FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: VQQ41

Calculation Name: 3MDK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MDK

Chain ID: A

ChEMBL ID:

UniProt ID: Q88N92

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2354863.250024
FMO2-HF: Nuclear repulsion 2273640.763537
FMO2-HF: Total energy -81222.486487
FMO2-MP2: Total energy -81455.628794


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:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-124.585-113.578.453-5.91-13.555-0.049
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.918 / q_NPA : 0.965
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].
3A8ALA0-0.023-0.0222.713-11.866-9.0340.806-1.706-1.931-0.007
4A9CYS00.011-0.0035.3545.2445.334-0.001-0.005-0.0840.000
5A10TYR0-0.0110.0138.310-1.589-1.5890.0000.0000.0000.000
6A11SER00.0500.00610.9161.8051.8050.0000.0000.0000.000
7A12ASP-1-0.766-0.88412.930-17.479-17.4790.0000.0000.0000.000
8A13PRO00.0070.00013.3480.2950.2950.0000.0000.0000.000
9A14ALA00.0350.03014.9130.4650.4650.0000.0000.0000.000
10A15ASP-1-0.776-0.84717.972-15.606-15.6060.0000.0000.0000.000
11A16HIS0-0.073-0.05918.027-1.310-1.3100.0000.0000.0000.000
12A17TYR0-0.032-0.05019.291-0.333-0.3330.0000.0000.0000.000
13A18SER0-0.019-0.04414.526-1.175-1.1750.0000.0000.0000.000
14A19HIS0-0.0290.00114.560-0.631-0.6310.0000.0000.0000.000
15A20ARG10.8720.90915.37013.57713.5770.0000.0000.0000.000
16A21VAL0-0.016-0.00611.385-0.324-0.3240.0000.0000.0000.000
17A22ARG10.7840.85810.05621.04321.0430.0000.0000.0000.000
18A23LEU0-0.0070.00911.503-1.232-1.2320.0000.0000.0000.000
19A24VAL00.0440.00713.256-0.109-0.1090.0000.0000.0000.000
20A25LEU0-0.042-0.0267.353-0.490-0.4900.0000.0000.0000.000
21A26ALA0-0.0050.00110.060-1.219-1.2190.0000.0000.0000.000
22A27GLU-1-0.807-0.87611.159-16.502-16.5020.0000.0000.0000.000
23A28LYS10.7130.84611.27718.69218.6920.0000.0000.0000.000
24A29GLY00.0110.0259.8510.0530.0530.0000.0000.0000.000
25A30VAL0-0.049-0.0136.635-1.763-1.7630.0000.0000.0000.000
26A31SER0-0.022-0.0202.598-13.729-12.1422.434-1.430-2.590-0.017
27A32VAL00.020-0.0012.541-6.473-3.2331.151-1.629-2.761-0.017
28A33GLN0-0.087-0.0422.520-17.167-13.2433.900-2.221-5.603-0.008
29A34LEU00.0240.0103.5469.3998.7410.1631.081-0.5860.000
30A35ILE0-0.054-0.0296.078-1.186-1.1860.0000.0000.0000.000
31A36ASP-1-0.847-0.9358.469-24.072-24.0720.0000.0000.0000.000
32A37VAL0-0.076-0.05311.3420.5420.5420.0000.0000.0000.000
33A38ASP-1-0.804-0.90414.686-14.551-14.5510.0000.0000.0000.000
34A39PRO0-0.005-0.00718.0560.2170.2170.0000.0000.0000.000
35A40ALA0-0.064-0.01820.7580.5300.5300.0000.0000.0000.000
36A41HIS0-0.083-0.04319.9260.4530.4530.0000.0000.0000.000
37A42LEU00.0190.02118.721-0.939-0.9390.0000.0000.0000.000
38A43PRO00.0210.01014.3560.4010.4010.0000.0000.0000.000
39A44ARG10.9580.97016.69314.91914.9190.0000.0000.0000.000
40A45LYS10.9910.99111.41323.66923.6690.0000.0000.0000.000
41A46LEU0-0.0270.01014.142-0.607-0.6070.0000.0000.0000.000
42A47ALA00.000-0.01515.2740.5430.5430.0000.0000.0000.000
43A48GLU-1-0.976-0.99615.642-17.247-17.2470.0000.0000.0000.000
44A49VAL0-0.010-0.00112.9900.3410.3410.0000.0000.0000.000
