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: 664KZ

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2071965.003851
FMO2-HF: Nuclear repulsion 1997562.260678
FMO2-HF: Total energy -74402.743173
FMO2-MP2: Total energy -74623.474642


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.
-5.925-2.9492.437-2.185-3.2270.002
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 : 0.016 / q_NPA : -0.005
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].
3C36GLY00.0160.0103.794-1.807-0.384-0.018-0.600-0.8050.002
4C37PRO00.0190.0024.185-0.061-0.055-0.001-0.0290.0250.000
5C38LEU0-0.0040.0104.7540.1620.229-0.001-0.013-0.0530.000
6C39PRO00.0020.0147.351-0.166-0.1660.0000.0000.0000.000
7C40ASP-1-0.879-0.94411.0270.1550.1550.0000.0000.0000.000
8C41ALA0-0.018-0.02613.564-0.002-0.0020.0000.0000.0000.000
9C42LYS10.9510.97314.660-0.066-0.0660.0000.0000.0000.000
10C43PRO00.0930.04616.788-0.010-0.0100.0000.0000.0000.000
11C44LEU00.0580.04011.815-0.003-0.0030.0000.0000.0000.000
12C45VAL00.0080.00016.203-0.017-0.0170.0000.0000.0000.000
13C46GLU-1-0.949-0.95418.1690.0270.0270.0000.0000.0000.000
14C47GLU-1-0.911-0.97717.5530.0600.0600.0000.0000.0000.000
15C48ALA00.0470.01517.249-0.008-0.0080.0000.0000.0000.000
16C49THR0-0.067-0.03319.353-0.012-0.0120.0000.0000.0000.000
17C50ALA0-0.021-0.01122.605-0.005-0.0050.0000.0000.0000.000
18C51GLN0-0.039-0.01720.468-0.008-0.0080.0000.0000.0000.000
19C52THR0-0.049-0.04721.364-0.007-0.0070.0000.0000.0000.000
20C53LYS10.8280.90223.7800.0020.0020.0000.0000.0000.000
21C54ALA0-0.0240.00326.575-0.001-0.0010.0000.0000.0000.000
22C55LEU0-0.0350.00522.964-0.001-0.0010.0000.0000.0000.000
23C56LYS10.8780.94226.7530.0120.0120.0000.0000.0000.000
24C57SER0-0.009-0.03727.9140.0000.0000.0000.0000.0000.000
25C58ALA00.0120.00923.4380.0000.0000.0000.0000.0000.000
26C59HIS0-0.055-0.02421.956-0.004-0.0040.0000.0000.0000.000
27C60MET00.000-0.01122.628-0.005-0.0050.0000.0000.0000.000
28C61VAL00.0130.00420.4730.0030.0030.0000.0000.0000.000
29C62LEU0-0.026-0.01021.544-0.007-0.0070.0000.0000.0000.000
30C63THR00.0420.00421.005-0.003-0.0030.0000.0000.0000.000
31C64VAL0-0.034-0.01323.3060.0000.0000.0000.0000.0000.000
32C65ASN0-0.028-0.00119.606-0.001-0.0010.0000.0000.0000.000
33C66GLY00.0370.02223.8550.0050.0050.0000.0000.0000.000
34C67LYS10.8640.91026.7620.0450.0450.0000.0000.0000.000
35C68ILE00.0650.03126.2810.0010.0010.0000.0000.0000.000
36C69PRO0-0.075-0.05230.5730.0010.0010.0000.0000.0000.000
37C70GLY00.0580.03234.2170.0010.0010.0000.0000.0000.000
38C71LEU00.0090.01929.1570.0010.0010.0000.0000.0000.000
39C72SER00.0030.00333.232-0.002-0.0020.0000.0000.0000.000
40C73LEU00.0040.00228.915-0.001-0.0010.0000.0000.0000.000
41C74LYS10.8260.91028.2050.0520.0520.0000.0000.0000.000
42C75THR00.025-0.00524.662-0.008-0.0080.0000.0000.0000.000
43C76LEU0-0.0190.00525.9870.0070.0070.0000.0000.0000.000
44C77SER0-0.0440.00324.998-0.008-0.0080.0000.0000.0000.000
45C78GLY00.0700.02426.1990.0060.0060.0000.0000.0000.000
46C79ASP-1-0.887-0.87926.688-0.051-0.0510.0000.0000.0000.000
47C80LEU00.0330.02028.3730.0030.0030.0000.0000.0000.000
48C81THR00.006-0.01229.4100.0000.0000.0000.0000.0000.000
