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: 3J8LL

Calculation Name: 3MEP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MEP

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D507

Base Structure: X-ray

Registration Date: 2023-09-23

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2028731.386603
FMO2-HF: Nuclear repulsion 1957131.886722
FMO2-HF: Total energy -71599.499881
FMO2-MP2: Total energy -71808.478035


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:12:GLN)


Summations of interaction energy for fragment #1(A:12:GLN)
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.
-27.926-30.65712.379-5.16-4.4870.053
Interaction energy analysis for fragmet #1(A:12:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.006
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].
3A14THR00.001-0.0093.856-1.0910.207-0.009-0.509-0.7800.001
4A15TRP00.0390.0006.2790.5360.5360.0000.0000.0000.000
5A16ILE0-0.0210.01210.120-0.178-0.1780.0000.0000.0000.000
6A17ASN0-0.027-0.03213.1270.0380.0380.0000.0000.0000.000
7A18ARG10.9250.96812.3000.0740.0740.0000.0000.0000.000
8A19PRO00.0240.03514.534-0.033-0.0330.0000.0000.0000.000
9A20GLU-1-0.879-0.93017.1060.0600.0600.0000.0000.0000.000
10A21TYR0-0.074-0.06018.848-0.001-0.0010.0000.0000.0000.000
11A22SER0-0.033-0.02414.5480.0180.0180.0000.0000.0000.000
12A23GLU-1-0.855-0.90915.1150.4730.4730.0000.0000.0000.000
13A24VAL0-0.026-0.0278.5610.0490.0490.0000.0000.0000.000
14A25SER0-0.0120.01111.722-0.051-0.0510.0000.0000.0000.000
15A26GLU-1-0.991-1.0019.7941.3971.3970.0000.0000.0000.000
16A27ASP-1-0.933-0.96210.8491.1851.1850.0000.0000.0000.000
17A28ARG10.7900.87013.741-0.676-0.6760.0000.0000.0000.000
18A29ILE0-0.018-0.0089.6190.0840.0840.0000.0000.0000.000
19A30VAL0-0.015-0.00514.187-0.077-0.0770.0000.0000.0000.000
20A31ILE0-0.023-0.01814.380-0.014-0.0140.0000.0000.0000.000
21A32VAL00.0100.00917.607-0.012-0.0120.0000.0000.0000.000
22A33SER0-0.011-0.01020.475-0.026-0.0260.0000.0000.0000.000
23A34ASP-1-0.738-0.87420.8800.0850.0850.0000.0000.0000.000
24A35ALA0-0.036-0.03023.5190.0090.0090.0000.0000.0000.000
25A36ASN0-0.062-0.02526.358-0.006-0.0060.0000.0000.0000.000
26A37THR00.0070.01322.159-0.002-0.0020.0000.0000.0000.000
27A38ASP-1-0.789-0.93123.6570.1750.1750.0000.0000.0000.000
28A39PHE0-0.024-0.00616.871-0.007-0.0070.0000.0000.0000.000
29A40TRP0-0.037-0.02622.6820.0290.0290.0000.0000.0000.000
30A41GLU-1-0.812-0.87824.6400.0200.0200.0000.0000.0000.000
31A42ASN0-0.028-0.02026.6560.0010.0010.0000.0000.0000.000
32A43THR00.001-0.02030.388-0.001-0.0010.0000.0000.0000.000
33A44TYR0-0.0190.01132.4770.0060.0060.0000.0000.0000.000
34A45TYR0-0.024-0.02932.127-0.001-0.0010.0000.0000.0000.000
35A46ASP-1-0.964-0.96733.3370.0420.0420.0000.0000.0000.000
36A47PHE0-0.014-0.00629.312-0.008-0.0080.0000.0000.0000.000
