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: 22M9R

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2071144.568405
FMO2-HF: Nuclear repulsion 1996742.724267
FMO2-HF: Total energy -74401.844138
FMO2-MP2: Total energy -74622.663804


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.
-1.841.2215.529-3.555-5.0340.002
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 : 0.032 / q_NPA : 0.002
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].
3C36GLY00.0130.0093.794-0.7690.734-0.017-0.631-0.8550.003
4C37PRO00.010-0.0054.163-0.405-0.404-0.001-0.0330.0330.000
5C38LEU0-0.006-0.0014.615-0.0700.011-0.001-0.019-0.0600.000
6C39PRO00.0080.0187.324-0.063-0.0630.0000.0000.0000.000
7C40ASP-1-0.876-0.94511.000-0.111-0.1110.0000.0000.0000.000
8C41ALA0-0.016-0.02513.3910.0050.0050.0000.0000.0000.000
9C42LYS10.9570.97214.4580.0460.0460.0000.0000.0000.000
10C43PRO00.0940.04516.7170.0130.0130.0000.0000.0000.000
11C44LEU00.0660.04511.7140.0070.0070.0000.0000.0000.000
12C45VAL00.0060.00116.1680.0190.0190.0000.0000.0000.000
13C46GLU-1-0.965-0.95818.058-0.042-0.0420.0000.0000.0000.000
14C47GLU-1-0.945-0.99017.608-0.111-0.1110.0000.0000.0000.000
15C48ALA00.0390.01217.2650.0080.0080.0000.0000.0000.000
16C49THR0-0.066-0.03719.3810.0150.0150.0000.0000.0000.000
17C50ALA0-0.023-0.01522.5770.0060.0060.0000.0000.0000.000
18C51GLN00.0030.00220.4330.0130.0130.0000.0000.0000.000
19C52THR0-0.043-0.03621.3040.0110.0110.0000.0000.0000.000
20C53LYS10.8780.94223.836-0.003-0.0030.0000.0000.0000.000
21C54ALA0-0.0200.00826.6380.0010.0010.0000.0000.0000.000
22C55LEU0-0.0390.00523.0460.0020.0020.0000.0000.0000.000
23C56LYS10.8720.93126.715-0.028-0.0280.0000.0000.0000.000
24C57SER0-0.030-0.04027.7750.0010.0010.0000.0000.0000.000
25C58ALA00.0180.00823.396-0.001-0.0010.0000.0000.0000.000
26C59HIS0-0.039-0.01522.4500.0080.0080.0000.0000.0000.000
27C60MET0-0.016-0.01422.6740.0050.0050.0000.0000.0000.000
28C61VAL00.0200.00720.789-0.003-0.0030.0000.0000.0000.000
29C62LEU0-0.027-0.00821.5610.0080.0080.0000.0000.0000.000
30C63THR00.024-0.00521.0360.0060.0060.0000.0000.0000.000
31C64VAL0-0.024-0.00623.144-0.001-0.0010.0000.0000.0000.000
32C65ASN0-0.041-0.01020.1620.0040.0040.0000.0000.0000.000
33C66GLY00.0280.01823.920-0.008-0.0080.0000.0000.0000.000
34C67LYS10.8640.93626.919-0.070-0.0700.0000.0000.0000.000
35C68ILE00.0750.03526.119-0.003-0.0030.0000.0000.0000.000
36C69PRO0-0.067-0.06930.412-0.001-0.0010.0000.0000.0000.000
37C70GLY00.0710.03933.939-0.001-0.0010.0000.0000.0000.000
38C71LEU00.0030.01628.977-0.001-0.0010.0000.0000.0000.000
39C72SER0-0.019-0.01533.0910.0020.0020.0000.0000.0000.000
40C73LEU00.0110.01128.8790.0020.0020.0000.0000.0000.000
41C74LYS10.8700.94528.380-0.096-0.0960.0000.0000.0000.000
42C75THR00.020-0.00625.1550.0110.0110.0000.0000.0000.000
43C76LEU0-0.0210.00526.221-0.010-0.0100.0000.0000.0000.000
44C77SER0-0.035-0.00125.5720.0120.0120.0000.0000.0000.000
45C78GLY00.0700.02126.606-0.008-0.0080.0000.0000.0000.000
46C79ASP-1-0.891-0.86826.9410.1000.1000.0000.0000.0000.000
47C80LEU00.0330.01728.396-0.005-0.0050.0000.0000.0000.000
48C81THR0-0.018-0.02329.365-0.001-0.0010.0000.0000.0000.000
