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: NNJKQ

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 OptH
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 -2026143.039545
FMO2-HF: Nuclear repulsion 1954544.913161
FMO2-HF: Total energy -71598.126383
FMO2-MP2: Total energy -71807.170798


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.
0.5053.4720.031-1.206-1.790.002
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 : -0.017 / 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].
3A14THR0-0.015-0.0043.660-0.8311.286-0.009-1.007-1.1010.002
4A15TRP00.0480.0046.1680.3780.3780.0000.0000.0000.000
5A16ILE00.0040.0329.954-0.187-0.1870.0000.0000.0000.000
6A17ASN0-0.062-0.03913.0540.1110.1110.0000.0000.0000.000
7A18ARG10.9050.95611.4430.6180.6180.0000.0000.0000.000
8A19PRO00.0160.03314.0100.0340.0340.0000.0000.0000.000
9A20GLU-1-0.939-0.96716.476-0.141-0.1410.0000.0000.0000.000
10A21TYR0-0.097-0.05518.4510.0680.0680.0000.0000.0000.000
11A22SER0-0.049-0.03714.338-0.067-0.0670.0000.0000.0000.000
12A23GLU-1-0.885-0.94414.8880.4020.4020.0000.0000.0000.000
13A24VAL0-0.028-0.0168.401-0.139-0.1390.0000.0000.0000.000
14A25SER0-0.035-0.01211.6230.2150.2150.0000.0000.0000.000
15A26GLU-1-0.972-0.9889.9701.9591.9590.0000.0000.0000.000
16A27ASP-1-0.941-0.96511.0301.0101.0100.0000.0000.0000.000
17A28ARG10.8200.89213.307-0.611-0.6110.0000.0000.0000.000
18A29ILE0-0.035-0.0089.9740.0640.0640.0000.0000.0000.000
19A30VAL00.0300.02114.267-0.077-0.0770.0000.0000.0000.000
20A31ILE0-0.022-0.01414.358-0.037-0.0370.0000.0000.0000.000
21A32VAL00.0140.01417.3810.0220.0220.0000.0000.0000.000
22A33SER0-0.0500.02620.002-0.028-0.0280.0000.0000.0000.000
23A34ASP-1-0.738-0.88620.079-0.313-0.3130.0000.0000.0000.000
24A35ALA0-0.070-0.06822.9010.0020.0020.0000.0000.0000.000
25A36ASN0-0.063-0.02125.746-0.010-0.0100.0000.0000.0000.000
26A37THR00.0100.01221.556-0.020-0.0200.0000.0000.0000.000
27A38ASP-1-0.817-0.94623.469-0.366-0.3660.0000.0000.0000.000
28A39PHE0-0.039-0.00716.949-0.041-0.0410.0000.0000.0000.000
29A40TRP0-0.037-0.03022.7840.0300.0300.0000.0000.0000.000
30A41GLU-1-0.782-0.86924.723-0.538-0.5380.0000.0000.0000.000
31A42ASN00.0120.00926.7350.0190.0190.0000.0000.0000.000
32A43THR0-0.044-0.04830.3630.0250.0250.0000.0000.0000.000
33A44TYR0-0.046-0.01532.1450.0060.0060.0000.0000.0000.000
34A45TYR0-0.007-0.02031.9500.0190.0190.0000.0000.0000.000
35A46ASP-1-0.942-0.94833.604-0.253-0.2530.0000.0000.0000.000
36A47PHE0-0.050-0.02629.1750.0060.0060.0000.0000.0000.000
37A48SER0-0.053-0.05225.632-0.012-0.0120.0000.0000.0000.000
38A49HIS0-0.044-0.01125.110-0.015-0.0150.0000.0000.0000.000
39A50TYR00.0950.02415.247-0.040-0.0400.0000.0000.0000.000
40A51THR00.0170.00120.329-0.055-0.0550.0000.0000.0000.000