45A50ASN0-0.022-0.01916.2631.0781.0780.0000.0000.0000.000
46A51PRO0-0.0090.00618.4970.0850.0850.0000.0000.0000.000
47A52TYR0-0.031-0.02021.4790.8340.8340.0000.0000.0000.000
48A53GLY0-0.028-0.00119.5890.1910.1910.0000.0000.0000.000
49A54SER00.0300.02218.5990.0830.0830.0000.0000.0000.000
50A55VAL0-0.033-0.00114.942-1.190-1.1900.0000.0000.0000.000
51A56PRO00.0290.01213.3950.8730.8730.0000.0000.0000.000
52A57THR0-0.072-0.04712.7021.5921.5920.0000.0000.0000.000
53A58LEU0-0.036-0.0147.964-2.283-2.2830.0000.0000.0000.000
54A59VAL00.004-0.0098.3922.2502.2500.0000.0000.0000.000
55A60ASP-1-0.845-0.9145.888-35.521-35.5210.0000.0000.0000.000
56A61ARG10.8950.9396.68924.17924.1790.0000.0000.0000.000
57A62ASP-1-0.944-0.9798.410-18.157-18.1570.0000.0000.0000.000
58A63LEU0-0.0220.00710.3971.2001.2000.0000.0000.0000.000
59A64ALA00.0220.00011.155-1.760-1.7600.0000.0000.0000.000
60A65LEU0-0.0360.00112.9601.4471.4470.0000.0000.0000.000
61A66TYR00.0510.00314.041-0.963-0.9630.0000.0000.0000.000
62A67GLU-1-0.730-0.83116.664-13.649-13.6490.0000.0000.0000.000
63A68SER00.0060.00517.151-0.431-0.4310.0000.0000.0000.000
64A69THR0-0.052-0.07517.641-0.443-0.4430.0000.0000.0000.000
65A70VAL00.0280.02117.586-0.079-0.0790.0000.0000.0000.000
66A71VAL0-0.0110.00212.545-0.555-0.5550.0000.0000.0000.000
67A72MET0-0.029-0.02014.403-0.780-0.7800.0000.0000.0000.000
68A73GLU-1-0.771-0.84416.241-13.439-13.4390.0000.0000.0000.000
69A74TYR00.0520.0429.3620.2330.2330.0000.0000.0000.000
70A75LEU0-0.048-0.0349.622-0.614-0.6140.0000.0000.0000.000
71A76GLU-1-0.779-0.88713.242-15.853-15.8530.0000.0000.0000.000
72A77GLU-1-0.980-0.98816.396-13.647-13.6470.0000.0000.0000.000
73A78ARG10.8210.9198.94822.94922.9490.0000.0000.0000.000
74A79TYR0-0.023-0.0166.955-0.882-0.8820.0000.0000.0000.000
75A80PRO00.0390.02512.7610.0640.0640.0000.0000.0000.000
76A81HIS0-0.065-0.00615.3520.8680.8680.0000.0000.0000.000
77A82PRO00.0500.02015.069-1.025-1.0250.0000.0000.0000.000
78A83PRO00.0300.01617.929-0.739-0.7390.0000.0000.0000.000
79A84LEU00.0270.01316.4370.1030.1030.0000.0000.0000.000
80A85MET0-0.047-0.02220.5870.4910.4910.0000.0000.0000.000
81A86PRO00.0500.03623.3570.0880.0880.0000.0000.0000.000
82A87VAL00.0510.02024.901-0.127-0.1270.0000.0000.0000.000
83A88TYR0-0.005-0.00526.8880.1050.1050.0000.0000.0000.000
84A89PRO00.0300.00130.073-0.109-0.1090.0000.0000.0000.000
85A90VAL00.0230.01231.216-0.102-0.1020.0000.0000.0000.000
86A91ALA00.0300.01730.847-0.024-0.0240.0000.0000.0000.000
87A92ARG10.9480.98322.04012.23912.2390.0000.0000.0000.000
88A93GLY00.0150.01028.255-0.253-0.2530.0000.0000.0000.000
89A94ASN0-0.004-0.01530.7680.0570.0570.0000.0000.0000.000
90A95SER00.0420.02226.4020.0170.0170.0000.0000.0000.000
91A96ARG10.8250.85923.07211.99711.9970.0000.0000.0000.000
92A97LEU0-0.032-0.00327.572-0.056-0.0560.0000.0000.0000.000
93A98LEU00.0010.00729.3360.0860.0860.0000.0000.0000.000
94A99MET00.0360.01721.912-0.027-0.0270.0000.0000.0000.000
95A100HIS0-0.010-0.00426.9500.2260.2260.0000.0000.0000.000
96A101ARG10.8560.90129.1888.9988.9980.0000.0000.0000.000
97A102ILE00.0300.03026.5750.1630.1630.0000.0000.0000.000
