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: ZYZKN

Calculation Name: 3MH9-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MH9

Chain ID: C

ChEMBL ID:

UniProt ID: P9WK45

Base Structure: X-ray

Registration Date: 2023-03-14

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2072123.633711
FMO2-HF: Nuclear repulsion 1997720.665208
FMO2-HF: Total energy -74402.968503
FMO2-MP2: Total energy -74623.708392


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(C:34:SER)


Summations of interaction energy for fragment #1(C:34:SER)
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.
-7.972-3.4290.923-2.247-3.22-0.008
Interaction energy analysis for fragmet #1(C:34:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.001
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].
3C36GLY00.0230.0143.872-1.507-0.203-0.014-0.610-0.6800.002
4C37PRO00.0250.0134.599-0.038-0.068-0.001-0.0110.0420.000
5C38LEU0-0.0020.0164.7000.0730.135-0.001-0.014-0.0470.000
6C39PRO00.0100.0157.731-0.101-0.1010.0000.0000.0000.000
7C40ASP-1-0.904-0.95811.5070.0890.0890.0000.0000.0000.000
8C41ALA0-0.015-0.02213.475-0.012-0.0120.0000.0000.0000.000
9C42LYS10.9230.97914.693-0.029-0.0290.0000.0000.0000.000
10C43PRO00.1120.04817.306-0.008-0.0080.0000.0000.0000.000
11C44LEU00.0460.03312.051-0.007-0.0070.0000.0000.0000.000
12C45VAL00.0240.00716.358-0.017-0.0170.0000.0000.0000.000
13C46GLU-1-0.928-0.94718.419-0.014-0.0140.0000.0000.0000.000
14C47GLU-1-0.896-0.96918.000-0.024-0.0240.0000.0000.0000.000
15C48ALA00.0450.02017.597-0.005-0.0050.0000.0000.0000.000
16C49THR0-0.063-0.03319.724-0.006-0.0060.0000.0000.0000.000
17C50ALA0-0.036-0.01823.015-0.001-0.0010.0000.0000.0000.000
18C51GLN0-0.042-0.02120.7010.0010.0010.0000.0000.0000.000
19C52THR0-0.043-0.04521.593-0.004-0.0040.0000.0000.0000.000
20C53LYS10.8050.88224.0200.0370.0370.0000.0000.0000.000
21C54ALA0-0.0120.00826.7580.0030.0030.0000.0000.0000.000
22C55LEU0-0.0280.00322.728-0.001-0.0010.0000.0000.0000.000
23C56LYS10.8790.93926.6690.0400.0400.0000.0000.0000.000
24C57SER0-0.018-0.03228.0120.0020.0020.0000.0000.0000.000
25C58ALA00.0230.01023.377-0.003-0.0030.0000.0000.0000.000
26C59HIS0-0.043-0.01921.654-0.002-0.0020.0000.0000.0000.000
27C60MET0-0.025-0.02722.576-0.011-0.0110.0000.0000.0000.000
28C61VAL00.0180.01320.4880.0080.0080.0000.0000.0000.000
29C62LEU0-0.024-0.00421.531-0.011-0.0110.0000.0000.0000.000
30C63THR00.0380.00321.0400.0000.0000.0000.0000.0000.000
31C64VAL0-0.038-0.01923.261-0.001-0.0010.0000.0000.0000.000
32C65ASN0-0.033-0.00319.1690.0000.0000.0000.0000.0000.000
33C66GLY00.0100.00623.5610.0060.0060.0000.0000.0000.000
34C67LYS10.8350.90026.3630.0560.0560.0000.0000.0000.000
35C68ILE00.0660.03926.1220.0020.0020.0000.0000.0000.000
36C69PRO0-0.032-0.03430.3320.0010.0010.0000.0000.0000.000
37C70GLY00.0380.01733.658-0.001-0.0010.0000.0000.0000.000
38C71LEU00.0200.02928.9110.0010.0010.0000.0000.0000.000
39C72SER00.0060.00232.913-0.002-0.0020.0000.0000.0000.000
40C73LEU00.0020.00628.2970.0000.0000.0000.0000.0000.000
41C74LYS10.8170.90827.9530.0610.0610.0000.0000.0000.000
42C75THR00.021-0.01024.403-0.009-0.0090.0000.0000.0000.000
43C76LEU0-0.038-0.00825.7580.0090.0090.0000.0000.0000.000
