Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VR381

Calculation Name: 3MTV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MTV

Chain ID: A

ChEMBL ID:

UniProt ID: B2ZAB4

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241825.430598
FMO2-HF: Nuclear repulsion 2162045.176539
FMO2-HF: Total energy -79780.254058
FMO2-MP2: Total energy -80016.409476


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-1.863-0.2153.797-3.262-2.183-0.003
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.025
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].
3A3VAL0-0.050-0.0243.9900.5182.073-0.006-0.916-0.6330.001
4A4TYR0-0.031-0.0356.3780.3850.3850.0000.0000.0000.000
5A5ASP-1-0.794-0.88710.188-0.151-0.1510.0000.0000.0000.000
6A6ILE0-0.030-0.02312.366-0.017-0.0170.0000.0000.0000.000
7A7GLY00.0060.00815.2380.0470.0470.0000.0000.0000.000
8A8ARG10.8290.88517.4850.1720.1720.0000.0000.0000.000
9A9GLY00.0160.01818.6920.0210.0210.0000.0000.0000.000
10A10ALA0-0.018-0.00114.4700.0240.0240.0000.0000.0000.000
11A11VAL0-0.017-0.00910.016-0.056-0.0560.0000.0000.0000.000
12A12MET0-0.018-0.0159.2740.1530.1530.0000.0000.0000.000
13A13TYR0-0.0070.0014.248-0.223-0.154-0.001-0.010-0.0590.000
14A14VAL0-0.001-0.0244.5660.5140.642-0.001-0.015-0.1110.000
15A15ALA00.0560.0301.979-2.071-2.2983.797-2.305-1.266-0.004
16A16GLY00.0270.0333.7480.4050.5280.008-0.016-0.1140.000
17A17GLY00.004-0.0017.269-0.405-0.4050.0000.0000.0000.000
18A18LYS10.8760.9327.777-0.956-0.9560.0000.0000.0000.000
19A19VAL00.0350.0206.857-0.002-0.0020.0000.0000.0000.000
20A20SER00.0090.0037.9350.0720.0720.0000.0000.0000.000
21A21TRP00.0390.0119.585-0.165-0.1650.0000.0000.0000.000
22A22ALA00.0360.02410.7220.0820.0820.0000.0000.0000.000
23A23PRO00.020-0.00712.489-0.061-0.0610.0000.0000.0000.000
24A24ARG10.8340.94613.6810.2350.2350.0000.0000.0000.000
25A25GLY00.0590.01714.2810.0040.0040.0000.0000.0000.000
26A26GLY00.0650.02917.028-0.005-0.0050.0000.0000.0000.000
27A27ASN0-0.063-0.02218.378-0.034-0.0340.0000.0000.0000.000
28A28GLU-1-0.824-0.92317.458-0.135-0.1350.0000.0000.0000.000
29A29VAL0-0.073-0.02913.035-0.043-0.0430.0000.0000.0000.000
30A30LYS10.8410.90014.6910.2420.2420.0000.0000.0000.000
31A31PHE00.0440.0299.135-0.019-0.0190.0000.0000.0000.000
32A32GLU-1-0.884-0.94111.892-0.900-0.9000.0000.0000.0000.000
33A33PRO0-0.019-0.01012.782-0.013-0.0130.0000.0000.0000.000
34A34VAL00.0380.02812.477-0.067-0.0670.0000.0000.0000.000
35A35PRO00.0800.04311.8080.1420.1420.0000.0000.0000.000
36A36LYS10.7510.87014.9250.4140.4140.0000.0000.0000.000
37A37GLU-1-0.836-0.92615.415-0.408-0.4080.0000.0000.0000.000
38A38LEU00.0480.01610.4220.0250.0250.0000.0000.0000.000
39A39LYS10.9330.97314.6150.3440.3440.0000.0000.0000.000
40A40LEU0-0.031-0.00517.0440.0390.0390.0000.0000.0000.000
41A41VAL00.070-0.00212.2470.0370.0370.0000.0000.0000.000
42A42ALA00.0400.04714.3850.0360.0360.0000.0000.0000.000
43A43ASN00.0430.01915.2490.0310.0310.0000.0000.0000.000
44A44ARG10.9401.00417.3370.0800.0800.0000.0000.0000.000
45A45LEU00.0770.04212.2470.0220.0220.0000.0000.0000.000
46A46HIS00.0080.01516.0510.0190.0190.0000.0000.0000.000
