Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LL5J9

Calculation Name: 3GR0-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GR0

Chain ID: A

ChEMBL ID:

UniProt ID: P41783

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2032157.387023
FMO2-HF: Nuclear repulsion 1956279.718222
FMO2-HF: Total energy -75877.668801
FMO2-MP2: Total energy -76101.806328


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(A:176:ACE )


Summations of interaction energy for fragment #1(A:176:ACE )
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.
0.7241.957-0.002-0.621-0.611-0.001
Interaction energy analysis for fragmet #1(A:176:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.006
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].
3A178GLY 00.0360.0313.8500.3461.519-0.002-0.607-0.564-0.001
4A179GLN 0-0.002-0.0015.8780.1040.1040.0000.0000.0000.000
5A180GLU -1-0.840-0.9317.632-0.558-0.5580.0000.0000.0000.000
6A181LYS 10.8720.9254.3540.0370.0970.000-0.014-0.0470.000
7A182GLU -1-0.889-0.9427.191-0.091-0.0910.0000.0000.0000.000
8A183ARG 10.8210.92510.5380.4010.4010.0000.0000.0000.000
9A184PHE 0-0.031-0.0168.7140.0490.0490.0000.0000.0000.000
10A185GLN 00.004-0.0018.6380.0060.0060.0000.0000.0000.000
11A186VAL 00.0130.0155.4740.0030.0030.0000.0000.0000.000
12A187LEU 0-0.056-0.0318.1430.1790.1790.0000.0000.0000.000
13A188PRO 00.0070.00710.691-0.027-0.0270.0000.0000.0000.000
14A189GLY 00.0610.02812.5370.0090.0090.0000.0000.0000.000
15A190ARG 10.7790.85316.0410.0930.0930.0000.0000.0000.000
16A191ASP -1-0.775-0.85218.027-0.127-0.1270.0000.0000.0000.000
17A192LYS 10.8900.93816.4430.0230.0230.0000.0000.0000.000
18A193MET 0-0.0180.02615.251-0.003-0.0030.0000.0000.0000.000
19A194LEU 0-0.021-0.0108.6470.0060.0060.0000.0000.0000.000
20A195TYR 0-0.051-0.07311.899-0.003-0.0030.0000.0000.0000.000
21A196VAL 00.0100.0069.786-0.060-0.0600.0000.0000.0000.000
22A197ALA 0-0.018-0.01211.4020.0880.0880.0000.0000.0000.000
23A198ALA 00.0470.01912.696-0.075-0.0750.0000.0000.0000.000
24A199GLN 00.0610.02714.9780.0570.0570.0000.0000.0000.000
25A200ASN 0-0.010-0.00217.5590.0280.0280.0000.0000.0000.000
26A201GLU -1-0.804-0.89219.105-0.209-0.2090.0000.0000.0000.000
27A202ARG 10.9670.97819.6250.1940.1940.0000.0000.0000.000
28A203ASP -1-0.860-0.93615.154-0.376-0.3760.0000.0000.0000.000
29A204THR 0-0.010-0.01715.664-0.055-0.0550.0000.0000.0000.000
30A205LEU 0-0.014-0.01317.370-0.012-0.0120.0000.0000.0000.000
31A206TRP 00.0000.01210.9610.0050.0050.0000.0000.0000.000
32A207ALA 00.0230.00612.821-0.022-0.0220.0000.0000.0000.000
33A208ARG 10.7710.82814.1260.2300.2300.0000.0000.0000.000
34A209GLN 0-0.0090.00516.7020.0270.0270.0000.0000.0000.000