44C77SER0-0.044-0.01324.946-0.012-0.0120.0000.0000.0000.000
45C78GLY00.0760.02725.9170.0100.0100.0000.0000.0000.000
46C79ASP-1-0.835-0.84926.327-0.093-0.0930.0000.0000.0000.000
47C80LEU00.0240.01328.3320.0060.0060.0000.0000.0000.000
48C81THR0-0.002-0.01429.373-0.002-0.0020.0000.0000.0000.000
49C82THR00.0240.01931.3470.0030.0030.0000.0000.0000.000
50C83ASN0-0.0070.01133.8120.0010.0010.0000.0000.0000.000
51C84PRO00.005-0.01136.9640.0010.0010.0000.0000.0000.000
52C85THR00.016-0.01435.263-0.002-0.0020.0000.0000.0000.000
53C86ALA0-0.045-0.00635.0820.0020.0020.0000.0000.0000.000
54C87ALA00.006-0.00332.367-0.004-0.0040.0000.0000.0000.000
55C88THR00.0050.00031.7680.0040.0040.0000.0000.0000.000
56C89GLY00.0480.01930.567-0.006-0.0060.0000.0000.0000.000
57C90ASN00.0080.03028.9690.0000.0000.0000.0000.0000.000
58C91TRP00.020-0.00229.684-0.007-0.0070.0000.0000.0000.000
59C92LYS10.8580.92828.9380.0670.0670.0000.0000.0000.000
60C93LEU00.005-0.00530.746-0.004-0.0040.0000.0000.0000.000
61C94THR0-0.025-0.03933.186-0.001-0.0010.0000.0000.0000.000
62C95LEU0-0.010-0.01035.1880.0010.0010.0000.0000.0000.000
63C96GLY0-0.008-0.00438.9300.0020.0020.0000.0000.0000.000
64C97GLY00.0080.00738.414-0.002-0.0020.0000.0000.0000.000
65C98SER0-0.038-0.02937.9980.0020.0020.0000.0000.0000.000
66C99ASP-1-0.764-0.84432.018-0.059-0.0590.0000.0000.0000.000
67C100ILE0-0.029-0.02135.0730.0030.0030.0000.0000.0000.000
68C101ASP-1-0.805-0.88032.286-0.063-0.0630.0000.0000.0000.000
69C102ALA0-0.040-0.01934.0990.0040.0040.0000.0000.0000.000
70C103ASP-1-0.865-0.93133.854-0.056-0.0560.0000.0000.0000.000
71C104PHE0-0.050-0.03430.8020.0030.0030.0000.0000.0000.000
72C105VAL0-0.009-0.01534.999-0.002-0.0020.0000.0000.0000.000
73C106VAL0-0.028-0.00436.1720.0020.0020.0000.0000.0000.000
74C107PHE00.013-0.00837.624-0.001-0.0010.0000.0000.0000.000
75C108ASP-1-0.817-0.90740.431-0.027-0.0270.0000.0000.0000.000
76C109GLY00.0060.00840.6570.0010.0010.0000.0000.0000.000
77C110ILE0-0.049-0.00741.6830.0000.0000.0000.0000.0000.000
78C111LEU00.0180.00437.593-0.002-0.0020.0000.0000.0000.000
79C112TYR0-0.041-0.04439.7300.0020.0020.0000.0000.0000.000
80C113ALA00.0380.00838.587-0.003-0.0030.0000.0000.0000.000
81C114THR0-0.039-0.01638.5140.0020.0020.0000.0000.0000.000
82C115LEU00.0260.03040.312-0.001-0.0010.0000.0000.0000.000
83C116THR00.0080.00142.2240.0000.0000.0000.0000.0000.000
84C117PRO00.0710.01539.3790.0000.0000.0000.0000.0000.000
85C118ASN0-0.015-0.00938.8760.0010.0010.0000.0000.0000.000
86C119GLN0-0.085-0.03241.5050.0030.0030.0000.0000.0000.000
87C120TRP00.0160.00937.0510.0000.0000.0000.0000.0000.000
88C121SER0-0.065-0.02743.4420.0020.0020.0000.0000.0000.000
89C122ASP-1-0.814-0.90543.676-0.030-0.0300.0000.0000.0000.000
90C123PHE0-0.050-0.03042.4520.0010.0010.0000.0000.0000.000
91C124GLY00.0420.03844.5400.0000.0000.0000.0000.0000.000
92C125PRO00.000-0.01043.536-0.002-0.0020.0000.0000.0000.000
93C126ALA00.0310.00637.977-0.001-0.0010.0000.0000.0000.000
94C127ALA0-0.036-0.02739.029-0.002-0.0020.0000.0000.0000.000
95C128ASP-1-0.904-0.93940.203-0.029-0.0290.0000.0000.0000.000
96C129ILE0-0.095-0.04037.3310.0000.0000.0000.0000.0000.000
97C130TYR0-0.067-0.06230.327-0.002-0.0020.0000.0000.0000.000
98C131ASP-1-0.814-0.89535.858-0.043-0.0430.0000.0000.0000.000