47A47THR0-0.024-0.01417.2090.0150.0150.0000.0000.0000.000
48A48SER0-0.052-0.04719.6050.0180.0180.0000.0000.0000.000
49A49PHE00.0160.01616.6430.0190.0190.0000.0000.0000.000
50A50PRO00.0460.01918.050-0.026-0.0260.0000.0000.0000.000
51A51PRO0-0.002-0.00614.5200.0330.0330.0000.0000.0000.000
52A52HIS00.0060.01711.6910.0450.0450.0000.0000.0000.000
53A53HIS0-0.066-0.00912.7560.0870.0870.0000.0000.0000.000
54A54VAL00.0360.0248.947-0.029-0.0290.0000.0000.0000.000
55A55VAL00.0180.01811.295-0.042-0.0420.0000.0000.0000.000
56A56ASP-1-0.769-0.85211.6300.3130.3130.0000.0000.0000.000
57A57MET0-0.043-0.01913.054-0.039-0.0390.0000.0000.0000.000
58A58SER0-0.026-0.04115.132-0.038-0.0380.0000.0000.0000.000
59A59LYS10.7970.88616.426-0.253-0.2530.0000.0000.0000.000
60A60PHE00.0300.02516.6360.0040.0040.0000.0000.0000.000
61A61THR00.0160.00920.461-0.019-0.0190.0000.0000.0000.000
62A62PHE0-0.017-0.02617.968-0.008-0.0080.0000.0000.0000.000
63A63ILE00.0380.01923.559-0.004-0.0040.0000.0000.0000.000
64A64THR0-0.0050.00426.229-0.006-0.0060.0000.0000.0000.000
65A65PRO0-0.016-0.02224.7450.0070.0070.0000.0000.0000.000
66A66GLY00.0150.01927.129-0.003-0.0030.0000.0000.0000.000
67A67SER0-0.031-0.02529.2680.0030.0030.0000.0000.0000.000
68A68GLY00.0590.03127.9680.0040.0040.0000.0000.0000.000
69A69VAL0-0.0090.00527.078-0.002-0.0020.0000.0000.0000.000
70A70SER00.018-0.01323.3570.0090.0090.0000.0000.0000.000
71A71MET0-0.014-0.00421.6640.0050.0050.0000.0000.0000.000
72A72ARG10.7760.88719.945-0.019-0.0190.0000.0000.0000.000
73A73VAL00.0210.02523.534-0.012-0.0120.0000.0000.0000.000
74A74GLU-1-0.853-0.92422.7640.0510.0510.0000.0000.0000.000
75A75TYR0-0.048-0.00922.688-0.009-0.0090.0000.0000.0000.000
76A76GLN00.0270.01127.0170.0040.0040.0000.0000.0000.000
77A77TYR0-0.010-0.00729.2010.0050.0050.0000.0000.0000.000
78A78GLY0-0.018-0.02025.454-0.004-0.0040.0000.0000.0000.000
79A79CYS0-0.101-0.05422.518-0.013-0.0130.0000.0000.0000.000
80A80LEU00.0250.01721.2350.0000.0000.0000.0000.0000.000
81A81PRO00.0980.06725.052-0.005-0.0050.0000.0000.0000.000
82A82ALA00.0170.00627.5190.0120.0120.0000.0000.0000.000
83A83ASP-1-0.885-0.92729.7230.0610.0610.0000.0000.0000.000
84A84THR0-0.110-0.08125.1510.0110.0110.0000.0000.0000.000
85A85VAL0-0.015-0.00823.8320.0190.0190.0000.0000.0000.000
86A86PRO0-0.0010.00025.516-0.008-0.0080.0000.0000.0000.000
87A87GLU-1-0.844-0.90528.7570.0690.0690.0000.0000.0000.000
88A88GLY0-0.022-0.00131.467-0.005-0.0050.0000.0000.0000.000
89A89ASN0-0.024-0.04432.3250.0050.0050.0000.0000.0000.000
90A90CYS0-0.0710.00731.6510.0030.0030.0000.0000.0000.000
91A91TRP00.021-0.02234.1300.0010.0010.0000.0000.0000.000
92A92TRP00.0160.00335.843-0.001-0.0010.0000.0000.0000.000
93A93ARG10.9550.98833.747-0.108-0.1080.0000.0000.0000.000
94A94LEU0-0.022-0.03035.750-0.001-0.0010.0000.0000.0000.000
95A95LEU0-0.083-0.04239.575-0.002-0.0020.0000.0000.0000.000
96A96ASP-1-0.843-0.93341.6070.0770.0770.0000.0000.0000.000
97A97SER0-0.031-0.01144.249-0.002-0.0020.0000.0000.0000.000
98A98LEU0-0.094-0.04145.953-0.003-0.0030.0000.0000.0000.000
99A99PRO00.0490.03348.6500.0000.0000.0000.0000.0000.000