35A210VAL 0-0.032-0.00811.1000.0270.0270.0000.0000.0000.000
36A211LEU 0-0.025-0.02211.192-0.001-0.0010.0000.0000.0000.000
37A212ALA 00.0180.01214.4060.0320.0320.0000.0000.0000.000
38A213ARG 10.8690.94815.8770.2920.2920.0000.0000.0000.000
39A214GLY 0-0.0050.00214.1820.0270.0270.0000.0000.0000.000
40A215ASP -1-0.880-0.92815.270-0.139-0.1390.0000.0000.0000.000
41A216TYR 0-0.006-0.01511.003-0.020-0.0200.0000.0000.0000.000
42A217ASP -1-0.870-0.93414.839-0.232-0.2320.0000.0000.0000.000
43A218LYS 10.8610.92917.6590.1750.1750.0000.0000.0000.000
44A219ASN 0-0.054-0.03314.6000.0200.0200.0000.0000.0000.000
45A220ALA 0-0.0010.00412.088-0.011-0.0110.0000.0000.0000.000
46A221ARG 10.9390.97114.0140.1950.1950.0000.0000.0000.000
47A222VAL 00.0010.01713.994-0.050-0.0500.0000.0000.0000.000
48A223ILE 0-0.0190.00515.2590.0550.0550.0000.0000.0000.000
49A224ASN 00.039-0.00116.670-0.010-0.0100.0000.0000.0000.000
50A225GLU -1-0.808-0.91719.254-0.114-0.1140.0000.0000.0000.000
51A226ASN 00.003-0.01422.0470.0230.0230.0000.0000.0000.000
52A227GLU -1-0.803-0.87121.936-0.185-0.1850.0000.0000.0000.000
53A228GLU -1-0.736-0.81320.564-0.149-0.1490.0000.0000.0000.000
54A229ASN 0-0.035-0.03323.7210.0240.0240.0000.0000.0000.000
55A230LYS 10.9300.96626.8910.1280.1280.0000.0000.0000.000
56A231ARG 10.7850.87022.4570.1390.1390.0000.0000.0000.000
57A232ILE 00.008-0.00724.6870.0080.0080.0000.0000.0000.000
58A233SER 0-0.0010.01028.7250.0100.0100.0000.0000.0000.000
59A234ILE 00.0340.04431.2620.0050.0050.0000.0000.0000.000
60A235TRP 00.0120.00330.6660.0060.0060.0000.0000.0000.000
61A236LEU 0-0.037-0.03631.8030.0060.0060.0000.0000.0000.000
62A237ASP -1-0.886-0.93234.609-0.057-0.0570.0000.0000.0000.000
63A238THR 0-0.074-0.03136.2550.0040.0040.0000.0000.0000.000
64A239TYR 0-0.049-0.02834.6810.0050.0050.0000.0000.0000.000
65A240TYR 0-0.074-0.05135.2790.0030.0030.0000.0000.0000.000
66A241PRO 00.0740.04538.296-0.001-0.0010.0000.0000.0000.000
67A242GLN 0-0.019-0.01140.500-0.001-0.0010.0000.0000.0000.000
68A243LEU 0-0.045-0.00135.0480.0010.0010.0000.0000.0000.000
69A244ALA 00.0040.00339.059-0.002-0.0020.0000.0000.0000.000
70A245TYR 0-0.033-0.06232.3670.0030.0030.0000.0000.0000.000
71A246TYR 0-0.061-0.04833.5490.0000.0000.0000.0000.0000.000
72A247ARG 10.9090.95626.8010.0990.0990.0000.0000.0000.000
73A248ILE 00.0060.00624.6440.0060.0060.0000.0000.0000.000
74A249HIS 10.8430.93824.4680.0810.0810.0000.0000.0000.000
75A250PHE 00.018-0.01119.2520.0060.0060.0000.0000.0000.000
76A251ASP -1-0.885-0.93918.832-0.120-0.1200.0000.0000.0000.000
77A252GLU -1-0.912-0.95217.569-0.051-0.0510.0000.0000.0000.000
78A253PRO 00.0050.00014.5830.0080.0080.0000.0000.0000.000
79A254ARG 10.9730.98610.4250.0900.0900.0000.0000.0000.000
