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: YV1Q2

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2435640.543677
FMO2-HF: Nuclear repulsion 2351639.604066
FMO2-HF: Total energy -84000.939611
FMO2-MP2: Total energy -84243.270938


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.
1.3944.4350.162-1.45-1.7510.005
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 : 0.000 / 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].
3C4GLN0-0.017-0.0163.683-1.2340.8900.000-1.076-1.0480.002
4C5MET0-0.053-0.0254.4762.7942.9810.000-0.028-0.1580.000
5C6ARG10.9180.9546.835-2.736-2.7360.0000.0000.0000.000
6C7ILE00.0100.0149.625-0.096-0.0960.0000.0000.0000.000
7C8PRO00.0000.01713.2880.0160.0160.0000.0000.0000.000
8C9CYS0-0.023-0.00516.164-0.069-0.0690.0000.0000.0000.000
9C10VAL00.0200.02118.6530.0170.0170.0000.0000.0000.000
10C11ILE00.0040.01220.418-0.026-0.0260.0000.0000.0000.000
11C12MET0-0.028-0.01124.0650.0010.0010.0000.0000.0000.000
12C13ARG10.8680.94427.844-0.122-0.1220.0000.0000.0000.000
13C14ALA00.0150.01031.0680.0020.0020.0000.0000.0000.000
14C15GLY00.0540.01233.066-0.008-0.0080.0000.0000.0000.000
15C16THR0-0.075-0.04635.8910.0040.0040.0000.0000.0000.000
16C17SER0-0.046-0.01832.070-0.007-0.0070.0000.0000.0000.000
17C18LYS10.9500.97426.405-0.139-0.1390.0000.0000.0000.000
18C19GLY00.0160.00827.406-0.011-0.0110.0000.0000.0000.000
19C20ILE0-0.0020.00320.6310.0200.0200.0000.0000.0000.000
20C21PHE00.000-0.01823.450-0.021-0.0210.0000.0000.0000.000
21C22LEU00.0080.00018.6920.0390.0390.0000.0000.0000.000
22C23LYS10.9490.97421.260-0.351-0.3510.0000.0000.0000.000
23C24GLY00.008-0.00421.0200.0160.0160.0000.0000.0000.000
24C25ASN0-0.043-0.04320.446-0.023-0.0230.0000.0000.0000.000
25C26ASP-1-0.895-0.93516.8860.4450.4450.0000.0000.0000.000
26C27LEU0-0.016-0.01416.0390.0420.0420.0000.0000.0000.000
27C28PRO0-0.0130.00015.454-0.013-0.0130.0000.0000.0000.000
28C29ALA00.0120.01417.874-0.005-0.0050.0000.0000.0000.000
29C30ASP-1-0.847-0.93019.829-0.063-0.0630.0000.0000.0000.000
30C31GLN00.0330.00420.8020.0190.0190.0000.0000.0000.000
31C32GLU-1-0.816-0.86520.206-0.157-0.1570.0000.0000.0000.000
32C33LEU0-0.005-0.01214.436-0.002-0.0020.0000.0000.0000.000
33C34ARG10.8260.90017.719-0.101-0.1010.0000.0000.0000.000
34C35ASP-1-0.773-0.88419.6610.0440.0440.0000.0000.0000.000
35C36LYS10.8160.88616.8970.2160.2160.0000.0000.0000.000
36C37VAL0-0.018-0.01213.9410.0020.0020.0000.0000.0000.000
37C38ILE00.0260.02416.3700.0520.0520.0000.0000.0000.000
38C39LEU0-0.012-0.00619.4060.0160.0160.0000.0000.0000.000
39C40ARG10.7970.88714.1840.1100.1100.0000.0000.0000.000
40C41ILE00.0020.01915.6420.0320.0320.0000.0000.0000.000
41C42PHE0-0.006-0.01517.0710.0200.0200.0000.0000.0000.000