41A52GLY00.0250.02319.8550.0300.0300.0000.0000.0000.000
42A53HIS00.0240.02916.023-0.024-0.0240.0000.0000.0000.000
43A54VAL00.009-0.00411.8130.0700.0700.0000.0000.0000.000
44A55TYR00.0160.0126.206-0.091-0.0910.0000.0000.0000.000
45A56GLY00.010-0.0098.0300.5150.5150.0000.0000.0000.000
46A57LYS10.9330.9872.966-0.3270.3240.042-0.190-0.5030.000
47A58GLU-1-0.880-0.9334.516-1.801-1.619-0.001-0.008-0.1720.000
48A59THR0-0.057-0.0255.195-0.426-0.409-0.001-0.001-0.0140.000
49A60GLU-1-0.878-0.9517.890-1.473-1.4730.0000.0000.0000.000
50A61SER0-0.065-0.03010.9620.1840.1840.0000.0000.0000.000
51A62ASP-1-0.877-0.92412.701-0.626-0.6260.0000.0000.0000.000
52A63PHE0-0.033-0.04412.297-0.022-0.0220.0000.0000.0000.000
53A64THR00.003-0.00714.400-0.002-0.0020.0000.0000.0000.000
54A65PHE0-0.0060.00111.0520.0150.0150.0000.0000.0000.000
55A66GLN00.0390.02714.861-0.011-0.0110.0000.0000.0000.000
56A67VAL00.0210.01815.4500.0350.0350.0000.0000.0000.000
57A68ARG10.7670.85417.237-0.146-0.1460.0000.0000.0000.000
58A69VAL0-0.002-0.02019.1760.0120.0120.0000.0000.0000.000
59A70LYS10.9280.97321.064-0.134-0.1340.0000.0000.0000.000
60A71ALA00.0300.01622.9880.0060.0060.0000.0000.0000.000
61A72ASP-1-0.935-0.95324.5950.0020.0020.0000.0000.0000.000
62A73PHE0-0.054-0.03924.756-0.011-0.0110.0000.0000.0000.000
63A74SER0-0.051-0.02929.2020.0170.0170.0000.0000.0000.000
64A75ALA0-0.0230.00330.7900.0040.0040.0000.0000.0000.000
65A76LEU0-0.001-0.00431.473-0.007-0.0070.0000.0000.0000.000
66A77TYR0-0.002-0.02329.424-0.007-0.0070.0000.0000.0000.000
67A78ASP-1-0.745-0.85727.241-0.200-0.2000.0000.0000.0000.000
68A79GLN00.0140.00423.587-0.027-0.0270.0000.0000.0000.000
69A80ALA00.0240.00921.138-0.012-0.0120.0000.0000.0000.000
70A81GLY0-0.028-0.01319.6220.0400.0400.0000.0000.0000.000
71A82ILE0-0.081-0.01916.117-0.027-0.0270.0000.0000.0000.000
72A83PHE00.0650.01113.7780.0350.0350.0000.0000.0000.000
73A84ILE0-0.017-0.01913.644-0.121-0.1210.0000.0000.0000.000
74A85GLY00.0210.00812.9540.1410.1410.0000.0000.0000.000
75A86GLY00.007-0.00413.127-0.159-0.1590.0000.0000.0000.000
76A87THR0-0.040-0.02314.906-0.089-0.0890.0000.0000.0000.000
77A88GLU-1-0.863-0.94717.131-0.863-0.8630.0000.0000.0000.000
78A89THR00.0010.01419.3100.0400.0400.0000.0000.0000.000
79A90ALA0-0.018-0.00519.0350.0670.0670.0000.0000.0000.000
80A91TRP0-0.0110.01517.417-0.115-0.1150.0000.0000.0000.000
81A92ILE0-0.009-0.01217.8270.1050.1050.0000.0000.0000.000
82A93LYS10.8700.94118.0480.3560.3560.0000.0000.0000.000
83A94ALA0-0.012-0.02620.0900.0540.0540.0000.0000.0000.000
84A95GLY00.0210.01221.050-0.023-0.0230.0000.0000.0000.000
85A96ILE0-0.0120.00723.5460.0100.0100.0000.0000.0000.000
86A97GLU-1-0.909-0.96625.886-0.307-0.3070.0000.0000.0000.000
87A98PHE0-0.0080.00128.4430.0210.0210.0000.0000.0000.000