49C82THR00.0440.01731.3040.0010.0010.0000.0000.0000.000
50C83ASN0-0.0420.02233.8170.0010.0010.0000.0000.0000.000
51C84PRO00.037-0.00736.9690.0010.0010.0000.0000.0000.000
52C85THR00.013-0.02034.8850.0000.0000.0000.0000.0000.000
53C86ALA0-0.040-0.00234.9000.0010.0010.0000.0000.0000.000
54C87ALA0-0.004-0.01132.387-0.002-0.0020.0000.0000.0000.000
55C88THR00.0000.00332.0030.0020.0020.0000.0000.0000.000
56C89GLY00.0600.02530.617-0.003-0.0030.0000.0000.0000.000
57C90ASN0-0.0140.02128.5760.0000.0000.0000.0000.0000.000
58C91TRP00.034-0.00129.878-0.004-0.0040.0000.0000.0000.000
59C92LYS10.8560.93029.3720.0550.0550.0000.0000.0000.000
60C93LEU0-0.013-0.01431.156-0.003-0.0030.0000.0000.0000.000
61C94THR0-0.009-0.02333.391-0.001-0.0010.0000.0000.0000.000
62C95LEU0-0.007-0.00635.4180.0010.0010.0000.0000.0000.000
63C96GLY00.0050.00739.1520.0010.0010.0000.0000.0000.000
64C97GLY0-0.004-0.00638.263-0.002-0.0020.0000.0000.0000.000
65C98SER0-0.041-0.02738.3470.0010.0010.0000.0000.0000.000
66C99ASP-1-0.772-0.85532.258-0.051-0.0510.0000.0000.0000.000
67C100ILE0-0.024-0.02235.4180.0020.0020.0000.0000.0000.000
68C101ASP-1-0.821-0.88832.406-0.050-0.0500.0000.0000.0000.000
69C102ALA0-0.036-0.01934.2720.0030.0030.0000.0000.0000.000
70C103ASP-1-0.864-0.92934.173-0.038-0.0380.0000.0000.0000.000
71C104PHE0-0.044-0.04030.9290.0020.0020.0000.0000.0000.000
72C105VAL00.000-0.01235.285-0.001-0.0010.0000.0000.0000.000
73C106VAL0-0.029-0.00436.1990.0010.0010.0000.0000.0000.000
74C107PHE00.019-0.01337.7600.0000.0000.0000.0000.0000.000
75C108ASP-1-0.890-0.94140.468-0.013-0.0130.0000.0000.0000.000
76C109GLY0-0.005-0.00741.1780.0010.0010.0000.0000.0000.000
77C110ILE0-0.053-0.00642.2970.0000.0000.0000.0000.0000.000
78C111LEU00.0130.00737.633-0.001-0.0010.0000.0000.0000.000
79C112TYR0-0.041-0.03040.1180.0010.0010.0000.0000.0000.000
80C113ALA00.0430.00738.750-0.002-0.0020.0000.0000.0000.000
81C114THR0-0.042-0.00938.8560.0010.0010.0000.0000.0000.000
82C115LEU00.0030.02140.404-0.001-0.0010.0000.0000.0000.000
83C116THR00.015-0.00442.6650.0000.0000.0000.0000.0000.000
84C117PRO00.0470.00439.9510.0000.0000.0000.0000.0000.000
85C118ASN0-0.013-0.00539.1070.0010.0010.0000.0000.0000.000
86C119GLN0-0.041-0.01241.7960.0020.0020.0000.0000.0000.000
87C120TRP0-0.007-0.00137.3380.0000.0000.0000.0000.0000.000
88C121SER0-0.020-0.00143.6890.0010.0010.0000.0000.0000.000
89C122ASP-1-0.839-0.92143.959-0.017-0.0170.0000.0000.0000.000
90C123PHE0-0.069-0.04442.5190.0000.0000.0000.0000.0000.000
91C124GLY00.0430.03844.5810.0000.0000.0000.0000.0000.000
92C125PRO00.022-0.00543.694-0.001-0.0010.0000.0000.0000.000
93C126ALA00.0380.00938.273-0.001-0.0010.0000.0000.0000.000
94C127ALA0-0.047-0.02639.214-0.001-0.0010.0000.0000.0000.000
95C128ASP-1-0.905-0.94240.328-0.017-0.0170.0000.0000.0000.000
96C129ILE0-0.097-0.03737.148-0.001-0.0010.0000.0000.0000.000
97C130TYR0-0.066-0.06730.535-0.001-0.0010.0000.0000.0000.000
98C131ASP-1-0.810-0.90135.816-0.022-0.0220.0000.0000.0000.000
99C132PRO00.0190.00432.035-0.001-0.0010.0000.0000.0000.000
100C133ALA0-0.004-0.00831.371-0.002-0.0020.0000.0000.0000.000
