FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 493MN

Calculation Name: 3WGO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WGO

Chain ID: A

ChEMBL ID:

UniProt ID: Q890V3

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 323
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4627650.783807
FMO2-HF: Nuclear repulsion 4501691.086804
FMO2-HF: Total energy -125959.697003
FMO2-MP2: Total energy -126327.560775


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(A:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-50.42-47.8728.038-5.073-5.512-0.045
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.990 / q_NPA : 0.980
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].
3A6ARG10.8190.9103.71037.36639.178-0.005-0.760-1.0470.004
4A7ILE00.0520.0245.7383.2193.2190.0000.0000.0000.000
5A8GLY00.0190.0138.5950.0960.0960.0000.0000.0000.000
6A9ILE0-0.034-0.01511.9920.4480.4480.0000.0000.0000.000
7A10VAL00.0150.00414.7590.3760.3760.0000.0000.0000.000
8A11GLY00.0190.01618.3360.4940.4940.0000.0000.0000.000
9A12TYR0-0.021-0.04617.896-0.003-0.0030.0000.0000.0000.000
10A13GLY00.0480.02521.0470.3980.3980.0000.0000.0000.000
11A14ASN00.001-0.01621.678-0.460-0.4600.0000.0000.0000.000
12A15ILE00.0550.04319.047-0.232-0.2320.0000.0000.0000.000
13A16GLY00.0610.03817.594-0.601-0.6010.0000.0000.0000.000
14A17LYS10.8500.91816.78011.16111.1610.0000.0000.0000.000
15A18GLY00.0270.01617.593-0.281-0.2810.0000.0000.0000.000
16A19VAL0-0.002-0.00313.047-0.547-0.5470.0000.0000.0000.000
17A20GLU-1-0.827-0.89212.934-16.016-16.0160.0000.0000.0000.000
18A21LYS10.8140.88812.86812.49212.4920.0000.0000.0000.000
19A22ALA00.0700.03913.565-0.373-0.3730.0000.0000.0000.000
20A23ILE00.004-0.0047.326-0.723-0.7230.0000.0000.0000.000
21A24LYS10.7940.8958.76515.17415.1740.0000.0000.0000.000
22A25GLN0-0.029-0.00610.9230.8290.8290.0000.0000.0000.000
23A26ASN0-0.022-0.0107.5770.4880.4880.0000.0000.0000.000
24A27ASP-1-0.846-0.9176.272-25.602-25.6020.0000.0000.0000.000
25A28ASP-1-0.837-0.9003.193-34.144-33.1790.030-0.380-0.614-0.002
26A29MET0-0.066-0.0261.961-14.206-15.4527.993-3.717-3.030-0.046
27A30GLU-1-0.871-0.8953.280-33.203-32.4930.018-0.133-0.595-0.001
28A31LEU0-0.0310.0004.6241.0220.996-0.001-0.0040.0310.000
29A32GLH0-0.050-0.0676.6211.0781.0780.0000.0000.0000.000
30A33ALA0-0.025-0.0229.8421.2041.2040.0000.0000.0000.000
31A34ILE00.0050.01313.420-0.294-0.2940.0000.0000.0000.000
32A35PHE00.0430.02914.3950.8760.8760.0000.0000.0000.000
33A36THR0-0.035-0.03518.7110.3800.3800.0000.0000.0000.000
34A37ARG10.9190.92722.03311.10111.1010.0000.0000.0000.000
35A38ARG10.8280.92425.5809.5739.5730.0000.0000.0000.000
