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: JQ7N9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2026843.76764
FMO2-HF: Nuclear repulsion 1955244.69938
FMO2-HF: Total energy -71599.068261
FMO2-MP2: Total energy -71808.009952


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.
-1.4071.5410.051-1.193-1.8040.004
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 : -0.009 / q_NPA : -0.016
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].
3A14THR0-0.008-0.0073.801-1.0351.047-0.015-0.987-1.0800.004
4A15TRP00.039-0.0026.3910.3080.3080.0000.0000.0000.000
5A16ILE00.0000.03010.174-0.166-0.1660.0000.0000.0000.000
6A17ASN0-0.039-0.03313.1100.0780.0780.0000.0000.0000.000
7A18ARG10.9140.96611.8880.2220.2220.0000.0000.0000.000
8A19PRO00.0240.03814.2670.0050.0050.0000.0000.0000.000
9A20GLU-1-0.894-0.93416.6510.0110.0110.0000.0000.0000.000
10A21TYR0-0.094-0.07618.6010.0420.0420.0000.0000.0000.000
11A22SER0-0.030-0.02414.582-0.025-0.0250.0000.0000.0000.000
12A23GLU-1-0.843-0.91014.9660.4700.4700.0000.0000.0000.000
13A24VAL0-0.033-0.0228.458-0.069-0.0690.0000.0000.0000.000
14A25SER0-0.021-0.00111.6250.1150.1150.0000.0000.0000.000
15A26GLU-1-0.974-0.9949.7771.7081.7080.0000.0000.0000.000
16A27ASP-1-0.948-0.96510.8371.0111.0110.0000.0000.0000.000
17A28ARG10.8000.87013.220-0.676-0.6760.0000.0000.0000.000
18A29ILE0-0.045-0.0129.8110.0920.0920.0000.0000.0000.000
19A30VAL00.0220.01714.315-0.090-0.0900.0000.0000.0000.000
20A31ILE0-0.029-0.01814.582-0.011-0.0110.0000.0000.0000.000
21A32VAL00.0030.00617.516-0.003-0.0030.0000.0000.0000.000
22A33SER0-0.034-0.03120.167-0.015-0.0150.0000.0000.0000.000
23A34ASP-1-0.766-0.89520.343-0.084-0.0840.0000.0000.0000.000
24A35ALA0-0.065-0.06023.0910.0000.0000.0000.0000.0000.000
25A36ASN0-0.064-0.02525.954-0.009-0.0090.0000.0000.0000.000
26A37THR00.0160.01621.889-0.015-0.0150.0000.0000.0000.000
27A38ASP-1-0.812-0.93323.595-0.143-0.1430.0000.0000.0000.000
28A39PHE0-0.048-0.01717.080-0.025-0.0250.0000.0000.0000.000
29A40TRP0-0.024-0.01822.9330.0220.0220.0000.0000.0000.000
30A41GLU-1-0.781-0.85924.850-0.281-0.2810.0000.0000.0000.000
31A42ASN0-0.022-0.01526.9010.0150.0150.0000.0000.0000.000
32A43THR0-0.026-0.02930.5220.0130.0130.0000.0000.0000.000
33A44TYR0-0.039-0.01132.2880.0050.0050.0000.0000.0000.000
34A45TYR0-0.004-0.02132.1020.0070.0070.0000.0000.0000.000
35A46ASP-1-0.945-0.94733.656-0.128-0.1280.0000.0000.0000.000
36A47PHE0-0.046-0.02629.5220.0030.0030.0000.0000.0000.000
37A48SER0-0.049-0.05425.869-0.006-0.0060.0000.0000.0000.000
38A49HIS0-0.055-0.01125.248-0.011-0.0110.0000.0000.0000.000
39A50TYR00.0840.00915.553-0.012-0.0120.0000.0000.0000.000
40A51THR00.0150.00020.541-0.033-0.0330.0000.0000.0000.000
41A52GLY00.0200.02219.9490.0250.0250.0000.0000.0000.000