98A103GLN00.003-0.00325.470-0.421-0.4210.0000.0000.0000.000
99A104ARG10.9010.94528.4289.0249.0240.0000.0000.0000.000
100A105ASP-1-0.843-0.91031.976-8.885-8.8850.0000.0000.0000.000
101A106TRP0-0.024-0.02329.5530.0600.0600.0000.0000.0000.000
102A107CYS0-0.0090.02525.862-0.150-0.1500.0000.0000.0000.000
103A108ALA00.0440.04328.314-0.060-0.0600.0000.0000.0000.000
104A109LEU0-0.018-0.00930.8580.1390.1390.0000.0000.0000.000
105A110ALA00.012-0.00427.6030.0950.0950.0000.0000.0000.000
106A111ASP-1-0.751-0.84626.452-12.261-12.2610.0000.0000.0000.000
107A112THR0-0.065-0.03428.8590.1780.1780.0000.0000.0000.000
108A113VAL0-0.055-0.03330.9220.1620.1620.0000.0000.0000.000
109A114LEU0-0.002-0.00525.2180.0910.0910.0000.0000.0000.000
110A115ASP-1-0.820-0.88828.812-10.574-10.5740.0000.0000.0000.000
111A116PRO0-0.012-0.01128.5050.4340.4340.0000.0000.0000.000
112A117ARG10.8750.93531.5609.8289.8280.0000.0000.0000.000
113A118SER0-0.0070.01633.7160.3610.3610.0000.0000.0000.000
114A119SER00.0010.00135.7020.1000.1000.0000.0000.0000.000
115A120GLU-1-0.778-0.91038.043-8.692-8.6920.0000.0000.0000.000
116A121ALA0-0.046-0.00839.767-0.012-0.0120.0000.0000.0000.000
117A122ALA00.0450.02138.0410.0030.0030.0000.0000.0000.000
118A123ARG10.8200.90733.3769.1619.1610.0000.0000.0000.000
119A124THR0-0.050-0.04136.661-0.104-0.1040.0000.0000.0000.000
120A125GLU-1-0.945-0.96839.315-7.778-7.7780.0000.0000.0000.000
121A126ALA00.0340.02934.707-0.005-0.0050.0000.0000.0000.000
122A127ARG10.9030.94533.5308.9818.9810.0000.0000.0000.000
123A128LYS10.8180.89435.8407.3607.3600.0000.0000.0000.000
124A129ALA00.0220.00937.7110.0580.0580.0000.0000.0000.000
125A130LEU00.0340.02530.3810.0020.0020.0000.0000.0000.000
126A131ARG10.8910.93934.9797.9937.9930.0000.0000.0000.000
127A132GLU-1-0.801-0.88836.215-7.536-7.5360.0000.0000.0000.000
128A133SER0-0.0120.00535.6400.1220.1220.0000.0000.0000.000
129A134LEU00.0200.01030.902-0.002-0.0020.0000.0000.0000.000
130A135THR0-0.060-0.04234.6790.0250.0250.0000.0000.0000.000
131A136GLY0-0.041-0.01437.5400.1350.1350.0000.0000.0000.000
132A137VAL00.011-0.00233.9020.1250.1250.0000.0000.0000.000
133A138SER00.0400.02335.284-0.145-0.1450.0000.0000.0000.000
134A139PRO0-0.034-0.01836.316-0.121-0.1210.0000.0000.0000.000
135A140LEU00.0580.03235.3200.0210.0210.0000.0000.0000.000
136A141PHE0-0.048-0.03029.303-0.134-0.1340.0000.0000.0000.000
137A142SER0-0.079-0.05433.888-0.125-0.1250.0000.0000.0000.000
138A143GLU-1-0.993-0.99136.359-8.063-8.0630.0000.0000.0000.000
139A144PHE0-0.0270.00332.0560.0720.0720.0000.0000.0000.000
140A145ALA0-0.0050.00729.072-0.069-0.0690.0000.0000.0000.000
141A146CYS0-0.071-0.01925.148-0.393-0.3930.0000.0000.0000.000
142A147PHE00.035-0.00227.3890.4950.4950.0000.0000.0000.000
143A148MET0-0.051-0.01629.299-0.066-0.0660.0000.0000.0000.000
144A149SER0-0.0100.00127.2870.1450.1450.0000.0000.0000.000
145A150ASP-1-0.833-0.92429.811-9.792-9.7920.0000.0000.0000.000
146A151GLU-1-0.973-0.97824.207-12.240-12.2400.0000.0000.0000.000
147A152GLN0-0.022-0.02119.9960.6820.6820.0000.0000.0000.000
148A153SER00.035-0.00422.158-0.084-0.0840.0000.0000.0000.000
149A154LEU00.053-0.00217.762-0.320-0.3200.0000.0000.0000.000
