000
144B142LEU00.001-0.01436.621-0.002-0.0020.0000.0000.0000.000
145B143GLU-1-0.761-0.87740.492-0.054-0.0540.0000.0000.0000.000
146B144ALA0-0.0050.00643.4630.0010.0010.0000.0000.0000.000
147B145GLU-1-0.902-0.97239.223-0.068-0.0680.0000.0000.0000.000
148B146ALA0-0.069-0.02340.148-0.003-0.0030.0000.0000.0000.000
149B147ILE0-0.061-0.00841.1410.0010.0010.0000.0000.0000.000
150B148ALA0-0.029-0.03642.0040.0010.0010.0000.0000.0000.000
151B149GLU-1-0.780-0.84537.280-0.083-0.0830.0000.0000.0000.000
152B150LEU0-0.0090.00034.499-0.006-0.0060.0000.0000.0000.000
153B151ALA00.004-0.01234.996-0.006-0.0060.0000.0000.0000.000
154B152SER0-0.065-0.01435.998-0.003-0.0030.0000.0000.0000.000
155B153HIS00.0220.00730.980-0.005-0.0050.0000.0000.0000.000
156B154PHE0-0.020-0.01126.4230.0020.0020.0000.0000.0000.000
157B155ASP-1-0.745-0.86227.208-0.132-0.1320.0000.0000.0000.000
158B156ILE00.0170.00124.2310.0000.0000.0000.0000.0000.000
159B157ALA0-0.0260.00227.0610.0020.0020.0000.0000.0000.000
160B158ALA00.0250.02530.2330.0040.0040.0000.0000.0000.000
161B159ILE0-0.007-0.00323.9390.0030.0030.0000.0000.0000.000
162B160SER0-0.006-0.02127.722-0.001-0.0010.0000.0000.0000.000
163B161VAL00.0230.00828.7540.0050.0050.0000.0000.0000.000
164B162ALA00.0220.01029.7540.0050.0050.0000.0000.0000.000
165B163CYS0-0.062-0.02426.5940.0010.0010.0000.0000.0000.000
166B164ALA00.000-0.00529.2340.0050.0050.0000.0000.0000.000
167B165LEU00.0010.00231.9970.0050.0050.0000.0000.0000.000
168B166GLY00.0060.00731.5990.0040.0040.0000.0000.0000.000
169B167TYR0-0.011-0.02930.0870.0050.0050.0000.0000.0000.000
170B168LEU00.0150.01032.3170.0050.0050.0000.0000.0000.000
171B169ASP-1-0.765-0.84535.178-0.062-0.0620.0000.0000.0000.000
172B170PHE0-0.091-0.04330.0250.0030.0030.0000.0000.0000.000
173B171ARG10.8360.90930.7510.0670.0670.0000.0000.0000.000
174B172HIS0-0.044-0.01735.7220.0050.0050.0000.0000.0000.000
175B173PRO00.0550.03438.4690.0000.0000.0000.0000.0000.000
176B174ASP-1-0.921-0.95840.814-0.043-0.0430.0000.0000.0000.000
177B175LEU0-0.051-0.04839.9360.0010.0010.0000.0000.0000.000
178B176GLU-1-0.985-0.98243.297-0.045-0.0450.0000.0000.0000.000
179B177TRP00.0500.01237.7670.0010.0010.0000.0000.0000.000
180B178ARG10.8380.89137.7280.0610.0610.0000.0000.0000.000
181B179GLN0-0.046-0.00943.764-0.001-0.0010.0000.0000.0000.000
182B180ASP-1-0.901-0.94846.809-0.043-0.0430.0000.0000.0000.000
183B181HIS10.7820.89143.5750.0500.0500.0000.0000.0000.000
184B182PRO00.0560.02644.070-0.003-0.0030.0000.0000.0000.000
185B183GLN00.012-0.00844.351-0.003-0.0030.0000.0000.0000.000
186B184LEU00.007-0.00238.001-0.003-0.0030.0000.0000.0000.000
187B185ALA0-0.033-0.02139.712-0.004-0.0040.0000.0000.0000.000
188B186ALA0-0.023-0.00540.471-0.002-0.0020.0000.0000.0000.000
189B187TRP00.0530.02033.034-0.002-0.0020.0000.0000.0000.000
190B188TYR00.019-0.00432.660-0.006-0.0060.0000.0000.0000.000
191B189PHE0-0.034-0.00835.726-0.004-0.0040.0000.0000.0000.000
192B190GLU-1-0.895-0.93436.033-0.074-0.0740.0000.0000.0000.000
193B191ILE0-0.034-0.01931.606-0.005-0.0050.0000.0000.0000.000
194B192SER0-0.030-0.02731.518-0.009-0.0090.0000.0000.0000.000
195B193GLN0-0.092-0.05231.801-0.003-0.0030.0000.0000.0000.000
196B194ARG10.8310.91527.2880.1290.1290.0000.0000.0000.000
197B195PRO00.0300.00225.898-0.003-0.0030.0000.0000.0000.000
198B196SER0-0.032-0.03023.6650.0010.0010.0000.0000.0000.000
199B197MET00.0070.03024.678-0.010-0.0100.0000.0000.0000.000
200B198LEU00.0170.00827.5000.0030.0030.0000.0000.0000.000
201B199ALA0-0.019-0.01022.8990.0070.0070.0000.0000.0000.000
202B200THR0-0.048-0.02721.860-0.004-0.0040.0000.0000.0000.000
203B201ARG10.8630.93724.4110.0910.0910.0000.0000.0000.000
204B202PRO00.0260.02926.882-0.003-0.0030.0000.0000.0000.000
205B203PRO0-0.052-0.03427.1630.0040.0040.0000.0000.0000.000
206B204NME00.0180.02129.5990.0020.0020.0000.0000.0000.000
207B301ACT-1-1.009-1.00341.797-0.035-0.0350.0000.0000.0000.000
208B302GSF-2-1.838-1.90632.791-0.094-0.0940.0000.0000.0000.000