36A39ASP-1-0.809-0.90426.546-9.550-9.5500.0000.0000.0000.000
37A40ILE00.0280.00427.145-0.172-0.1720.0000.0000.0000.000
38A41ASN00.0020.01328.521-0.126-0.1260.0000.0000.0000.000
39A42LYS10.8240.91023.92911.20311.2030.0000.0000.0000.000
40A43VAL00.0330.01727.7390.2060.2060.0000.0000.0000.000
41A44ASP-1-0.810-0.89025.918-10.703-10.7030.0000.0000.0000.000
42A45SER0-0.043-0.04421.133-0.081-0.0810.0000.0000.0000.000
43A46ASN0-0.072-0.04223.088-0.090-0.0900.0000.0000.0000.000
44A47ASN00.0540.04320.957-0.332-0.3320.0000.0000.0000.000
45A48SER0-0.006-0.00218.162-0.214-0.2140.0000.0000.0000.000
46A49LYS10.9560.97410.01121.21021.2100.0000.0000.0000.000
47A50LEU0-0.023-0.01015.972-0.302-0.3020.0000.0000.0000.000
48A51VAL00.0030.00716.7760.1810.1810.0000.0000.0000.000
49A52HIS00.0490.05019.708-0.146-0.1460.0000.0000.0000.000
50A53ILE00.005-0.01321.212-0.344-0.3440.0000.0000.0000.000
51A54SER0-0.012-0.02822.453-0.311-0.3110.0000.0000.0000.000
52A55ARG10.9240.95518.30414.32714.3270.0000.0000.0000.000
53A56LEU0-0.029-0.00617.676-0.529-0.5290.0000.0000.0000.000
54A57GLU-1-0.852-0.93217.592-14.631-14.6310.0000.0000.0000.000
55A58LEU0-0.014-0.00118.213-0.683-0.6830.0000.0000.0000.000
56A59TYR0-0.023-0.01313.015-0.298-0.2980.0000.0000.0000.000
57A60LYS10.9100.92913.18116.51016.5100.0000.0000.0000.000
58A61ASP-1-0.835-0.89311.994-20.277-20.2770.0000.0000.0000.000
59A62THR0-0.032-0.0159.249-3.055-3.0550.0000.0000.0000.000
60A63VAL0-0.034-0.0228.398-1.944-1.9440.0000.0000.0000.000
61A64ASP-1-0.809-0.8765.995-36.502-36.5020.0000.0000.0000.000
62A65VAL0-0.008-0.0089.2501.4861.4860.0000.0000.0000.000
63A66MET0-0.0290.01611.393-0.414-0.4140.0000.0000.0000.000
64A67ILE00.0270.00311.6490.7580.7580.0000.0000.0000.000
65A68LEU00.0070.00315.4090.3460.3460.0000.0000.0000.000
66A69CYS0-0.060-0.01116.9620.3510.3510.0000.0000.0000.000
67A70GLY0-0.033-0.02319.8080.3920.3920.0000.0000.0000.000
68A71GLY00.011-0.00323.531-0.007-0.0070.0000.0000.0000.000
69A72SER0-0.013-0.02326.2580.2940.2940.0000.0000.0000.000
70A73ALA00.0660.02327.962-0.218-0.2180.0000.0000.0000.000
71A74THR0-0.007-0.01528.963-0.039-0.0390.0000.0000.0000.000
72A75ASP-1-0.848-0.89227.752-9.690-9.6900.0000.0000.0000.000
73A76LEU0-0.066-0.03423.248-0.204-0.2040.0000.0000.0000.000
74A77VAL0-0.0210.00726.740-0.257-0.2570.0000.0000.0000.000
75A78GLU-1-0.830-0.91929.026-9.539-9.5390.0000.0000.0000.000
76A79GLN0-0.005-0.00524.226-0.509-0.5090.0000.0000.0000.000
77A80GLY00.0290.01322.970-0.492-0.4920.0000.0000.0000.000
78A81PRO00.0380.00922.810-0.555-0.5550.0000.0000.0000.000
79A82MET0-0.0030.01724.137-0.150-0.1500.0000.0000.0000.000
80A83ILE0-0.024-0.00318.142-0.393-0.3930.0000.0000.0000.000