42A53HIS00.0190.02216.228-0.023-0.0230.0000.0000.0000.000
43A54VAL00.004-0.01012.3440.0580.0580.0000.0000.0000.000
44A55TYR00.0030.0075.9060.1300.1300.0000.0000.0000.000
45A56GLY00.018-0.0048.0590.3600.3600.0000.0000.0000.000
46A57LYS10.9350.9882.798-2.681-2.0140.068-0.195-0.5400.000
47A58GLU-1-0.874-0.9314.648-1.126-0.943-0.001-0.009-0.1720.000
48A59THR0-0.066-0.0365.188-0.173-0.157-0.001-0.002-0.0120.000
49A60GLU-1-0.819-0.8997.853-0.943-0.9430.0000.0000.0000.000
50A61SER0-0.035-0.01010.8880.0940.0940.0000.0000.0000.000
51A62ASP-1-0.890-0.93612.600-0.277-0.2770.0000.0000.0000.000
52A63PHE0-0.008-0.02712.1170.0150.0150.0000.0000.0000.000
53A64THR00.0130.00014.246-0.039-0.0390.0000.0000.0000.000
54A65PHE0-0.0050.00511.0910.0380.0380.0000.0000.0000.000
55A66GLN00.0430.02614.722-0.066-0.0660.0000.0000.0000.000
56A67VAL00.0160.01515.3560.0620.0620.0000.0000.0000.000
57A68ARG10.7450.84017.254-0.281-0.2810.0000.0000.0000.000
58A69VAL0-0.016-0.02619.2320.0310.0310.0000.0000.0000.000
59A70LYS10.8820.94121.096-0.295-0.2950.0000.0000.0000.000
60A71ALA00.0250.01522.9570.0120.0120.0000.0000.0000.000
61A72ASP-1-0.923-0.94724.6370.1110.1110.0000.0000.0000.000
62A73PHE0-0.045-0.03824.876-0.011-0.0110.0000.0000.0000.000
63A74SER0-0.044-0.02429.2440.0040.0040.0000.0000.0000.000
64A75ALA0-0.028-0.00231.007-0.004-0.0040.0000.0000.0000.000
65A76LEU0-0.014-0.01531.482-0.001-0.0010.0000.0000.0000.000
66A77TYR00.009-0.01529.509-0.007-0.0070.0000.0000.0000.000
67A78ASP-1-0.716-0.83727.240-0.027-0.0270.0000.0000.0000.000
68A79GLN00.0100.00323.649-0.016-0.0160.0000.0000.0000.000
69A80ALA00.0230.00921.1740.0010.0010.0000.0000.0000.000
70A81GLY0-0.027-0.01519.6560.0130.0130.0000.0000.0000.000
71A82ILE0-0.087-0.02316.0810.0100.0100.0000.0000.0000.000
72A83PHE00.0610.00913.768-0.002-0.0020.0000.0000.0000.000
73A84ILE0-0.026-0.02113.691-0.048-0.0480.0000.0000.0000.000
74A85GLY00.0220.01013.0470.0680.0680.0000.0000.0000.000
75A86GLY00.012-0.00313.243-0.091-0.0910.0000.0000.0000.000
76A87THR0-0.035-0.02315.080-0.062-0.0620.0000.0000.0000.000
77A88GLU-1-0.857-0.93717.318-0.498-0.4980.0000.0000.0000.000
78A89THR0-0.0040.01019.5120.0300.0300.0000.0000.0000.000
79A90ALA0-0.019-0.00719.2650.0390.0390.0000.0000.0000.000
80A91TRP0-0.0210.00917.570-0.061-0.0610.0000.0000.0000.000
81A92ILE0-0.005-0.01217.9160.0560.0560.0000.0000.0000.000
82A93LYS10.8680.94018.1110.1420.1420.0000.0000.0000.000
83A94ALA0-0.005-0.01820.1490.0210.0210.0000.0000.0000.000
84A95GLY00.0200.01121.0570.0040.0040.0000.0000.0000.000
85A96ILE0-0.0090.00423.546-0.005-0.0050.0000.0000.0000.000
86A97GLU-1-0.896-0.96325.918-0.106-0.1060.0000.0000.0000.000
87A98PHE0-0.022-0.00228.4850.0080.0080.0000.0000.0000.000