101C134GLN0-0.071-0.04132.0720.0020.0020.0000.0000.0000.000
102C135VAL00.0160.00826.0440.0010.0010.0000.0000.0000.000
103C136LEU0-0.004-0.01225.338-0.001-0.0010.0000.0000.0000.000
104C137ASN00.0290.04528.5740.0040.0040.0000.0000.0000.000
105C138PRO00.0420.01629.309-0.001-0.0010.0000.0000.0000.000
106C139ASP-1-0.904-0.95029.810-0.006-0.0060.0000.0000.0000.000
107C140THR0-0.051-0.02731.4020.0010.0010.0000.0000.0000.000
108C141GLY00.0250.02528.351-0.002-0.0020.0000.0000.0000.000
109C142LEU00.001-0.03521.9510.0020.0020.0000.0000.0000.000
110C143ALA00.0000.00623.5370.0030.0030.0000.0000.0000.000
111C144ASN00.0200.01225.2630.0070.0070.0000.0000.0000.000
112C145VAL0-0.016-0.00822.0680.0020.0020.0000.0000.0000.000
113C146LEU0-0.012-0.00618.5230.0020.0020.0000.0000.0000.000
114C147ALA0-0.007-0.00222.2480.0060.0060.0000.0000.0000.000
115C148ASN0-0.095-0.03925.0230.0030.0030.0000.0000.0000.000
116C149PHE0-0.0210.00016.710-0.003-0.0030.0000.0000.0000.000
117C150ALA00.0090.00021.8450.0080.0080.0000.0000.0000.000
118C151ASP-1-0.910-0.95720.5510.0110.0110.0000.0000.0000.000
119C152ALA0-0.0110.00616.9150.0040.0040.0000.0000.0000.000
120C153LYS10.8880.92512.054-0.087-0.0870.0000.0000.0000.000
121C154ALA00.0180.0119.482-0.015-0.0150.0000.0000.0000.000
122C155GLU-1-0.846-0.8829.0930.1160.1160.0000.0000.0000.000
123C156GLY0-0.034-0.0355.2150.0840.0840.0000.0000.0000.000
124C157ARG10.7280.8421.990-2.079-1.2142.441-1.368-1.9380.001
125C158ASP-1-0.771-0.8513.656-3.044-2.4290.016-0.175-0.456-0.001
126C159THR0-0.0120.0005.8310.1540.1540.0000.0000.0000.000
127C160ILE00.0150.0157.2950.0750.0750.0000.0000.0000.000
128C161ASN0-0.015-0.01611.0160.0510.0510.0000.0000.0000.000
129C162GLY00.0100.00611.1790.0430.0430.0000.0000.0000.000
130C163GLN00.0170.02110.8560.0590.0590.0000.0000.0000.000
131C164ASN0-0.014-0.0036.438-0.339-0.3390.0000.0000.0000.000
132C165THR0-0.045-0.0317.1870.1940.1940.0000.0000.0000.000
133C166ILE00.0150.0016.573-0.061-0.0610.0000.0000.0000.000
134C167ARG10.8600.9366.1010.1920.1920.0000.0000.0000.000
135C168ILE0-0.012-0.0199.4040.1490.1490.0000.0000.0000.000
136C169SER0-0.019-0.02412.530-0.054-0.0540.0000.0000.0000.000
137C170GLY00.0920.02215.2640.0180.0180.0000.0000.0000.000
138C171LYS10.8110.89418.893-0.013-0.0130.0000.0000.0000.000
139C172VAL00.0370.03721.9360.0050.0050.0000.0000.0000.000
140C173SER00.0140.01824.441-0.004-0.0040.0000.0000.0000.000
141C174ALA00.0470.00428.192-0.002-0.0020.0000.0000.0000.000
142C175GLN0-0.031-0.01230.421-0.001-0.0010.0000.0000.0000.000
143C176ALA00.0580.02927.625-0.001-0.0010.0000.0000.0000.000
144C177VAL00.0100.00325.849-0.002-0.0020.0000.0000.0000.000
145C178ASN0-0.027-0.02428.373-0.004-0.0040.0000.0000.0000.000
146C179GLN0-0.011-0.00431.4040.0000.0000.0000.0000.0000.000
147C180ILE00.0160.03425.730-0.001-0.0010.0000.0000.0000.000
148C181ALA0-0.009-0.00528.590-0.003-0.0030.0000.0000.0000.000
149C182PRO00.0630.03730.595-0.001-0.0010.0000.0000.0000.000
150C183PRO0-0.015-0.01232.7130.0010.0010.0000.0000.0000.000
151C184PHE0-0.0010.00725.7360.0000.0000.0000.0000.0000.000
152C185ASN0-0.025-0.00931.2520.0000.0000.0000.0000.0000.000
153C186ALA00.0060.02129.7390.0000.0000.0000.0000.0000.000