42C43GLY00.0120.02819.0410.0020.0020.0000.0000.0000.000
43C44SER0-0.060-0.03819.950-0.013-0.0130.0000.0000.0000.000
44C45PRO0-0.072-0.03420.922-0.012-0.0120.0000.0000.0000.000
45C46ASP-1-0.821-0.94823.171-0.061-0.0610.0000.0000.0000.000
46C47VAL0-0.026-0.01925.1200.0170.0170.0000.0000.0000.000
47C48ARG10.8970.93425.0180.0450.0450.0000.0000.0000.000
48C49GLN0-0.0090.00122.8130.0250.0250.0000.0000.0000.000
49C50ILE0-0.022-0.00920.2580.0200.0200.0000.0000.0000.000
50C51ASP-1-0.880-0.92615.324-0.097-0.0970.0000.0000.0000.000
51C52GLY00.0220.00016.820-0.001-0.0010.0000.0000.0000.000
52C53LEU0-0.051-0.03717.5320.0060.0060.0000.0000.0000.000
53C54ALA0-0.078-0.01319.994-0.002-0.0020.0000.0000.0000.000
54C55GLY00.005-0.00123.533-0.004-0.0040.0000.0000.0000.000
55C56ALA0-0.0030.00126.135-0.008-0.0080.0000.0000.0000.000
56C57ASP-1-0.841-0.90427.8610.0400.0400.0000.0000.0000.000
57C58PRO00.0710.01930.1200.0090.0090.0000.0000.0000.000
58C59LEU0-0.072-0.04031.6320.0070.0070.0000.0000.0000.000
59C60THR0-0.083-0.05927.9180.0130.0130.0000.0000.0000.000
60C61SER00.0640.03426.1600.0150.0150.0000.0000.0000.000
61C62LYS10.8240.91227.188-0.082-0.0820.0000.0000.0000.000
62C63LEU0-0.0010.00222.8020.0190.0190.0000.0000.0000.000
63C64ALA0-0.0090.00125.785-0.017-0.0170.0000.0000.0000.000
64C65ILE0-0.005-0.00523.4650.0240.0240.0000.0000.0000.000
65C66ILE0-0.014-0.00825.362-0.018-0.0180.0000.0000.0000.000
66C67GLY00.0230.00525.6590.0230.0230.0000.0000.0000.000
67C68PRO00.005-0.00526.877-0.005-0.0050.0000.0000.0000.000
68C69SER0-0.0030.00030.131-0.007-0.0070.0000.0000.0000.000
69C70THR0-0.042-0.02232.960-0.002-0.0020.0000.0000.0000.000
70C71HIS0-0.010-0.00234.785-0.006-0.0060.0000.0000.0000.000
71C72PRO0-0.034-0.02238.3220.0040.0040.0000.0000.0000.000
72C73ASP-1-0.889-0.93340.8180.0580.0580.0000.0000.0000.000
73C74ALA0-0.050-0.02837.2730.0010.0010.0000.0000.0000.000
74C75ASP-1-0.822-0.88836.0920.1000.1000.0000.0000.0000.000
75C76VAL0-0.099-0.06431.0400.0090.0090.0000.0000.0000.000
76C77ASP-1-0.755-0.85030.8270.0790.0790.0000.0000.0000.000
77C78TYR0-0.030-0.03130.1960.0150.0150.0000.0000.0000.000
78C79THR0-0.016-0.01027.934-0.011-0.0110.0000.0000.0000.000
79C80PHE0-0.004-0.00428.5100.0130.0130.0000.0000.0000.000
80C81ALA00.0460.02126.812-0.010-0.0100.0000.0000.0000.000
81C82GLN0-0.0170.00328.5920.0150.0150.0000.0000.0000.000
82C83VAL0-0.0050.00423.512-0.012-0.0120.0000.0000.0000.000
83C84SER0-0.011-0.01326.9240.0050.0050.0000.0000.0000.000
84C85ILE00.0130.03926.283-0.001-0.0010.0000.0000.0000.000
85C86THR0-0.008-0.02526.514-0.008-0.0080.0000.0000.0000.000
86C87ASP-1-0.825-0.88128.146-0.045-0.0450.0000.0000.0000.000
87C88ALA0-0.038-0.00424.1800.0100.0100.0000.0000.0000.000
88C89VAL0-0.011-0.02025.481-0.003-0.0030.0000.0000.0000.000