100A100PRO00.1190.05549.3630.0010.0010.0000.0000.0000.000
101A101GLU-1-0.813-0.90949.5510.0470.0470.0000.0000.0000.000
102A102VAL0-0.017-0.00848.4980.0000.0000.0000.0000.0000.000
103A103GLN00.0130.02445.2370.0010.0010.0000.0000.0000.000
104A104TYR00.037-0.00345.6900.0000.0000.0000.0000.0000.000
105A105LYS10.8010.89346.790-0.045-0.0450.0000.0000.0000.000
106A106GLU-1-0.744-0.86143.7070.0640.0640.0000.0000.0000.000
107A107ILE0-0.055-0.00341.6660.0020.0020.0000.0000.0000.000
108A108ARG10.9630.97342.568-0.042-0.0420.0000.0000.0000.000
109A109HIS0-0.020-0.00144.084-0.002-0.0020.0000.0000.0000.000
110A110ALA0-0.040-0.02839.0040.0000.0000.0000.0000.0000.000
111A111ASN0-0.006-0.02839.9520.0010.0010.0000.0000.0000.000
112A112GLN0-0.076-0.00241.373-0.005-0.0050.0000.0000.0000.000
113A113PHE0-0.052-0.01839.0670.0000.0000.0000.0000.0000.000
114A114GLY00.0200.01136.611-0.002-0.0020.0000.0000.0000.000
115A115TYR00.004-0.03634.588-0.001-0.0010.0000.0000.0000.000
116A116GLN00.0400.06935.4620.0060.0060.0000.0000.0000.000
117A117THR0-0.048-0.03931.754-0.003-0.0030.0000.0000.0000.000
118A118LYS10.8820.94526.742-0.065-0.0650.0000.0000.0000.000
119A119HIS0-0.015-0.01726.3470.0080.0080.0000.0000.0000.000
120A120GLY00.0720.04729.2930.0100.0100.0000.0000.0000.000
121A121VAL0-0.051-0.03332.286-0.006-0.0060.0000.0000.0000.000
122A122PRO0-0.001-0.00331.5350.0080.0080.0000.0000.0000.000
123A123GLY00.0770.03831.4750.0090.0090.0000.0000.0000.000
124A124LYS10.8590.92931.600-0.120-0.1200.0000.0000.0000.000
125A125TYR0-0.0250.00535.603-0.005-0.0050.0000.0000.0000.000
126A126LEU00.0380.01334.103-0.004-0.0040.0000.0000.0000.000
127A127GLN0-0.013-0.02736.3730.0020.0020.0000.0000.0000.000
128A128ARG10.9740.99938.273-0.084-0.0840.0000.0000.0000.000
129A129ARG10.8270.91540.511-0.070-0.0700.0000.0000.0000.000
130A130LEU00.0980.01539.2890.0030.0030.0000.0000.0000.000
131A131GLN0-0.0160.01842.282-0.002-0.0020.0000.0000.0000.000
132A132VAL0-0.047-0.03744.029-0.003-0.0030.0000.0000.0000.000
133A133ASN0-0.087-0.05945.629-0.004-0.0040.0000.0000.0000.000
134A134GLY00.0140.03147.402-0.002-0.0020.0000.0000.0000.000
135A135LEU0-0.0120.00443.4710.0020.0020.0000.0000.0000.000
136A136ARG10.7820.85441.870-0.085-0.0850.0000.0000.0000.000
137A137ALA0-0.0310.01137.4070.0000.0000.0000.0000.0000.000
138A138VAL0-0.007-0.00838.2740.0040.0040.0000.0000.0000.000
139A139THR0-0.011-0.00633.5130.0050.0050.0000.0000.0000.000
140A140ASP-1-0.716-0.85335.4190.1170.1170.0000.0000.0000.000
141A141THR00.001-0.02734.0670.0060.0060.0000.0000.0000.000
142A142HIS0-0.100-0.03134.5810.0120.0120.0000.0000.0000.000
143A143GLY0-0.0030.01036.587-0.006-0.0060.0000.0000.0000.000
144A144PRO0-0.016-0.01035.9470.0070.0070.0000.0000.0000.000
145A145ILE00.0340.01433.5120.0010.0010.0000.0000.0000.000
146A146VAL00.0020.03228.2980.0060.0060.0000.0000.0000.000
147A147ILE0-0.036-0.01727.365-0.005-0.0050.0000.0000.0000.000
148A148GLN0-0.014-0.02524.7170.0040.0040.0000.0000.0000.000
149A149TYR0-0.0190.00017.948-0.005-0.0050.0000.0000.0000.000
150A150PHE00.0520.01217.7280.0160.0160.0000.0000.0000.000