88A99ASN00.017-0.01231.491-0.018-0.0180.0000.0000.0000.000
89A100ASP-1-0.921-0.94434.682-0.026-0.0260.0000.0000.0000.000
90A101GLY0-0.031-0.00336.9700.0040.0040.0000.0000.0000.000
91A102GLN00.002-0.00335.5610.0070.0070.0000.0000.0000.000
92A103PRO0-0.0150.00431.330-0.005-0.0050.0000.0000.0000.000
93A104SER0-0.019-0.02431.2730.0060.0060.0000.0000.0000.000
94A105ILE0-0.032-0.00725.6090.0000.0000.0000.0000.0000.000
95A106GLY00.019-0.00127.011-0.001-0.0010.0000.0000.0000.000
96A107CYS0-0.119-0.06122.869-0.006-0.0060.0000.0000.0000.000
97A108VAL00.0450.02223.7250.0100.0100.0000.0000.0000.000
98A109VAL00.003-0.00322.809-0.027-0.0270.0000.0000.0000.000
99A110THR00.0280.02222.2270.0330.0330.0000.0000.0000.000
100A111ASN00.0180.01622.423-0.048-0.0480.0000.0000.0000.000
101A112ASN0-0.057-0.03224.2560.0130.0130.0000.0000.0000.000
102A113ASN00.023-0.00626.1830.0050.0050.0000.0000.0000.000
103A114SER0-0.007-0.00525.386-0.006-0.0060.0000.0000.0000.000
104A115ASP-1-0.841-0.88827.013-0.126-0.1260.0000.0000.0000.000
105A116TRP0-0.014-0.00327.663-0.007-0.0070.0000.0000.0000.000
106A117SER00.0140.02328.7240.0050.0050.0000.0000.0000.000
107A118THR00.011-0.01329.3280.0000.0000.0000.0000.0000.000
108A119GLY00.0360.01631.5210.0010.0010.0000.0000.0000.000
109A120LEU00.0180.00632.9140.0030.0030.0000.0000.0000.000
110A121PHE00.0450.02128.504-0.001-0.0010.0000.0000.0000.000
111A122PRO0-0.058-0.02432.2390.0030.0030.0000.0000.0000.000
112A123GLY00.006-0.00631.3130.0050.0050.0000.0000.0000.000
113A124ASN00.0490.02529.968-0.014-0.0140.0000.0000.0000.000
114A125PRO00.011-0.00529.0820.0070.0070.0000.0000.0000.000
115A126GLY00.0410.02327.410-0.004-0.0040.0000.0000.0000.000
116A127ASP-1-0.855-0.90225.1120.2050.2050.0000.0000.0000.000
117A128PHE0-0.0360.00623.068-0.011-0.0110.0000.0000.0000.000
118A129TRP0-0.038-0.02021.0830.0030.0030.0000.0000.0000.000
119A130MET0-0.0220.00419.445-0.028-0.0280.0000.0000.0000.000
120A131ARG10.8430.91118.910-0.049-0.0490.0000.0000.0000.000
121A132VAL00.0010.01616.293-0.024-0.0240.0000.0000.0000.000
122A133THR0-0.052-0.03317.0710.0200.0200.0000.0000.0000.000
123A134SER00.0290.00715.447-0.028-0.0280.0000.0000.0000.000
124A135LYS10.9520.97516.7510.0800.0800.0000.0000.0000.000
125A136SER0-0.017-0.00819.1930.0210.0210.0000.0000.0000.000
126A137ASP-1-0.807-0.88919.230-0.322-0.3220.0000.0000.0000.000
127A138VAL0-0.050-0.00521.3390.0020.0020.0000.0000.0000.000
128A139ILE00.0140.01417.725-0.011-0.0110.0000.0000.0000.000
129A140ARG10.9320.96520.8930.0810.0810.0000.0000.0000.000
130A141ILE00.0240.00620.3980.0030.0030.0000.0000.0000.000
131A142GLN0-0.023-0.03122.3970.0060.0060.0000.0000.0000.000
132A143TYR00.0630.03323.0360.0020.0020.0000.0000.0000.000
133A144SER0-0.007-0.02625.1670.0070.0070.0000.0000.0000.000