80A255LYS 10.9080.96117.5190.0380.0380.0000.0000.0000.000
81A256PRO 00.0320.03320.6210.0020.0020.0000.0000.0000.000
82A257VAL 00.0010.00322.7890.0120.0120.0000.0000.0000.000
83A258PHE 0-0.017-0.02026.286-0.006-0.0060.0000.0000.0000.000
84A259TRP 00.0310.01328.9450.0060.0060.0000.0000.0000.000
85A260LEU 00.038-0.00231.974-0.002-0.0020.0000.0000.0000.000
86A261SER 0-0.057-0.04435.3520.0020.0020.0000.0000.0000.000
87A262ARG 10.9370.95537.4160.0290.0290.0000.0000.0000.000
88A263GLN 00.0270.01840.5770.0000.0000.0000.0000.0000.000
89A264ARG 10.8530.91139.9750.0400.0400.0000.0000.0000.000
90A265ASN 0-0.0090.00239.999-0.002-0.0020.0000.0000.0000.000
91A266THR 0-0.008-0.00441.9610.0010.0010.0000.0000.0000.000
92A267MET 0-0.0160.01637.8810.0000.0000.0000.0000.0000.000
93A268SER 00.0270.02141.5170.0010.0010.0000.0000.0000.000
94A269LYS 11.0140.98636.9660.0110.0110.0000.0000.0000.000
95A270LYS 11.0131.00837.6120.0140.0140.0000.0000.0000.000
96A271GLU -1-0.873-0.94637.860-0.025-0.0250.0000.0000.0000.000
97A272LEU 0-0.004-0.00435.557-0.003-0.0030.0000.0000.0000.000
98A273GLU -1-0.913-0.96333.504-0.020-0.0200.0000.0000.0000.000
99A274VAL 0-0.030-0.01032.979-0.002-0.0020.0000.0000.0000.000
100A275LEU 0-0.0120.01032.606-0.003-0.0030.0000.0000.0000.000
101A276SER 0-0.005-0.00329.095-0.004-0.0040.0000.0000.0000.000
102A277GLN 00.0320.00028.563-0.006-0.0060.0000.0000.0000.000
103A278LYS 10.8920.94828.7820.0350.0350.0000.0000.0000.000
104A279LEU 00.0150.01027.374-0.006-0.0060.0000.0000.0000.000
105A280ARG 10.9350.96523.0160.0300.0300.0000.0000.0000.000
106A281ALA 0-0.055-0.02223.838-0.008-0.0080.0000.0000.0000.000
107A282LEU 00.0130.01724.982-0.006-0.0060.0000.0000.0000.000
108A283MET 0-0.0280.00721.100-0.016-0.0160.0000.0000.0000.000
109A284PRO 00.0030.00518.8480.0070.0070.0000.0000.0000.000
110A285TYR 0-0.010-0.02215.4720.0090.0090.0000.0000.0000.000
111A286ALA 0-0.0210.00316.9120.0020.0020.0000.0000.0000.000
112A287ASP -1-0.914-0.94718.294-0.028-0.0280.0000.0000.0000.000
113A288SER 0-0.105-0.05720.6790.0110.0110.0000.0000.0000.000
114A289VAL 00.0730.03523.258-0.008-0.0080.0000.0000.0000.000
115A290ASN 0-0.0040.00425.7820.0060.0060.0000.0000.0000.000
116A291ILE 00.0130.01228.071-0.005-0.0050.0000.0000.0000.000
117A292THR 0-0.007-0.00330.6950.0050.0050.0000.0000.0000.000
118A293LEU 0-0.028-0.00932.753-0.003-0.0030.0000.0000.0000.000
119A294MET 0-0.025-0.01533.0660.0020.0020.0000.0000.0000.000
120A295ASP -1-0.833-0.93236.608-0.027-0.0270.0000.0000.0000.000
121A296ASP -1-0.667-0.79039.668-0.038-0.0380.0000.0000.0000.000
122A297VAL 0-0.037-0.01141.607-0.001-0.0010.0000.0000.0000.000
123A298THR 0-0.026-0.01337.9450.0000.0000.0000.0000.0000.000
