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: VQN21

Calculation Name: 3G7K-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G7K

Chain ID: C

ChEMBL ID:

UniProt ID: Q0QLE6

Base Structure: X-ray

Registration Date: 2023-09-22

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2442601.243798
FMO2-HF: Nuclear repulsion 2358599.487099
FMO2-HF: Total energy -84001.756699
FMO2-MP2: Total energy -84244.088054


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:2:SER)


Summations of interaction energy for fragment #1(C:2: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.
0.53.3580.006-1.378-1.4860.003
Interaction energy analysis for fragmet #1(C:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.022
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].
3C4GLN00.002-0.0063.574-0.5761.6570.004-1.084-1.1530.002
4C5MET0-0.041-0.0154.5080.5960.702-0.001-0.023-0.0820.000
5C6ARG10.9130.9567.150-1.076-1.0760.0000.0000.0000.000
6C7ILE00.0130.01310.007-0.054-0.0540.0000.0000.0000.000
7C8PRO0-0.020-0.00113.524-0.002-0.0020.0000.0000.0000.000
8C9CYS0-0.036-0.00816.621-0.029-0.0290.0000.0000.0000.000
9C10VAL00.0320.02519.1050.0050.0050.0000.0000.0000.000
10C11ILE00.0120.00920.225-0.008-0.0080.0000.0000.0000.000
11C12MET0-0.021-0.00524.1120.0020.0020.0000.0000.0000.000
12C13ARG10.8360.91527.939-0.012-0.0120.0000.0000.0000.000
13C14ALA00.0160.00731.2560.0030.0030.0000.0000.0000.000
14C15GLY00.0650.03433.361-0.002-0.0020.0000.0000.0000.000
15C16THR0-0.065-0.03635.7870.0000.0000.0000.0000.0000.000
16C17SER0-0.052-0.03832.233-0.003-0.0030.0000.0000.0000.000
17C18LYS10.9280.98025.6520.0090.0090.0000.0000.0000.000
18C19GLY00.0530.02327.246-0.004-0.0040.0000.0000.0000.000
19C20ILE0-0.033-0.01020.7100.0050.0050.0000.0000.0000.000
20C21PHE00.0180.00123.551-0.005-0.0050.0000.0000.0000.000
21C22LEU00.0120.00518.9600.0110.0110.0000.0000.0000.000
22C23LYS10.9260.95421.292-0.099-0.0990.0000.0000.0000.000
23C24GLY00.006-0.00121.6450.0030.0030.0000.0000.0000.000
24C25ASN0-0.043-0.02920.839-0.009-0.0090.0000.0000.0000.000
25C26ASP-1-0.865-0.92517.4710.1250.1250.0000.0000.0000.000
26C27LEU00.004-0.00916.4080.0120.0120.0000.0000.0000.000
27C28PRO0-0.017-0.00316.0200.0000.0000.0000.0000.0000.000
28C29ALA00.0200.01618.462-0.001-0.0010.0000.0000.0000.000
29C30ASP-1-0.837-0.90820.763-0.016-0.0160.0000.0000.0000.000
30C31GLN00.010-0.01421.5130.0050.0050.0000.0000.0000.000
31C32GLU-1-0.839-0.88920.469-0.058-0.0580.0000.0000.0000.000
32C33LEU00.020-0.01014.837-0.008-0.0080.0000.0000.0000.000
33C34ARG10.8220.90317.945-0.030-0.0300.0000.0000.0000.000
34C35ASP-1-0.745-0.86219.904-0.008-0.0080.0000.0000.0000.000
35C36LYS10.8000.90017.2890.0710.0710.0000.0000.0000.000
36C37VAL0-0.016-0.01414.320-0.009-0.0090.0000.0000.0000.000