81A84ALA00.0440.02419.497-0.697-0.6970.0000.0000.0000.000
82A85SER0-0.050-0.03520.366-0.291-0.2910.0000.0000.0000.000
83A86GLN0-0.071-0.04418.759-0.199-0.1990.0000.0000.0000.000
84A87PHE00.0040.00213.390-0.827-0.8270.0000.0000.0000.000
85A88ASN00.0300.02111.8161.8751.8750.0000.0000.0000.000
86A89THR0-0.019-0.00214.742-0.160-0.1600.0000.0000.0000.000
87A90VAL00.0140.01414.1640.1260.1260.0000.0000.0000.000
88A91ASP-1-0.783-0.87817.209-12.251-12.2510.0000.0000.0000.000
89A92SER00.0430.01220.320-0.212-0.2120.0000.0000.0000.000
90A93PHE0-0.056-0.02922.6880.4750.4750.0000.0000.0000.000
91A94ASP-1-0.828-0.92425.958-9.664-9.6640.0000.0000.0000.000
92A95ASN0-0.0020.00428.5120.3590.3590.0000.0000.0000.000
93A96HIS00.0730.00530.6300.1250.1250.0000.0000.0000.000
94A97GLY0-0.0100.00732.682-0.014-0.0140.0000.0000.0000.000
95A98ARG10.8950.93932.8858.5578.5570.0000.0000.0000.000
96A99ILE00.0430.04128.212-0.160-0.1600.0000.0000.0000.000
97A100PRO0-0.0060.00429.923-0.289-0.2890.0000.0000.0000.000
98A101GLN00.0990.03331.558-0.302-0.3020.0000.0000.0000.000
99A102HIS0-0.079-0.03524.7560.2260.2260.0000.0000.0000.000
100A103PHE00.017-0.00525.090-0.271-0.2710.0000.0000.0000.000
101A104GLU-1-0.930-0.96227.339-9.171-9.1710.0000.0000.0000.000
102A105ARG10.8760.92728.8679.7599.7590.0000.0000.0000.000
103A106MET00.0150.02022.020-0.266-0.2660.0000.0000.0000.000
104A107ASP-1-0.793-0.84924.164-11.973-11.9730.0000.0000.0000.000
105A108GLU-1-0.825-0.89625.346-10.323-10.3230.0000.0000.0000.000
106A109ILE0-0.020-0.00123.913-0.052-0.0520.0000.0000.0000.000
107A110SER00.008-0.01820.436-0.325-0.3250.0000.0000.0000.000
108A111LYS10.8040.87621.42910.70010.7000.0000.0000.0000.000
109A112LYS10.7460.86523.37210.30610.3060.0000.0000.0000.000
110A113ALA00.0040.01320.9820.0580.0580.0000.0000.0000.000
111A114GLY0-0.0060.01319.695-0.591-0.5910.0000.0000.0000.000
112A115ASN0-0.050-0.02016.463-1.836-1.8360.0000.0000.0000.000
113A116ILE0-0.002-0.00214.9680.6880.6880.0000.0000.0000.000
114A117SER0-0.015-0.02417.019-0.569-0.5690.0000.0000.0000.000
115A118LEU0-0.050-0.00917.1030.5380.5380.0000.0000.0000.000
116A119ILE0-0.027-0.00619.768-0.088-0.0880.0000.0000.0000.000
117A120SER0-0.062-0.04722.5620.0360.0360.0000.0000.0000.000
118A121THR0-0.011-0.01118.0330.3220.3220.0000.0000.0000.000
119A122GLY00.0720.01921.4040.0450.0450.0000.0000.0000.000
120A123TRP0-0.022-0.00622.175-0.053-0.0530.0000.0000.0000.000
121A124ASP-1-0.757-0.82524.915-9.137-9.1370.0000.0000.0000.000
122A125PRO00.0260.03226.0870.1350.1350.0000.0000.0000.000
123A126GLY00.0310.00023.756-0.375-0.3750.0000.0000.0000.000
124A127LEU00.0150.00020.9810.2500.2500.0000.0000.0000.000