89C90VAL0-0.011-0.00623.3660.0110.0110.0000.0000.0000.000
90C91ASP-1-0.826-0.90126.7660.0140.0140.0000.0000.0000.000
91C92TYR0-0.049-0.04624.5650.0180.0180.0000.0000.0000.000
92C93ASN0-0.040-0.01931.2830.0030.0030.0000.0000.0000.000
93C94GLY00.0240.01734.9860.0000.0000.0000.0000.0000.000
94C95ASN00.0260.00435.0150.0110.0110.0000.0000.0000.000
95C96CYS0-0.0420.00033.781-0.003-0.0030.0000.0000.0000.000
96C97GLY00.0720.02835.7920.0060.0060.0000.0000.0000.000
97C98ASN00.016-0.00535.8130.0040.0040.0000.0000.0000.000
98C99ILE00.0660.02229.7630.0060.0060.0000.0000.0000.000
99C100SER0-0.018-0.01232.6320.0080.0080.0000.0000.0000.000
100C101ALA00.0280.00234.8400.0020.0020.0000.0000.0000.000
101C102GLY0-0.0110.00131.5290.0040.0040.0000.0000.0000.000
102C103VAL0-0.022-0.00731.1370.0110.0110.0000.0000.0000.000
103C104GLY00.0670.04332.0420.0080.0080.0000.0000.0000.000
104C105PRO00.022-0.00232.6290.0070.0070.0000.0000.0000.000
105C106PHE00.0270.01124.4390.0120.0120.0000.0000.0000.000
106C107ALA00.0250.00129.2190.0130.0130.0000.0000.0000.000
107C108ILE00.0020.00731.2150.0040.0040.0000.0000.0000.000
108C109ASP-1-0.848-0.93628.9330.1880.1880.0000.0000.0000.000
109C110GLU-1-0.862-0.90724.4770.3130.3130.0000.0000.0000.000
110C111SER0-0.107-0.04828.0150.0010.0010.0000.0000.0000.000
111C112PHE0-0.028-0.01126.0510.0000.0000.0000.0000.0000.000
112C113VAL00.0180.01131.529-0.011-0.0110.0000.0000.0000.000
113C114LYS10.9090.96334.765-0.105-0.1050.0000.0000.0000.000
114C115ALA00.0230.01736.202-0.005-0.0050.0000.0000.0000.000
115C116VAL0-0.061-0.04437.994-0.002-0.0020.0000.0000.0000.000
116C117GLU-1-0.783-0.90541.2730.1080.1080.0000.0000.0000.000
117C118PRO0-0.071-0.04343.207-0.004-0.0040.0000.0000.0000.000
118C119MET0-0.0080.01643.0890.0040.0040.0000.0000.0000.000
119C120THR00.0100.01238.4690.0000.0000.0000.0000.0000.000
120C121ARG10.8060.89541.027-0.069-0.0690.0000.0000.0000.000
121C122VAL0-0.003-0.00135.7460.0030.0030.0000.0000.0000.000
122C123CYS0-0.092-0.04139.099-0.006-0.0060.0000.0000.0000.000
123C124ILE00.009-0.00334.6630.0050.0050.0000.0000.0000.000
124C125HIS00.027-0.00834.784-0.014-0.0140.0000.0000.0000.000
125C126ASN0-0.050-0.02434.098-0.001-0.0010.0000.0000.0000.000
126C127THR00.0330.01731.110-0.003-0.0030.0000.0000.0000.000
127C128ASN0-0.084-0.05431.5260.0010.0010.0000.0000.0000.000
128C129THR0-0.059-0.03034.882-0.008-0.0080.0000.0000.0000.000
129C130GLY00.0250.02737.589-0.005-0.0050.0000.0000.0000.000
130C131LYS10.8080.90339.065-0.039-0.0390.0000.0000.0000.000
131C132LEU00.0580.02839.2870.0040.0040.0000.0000.0000.000
132C133LEU0-0.071-0.03537.339-0.003-0.0030.0000.0000.0000.000
133C134TYR0-0.032-0.02540.4560.0050.0050.0000.0000.0000.000
134C135ALA00.0470.03238.639-0.002-0.0020.0000.0000.0000.000