134A145ILE00.0240.01226.5620.0040.0040.0000.0000.0000.000
135A146ASP-1-0.788-0.88628.8620.0960.0960.0000.0000.0000.000
136A147GLY00.0360.03825.3910.0140.0140.0000.0000.0000.000
137A148LYS10.8470.92526.189-0.112-0.1120.0000.0000.0000.000
138A149ASN0-0.087-0.05628.711-0.013-0.0130.0000.0000.0000.000
139A150TRP00.0120.00822.053-0.003-0.0030.0000.0000.0000.000
140A151PRO00.0170.02827.586-0.011-0.0110.0000.0000.0000.000
141A152LEU0-0.042-0.02926.360-0.002-0.0020.0000.0000.0000.000
142A153LEU0-0.0290.00124.6290.0040.0040.0000.0000.0000.000
143A154ARG10.8260.87924.7640.1300.1300.0000.0000.0000.000
144A155LEU0-0.039-0.02225.1660.0040.0040.0000.0000.0000.000
145A156CYS00.0050.01523.2570.0050.0050.0000.0000.0000.000
146A157THR00.0230.00323.5290.0080.0080.0000.0000.0000.000
147A158TRP0-0.054-0.06115.0810.0260.0260.0000.0000.0000.000
148A159PRO0-0.0030.01119.9160.0060.0060.0000.0000.0000.000
149A160GLY00.0410.03617.858-0.008-0.0080.0000.0000.0000.000
150A161THR0-0.015-0.01816.3960.0130.0130.0000.0000.0000.000
151A162ARG10.8510.90914.4850.4010.4010.0000.0000.0000.000
152A163LYS10.8750.9309.2411.3191.3190.0000.0000.0000.000
153A164ARG10.8570.94110.8290.5280.5280.0000.0000.0000.000
154A165PHE00.0060.0077.431-0.194-0.1940.0000.0000.0000.000
155A166ILE0-0.019-0.0038.8550.2530.2530.0000.0000.0000.000
156A167GLY00.030-0.0029.180-0.152-0.1520.0000.0000.0000.000
157A168VAL00.0000.01611.4220.0580.0580.0000.0000.0000.000
158A169MET00.0070.00314.244-0.092-0.0920.0000.0000.0000.000
159A170CYS0-0.036-0.01217.0350.0600.0600.0000.0000.0000.000
160A171CYS0-0.056-0.01719.911-0.048-0.0480.0000.0000.0000.000
161A172SER00.0720.04422.8470.0320.0320.0000.0000.0000.000
162A173PRO00.0240.03426.042-0.001-0.0010.0000.0000.0000.000
163A174LYS10.9270.96428.2040.0870.0870.0000.0000.0000.000
164A175ARG10.8380.92628.264-0.007-0.0070.0000.0000.0000.000
165A176LYS10.9340.95025.0630.0000.0000.0000.0000.0000.000
166A177GLY0-0.018-0.00924.9760.0110.0110.0000.0000.0000.000
167A178LEU0-0.0540.00223.9810.0220.0220.0000.0000.0000.000
168A179SER00.0120.00622.162-0.002-0.0020.0000.0000.0000.000
169A180ALA00.002-0.01119.8120.0000.0000.0000.0000.0000.000
170A181GLU-1-0.814-0.88118.7840.3630.3630.0000.0000.0000.000
171A182PHE0-0.036-0.03015.157-0.042-0.0420.0000.0000.0000.000
172A183THR00.0330.00515.8990.0850.0850.0000.0000.0000.000
173A184GLU-1-0.800-0.90217.0890.2480.2480.0000.0000.0000.000
174A185ILE0-0.0210.00411.026-0.076-0.0760.0000.0000.0000.000
175A186LEU0-0.020-0.01113.1460.1130.1130.0000.0000.0000.000
176A187LEU00.0080.0137.802-0.132-0.1320.0000.0000.0000.000
177A188THR0-0.022-0.01411.8260.1020.1020.0000.0000.0000.000
178A189THR00.0610.04613.499-0.086-0.0860.0000.0000.0000.000
179A190PRO0-0.028-0.01315.6870.0330.0330.0000.0000.0000.000