125A128PHE00.002-0.00224.7680.2560.2560.0000.0000.0000.000
126A129SER0-0.003-0.00626.9660.3650.3650.0000.0000.0000.000
127A130LEU00.0260.02122.7220.2390.2390.0000.0000.0000.000
128A131ASN0-0.032-0.03026.8150.3580.3580.0000.0000.0000.000
129A132ARG10.7920.86729.7129.3269.3260.0000.0000.0000.000
130A133LEU00.0390.03429.0040.2360.2360.0000.0000.0000.000
131A134LEU00.0090.01728.7850.1810.1810.0000.0000.0000.000
132A135GLY00.0380.00531.6480.1970.1970.0000.0000.0000.000
133A136GLU-1-0.841-0.92134.954-7.524-7.5240.0000.0000.0000.000
134A137SER0-0.047-0.03733.5300.1700.1700.0000.0000.0000.000
135A138ILE0-0.035-0.01332.7050.1080.1080.0000.0000.0000.000
136A139LEU0-0.0070.00336.2490.2260.2260.0000.0000.0000.000
137A140PRO00.0330.03439.0410.1160.1160.0000.0000.0000.000
138A141LYS10.8680.92740.9566.8736.8730.0000.0000.0000.000
139A142GLY00.0510.01742.1300.0150.0150.0000.0000.0000.000
140A143LYS10.7790.89042.0766.6286.6280.0000.0000.0000.000
141A144THR00.0140.01735.749-0.060-0.0600.0000.0000.0000.000
142A145HIS0-0.057-0.02838.1490.0050.0050.0000.0000.0000.000
143A146THR0-0.0030.00933.419-0.110-0.1100.0000.0000.0000.000
144A147PHE0-0.006-0.00535.5560.2430.2430.0000.0000.0000.000
145A148TRP0-0.011-0.02032.331-0.128-0.1280.0000.0000.0000.000
146A149GLY00.012-0.02133.8070.2240.2240.0000.0000.0000.000
147A150LYS10.9090.96335.1987.4257.4250.0000.0000.0000.000
148A151GLY00.0340.01433.404-0.173-0.1730.0000.0000.0000.000
149A152VAL0-0.0370.00832.9070.1770.1770.0000.0000.0000.000
150A153SER0-0.020-0.02432.969-0.265-0.2650.0000.0000.0000.000
151A154LEU0-0.026-0.03128.8490.0250.0250.0000.0000.0000.000
152A155GLY00.0920.05333.5320.1650.1650.0000.0000.0000.000
153A156HIS00.0290.01335.5050.0420.0420.0000.0000.0000.000
154A157SER0-0.019-0.01636.2440.2620.2620.0000.0000.0000.000
155A158ASP-1-0.845-0.91035.046-7.969-7.9690.0000.0000.0000.000
156A159ALA0-0.0330.00638.2130.0850.0850.0000.0000.0000.000
157A160ILE00.008-0.01041.2060.1530.1530.0000.0000.0000.000
158A161ARG10.8230.89635.5487.8587.8580.0000.0000.0000.000
159A162ARG10.8550.93039.5647.2037.2030.0000.0000.0000.000
160A163VAL0-0.046-0.00744.7660.1120.1120.0000.0000.0000.000
161A164GLN0-0.044-0.02547.8470.0180.0180.0000.0000.0000.000
162A165GLY00.0370.01949.4370.1460.1460.0000.0000.0000.000
163A166VAL0-0.041-0.01044.761-0.016-0.0160.0000.0000.0000.000
164A167LYS10.8910.97544.9016.3906.3900.0000.0000.0000.000
165A168ASN0-0.028-0.02838.731-0.286-0.2860.0000.0000.0000.000
166A169GLY00.0160.00440.5620.1790.1790.0000.0000.0000.000
167A170ILE0-0.068-0.01835.222-0.229-0.2290.0000.0000.0000.000
168A171GLN00.0400.01638.0360.0490.0490.0000.0000.0000.000