37A48SER0-0.047-0.04525.4210.0070.0070.0000.0000.0000.000
38A49HIS0-0.048-0.01224.807-0.018-0.0180.0000.0000.0000.000
39A50TYR00.0870.02215.0160.0490.0490.0000.0000.0000.000
40A51THR00.0320.01519.939-0.019-0.0190.0000.0000.0000.000
41A52GLY00.0090.00020.2330.0030.0030.0000.0000.0000.000
42A53HIS00.0080.01216.419-0.019-0.0190.0000.0000.0000.000
43A54VAL00.000-0.01412.3260.0720.0720.0000.0000.0000.000
44A55TYR0-0.0130.0065.7890.2270.2270.0000.0000.0000.000
45A56GLY00.0330.0028.2880.2320.2320.0000.0000.0000.000
46A57LYS10.8800.9341.948-31.862-35.89112.388-4.651-3.7070.052
47A58GLU-1-0.862-0.9244.941-0.217-0.2170.0000.0000.0000.000
48A59THR0-0.046-0.0285.4171.6481.6480.0000.0000.0000.000
49A60GLU-1-0.805-0.8958.113-0.330-0.3300.0000.0000.0000.000
50A61SER0-0.056-0.01510.948-0.061-0.0610.0000.0000.0000.000
51A62ASP-1-0.841-0.90412.9240.5650.5650.0000.0000.0000.000
52A63PHE0-0.022-0.02512.5380.1390.1390.0000.0000.0000.000
53A64THR0-0.016-0.02214.652-0.191-0.1910.0000.0000.0000.000
54A65PHE00.003-0.00210.9850.1780.1780.0000.0000.0000.000
55A66GLN00.0240.01314.770-0.224-0.2240.0000.0000.0000.000
56A67VAL00.0260.02015.1980.1390.1390.0000.0000.0000.000
57A68ARG10.7440.83617.096-0.573-0.5730.0000.0000.0000.000
58A69VAL0-0.011-0.01618.9060.0600.0600.0000.0000.0000.000
59A70LYS10.8650.93220.908-0.573-0.5730.0000.0000.0000.000
60A71ALA00.0100.00722.7950.0160.0160.0000.0000.0000.000
61A72ASP-1-0.854-0.90524.5960.2720.2720.0000.0000.0000.000
62A73PHE0-0.053-0.03324.950-0.021-0.0210.0000.0000.0000.000
63A74SER0-0.061-0.03429.169-0.013-0.0130.0000.0000.0000.000
64A75ALA0-0.015-0.00631.008-0.014-0.0140.0000.0000.0000.000
65A76LEU0-0.005-0.00631.4400.0110.0110.0000.0000.0000.000
66A77TYR00.031-0.00229.410-0.012-0.0120.0000.0000.0000.000
67A78ASP-1-0.700-0.81027.1010.1990.1990.0000.0000.0000.000
68A79GLN0-0.048-0.04023.4930.0180.0180.0000.0000.0000.000
69A80ALA00.0330.01321.1960.0070.0070.0000.0000.0000.000
70A81GLY0-0.022-0.02019.641-0.019-0.0190.0000.0000.0000.000
71A82ILE0-0.071-0.02015.9600.0750.0750.0000.0000.0000.000
72A83PHE00.0610.01513.767-0.078-0.0780.0000.0000.0000.000
73A84ILE0-0.026-0.01813.9640.1380.1380.0000.0000.0000.000
74A85GLY00.0380.01613.287-0.081-0.0810.0000.0000.0000.000
75A86GLY0-0.016-0.01213.1310.0720.0720.0000.0000.0000.000
76A87THR0-0.040-0.02014.912-0.064-0.0640.0000.0000.0000.000
77A88GLU-1-0.867-0.93917.136-0.073-0.0730.0000.0000.0000.000
78A89THR0-0.0040.00119.1020.0170.0170.0000.0000.0000.000
79A90ALA0-0.018-0.00419.0340.0150.0150.0000.0000.0000.000
80A91TRP0-0.0140.00317.5190.0380.0380.0000.0000.0000.000
81A92ILE00.004-0.01218.019-0.012-0.0120.0000.0000.0000.000
82A93LYS10.8590.95118.243-0.163-0.1630.0000.0000.0000.000
83A94ALA0-0.001-0.01120.261-0.029-0.0290.0000.0000.0000.000
84A95GLY00.0210.00521.0620.0560.0560.0000.0000.0000.000
85A96ILE0-0.0090.01523.406-0.029-0.0290.0000.0000.0000.000