37C38ILE0-0.0020.00716.8170.0080.0080.0000.0000.0000.000
38C39LEU0-0.009-0.00419.966-0.001-0.0010.0000.0000.0000.000
39C40ARG10.7910.88814.1590.1510.1510.0000.0000.0000.000
40C41ILE0-0.0110.00615.9010.0020.0020.0000.0000.0000.000
41C42PHE0-0.001-0.01117.1790.0040.0040.0000.0000.0000.000
42C43GLY00.0050.01618.322-0.001-0.0010.0000.0000.0000.000
43C44SER0-0.064-0.03519.324-0.007-0.0070.0000.0000.0000.000
44C45PRO0-0.055-0.02920.516-0.008-0.0080.0000.0000.0000.000
45C46ASP-1-0.789-0.91622.217-0.105-0.1050.0000.0000.0000.000
46C47VAL0-0.028-0.01124.2030.0070.0070.0000.0000.0000.000
47C48ARG10.8880.92724.1470.0900.0900.0000.0000.0000.000
48C49GLN0-0.015-0.02022.2170.0080.0080.0000.0000.0000.000
49C50ILE0-0.016-0.00619.3990.0040.0040.0000.0000.0000.000
50C51ASP-1-0.841-0.90314.780-0.254-0.2540.0000.0000.0000.000
51C52GLY00.026-0.00116.232-0.004-0.0040.0000.0000.0000.000
52C53LEU0-0.042-0.02216.9660.0030.0030.0000.0000.0000.000
53C54ALA0-0.045-0.00419.5610.0070.0070.0000.0000.0000.000
54C55GLY0-0.019-0.02223.067-0.002-0.0020.0000.0000.0000.000
55C56ALA0-0.030-0.00125.8880.0010.0010.0000.0000.0000.000
56C57ASP-1-0.808-0.89327.645-0.018-0.0180.0000.0000.0000.000
57C58PRO00.0610.02029.9530.0030.0030.0000.0000.0000.000
58C59LEU0-0.053-0.01231.9610.0040.0040.0000.0000.0000.000
59C60THR0-0.049-0.04427.6190.0020.0020.0000.0000.0000.000
60C61SER0-0.0180.00026.0320.0020.0020.0000.0000.0000.000
61C62LYS10.8150.90527.0530.0050.0050.0000.0000.0000.000
62C63LEU00.0110.00523.1150.0040.0040.0000.0000.0000.000
63C64ALA0-0.007-0.00326.244-0.004-0.0040.0000.0000.0000.000
64C65ILE00.0010.00223.6070.0070.0070.0000.0000.0000.000
65C66ILE0-0.0080.00225.599-0.005-0.0050.0000.0000.0000.000
66C67GLY00.008-0.00626.0920.0070.0070.0000.0000.0000.000
67C68PRO00.012-0.00527.470-0.002-0.0020.0000.0000.0000.000
68C69SER00.0060.02230.728-0.002-0.0020.0000.0000.0000.000
69C70THR0-0.055-0.03333.4100.0010.0010.0000.0000.0000.000
70C71HIS0-0.034-0.01235.165-0.001-0.0010.0000.0000.0000.000
71C72PRO0-0.021-0.02538.7040.0010.0010.0000.0000.0000.000
72C73ASP-1-0.894-0.93541.2730.0140.0140.0000.0000.0000.000
73C74ALA0-0.024-0.01938.034-0.001-0.0010.0000.0000.0000.000
74C75ASP-1-0.842-0.90836.3120.0230.0230.0000.0000.0000.000
75C76VAL0-0.088-0.04831.2480.0030.0030.0000.0000.0000.000
76C77ASP-1-0.743-0.83531.2130.0170.0170.0000.0000.0000.000
77C78TYR0-0.028-0.03530.5440.0030.0030.0000.0000.0000.000
78C79THR00.007-0.00428.273-0.003-0.0030.0000.0000.0000.000
79C80PHE0-0.021-0.01128.5800.0020.0020.0000.0000.0000.000
80C81ALA00.0500.02227.099-0.001-0.0010.0000.0000.0000.000
81C82GLN0-0.019-0.01328.6760.0030.0030.0000.0000.0000.000
82C83VAL0-0.015-0.00123.473-0.002-0.0020.0000.0000.0000.000
83C84SER0-0.018-0.01426.924-0.001-0.0010.0000.0000.0000.000