135C136GLU-1-0.883-0.91740.5880.0700.0700.0000.0000.0000.000
136C137VAL0-0.007-0.02236.7270.0000.0000.0000.0000.0000.000
137C138GLU-1-0.825-0.91240.1700.0890.0890.0000.0000.0000.000
138C139VAL0-0.089-0.03937.5390.0080.0080.0000.0000.0000.000
139C140GLU-1-0.833-0.89638.1830.1070.1070.0000.0000.0000.000
140C141ASP-1-0.889-0.94036.9110.1350.1350.0000.0000.0000.000
141C142GLY0-0.088-0.05135.3740.0090.0090.0000.0000.0000.000
142C143LYS10.8360.92429.560-0.180-0.1800.0000.0000.0000.000
143C144ALA00.0210.01533.634-0.011-0.0110.0000.0000.0000.000
144C145LYS10.8060.89135.149-0.104-0.1040.0000.0000.0000.000
145C146VAL00.0160.00433.4100.0000.0000.0000.0000.0000.000
146C147SER0-0.033-0.02036.768-0.003-0.0030.0000.0000.0000.000
147C148GLY00.0750.02939.803-0.001-0.0010.0000.0000.0000.000
148C149ASP-1-0.956-0.97543.3470.0770.0770.0000.0000.0000.000
149C150CYS0-0.0060.01043.436-0.006-0.0060.0000.0000.0000.000
150C151LYS10.8460.91743.146-0.060-0.0600.0000.0000.0000.000
151C152ILE00.0120.01338.868-0.003-0.0030.0000.0000.0000.000
152C153ASP-1-0.804-0.90442.4160.0560.0560.0000.0000.0000.000
153C154GLY0-0.001-0.01040.1060.0000.0000.0000.0000.0000.000
154C155VAL0-0.051-0.02236.6920.0040.0040.0000.0000.0000.000
155C156PRO0-0.039-0.02237.400-0.003-0.0030.0000.0000.0000.000
156C157GLY0-0.0030.00639.2220.0050.0050.0000.0000.0000.000
157C158THR0-0.029-0.00541.552-0.003-0.0030.0000.0000.0000.000
158C159ASN0-0.012-0.01737.3090.0060.0060.0000.0000.0000.000
159C160ALA00.0380.03039.297-0.006-0.0060.0000.0000.0000.000
160C161PRO0-0.053-0.02540.3260.0010.0010.0000.0000.0000.000
161C162GLU-1-0.798-0.91237.5800.1060.1060.0000.0000.0000.000
162C163LEU0-0.056-0.01441.525-0.004-0.0040.0000.0000.0000.000
163C164MET00.0080.01638.0510.0040.0040.0000.0000.0000.000
164C165ASP-1-0.796-0.92542.5730.0500.0500.0000.0000.0000.000
165C166PHE0-0.016-0.01739.8380.0020.0020.0000.0000.0000.000
166C167SER0-0.011-0.00344.833-0.002-0.0020.0000.0000.0000.000
167C168ASP-1-0.803-0.87344.9920.0470.0470.0000.0000.0000.000
168C169THR0-0.037-0.04842.6130.0000.0000.0000.0000.0000.000
169C170ALA0-0.024-0.00644.826-0.003-0.0030.0000.0000.0000.000
170C171GLY0-0.030-0.02047.5060.0000.0000.0000.0000.0000.000
171C172ALA0-0.022-0.01843.353-0.002-0.0020.0000.0000.0000.000
172C173ALA00.0430.03343.0080.0000.0000.0000.0000.0000.000
173C174THR0-0.025-0.01944.239-0.001-0.0010.0000.0000.0000.000
174C175GLY00.0370.02747.712-0.002-0.0020.0000.0000.0000.000
175C176LYS10.8740.91848.860-0.015-0.0150.0000.0000.0000.000
176C177VAL00.0370.04650.9360.0000.0000.0000.0000.0000.000
177C333ASP-1-0.897-0.95056.2700.0360.0360.0000.0000.0000.000
178C334THR0-0.044-0.03052.5510.0000.0000.0000.0000.0000.000