151A151SER0-0.026-0.02814.4030.0250.0250.0000.0000.0000.000
152A152VAL00.000-0.00213.2140.0870.0870.0000.0000.0000.000
153A153LYS10.8900.94415.426-0.661-0.6610.0000.0000.0000.000
154A154GLU-1-0.862-0.92716.2090.4920.4920.0000.0000.0000.000
155A155SER00.016-0.00818.645-0.050-0.0500.0000.0000.0000.000
156A156TRP0-0.080-0.05418.743-0.005-0.0050.0000.0000.0000.000
157A157ILE00.0110.01620.605-0.026-0.0260.0000.0000.0000.000
158A158ARG10.9270.93223.121-0.201-0.2010.0000.0000.0000.000
159A159HIS0-0.010-0.02225.970-0.028-0.0280.0000.0000.0000.000
160A160LEU0-0.0210.00128.2200.0110.0110.0000.0000.0000.000
161A161LYS10.8790.96827.434-0.194-0.1940.0000.0000.0000.000
162A162LEU0-0.002-0.01632.2310.0060.0060.0000.0000.0000.000
163A163VAL0-0.061-0.05232.4330.0060.0060.0000.0000.0000.000
164A164GLU-1-0.884-0.95032.3130.1180.1180.0000.0000.0000.000
165A165GLU-1-0.841-0.87332.5270.1080.1080.0000.0000.0000.000
166A166PRO00.0180.00529.0300.0110.0110.0000.0000.0000.000
167A167SER0-0.025-0.02524.535-0.011-0.0110.0000.0000.0000.000
168A168LEU00.0470.04625.048-0.006-0.0060.0000.0000.0000.000
169A169PRO00.019-0.00521.2260.0280.0280.0000.0000.0000.000
170A170GLY0-0.001-0.00418.268-0.005-0.0050.0000.0000.0000.000
171A171PHE0-0.031-0.02619.1320.0180.0180.0000.0000.0000.000
172A172GLU-1-0.934-0.96318.4900.4050.4050.0000.0000.0000.000
173A173ASP-1-0.853-0.92821.9460.2140.2140.0000.0000.0000.000
174A174LEU0-0.058-0.03523.2760.0200.0200.0000.0000.0000.000
175A175LEU0-0.026-0.02525.0660.0010.0010.0000.0000.0000.000
176A176ARG10.9220.98628.752-0.162-0.1620.0000.0000.0000.000
177A177ILE0-0.032-0.02432.263-0.001-0.0010.0000.0000.0000.000
178A178ARG10.7920.84735.316-0.108-0.1080.0000.0000.0000.000
179A179VAL0-0.034-0.02838.9020.0020.0020.0000.0000.0000.000
180A180GLU-1-0.791-0.86841.1260.0880.0880.0000.0000.0000.000
181A181PRO00.0720.02044.6420.0000.0000.0000.0000.0000.000
182A182ASN0-0.047-0.01345.4230.0030.0030.0000.0000.0000.000
183A183THR00.020-0.01447.165-0.002-0.0020.0000.0000.0000.000
184A184SER0-0.025-0.00849.667-0.004-0.0040.0000.0000.0000.000
185A185PRO00.0180.01148.9480.0030.0030.0000.0000.0000.000
186A186LEU00.0130.00342.3810.0010.0010.0000.0000.0000.000
187A187ALA00.0410.02445.827-0.002-0.0020.0000.0000.0000.000
188A188GLY00.0390.03745.0570.0030.0030.0000.0000.0000.000
189A189LYS10.8940.91843.381-0.094-0.0940.0000.0000.0000.000
190A190ASP-1-0.827-0.91139.7070.1130.1130.0000.0000.0000.000
191A191GLU-1-0.761-0.83338.5270.1180.1180.0000.0000.0000.000
192A192LYS10.7890.87336.444-0.128-0.1280.0000.0000.0000.000
193A193ILE00.0490.04437.6240.0030.0030.0000.0000.0000.000
194A194PHE00.0200.00830.1960.0070.0070.0000.0000.0000.000
195A195ARG10.9560.99332.403-0.152-0.1520.0000.0000.0000.000
196A196PHE00.0620.02331.8270.0120.0120.0000.0000.0000.000
197A197GLY00.0180.03429.0820.0060.0060.0000.0000.0000.000
198A198SER0-0.009-0.01929.578-0.015-0.0150.0000.0000.0000.000
199A199HIS0-0.010-0.02826.8890.0070.0070.0000.0000.0000.000
200A200LYS10.8860.97322.337-0.239-0.2390.0000.0000.0000.000
201A201TRP0-0.0130.00226.996-0.019-0.0190.0000.0000.0000.000
202A202TYR00.0170.00127.8830.0070.0070.0000.0000.0000.000