86A97GLU-1-0.887-0.96025.6350.2100.2100.0000.0000.0000.000
87A98PHE0-0.031-0.00428.212-0.006-0.0060.0000.0000.0000.000
88A99ASN00.0040.00031.241-0.007-0.0070.0000.0000.0000.000
89A100ASP-1-0.887-0.94734.5580.1210.1210.0000.0000.0000.000
90A101GLY0-0.0280.00136.573-0.004-0.0040.0000.0000.0000.000
91A102GLN0-0.036-0.01135.4350.0010.0010.0000.0000.0000.000
92A103PRO0-0.008-0.00331.5010.0040.0040.0000.0000.0000.000
93A104SER0-0.013-0.02531.415-0.008-0.0080.0000.0000.0000.000
94A105ILE0-0.033-0.01525.8050.0200.0200.0000.0000.0000.000
95A106GLY00.0290.00127.123-0.020-0.0200.0000.0000.0000.000
96A107CYS0-0.111-0.05922.9780.0340.0340.0000.0000.0000.000
97A108VAL00.0430.02723.928-0.024-0.0240.0000.0000.0000.000
98A109VAL0-0.003-0.00622.9030.0300.0300.0000.0000.0000.000
99A110THR00.0130.01322.129-0.023-0.0230.0000.0000.0000.000
100A111ASN0-0.005-0.00922.446-0.005-0.0050.0000.0000.0000.000
101A112ASN0-0.037-0.03024.279-0.022-0.0220.0000.0000.0000.000
102A113ASN00.0240.01626.111-0.015-0.0150.0000.0000.0000.000
103A114SER0-0.002-0.00125.3520.0110.0110.0000.0000.0000.000
104A115ASP-1-0.807-0.85027.2000.1620.1620.0000.0000.0000.000
105A116TRP00.003-0.00527.4220.0210.0210.0000.0000.0000.000
106A117SER0-0.0120.00828.561-0.009-0.0090.0000.0000.0000.000
107A118THR00.0170.00229.2030.0240.0240.0000.0000.0000.000
108A119GLY00.0280.01331.478-0.013-0.0130.0000.0000.0000.000
109A120LEU00.0270.01333.0070.0090.0090.0000.0000.0000.000
110A121PHE00.0410.01728.4400.0120.0120.0000.0000.0000.000
111A122PRO0-0.049-0.01732.009-0.007-0.0070.0000.0000.0000.000
112A123GLY00.0040.00031.311-0.002-0.0020.0000.0000.0000.000
113A124ASN00.0310.01329.838-0.023-0.0230.0000.0000.0000.000
114A125PRO00.002-0.00528.8680.0220.0220.0000.0000.0000.000
115A126GLY00.0490.02027.3640.0140.0140.0000.0000.0000.000
116A127ASP-1-0.855-0.90224.9630.4430.4430.0000.0000.0000.000
117A128PHE0-0.0280.01023.022-0.018-0.0180.0000.0000.0000.000
118A129TRP0-0.042-0.02721.1000.0230.0230.0000.0000.0000.000
119A130MET0-0.0110.01019.298-0.067-0.0670.0000.0000.0000.000
120A131ARG10.8020.89318.780-0.514-0.5140.0000.0000.0000.000
121A132VAL00.0280.02616.535-0.080-0.0800.0000.0000.0000.000
122A133THR0-0.014-0.00817.6200.1110.1110.0000.0000.0000.000
123A134SER00.0270.02215.795-0.107-0.1070.0000.0000.0000.000
124A135LYS10.9420.96216.995-0.321-0.3210.0000.0000.0000.000
125A136SER0-0.007-0.01619.438-0.062-0.0620.0000.0000.0000.000
126A137ASP-1-0.791-0.84319.2470.2730.2730.0000.0000.0000.000
127A138VAL0-0.036-0.00821.371-0.031-0.0310.0000.0000.0000.000
128A139ILE00.0120.01117.8600.0590.0590.0000.0000.0000.000
129A140ARG10.9340.96221.162-0.387-0.3870.0000.0000.0000.000
130A141ILE00.0220.01520.5230.0590.0590.0000.0000.0000.000
131A142GLN0-0.015-0.02122.629-0.011-0.0110.0000.0000.0000.000
132A143TYR00.0670.03923.0450.0360.0360.0000.0000.0000.000