99C132PRO00.012-0.00731.823-0.002-0.0020.0000.0000.0000.000
100C133ALA00.0100.00031.155-0.004-0.0040.0000.0000.0000.000
101C134GLN0-0.063-0.03131.8380.0010.0010.0000.0000.0000.000
102C135VAL00.0400.02025.9870.0000.0000.0000.0000.0000.000
103C136LEU0-0.018-0.01925.127-0.004-0.0040.0000.0000.0000.000
104C137ASN00.0190.03128.5640.0030.0030.0000.0000.0000.000
105C138PRO00.0460.01229.437-0.002-0.0020.0000.0000.0000.000
106C139ASP-1-0.882-0.94229.718-0.033-0.0330.0000.0000.0000.000
107C140THR0-0.062-0.02831.4450.0020.0020.0000.0000.0000.000
108C141GLY00.0330.03228.246-0.002-0.0020.0000.0000.0000.000
109C142LEU0-0.009-0.03421.7620.0020.0020.0000.0000.0000.000
110C143ALA00.0050.01323.6570.0000.0000.0000.0000.0000.000
111C144ASN00.0050.00925.5430.0060.0060.0000.0000.0000.000
112C145VAL0-0.021-0.01322.2200.0030.0030.0000.0000.0000.000
113C146LEU0-0.020-0.01218.8160.0020.0020.0000.0000.0000.000
114C147ALA00.0030.00722.4820.0060.0060.0000.0000.0000.000
115C148ASN0-0.050-0.01125.0730.0060.0060.0000.0000.0000.000
116C149PHE0-0.033-0.00816.870-0.002-0.0020.0000.0000.0000.000
117C150ALA00.0320.01921.6540.0060.0060.0000.0000.0000.000
118C151ASP-1-0.913-0.95920.534-0.016-0.0160.0000.0000.0000.000
119C152ALA0-0.0080.01217.3280.0050.0050.0000.0000.0000.000
120C153LYS10.8930.93312.022-0.055-0.0550.0000.0000.0000.000
121C154ALA00.0340.0199.632-0.017-0.0170.0000.0000.0000.000
122C155GLU-1-0.838-0.8858.8460.0750.0750.0000.0000.0000.000
123C156GLY0-0.024-0.0204.876-0.0510.025-0.001-0.009-0.0670.000
124C157ARG10.7310.8282.423-1.3670.0080.456-0.628-1.2030.001
125C158ASP-1-0.763-0.8532.786-5.697-3.9410.484-0.975-1.265-0.011
126C159THR0-0.016-0.0065.4440.2390.2390.0000.0000.0000.000
127C160ILE00.0150.0107.1980.1330.1330.0000.0000.0000.000
128C161ASN0-0.023-0.02110.9430.0450.0450.0000.0000.0000.000
129C162GLY00.0100.01111.6530.0530.0530.0000.0000.0000.000
130C163GLN00.0060.01211.0960.0500.0500.0000.0000.0000.000
131C164ASN0-0.009-0.0076.963-0.311-0.3110.0000.0000.0000.000
132C165THR0-0.042-0.0247.3380.2560.2560.0000.0000.0000.000
133C166ILE00.0080.0036.857-0.168-0.1680.0000.0000.0000.000
134C167ARG10.8260.9095.8180.2750.2750.0000.0000.0000.000
135C168ILE0-0.007-0.0139.2100.1670.1670.0000.0000.0000.000
136C169SER0-0.022-0.02712.480-0.051-0.0510.0000.0000.0000.000
137C170GLY00.0830.01615.0600.0150.0150.0000.0000.0000.000
138C171LYS10.8020.88618.7630.0130.0130.0000.0000.0000.000
139C172VAL00.0260.03221.9030.0030.0030.0000.0000.0000.000
140C173SER00.010-0.01124.3600.0000.0000.0000.0000.0000.000
141C174ALA00.026-0.00328.165-0.003-0.0030.0000.0000.0000.000
142C175GLN0-0.025-0.00530.428-0.001-0.0010.0000.0000.0000.000
143C176ALA00.0700.03627.620-0.001-0.0010.0000.0000.0000.000
144C177VAL0-0.007-0.00525.851-0.003-0.0030.0000.0000.0000.000
145C178ASN0-0.030-0.02328.360-0.004-0.0040.0000.0000.0000.000
146C179GLN00.0040.00331.2480.0010.0010.0000.0000.0000.000
147C180ILE00.0140.02925.435-0.001-0.0010.0000.0000.0000.000
148C181ALA0-0.0030.00028.386-0.003-0.0030.0000.0000.0000.000
149C182PRO00.0680.03730.3680.0000.0000.0000.0000.0000.000
150C183PRO0-0.023-0.01532.6270.0020.0020.0000.0000.0000.000
151C184PHE00.0020.01225.5880.0010.0010.0000.0000.0000.000