84C85ILE0-0.0060.02125.961-0.003-0.0030.0000.0000.0000.000
85C86THR0-0.011-0.04726.267-0.007-0.0070.0000.0000.0000.000
86C87ASP-1-0.836-0.87227.650-0.041-0.0410.0000.0000.0000.000
87C88ALA0-0.020-0.00524.2240.0000.0000.0000.0000.0000.000
88C89VAL00.0060.00125.5400.0030.0030.0000.0000.0000.000
89C90VAL00.006-0.00123.766-0.001-0.0010.0000.0000.0000.000
90C91ASP-1-0.825-0.90127.109-0.009-0.0090.0000.0000.0000.000
91C92TYR0-0.022-0.03624.9910.0050.0050.0000.0000.0000.000
92C93ASN0-0.063-0.02831.5350.0040.0040.0000.0000.0000.000
93C94GLY00.001-0.00635.029-0.001-0.0010.0000.0000.0000.000
94C95ASN00.0370.02634.9940.0020.0020.0000.0000.0000.000
95C96CYS0-0.0410.00134.016-0.002-0.0020.0000.0000.0000.000
96C97GLY00.0770.02735.7780.0020.0020.0000.0000.0000.000
97C98ASN00.0100.01135.8310.0020.0020.0000.0000.0000.000
98C99ILE00.0570.01530.4440.0010.0010.0000.0000.0000.000
99C100SER0-0.010-0.01632.9750.0030.0030.0000.0000.0000.000
100C101ALA00.0650.02935.2720.0020.0020.0000.0000.0000.000
101C102GLY0-0.025-0.01431.6290.0010.0010.0000.0000.0000.000
102C103VAL0-0.032-0.01431.4610.0040.0040.0000.0000.0000.000
103C104GLY00.0620.04032.6080.0030.0030.0000.0000.0000.000
104C105PRO00.000-0.00932.7190.0020.0020.0000.0000.0000.000
105C106PHE00.0390.01524.8480.0040.0040.0000.0000.0000.000
106C107ALA00.007-0.00229.7960.0050.0050.0000.0000.0000.000
107C108ILE00.0180.01631.7600.0020.0020.0000.0000.0000.000
108C109ASP-1-0.855-0.93929.1230.0380.0380.0000.0000.0000.000
109C110GLU-1-0.848-0.91824.6740.0790.0790.0000.0000.0000.000
110C111SER0-0.078-0.03428.1660.0020.0020.0000.0000.0000.000
111C112PHE0-0.027-0.00626.1490.0010.0010.0000.0000.0000.000
112C113VAL00.0180.01931.618-0.003-0.0030.0000.0000.0000.000
113C114LYS10.8940.94935.166-0.024-0.0240.0000.0000.0000.000
114C115ALA00.0420.03036.328-0.002-0.0020.0000.0000.0000.000
115C116VAL0-0.053-0.04038.1940.0000.0000.0000.0000.0000.000
116C117GLU-1-0.826-0.88941.6110.0190.0190.0000.0000.0000.000
117C118PRO0-0.037-0.03843.573-0.001-0.0010.0000.0000.0000.000
118C119MET0-0.024-0.00443.5080.0000.0000.0000.0000.0000.000
119C120THR00.0130.01138.8170.0010.0010.0000.0000.0000.000
120C121ARG10.7920.88541.325-0.012-0.0120.0000.0000.0000.000
121C122VAL0-0.013-0.00536.3690.0010.0010.0000.0000.0000.000
122C123CYS0-0.075-0.02939.591-0.002-0.0020.0000.0000.0000.000
123C124ILE00.014-0.00334.9140.0020.0020.0000.0000.0000.000
124C125HIS00.022-0.00935.304-0.004-0.0040.0000.0000.0000.000
125C126ASN0-0.029-0.01834.2660.0000.0000.0000.0000.0000.000
126C127THR00.007-0.02031.463-0.001-0.0010.0000.0000.0000.000
127C128ASN0-0.085-0.05131.6150.0010.0010.0000.0000.0000.000
128C129THR0-0.059-0.03535.051-0.002-0.0020.0000.0000.0000.000
129C130GLY00.0090.02337.755-0.001-0.0010.0000.0000.0000.000