49C82THR00.0790.02731.427-0.002-0.0020.0000.0000.0000.000
50C83ASN0-0.0430.02633.860-0.002-0.0020.0000.0000.0000.000
51C84PRO00.043-0.00336.968-0.002-0.0020.0000.0000.0000.000
52C85THR00.016-0.01834.9980.0010.0010.0000.0000.0000.000
53C86ALA0-0.042-0.00534.949-0.001-0.0010.0000.0000.0000.000
54C87ALA00.000-0.00832.4820.0030.0030.0000.0000.0000.000
55C88THR0-0.0060.00032.270-0.003-0.0030.0000.0000.0000.000
56C89GLY00.0620.02631.0950.0060.0060.0000.0000.0000.000
57C90ASN0-0.0310.01429.099-0.002-0.0020.0000.0000.0000.000
58C91TRP00.037-0.00630.3390.0060.0060.0000.0000.0000.000
59C92LYS10.8600.92929.881-0.109-0.1090.0000.0000.0000.000
60C93LEU0-0.026-0.01531.3930.0020.0020.0000.0000.0000.000
61C94THR00.0110.00133.4180.0030.0030.0000.0000.0000.000
62C95LEU0-0.015-0.01035.549-0.003-0.0030.0000.0000.0000.000
63C96GLY00.0130.01239.227-0.001-0.0010.0000.0000.0000.000
64C97GLY0-0.011-0.01038.3830.0020.0020.0000.0000.0000.000
65C98SER0-0.040-0.02638.6480.0000.0000.0000.0000.0000.000
66C99ASP-1-0.819-0.90432.9100.0920.0920.0000.0000.0000.000
67C100ILE0-0.034-0.02935.818-0.002-0.0020.0000.0000.0000.000
68C101ASP-1-0.804-0.87533.3250.1000.1000.0000.0000.0000.000
69C102ALA0-0.052-0.02934.866-0.005-0.0050.0000.0000.0000.000
70C103ASP-1-0.851-0.91934.7600.0840.0840.0000.0000.0000.000
71C104PHE0-0.049-0.04131.199-0.005-0.0050.0000.0000.0000.000
72C105VAL0-0.002-0.01335.7310.0020.0020.0000.0000.0000.000
73C106VAL0-0.031-0.00536.217-0.002-0.0020.0000.0000.0000.000
74C107PHE00.020-0.01837.8540.0000.0000.0000.0000.0000.000
75C108ASP-1-0.891-0.93940.5460.0300.0300.0000.0000.0000.000
76C109GLY0-0.012-0.01041.256-0.001-0.0010.0000.0000.0000.000
77C110ILE0-0.0320.00542.3450.0000.0000.0000.0000.0000.000
78C111LEU00.0070.00337.6080.0030.0030.0000.0000.0000.000
79C112TYR00.0070.00140.304-0.002-0.0020.0000.0000.0000.000
80C113ALA00.0450.00839.1860.0030.0030.0000.0000.0000.000
81C114THR0-0.047-0.01039.563-0.002-0.0020.0000.0000.0000.000
82C115LEU00.0110.02140.9920.0020.0020.0000.0000.0000.000
83C116THR00.006-0.00443.3160.0010.0010.0000.0000.0000.000
84C117PRO00.0460.00441.0360.0000.0000.0000.0000.0000.000
85C118ASN0-0.020-0.01040.370-0.002-0.0020.0000.0000.0000.000
86C119GLN0-0.029-0.00642.563-0.005-0.0050.0000.0000.0000.000
87C120TRP0-0.011-0.00537.9790.0000.0000.0000.0000.0000.000
88C121SER0-0.023-0.00544.169-0.003-0.0030.0000.0000.0000.000
89C122ASP-1-0.907-0.95744.2940.0380.0380.0000.0000.0000.000
90C123PHE0-0.060-0.04542.523-0.001-0.0010.0000.0000.0000.000
91C124GLY00.0410.03444.5580.0000.0000.0000.0000.0000.000
92C125PRO00.022-0.00743.6970.0020.0020.0000.0000.0000.000
93C126ALA00.0530.01738.2400.0010.0010.0000.0000.0000.000
94C127ALA0-0.050-0.03039.1670.0020.0020.0000.0000.0000.000
95C128ASP-1-0.913-0.94140.2740.0330.0330.0000.0000.0000.000
96C129ILE0-0.095-0.03736.8640.0010.0010.0000.0000.0000.000
97C130TYR0-0.083-0.08230.5570.0020.0020.0000.0000.0000.000
98C131ASP-1-0.812-0.89835.7740.0430.0430.0000.0000.0000.000
99C132PRO00.0190.00332.3030.0010.0010.0000.0000.0000.000
100C133ALA0-0.018-0.01831.3770.0030.0030.0000.0000.0000.000
101C134GLN0-0.061-0.02832.071-0.004-0.0040.0000.0000.0000.000