179C335VAL0-0.062-0.02452.953-0.002-0.0020.0000.0000.0000.000
180C336ARG10.9300.95652.510-0.032-0.0320.0000.0000.0000.000
181C337ILE00.0550.01748.421-0.002-0.0020.0000.0000.0000.000
182C338GLY0-0.0160.00750.0980.0020.0020.0000.0000.0000.000
183C339HIS00.0060.00743.425-0.003-0.0030.0000.0000.0000.000
184C340PRO00.028-0.00943.2880.0000.0000.0000.0000.0000.000
185C341ALA0-0.0100.00642.658-0.001-0.0010.0000.0000.0000.000
186C342GLY0-0.0150.00144.7190.0030.0030.0000.0000.0000.000
187C343VAL0-0.047-0.03047.574-0.003-0.0030.0000.0000.0000.000
188C344ILE0-0.024-0.02244.2750.0030.0030.0000.0000.0000.000
189C345PRO0-0.0310.00648.296-0.003-0.0030.0000.0000.0000.000
190C346VAL00.001-0.00747.5780.0030.0030.0000.0000.0000.000
191C347VAL00.005-0.00450.034-0.003-0.0030.0000.0000.0000.000
192C348SER00.0000.00252.0890.0000.0000.0000.0000.0000.000
193C349ILE00.0550.01653.2360.0000.0000.0000.0000.0000.000
194C350VAL0-0.031-0.01255.8590.0000.0000.0000.0000.0000.000
195C351LYS10.8410.89957.648-0.033-0.0330.0000.0000.0000.000
196C352ASP-1-0.917-0.96159.4490.0200.0200.0000.0000.0000.000
197C353GLY00.0530.03956.4890.0000.0000.0000.0000.0000.000
198C354LYS10.8140.89754.117-0.036-0.0360.0000.0000.0000.000
199C355VAL00.0090.00550.451-0.001-0.0010.0000.0000.0000.000
200C356GLU-1-0.849-0.89252.4190.0370.0370.0000.0000.0000.000
201C357LYS10.9520.94849.592-0.052-0.0520.0000.0000.0000.000
202C358ALA0-0.0070.00547.952-0.003-0.0030.0000.0000.0000.000
203C359ALA00.0130.02846.6580.0030.0030.0000.0000.0000.000
204C360LEU0-0.015-0.01043.325-0.003-0.0030.0000.0000.0000.000
205C361ILE00.0350.02943.9720.0030.0030.0000.0000.0000.000
206C362ARG10.8190.90439.073-0.074-0.0740.0000.0000.0000.000
207C363THR00.0920.02937.5170.0030.0030.0000.0000.0000.000
208C364ALA00.0090.01333.3390.0000.0000.0000.0000.0000.000
209C365ARG10.9190.96529.331-0.172-0.1720.0000.0000.0000.000
210C366ARG10.8660.91824.772-0.264-0.2640.0000.0000.0000.000
211C367ILE0-0.095-0.04725.814-0.008-0.0080.0000.0000.0000.000
212C368MET0-0.016-0.01818.608-0.004-0.0040.0000.0000.0000.000
213C369GLU-1-0.807-0.88820.9160.3130.3130.0000.0000.0000.000
214C370GLY00.0040.00317.1920.0120.0120.0000.0000.0000.000
215C371TYR0-0.024-0.02912.2010.0450.0450.0000.0000.0000.000
216C372VAL00.0190.02013.4310.0370.0370.0000.0000.0000.000
217C373TYR0-0.030-0.0147.1100.3940.3940.0000.0000.0000.000
218C374VAL00.0810.0439.475-0.239-0.2390.0000.0000.0000.000
219C375GLU-1-0.789-0.8958.376-0.583-0.5830.0000.0000.0000.000
220C376LYS10.8720.9152.7901.2551.9850.162-0.346-0.5450.003
221C377ALA00.0240.0168.4210.1370.1370.0000.0000.0000.000
222C378LYS10.8180.90310.4010.6870.6870.0000.0000.0000.000
223C379LEU0-0.027-0.00910.8230.1540.1540.0000.0000.0000.000
224C380VAL0-0.037-0.00113.7510.0350.0350.0000.0000.0000.000