88A99ASN0-0.009-0.03931.457-0.032-0.0320.0000.0000.0000.000
89A100ASP-1-0.930-0.94434.622-0.118-0.1180.0000.0000.0000.000
90A101GLY0-0.032-0.00436.9360.0090.0090.0000.0000.0000.000
91A102GLN00.011-0.00135.5260.0060.0060.0000.0000.0000.000
92A103PRO0-0.029-0.00131.298-0.012-0.0120.0000.0000.0000.000
93A104SER00.006-0.00431.5100.0150.0150.0000.0000.0000.000
94A105ILE0-0.0160.00325.811-0.013-0.0130.0000.0000.0000.000
95A106GLY00.018-0.00427.0080.0090.0090.0000.0000.0000.000
96A107CYS0-0.114-0.05322.898-0.022-0.0220.0000.0000.0000.000
97A108VAL00.0380.02223.6750.0290.0290.0000.0000.0000.000
98A109VAL0-0.010-0.01522.739-0.053-0.0530.0000.0000.0000.000
99A110THR00.0330.02422.1400.0650.0650.0000.0000.0000.000
100A111ASN00.0230.01722.306-0.088-0.0880.0000.0000.0000.000
101A112ASN0-0.044-0.02124.1080.0100.0100.0000.0000.0000.000
102A113ASN00.026-0.00526.0290.0030.0030.0000.0000.0000.000
103A114SER0-0.013-0.00625.296-0.013-0.0130.0000.0000.0000.000
104A115ASP-1-0.914-0.91926.924-0.285-0.2850.0000.0000.0000.000
105A116TRP00.002-0.00927.594-0.022-0.0220.0000.0000.0000.000
106A117SER00.0360.02828.6860.0130.0130.0000.0000.0000.000
107A118THR0-0.002-0.01729.295-0.010-0.0100.0000.0000.0000.000
108A119GLY00.0330.01231.4970.0080.0080.0000.0000.0000.000
109A120LEU00.0230.00932.917-0.001-0.0010.0000.0000.0000.000
110A121PHE00.0350.02028.451-0.007-0.0070.0000.0000.0000.000
111A122PRO0-0.057-0.02632.1810.0080.0080.0000.0000.0000.000
112A123GLY00.017-0.00331.2890.0110.0110.0000.0000.0000.000
113A124ASN00.0480.03030.213-0.014-0.0140.0000.0000.0000.000
114A125PRO00.010-0.00529.053-0.001-0.0010.0000.0000.0000.000
115A126GLY00.0530.02527.375-0.017-0.0170.0000.0000.0000.000
116A127ASP-1-0.866-0.89725.3830.0870.0870.0000.0000.0000.000
117A128PHE0-0.0280.00623.174-0.005-0.0050.0000.0000.0000.000
118A129TRP0-0.0250.00121.085-0.012-0.0120.0000.0000.0000.000
119A130MET0-0.022-0.00419.468-0.011-0.0110.0000.0000.0000.000
120A131ARG10.8640.91819.0430.1320.1320.0000.0000.0000.000
121A132VAL00.0090.01316.343-0.005-0.0050.0000.0000.0000.000
122A133THR0-0.042-0.01317.1870.0110.0110.0000.0000.0000.000
123A134SER00.0210.00115.531-0.015-0.0150.0000.0000.0000.000
124A135LYS10.9530.97416.8540.2460.2460.0000.0000.0000.000
125A136SER0-0.048-0.02419.1850.0520.0520.0000.0000.0000.000
126A137ASP-1-0.895-0.94519.277-0.580-0.5800.0000.0000.0000.000
127A138VAL0-0.050-0.01121.3650.0090.0090.0000.0000.0000.000
128A139ILE00.0220.01617.707-0.036-0.0360.0000.0000.0000.000
129A140ARG10.9330.96320.9640.2870.2870.0000.0000.0000.000
130A141ILE00.0160.00320.394-0.016-0.0160.0000.0000.0000.000
131A142GLN0-0.042-0.04822.4800.0090.0090.0000.0000.0000.000
132A143TYR00.0680.04023.119-0.015-0.0150.0000.0000.0000.000
133A144SER00.003-0.01925.2550.0240.0240.0000.0000.0000.000