130C131LYS10.7660.88339.351-0.006-0.0060.0000.0000.0000.000
131C132LEU00.0380.02339.4980.0010.0010.0000.0000.0000.000
132C133LEU0-0.047-0.01937.577-0.002-0.0020.0000.0000.0000.000
133C134TYR0-0.060-0.05840.6860.0020.0020.0000.0000.0000.000
134C135ALA00.0530.02039.063-0.001-0.0010.0000.0000.0000.000
135C136GLU-1-0.884-0.92241.0770.0110.0110.0000.0000.0000.000
136C137VAL00.009-0.00337.165-0.001-0.0010.0000.0000.0000.000
137C138GLU-1-0.832-0.92840.6180.0120.0120.0000.0000.0000.000
138C139VAL0-0.085-0.04938.0030.0020.0020.0000.0000.0000.000
139C140GLU-1-0.816-0.89338.6170.0140.0140.0000.0000.0000.000
140C141ASP-1-0.884-0.93336.9800.0240.0240.0000.0000.0000.000
141C142GLY0-0.068-0.02536.2300.0030.0030.0000.0000.0000.000
142C143LYS10.7880.88830.343-0.037-0.0370.0000.0000.0000.000
143C144ALA00.0450.02333.617-0.003-0.0030.0000.0000.0000.000
144C145LYS10.7970.90235.300-0.014-0.0140.0000.0000.0000.000
145C146VAL00.011-0.00833.711-0.001-0.0010.0000.0000.0000.000
146C147SER0-0.030-0.01437.185-0.002-0.0020.0000.0000.0000.000
147C148GLY00.0710.02139.9370.0010.0010.0000.0000.0000.000
148C149ASP-1-0.913-0.95043.2050.0050.0050.0000.0000.0000.000
149C150CYS0-0.033-0.01143.431-0.001-0.0010.0000.0000.0000.000
150C151LYS10.8410.91943.1100.0030.0030.0000.0000.0000.000
151C152ILE0-0.0030.00139.1920.0000.0000.0000.0000.0000.000
152C153ASP-1-0.805-0.89542.527-0.004-0.0040.0000.0000.0000.000
153C154GLY00.000-0.00840.0310.0000.0000.0000.0000.0000.000
154C155VAL0-0.049-0.02036.9970.0000.0000.0000.0000.0000.000
155C156PRO0-0.015-0.01337.2130.0000.0000.0000.0000.0000.000
156C157GLY0-0.0010.00639.1340.0010.0010.0000.0000.0000.000
157C158THR0-0.039-0.02441.1830.0000.0000.0000.0000.0000.000
158C159ASN0-0.011-0.00637.5100.0000.0000.0000.0000.0000.000
159C160ALA00.0510.04639.306-0.001-0.0010.0000.0000.0000.000
160C161PRO0-0.041-0.00940.4530.0000.0000.0000.0000.0000.000
161C162GLU-1-0.799-0.91537.9710.0160.0160.0000.0000.0000.000
162C163LEU0-0.066-0.02741.705-0.002-0.0020.0000.0000.0000.000
163C164MET00.0030.02438.7890.0010.0010.0000.0000.0000.000
164C165ASP-1-0.794-0.92942.9990.0050.0050.0000.0000.0000.000
165C166PHE0-0.0090.00940.1780.0010.0010.0000.0000.0000.000
166C167SER00.005-0.01145.098-0.001-0.0010.0000.0000.0000.000
167C168ASP-1-0.780-0.84945.0670.0080.0080.0000.0000.0000.000
168C169THR00.000-0.01642.5960.0000.0000.0000.0000.0000.000
169C170ALA0-0.035-0.01644.968-0.001-0.0010.0000.0000.0000.000
170C171GLY00.0070.00348.1250.0000.0000.0000.0000.0000.000
171C172ALA0-0.018-0.00143.2040.0000.0000.0000.0000.0000.000
172C173ALA00.0660.03643.1550.0000.0000.0000.0000.0000.000
173C174THR0-0.023-0.01544.7670.0000.0000.0000.0000.0000.000
174C175GLY0-0.003-0.00247.9180.0000.0000.0000.0000.0000.000
175C176LYS10.8860.94049.5250.0000.0000.0000.0000.0000.000