169A172TYR0-0.013-0.02636.120-0.296-0.2960.0000.0000.0000.000
170A173ILE00.0620.04436.3410.2360.2360.0000.0000.0000.000
171A174ILE00.002-0.02238.254-0.152-0.1520.0000.0000.0000.000
172A175PRO0-0.040-0.00937.6770.1290.1290.0000.0000.0000.000
173A176ILE00.0220.02440.5730.0570.0570.0000.0000.0000.000
174A177LYS10.8040.87342.3416.7366.7360.0000.0000.0000.000
175A178GLY00.0520.02544.082-0.037-0.0370.0000.0000.0000.000
176A179ALA00.0550.02644.4490.0220.0220.0000.0000.0000.000
177A180LEU0-0.0240.00037.965-0.063-0.0630.0000.0000.0000.000
178A181ASP-1-0.781-0.88541.995-6.817-6.8170.0000.0000.0000.000
179A182LYS10.8130.90844.1945.9535.9530.0000.0000.0000.000
180A183ALA0-0.019-0.00941.3480.0280.0280.0000.0000.0000.000
181A184ARG10.7990.86136.8407.5417.5410.0000.0000.0000.000
182A185SER0-0.024-0.01542.2200.0160.0160.0000.0000.0000.000
183A186GLY0-0.0030.00644.5190.0880.0880.0000.0000.0000.000
184A187GLU-1-0.855-0.92845.450-5.855-5.8550.0000.0000.0000.000
185A188GLN0-0.058-0.00744.7540.0060.0060.0000.0000.0000.000
186A189CYS00.0110.01946.5170.0350.0350.0000.0000.0000.000
187A190ASP-1-0.816-0.90046.174-6.589-6.5890.0000.0000.0000.000
188A191PHE0-0.006-0.02043.8170.0450.0450.0000.0000.0000.000
189A192THR0-0.021-0.03846.388-0.101-0.1010.0000.0000.0000.000
190A193THR0-0.020-0.04743.078-0.121-0.1210.0000.0000.0000.000
191A194ARG10.8350.92644.9375.8545.8540.0000.0000.0000.000
192A195GLU-1-0.824-0.87147.697-5.994-5.9940.0000.0000.0000.000
193A196LYS10.8460.92539.2437.2787.2780.0000.0000.0000.000
194A197HIS00.0010.00438.892-0.298-0.2980.0000.0000.0000.000
195A198GLU-1-0.935-0.95243.022-6.283-6.2830.0000.0000.0000.000
196A199MET0-0.0350.00339.675-0.230-0.2300.0000.0000.0000.000
197A200VAL0-0.017-0.00742.4030.1870.1870.0000.0000.0000.000
198A201CYS0-0.031-0.01442.192-0.214-0.2140.0000.0000.0000.000
199A202TYR00.009-0.01642.0180.0980.0980.0000.0000.0000.000
200A203VAL00.0260.01142.828-0.175-0.1750.0000.0000.0000.000
201A204VAL0-0.014-0.00643.1240.0840.0840.0000.0000.0000.000
202A205PRO0-0.021-0.01445.853-0.047-0.0470.0000.0000.0000.000
203A206GLU-1-0.936-0.95448.796-5.625-5.6250.0000.0000.0000.000
204A207GLU-1-0.885-0.92750.182-5.987-5.9870.0000.0000.0000.000
205A208ASN0-0.068-0.05551.9880.0700.0700.0000.0000.0000.000
206A209ALA0-0.006-0.01054.3190.0950.0950.0000.0000.0000.000
207A210ASP-1-0.862-0.90953.750-5.373-5.3730.0000.0000.0000.000
208A211LEU00.0090.00355.239-0.002-0.0020.0000.0000.0000.000
209A212LYS10.9220.93753.4995.4835.4830.0000.0000.0000.000
210A213LYS10.9030.93754.3914.9424.9420.0000.0000.0000.000
211A214ILE00.0380.02053.9310.0440.0440.0000.0000.0000.000
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