102C135VAL00.0220.01325.984-0.001-0.0010.0000.0000.0000.000
103C136LEU0-0.024-0.02125.5080.0020.0020.0000.0000.0000.000
104C137ASN00.0310.04128.594-0.007-0.0070.0000.0000.0000.000
105C138PRO00.0010.00029.3000.0020.0020.0000.0000.0000.000
106C139ASP-1-0.901-0.96229.7460.0150.0150.0000.0000.0000.000
107C140THR0-0.043-0.02431.281-0.001-0.0010.0000.0000.0000.000
108C141GLY00.0200.02128.2690.0040.0040.0000.0000.0000.000
109C142LEU0-0.008-0.04221.891-0.002-0.0020.0000.0000.0000.000
110C143ALA0-0.0030.00323.441-0.001-0.0010.0000.0000.0000.000
111C144ASN00.0420.02125.162-0.009-0.0090.0000.0000.0000.000
112C145VAL0-0.028-0.01221.806-0.002-0.0020.0000.0000.0000.000
113C146LEU0-0.019-0.01218.4940.0010.0010.0000.0000.0000.000
114C147ALA0-0.013-0.00622.091-0.007-0.0070.0000.0000.0000.000
115C148ASN0-0.093-0.03724.822-0.009-0.0090.0000.0000.0000.000
116C149PHE0-0.0200.00116.3170.0030.0030.0000.0000.0000.000
117C150ALA00.0120.00121.566-0.008-0.0080.0000.0000.0000.000
118C151ASP-1-0.951-0.99520.5280.0130.0130.0000.0000.0000.000
119C152ALA0-0.0170.00516.5530.0050.0050.0000.0000.0000.000
120C153LYS10.9610.97512.083-0.023-0.0230.0000.0000.0000.000
121C154ALA00.0090.0119.4230.0360.0360.0000.0000.0000.000
122C155GLU-1-0.899-0.9379.1130.1060.1060.0000.0000.0000.000
123C156GLY0-0.048-0.0355.2390.0890.0890.0000.0000.0000.000
124C157ARG10.7340.8531.8691.0431.7985.523-2.630-3.6480.001
125C158ASP-1-0.779-0.8653.4970.8201.5410.025-0.242-0.504-0.002
126C159THR0-0.025-0.0115.700-0.423-0.4230.0000.0000.0000.000
127C160ILE00.0100.0117.734-0.003-0.0030.0000.0000.0000.000
128C161ASN0-0.008-0.01211.401-0.053-0.0530.0000.0000.0000.000
129C162GLY00.0080.00411.533-0.052-0.0520.0000.0000.0000.000
130C163GLN00.0160.02410.484-0.053-0.0530.0000.0000.0000.000
131C164ASN00.0130.0195.4210.3690.3690.0000.0000.0000.000
132C165THR0-0.038-0.0257.074-0.090-0.0900.0000.0000.0000.000
133C166ILE00.0260.0046.6330.0250.0250.0000.0000.0000.000
134C167ARG10.8830.9556.055-0.689-0.6890.0000.0000.0000.000
135C168ILE0-0.008-0.0169.1400.0250.0250.0000.0000.0000.000
136C169SER0-0.018-0.01812.204-0.011-0.0110.0000.0000.0000.000
137C170GLY00.0770.01714.853-0.021-0.0210.0000.0000.0000.000
138C171LYS10.8560.93518.500-0.019-0.0190.0000.0000.0000.000
139C172VAL00.0450.04121.674-0.007-0.0070.0000.0000.0000.000
140C173SER00.0220.02124.1170.0020.0020.0000.0000.0000.000
141C174ALA00.0490.00527.8640.0040.0040.0000.0000.0000.000
142C175GLN0-0.025-0.01130.0870.0020.0020.0000.0000.0000.000
143C176ALA00.0520.02327.3470.0010.0010.0000.0000.0000.000
144C177VAL00.0010.00325.6640.0040.0040.0000.0000.0000.000
145C178ASN0-0.020-0.02328.1130.0060.0060.0000.0000.0000.000
146C179GLN0-0.034-0.01031.086-0.002-0.0020.0000.0000.0000.000
147C180ILE00.0290.04225.5950.0010.0010.0000.0000.0000.000
148C181ALA0-0.013-0.00428.4190.0040.0040.0000.0000.0000.000
149C182PRO00.0630.03630.3970.0010.0010.0000.0000.0000.000
150C183PRO0-0.013-0.01332.334-0.002-0.0020.0000.0000.0000.000
151C184PHE0-0.0020.00225.5560.0000.0000.0000.0000.0000.000
152C185ASN0-0.033-0.01930.964-0.001-0.0010.0000.0000.0000.000
153C186ALA0-0.0100.01129.379-0.001-0.0010.0000.0000.0000.000