176C177VAL00.0280.03051.438-0.001-0.0010.0000.0000.0000.000
177C333ASP-1-0.870-0.94256.3340.0020.0020.0000.0000.0000.000
178C334THR0-0.050-0.03053.0760.0000.0000.0000.0000.0000.000
179C335VAL0-0.0240.00152.965-0.001-0.0010.0000.0000.0000.000
180C336ARG10.9430.95752.5580.0020.0020.0000.0000.0000.000
181C337ILE00.0200.01548.6850.0000.0000.0000.0000.0000.000
182C338GLY00.0080.01050.0670.0000.0000.0000.0000.0000.000
183C339HIS0-0.024-0.01743.735-0.001-0.0010.0000.0000.0000.000
184C340PRO00.016-0.01843.0570.0000.0000.0000.0000.0000.000
185C341ALA0-0.0040.01241.983-0.001-0.0010.0000.0000.0000.000
186C342GLY0-0.0050.00344.0570.0000.0000.0000.0000.0000.000
187C343VAL0-0.038-0.02247.0970.0000.0000.0000.0000.0000.000
188C344ILE0-0.001-0.00344.1910.0000.0000.0000.0000.0000.000
189C345PRO0-0.015-0.00248.1290.0000.0000.0000.0000.0000.000
190C346VAL0-0.014-0.01747.5800.0000.0000.0000.0000.0000.000
191C347VAL0-0.0040.00150.1510.0000.0000.0000.0000.0000.000
192C348SER0-0.019-0.00651.5110.0010.0010.0000.0000.0000.000
193C349ILE00.0120.00853.4910.0000.0000.0000.0000.0000.000
194C350VAL00.001-0.00856.0890.0000.0000.0000.0000.0000.000
195C351LYS10.8470.89957.593-0.004-0.0040.0000.0000.0000.000
196C352ASP-1-0.862-0.92559.1860.0010.0010.0000.0000.0000.000
197C353GLY0-0.010-0.00457.0260.0000.0000.0000.0000.0000.000
198C354LYS10.7950.87554.269-0.005-0.0050.0000.0000.0000.000
199C355VAL00.0190.02450.7460.0000.0000.0000.0000.0000.000
200C356GLU-1-0.827-0.87853.2530.0050.0050.0000.0000.0000.000
201C357LYS10.9220.93849.908-0.006-0.0060.0000.0000.0000.000
202C358ALA0-0.017-0.00848.139-0.001-0.0010.0000.0000.0000.000
203C359ALA00.0070.02246.9740.0000.0000.0000.0000.0000.000
204C360LEU0-0.026-0.01943.553-0.001-0.0010.0000.0000.0000.000
205C361ILE00.0330.03243.9670.0010.0010.0000.0000.0000.000
206C362ARG10.8190.90339.321-0.005-0.0050.0000.0000.0000.000
207C363THR00.0680.01237.8200.0000.0000.0000.0000.0000.000
208C364ALA00.0180.01133.397-0.001-0.0010.0000.0000.0000.000
209C365ARG10.8840.93429.074-0.019-0.0190.0000.0000.0000.000
210C366ARG10.8510.92125.078-0.059-0.0590.0000.0000.0000.000
211C367ILE0-0.101-0.04125.550-0.004-0.0040.0000.0000.0000.000
212C368MET0-0.010-0.01418.389-0.007-0.0070.0000.0000.0000.000
213C369GLU-1-0.824-0.90121.1400.0720.0720.0000.0000.0000.000
214C370GLY00.0160.01017.320-0.001-0.0010.0000.0000.0000.000
215C371TYR0-0.041-0.03012.7430.0300.0300.0000.0000.0000.000
216C372VAL00.0390.03313.906-0.004-0.0040.0000.0000.0000.000
217C373TYR0-0.026-0.0216.9190.2200.2200.0000.0000.0000.000
218C374VAL00.0510.0289.568-0.115-0.1150.0000.0000.0000.000
219C375GLU-1-0.801-0.9117.965-0.530-0.5300.0000.0000.0000.000
220C376LYS10.8690.9133.6721.3381.8570.003-0.271-0.2510.001
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