133A144SER0-0.013-0.03625.044-0.017-0.0170.0000.0000.0000.000
134A145ILE00.0420.01226.5670.0090.0090.0000.0000.0000.000
135A146ASP-1-0.781-0.86628.5070.3070.3070.0000.0000.0000.000
136A147GLY00.0520.04125.219-0.003-0.0030.0000.0000.0000.000
137A148LYS10.7990.89325.865-0.290-0.2900.0000.0000.0000.000
138A149ASN0-0.055-0.03528.579-0.013-0.0130.0000.0000.0000.000
139A150TRP0-0.0010.00321.7210.0210.0210.0000.0000.0000.000
140A151PRO0-0.0010.01527.701-0.004-0.0040.0000.0000.0000.000
141A152LEU0-0.039-0.03126.5770.0270.0270.0000.0000.0000.000
142A153LEU0-0.0200.00424.796-0.014-0.0140.0000.0000.0000.000
143A154ARG10.8080.86024.772-0.238-0.2380.0000.0000.0000.000
144A155LEU0-0.041-0.02625.3030.0340.0340.0000.0000.0000.000
145A156CYS0-0.019-0.00323.345-0.021-0.0210.0000.0000.0000.000
146A157THR00.0480.02023.9480.0240.0240.0000.0000.0000.000
147A158TRP0-0.047-0.04415.0120.0260.0260.0000.0000.0000.000
148A159PRO0-0.0220.00119.876-0.023-0.0230.0000.0000.0000.000
149A160GLY00.0570.03517.863-0.034-0.0340.0000.0000.0000.000
150A161THR0-0.020-0.00915.7990.0190.0190.0000.0000.0000.000
151A162ARG10.8320.86814.483-0.219-0.2190.0000.0000.0000.000
152A163LYS10.8430.9298.9920.3920.3920.0000.0000.0000.000
153A164ARG10.8440.91010.987-0.683-0.6830.0000.0000.0000.000
154A165PHE00.0080.0067.3510.3580.3580.0000.0000.0000.000
155A166ILE0-0.025-0.0089.071-0.150-0.1500.0000.0000.0000.000
156A167GLY00.022-0.0039.4550.3120.3120.0000.0000.0000.000
157A168VAL00.0050.01511.662-0.107-0.1070.0000.0000.0000.000
158A169MET00.000-0.00214.071-0.058-0.0580.0000.0000.0000.000
159A170CYS0-0.042-0.01316.848-0.004-0.0040.0000.0000.0000.000
160A171CYS0-0.0310.02019.768-0.038-0.0380.0000.0000.0000.000
161A172SER00.0510.01922.6700.0180.0180.0000.0000.0000.000
162A173PRO00.0270.03126.193-0.022-0.0220.0000.0000.0000.000
163A174LYS10.8660.92828.249-0.111-0.1110.0000.0000.0000.000
164A175ARG10.7810.89128.262-0.199-0.1990.0000.0000.0000.000
165A176LYS10.8080.89324.262-0.096-0.0960.0000.0000.0000.000
166A177GLY00.014-0.00125.148-0.001-0.0010.0000.0000.0000.000
167A178LEU0-0.056-0.01923.8740.0050.0050.0000.0000.0000.000
168A179SER0-0.049-0.02222.5080.0300.0300.0000.0000.0000.000
169A180ALA00.0540.01120.041-0.010-0.0100.0000.0000.0000.000
170A181GLU-1-0.799-0.87518.8660.5780.5780.0000.0000.0000.000
171A182PHE0-0.036-0.02215.161-0.007-0.0070.0000.0000.0000.000
172A183THR00.0300.00916.0620.0380.0380.0000.0000.0000.000
173A184GLU-1-0.788-0.89717.1560.5950.5950.0000.0000.0000.000
174A185ILE0-0.0220.00510.933-0.012-0.0120.0000.0000.0000.000
175A186LEU0-0.014-0.00112.9350.1230.1230.0000.0000.0000.000
176A187LEU00.0010.0047.831-0.089-0.0890.0000.0000.0000.000
177A188THR0-0.006-0.00211.4720.1180.1180.0000.0000.0000.000
178A189THR00.0660.03313.579-0.012-0.0120.0000.0000.0000.000
179A190PRO0-0.053-0.01915.833-0.053-0.0530.0000.0000.0000.000