154C187THR00.008-0.00931.334-0.002-0.0020.0000.0000.0000.000
155C188GLN0-0.016-0.00328.331-0.008-0.0080.0000.0000.0000.000
156C189PRO0-0.037-0.02726.2990.0040.0040.0000.0000.0000.000
157C190VAL00.0090.00323.4530.0000.0000.0000.0000.0000.000
158C191PRO0-0.0190.00620.8510.0000.0000.0000.0000.0000.000
159C192ALA00.0410.01519.0820.0060.0060.0000.0000.0000.000
160C193THR0-0.023-0.00712.6470.0050.0050.0000.0000.0000.000
161C194VAL0-0.008-0.00314.433-0.004-0.0040.0000.0000.0000.000
162C195TRP0-0.030-0.0279.081-0.021-0.0210.0000.0000.0000.000
163C196ILE0-0.004-0.00111.550-0.015-0.0150.0000.0000.0000.000
164C197GLN0-0.027-0.01011.234-0.043-0.0430.0000.0000.0000.000
165C198GLU-1-0.770-0.8716.271-1.625-1.6250.0000.0000.0000.000
166C199THR0-0.049-0.03010.107-0.008-0.0080.0000.0000.0000.000
167C200GLY0-0.001-0.01312.5100.0480.0480.0000.0000.0000.000
168C201ASP-1-0.870-0.94016.085-0.047-0.0470.0000.0000.0000.000
169C202HIS10.7820.90313.8260.1570.1570.0000.0000.0000.000
170C203GLN00.0650.02816.1570.0200.0200.0000.0000.0000.000
171C204LEU00.0240.01615.8070.0030.0030.0000.0000.0000.000
172C205ALA00.004-0.00813.3820.0020.0020.0000.0000.0000.000
173C206GLN00.0000.01213.2440.0160.0160.0000.0000.0000.000
174C207ALA00.0160.01815.660-0.009-0.0090.0000.0000.0000.000
175C208GLN0-0.0040.00116.442-0.009-0.0090.0000.0000.0000.000
176C209LEU0-0.032-0.01018.684-0.009-0.0090.0000.0000.0000.000
177C210ASP-1-0.848-0.93320.1840.1050.1050.0000.0000.0000.000
178C211ARG10.8460.92022.220-0.070-0.0700.0000.0000.0000.000
179C212GLY00.0250.01724.165-0.009-0.0090.0000.0000.0000.000
180C213SER0-0.036-0.02823.9950.0010.0010.0000.0000.0000.000
181C214GLY00.0370.02521.6310.0010.0010.0000.0000.0000.000
182C215ASN0-0.066-0.02822.6900.0080.0080.0000.0000.0000.000
183C216SER00.0100.00721.1860.0010.0010.0000.0000.0000.000
184C217VAL00.0180.01522.7620.0000.0000.0000.0000.0000.000
185C218GLN00.0150.00416.3330.0100.0100.0000.0000.0000.000
186C219MET00.0170.01119.706-0.010-0.0100.0000.0000.0000.000
187C220THR0-0.024-0.02816.1590.0020.0020.0000.0000.0000.000
188C221LEU0-0.041-0.02018.051-0.013-0.0130.0000.0000.0000.000
189C222SER00.008-0.00418.0120.0170.0170.0000.0000.0000.000
190C223LYS10.9020.95919.797-0.113-0.1130.0000.0000.0000.000
191C224TRP00.0620.01516.091-0.007-0.0070.0000.0000.0000.000
192C225GLY00.0030.00623.004-0.005-0.0050.0000.0000.0000.000
193C226GLH0-0.123-0.09625.937-0.003-0.0030.0000.0000.0000.000
194C227LYS10.9590.98027.486-0.040-0.0400.0000.0000.0000.000
195C228VAL00.0320.02129.8780.0040.0040.0000.0000.0000.000
196C229GLN0-0.053-0.02532.251-0.005-0.0050.0000.0000.0000.000
197C230VAL00.0210.00835.0500.0030.0030.0000.0000.0000.000
198C231THR0-0.036-0.00937.451-0.003-0.0030.0000.0000.0000.000
199C232LYS10.9610.98341.144-0.031-0.0310.0000.0000.0000.000
200C233PRO00.0200.02341.2490.0000.0000.0000.0000.0000.000
201C234PRO0-0.011-0.00643.620-0.002-0.0020.0000.0000.0000.000
202C235VAL00.0310.02346.8720.0010.0010.0000.0000.0000.000
203C236SER0-0.026-0.01549.325-0.001-0.0010.0000.0000.0000.000
204C237LYS10.9310.94952.578-0.028-0.0280.0000.0000.0000.000
205C238LEU00.0560.04654.048-0.001-0.0010.0000.0000.0000.000