150A155VAL00.0300.01421.151-0.061-0.0610.0000.0000.0000.000
151A156ASP-1-0.730-0.83122.523-12.416-12.4160.0000.0000.0000.000
152A157CYS0-0.045-0.01318.573-0.424-0.4240.0000.0000.0000.000
153A158CYS0-0.050-0.01920.377-0.405-0.4050.0000.0000.0000.000
154A159LEU0-0.0020.00522.7190.1680.1680.0000.0000.0000.000
155A160LEU00.001-0.00921.0200.1800.1800.0000.0000.0000.000
156A161PRO00.0160.01918.8930.2120.2120.0000.0000.0000.000
157A162ILE00.011-0.00321.1850.2400.2400.0000.0000.0000.000
158A163LEU00.0280.00724.8740.3210.3210.0000.0000.0000.000
159A164TRP0-0.012-0.01920.4630.4540.4540.0000.0000.0000.000
160A165ARG10.7910.86018.33515.71715.7170.0000.0000.0000.000
161A166LEU0-0.0120.00224.9890.3850.3850.0000.0000.0000.000
162A167PRO00.0240.01126.6520.3380.3380.0000.0000.0000.000
163A168VAL00.0250.01324.8550.2920.2920.0000.0000.0000.000
164A169LEU0-0.0220.00627.5380.2590.2590.0000.0000.0000.000
165A170GLY0-0.0060.01530.1690.3920.3920.0000.0000.0000.000
166A171ILE0-0.071-0.04232.0180.3990.3990.0000.0000.0000.000
167A172GLU-1-0.829-0.89832.394-8.908-8.9080.0000.0000.0000.000
168A173LEU0-0.010-0.00731.7610.2260.2260.0000.0000.0000.000
169A174PRO00.0150.00935.5820.0950.0950.0000.0000.0000.000
170A175ARG10.8870.91736.4508.3088.3080.0000.0000.0000.000
171A176GLN0-0.003-0.01139.583-0.045-0.0450.0000.0000.0000.000
172A177ALA0-0.0100.00935.8280.0430.0430.0000.0000.0000.000
173A178LYS10.8470.90135.3378.4268.4260.0000.0000.0000.000
174A179PRO00.0510.03834.636-0.231-0.2310.0000.0000.0000.000
175A180LEU00.0130.01430.204-0.309-0.3090.0000.0000.0000.000
176A181LEU00.001-0.01830.601-0.374-0.3740.0000.0000.0000.000
177A182ASP-1-0.773-0.86730.227-9.370-9.3700.0000.0000.0000.000
178A183TYR0-0.088-0.07625.647-0.395-0.3950.0000.0000.0000.000
179A184MET0-0.031-0.01726.159-0.358-0.3580.0000.0000.0000.000
180A185GLU-1-0.981-0.96925.498-10.620-10.6200.0000.0000.0000.000
181A186ARG10.8610.92225.78410.27410.2740.0000.0000.0000.000
182A187GLN0-0.013-0.02122.470-1.135-1.1350.0000.0000.0000.000
183A188PHE0-0.015-0.02121.090-0.660-0.6600.0000.0000.0000.000
184A189ALA00.0060.01620.237-0.708-0.7080.0000.0000.0000.000
185A190ARG10.7790.87118.71015.12815.1280.0000.0000.0000.000
186A191GLU-1-0.908-0.95915.338-17.743-17.7430.0000.0000.0000.000
187A192PRO00.0140.00913.640-0.937-0.9370.0000.0000.0000.000
188A193PHE00.0510.02113.968-0.990-0.9900.0000.0000.0000.000
189A194GLN00.0150.01515.431-0.962-0.9620.0000.0000.0000.000
190A195ALA0-0.039-0.01710.243-0.581-0.5810.0000.0000.0000.000
191A196SER0-0.054-0.03210.420-1.664-1.6640.0000.0000.0000.000
192A197LEU0-0.061-0.01012.404-0.383-0.3830.0000.0000.0000.000
193A198SER0-0.009-0.02112.390-1.159-1.1590.0000.0000.0000.000
194A199SER00.006-0.02013.4220.8200.8200.0000.0000.0000.000
195A200VAL00.0860.04015.3780.9710.9710.0000.0000.0000.000
196A201GLU-1-0.714-0.81615.552-18.210-18.2100.0000.0000.0000.000
197A202ARG10.8330.91114.37119.41519.4150.0000.0000.0000.000
198A203GLU-1-0.940-0.96218.987-14.237-14.2370.0000.0000.0000.000
199A204MET0-0.085-0.01720.1160.7280.7280.0000.0000.0000.000
200A205ARG10.7960.90823.16112.71212.7120.0000.0000.0000.000