154C187THR00.018-0.00331.6870.0010.0010.0000.0000.0000.000
155C188GLN0-0.023-0.00628.5620.0040.0040.0000.0000.0000.000
156C189PRO0-0.029-0.02426.642-0.002-0.0020.0000.0000.0000.000
157C190VAL00.0070.00223.949-0.002-0.0020.0000.0000.0000.000
158C191PRO0-0.0090.01020.9900.0040.0040.0000.0000.0000.000
159C192ALA00.0380.01619.438-0.008-0.0080.0000.0000.0000.000
160C193THR0-0.040-0.01812.9970.0110.0110.0000.0000.0000.000
161C194VAL0-0.0030.00114.727-0.020-0.0200.0000.0000.0000.000
162C195TRP0-0.029-0.0249.1580.0760.0760.0000.0000.0000.000
163C196ILE0-0.009-0.00211.589-0.018-0.0180.0000.0000.0000.000
164C197GLN0-0.0060.00211.1470.0260.0260.0000.0000.0000.000
165C198GLU-1-0.757-0.8727.1420.3710.3710.0000.0000.0000.000
166C199THR0-0.048-0.03010.5430.0140.0140.0000.0000.0000.000
167C200GLY00.005-0.00713.257-0.016-0.0160.0000.0000.0000.000
168C201ASP-1-0.862-0.92916.8610.0180.0180.0000.0000.0000.000
169C202HIS10.7880.91614.021-0.067-0.0670.0000.0000.0000.000
170C203GLN00.0580.02116.364-0.003-0.0030.0000.0000.0000.000
171C204LEU00.0210.01615.765-0.002-0.0020.0000.0000.0000.000
172C205ALA00.007-0.00713.292-0.006-0.0060.0000.0000.0000.000
173C206GLN00.0030.00513.308-0.020-0.0200.0000.0000.0000.000
174C207ALA00.0140.01815.7600.0180.0180.0000.0000.0000.000
175C208GLN0-0.024-0.02116.5540.0000.0000.0000.0000.0000.000
176C209LEU0-0.022-0.00618.9250.0120.0120.0000.0000.0000.000
177C210ASP-1-0.837-0.93520.497-0.071-0.0710.0000.0000.0000.000
178C211ARG10.8070.89022.5340.0450.0450.0000.0000.0000.000
179C212GLY00.0210.01424.3120.0050.0050.0000.0000.0000.000
180C213SER0-0.042-0.03523.7770.0000.0000.0000.0000.0000.000
181C214GLY00.0300.02221.480-0.001-0.0010.0000.0000.0000.000
182C215ASN0-0.055-0.01322.517-0.004-0.0040.0000.0000.0000.000
183C216SER00.0190.00820.2740.0030.0030.0000.0000.0000.000
184C217VAL00.0080.01123.055-0.001-0.0010.0000.0000.0000.000
185C218GLN00.0160.01716.2280.0010.0010.0000.0000.0000.000
186C219MET00.0050.00919.8410.0060.0060.0000.0000.0000.000
187C220THR0-0.020-0.02015.9600.0010.0010.0000.0000.0000.000
188C221LEU0-0.030-0.01217.9820.0120.0120.0000.0000.0000.000
189C222SER0-0.008-0.01418.027-0.014-0.0140.0000.0000.0000.000
190C223LYS10.8460.93019.9100.0590.0590.0000.0000.0000.000
191C224TRP00.0510.01116.3790.0060.0060.0000.0000.0000.000
192C225GLY00.0090.01123.3120.0040.0040.0000.0000.0000.000
193C226GLH0-0.085-0.07026.1630.0020.0020.0000.0000.0000.000
194C227LYS10.9580.98227.8480.0110.0110.0000.0000.0000.000
195C228VAL00.0220.01329.883-0.002-0.0020.0000.0000.0000.000
196C229GLN0-0.045-0.02332.3790.0020.0020.0000.0000.0000.000
197C230VAL00.0190.00734.870-0.002-0.0020.0000.0000.0000.000
198C231THR0-0.0060.00237.3690.0020.0020.0000.0000.0000.000
199C232LYS10.9190.96540.9290.0130.0130.0000.0000.0000.000
200C233PRO00.0090.01440.7530.0010.0010.0000.0000.0000.000
201C234PRO0-0.008-0.00743.2420.0010.0010.0000.0000.0000.000
202C235VAL00.0380.02446.432-0.001-0.0010.0000.0000.0000.000
203C236SER0-0.026-0.01148.8490.0010.0010.0000.0000.0000.000
204C237LYS10.9250.94652.0260.0100.0100.0000.0000.0000.000
205C238LEU00.0590.04853.5500.0000.0000.0000.0000.0000.000