152C185ASN0-0.025-0.01431.1030.0020.0020.0000.0000.0000.000
153C186ALA00.0080.02129.7290.0010.0010.0000.0000.0000.000
154C187THR0-0.004-0.01531.6520.0010.0010.0000.0000.0000.000
155C188GLN0-0.0070.00627.8220.0050.0050.0000.0000.0000.000
156C189PRO0-0.019-0.02426.488-0.003-0.0030.0000.0000.0000.000
157C190VAL00.0030.01523.8840.0000.0000.0000.0000.0000.000
158C191PRO0-0.006-0.00120.8380.0010.0010.0000.0000.0000.000
159C192ALA00.0310.02319.458-0.009-0.0090.0000.0000.0000.000
160C193THR0-0.065-0.04213.0130.0100.0100.0000.0000.0000.000
161C194VAL0-0.0030.00714.515-0.018-0.0180.0000.0000.0000.000
162C195TRP0-0.032-0.0218.9380.0860.0860.0000.0000.0000.000
163C196ILE00.0130.01211.690-0.003-0.0030.0000.0000.0000.000
164C197GLN00.0050.00711.367-0.003-0.0030.0000.0000.0000.000
165C198GLU-1-0.778-0.8727.667-0.077-0.0770.0000.0000.0000.000
166C199THR0-0.044-0.02610.9670.0340.0340.0000.0000.0000.000
167C200GLY00.014-0.00213.789-0.015-0.0150.0000.0000.0000.000
168C201ASP-1-0.878-0.93817.365-0.056-0.0560.0000.0000.0000.000
169C202HIS10.8110.92614.4750.0580.0580.0000.0000.0000.000
170C203GLN00.0500.01716.7160.0040.0040.0000.0000.0000.000
171C204LEU00.0110.00916.055-0.020-0.0200.0000.0000.0000.000
172C205ALA00.0100.00013.3530.0000.0000.0000.0000.0000.000
173C206GLN0-0.0070.00212.942-0.014-0.0140.0000.0000.0000.000
174C207ALA00.0180.01515.5940.0140.0140.0000.0000.0000.000
175C208GLN0-0.006-0.00416.3460.0110.0110.0000.0000.0000.000
176C209LEU00.0010.00518.7480.0120.0120.0000.0000.0000.000
177C210ASP-1-0.813-0.93620.542-0.083-0.0830.0000.0000.0000.000
178C211ARG10.8250.90422.4420.0570.0570.0000.0000.0000.000
179C212GLY0-0.0030.00024.5640.0070.0070.0000.0000.0000.000
180C213SER0-0.038-0.02423.0910.0000.0000.0000.0000.0000.000
181C214GLY00.0370.02621.016-0.001-0.0010.0000.0000.0000.000
182C215ASN0-0.055-0.01421.981-0.006-0.0060.0000.0000.0000.000
183C216SER00.0080.00219.5530.0050.0050.0000.0000.0000.000
184C217VAL00.0060.00722.7910.0000.0000.0000.0000.0000.000
185C218GLN00.0040.00615.972-0.001-0.0010.0000.0000.0000.000
186C219MET0-0.0050.00919.8150.0100.0100.0000.0000.0000.000
187C220THR0-0.017-0.02715.730-0.002-0.0020.0000.0000.0000.000
188C221LEU0-0.020-0.00617.6660.0210.0210.0000.0000.0000.000
189C222SER0-0.012-0.01417.796-0.025-0.0250.0000.0000.0000.000
190C223LYS10.8210.90919.7890.1050.1050.0000.0000.0000.000
191C224TRP00.0510.00916.4420.0110.0110.0000.0000.0000.000
192C225GLY00.0120.01523.3500.0030.0030.0000.0000.0000.000
193C226GLH0-0.086-0.06626.4440.0050.0050.0000.0000.0000.000
194C227LYS10.9460.97628.1190.0420.0420.0000.0000.0000.000
195C228VAL00.0290.01229.868-0.003-0.0030.0000.0000.0000.000
196C229GLN0-0.043-0.02132.4000.0020.0020.0000.0000.0000.000
197C230VAL00.0110.00834.837-0.002-0.0020.0000.0000.0000.000
198C231THR0-0.024-0.01137.3670.0020.0020.0000.0000.0000.000
199C232LYS10.8670.94040.6680.0270.0270.0000.0000.0000.000
200C233PRO00.0100.01340.4090.0010.0010.0000.0000.0000.000
201C234PRO0-0.013-0.01042.9490.0010.0010.0000.0000.0000.000
202C235VAL00.0460.02845.926-0.001-0.0010.0000.0000.0000.000
203C236SER0-0.0040.00048.5540.0010.0010.0000.0000.0000.000
204C237LYS10.9550.95851.8660.0170.0170.0000.0000.0000.000
205C238LEU0-0.0050.02053.6690.0000.0000.0000.0000.0000.000