134A145ILE00.0390.01726.546-0.004-0.0040.0000.0000.0000.000
135A146ASP-1-0.832-0.90328.8220.0050.0050.0000.0000.0000.000
136A147GLY00.0390.03325.3810.0220.0220.0000.0000.0000.000
137A148LYS10.8470.91626.184-0.051-0.0510.0000.0000.0000.000
138A149ASN0-0.069-0.03628.707-0.015-0.0150.0000.0000.0000.000
139A150TRP00.0030.00222.148-0.017-0.0170.0000.0000.0000.000
140A151PRO00.0140.03027.718-0.013-0.0130.0000.0000.0000.000
141A152LEU0-0.029-0.02626.443-0.015-0.0150.0000.0000.0000.000
142A153LEU0-0.0360.00024.5600.0120.0120.0000.0000.0000.000
143A154ARG10.8770.91324.7980.3410.3410.0000.0000.0000.000
144A155LEU0-0.036-0.01625.133-0.006-0.0060.0000.0000.0000.000
145A156CYS0-0.0270.00523.7440.0110.0110.0000.0000.0000.000
146A157THR00.0390.00323.5450.0080.0080.0000.0000.0000.000
147A158TRP0-0.052-0.04315.2470.0340.0340.0000.0000.0000.000
148A159PRO0-0.0100.00820.0350.0160.0160.0000.0000.0000.000
149A160GLY00.0560.03917.759-0.006-0.0060.0000.0000.0000.000
150A161THR0-0.016-0.01615.9830.0230.0230.0000.0000.0000.000
151A162ARG10.9130.94514.0960.7970.7970.0000.0000.0000.000
152A163LYS10.9470.9849.6861.9551.9550.0000.0000.0000.000
153A164ARG10.9190.98610.7631.1641.1640.0000.0000.0000.000
154A165PHE00.0160.0067.003-0.377-0.3770.0000.0000.0000.000
155A166ILE0-0.0150.0028.7740.4270.4270.0000.0000.0000.000
156A167GLY00.025-0.0089.184-0.369-0.3690.0000.0000.0000.000
157A168VAL0-0.0100.01511.4160.1610.1610.0000.0000.0000.000
158A169MET00.0080.00214.213-0.138-0.1380.0000.0000.0000.000
159A170CYS0-0.046-0.02217.0110.1110.1110.0000.0000.0000.000
160A171CYS0-0.047-0.00619.911-0.065-0.0650.0000.0000.0000.000
161A172SER00.009-0.04022.8470.0550.0550.0000.0000.0000.000
162A173PRO00.0180.02325.8600.0070.0070.0000.0000.0000.000
163A174LYS10.9360.96928.1440.2330.2330.0000.0000.0000.000
164A175ARG10.8480.94027.9580.1530.1530.0000.0000.0000.000
165A176LYS11.0080.98025.6820.0980.0980.0000.0000.0000.000
166A177GLY0-0.043-0.02324.8300.0240.0240.0000.0000.0000.000
167A178LEU0-0.0010.02123.7810.0310.0310.0000.0000.0000.000
168A179SER00.0190.01122.033-0.029-0.0290.0000.0000.0000.000
169A180ALA00.005-0.00719.7030.0110.0110.0000.0000.0000.000
170A181GLU-1-0.847-0.91018.7300.2280.2280.0000.0000.0000.000
171A182PHE0-0.035-0.02615.048-0.051-0.0510.0000.0000.0000.000
172A183THR00.0470.01215.8610.0960.0960.0000.0000.0000.000
173A184GLU-1-0.855-0.94917.0630.1110.1110.0000.0000.0000.000
174A185ILE0-0.0140.00710.930-0.104-0.1040.0000.0000.0000.000
175A186LEU0-0.017-0.01013.1500.1390.1390.0000.0000.0000.000
176A187LEU00.0050.0078.116-0.153-0.1530.0000.0000.0000.000
177A188THR0-0.020-0.00411.7220.1320.1320.0000.0000.0000.000
178A189THR00.0530.03013.721-0.113-0.1130.0000.0000.0000.000
179A190PRO0-0.031-0.01115.9010.0710.0710.0000.0000.0000.000