124A299ALA 00.0180.01638.034-0.001-0.0010.0000.0000.0000.000
125A300ALA 0-0.0250.01039.027-0.002-0.0020.0000.0000.0000.000
126A301GLY 00.0300.01842.0800.0000.0000.0000.0000.0000.000
127A302GLN 00.016-0.00535.115-0.003-0.0030.0000.0000.0000.000
128A303ALA 0-0.0070.01139.049-0.002-0.0020.0000.0000.0000.000
129A304GLU -1-0.832-0.88840.099-0.029-0.0290.0000.0000.0000.000
130A305ALA 0-0.030-0.00640.4310.0010.0010.0000.0000.0000.000
131A306GLY 00.0510.01339.0380.0010.0010.0000.0000.0000.000
132A307LEU 00.002-0.00239.828-0.001-0.0010.0000.0000.0000.000
133A308LYS 10.9350.96742.8530.0290.0290.0000.0000.0000.000
134A309GLN 0-0.066-0.03638.347-0.001-0.0010.0000.0000.0000.000
135A310GLN 0-0.047-0.02038.0090.0000.0000.0000.0000.0000.000
136A311ALA 0-0.0180.00143.1960.0000.0000.0000.0000.0000.000
137A312LEU 00.0220.02342.2470.0000.0000.0000.0000.0000.000
138A313PRO 00.0010.01946.6520.0010.0010.0000.0000.0000.000
139A314TYR 0-0.021-0.07646.792-0.002-0.0020.0000.0000.0000.000
140A315SER 0-0.029-0.01148.8600.0020.0020.0000.0000.0000.000
141A316ARG 10.8670.92846.1810.0290.0290.0000.0000.0000.000
142A317ARG 10.9190.95548.6450.0300.0300.0000.0000.0000.000
143A318ASN 00.0550.04248.772-0.003-0.0030.0000.0000.0000.000
144A319HIS 00.0610.07447.0330.0000.0000.0000.0000.0000.000
145A320LYS 10.8980.94549.2890.0270.0270.0000.0000.0000.000
146A321GLY 00.0480.02046.076-0.001-0.0010.0000.0000.0000.000
147A322GLY 00.0310.01644.218-0.002-0.0020.0000.0000.0000.000
148A323VAL 0-0.085-0.02544.1010.0030.0030.0000.0000.0000.000
149A324THR 00.055-0.02343.967-0.003-0.0030.0000.0000.0000.000
150A325PHE 0-0.053-0.02743.0230.0030.0030.0000.0000.0000.000
151A326VAL 0-0.008-0.00944.910-0.002-0.0020.0000.0000.0000.000
152A327ILE 00.0260.00442.2280.0020.0020.0000.0000.0000.000
153A328GLN 0-0.041-0.02346.8010.0000.0000.0000.0000.0000.000
154A329GLY 00.0050.01149.3900.0000.0000.0000.0000.0000.000
155A330ALA 0-0.026-0.00749.690-0.001-0.0010.0000.0000.0000.000
156A331LEU 00.003-0.01144.6690.0000.0000.0000.0000.0000.000
157A332ASP -1-0.812-0.88944.952-0.039-0.0390.0000.0000.0000.000
158A333ASP -1-0.862-0.94842.327-0.045-0.0450.0000.0000.0000.000
159A334VAL 0-0.057-0.03140.138-0.004-0.0040.0000.0000.0000.000
160A335GLU -1-0.886-0.95740.230-0.038-0.0380.0000.0000.0000.000
161A336ILE 0-0.041-0.01140.576-0.002-0.0020.0000.0000.0000.000
162A337LEU 0-0.045-0.02835.694-0.004-0.0040.0000.0000.0000.000
163A338ARG 10.9570.97636.6350.0440.0440.0000.0000.0000.000
164A339ALA 00.0690.03837.307-0.001-0.0010.0000.0000.0000.000
165A340ARG 10.9350.96535.9980.0590.0590.0000.0000.0000.000
166A341GLN 00.0250.01331.939-0.001-0.0010.0000.0000.0000.000
167A342PHE 0-0.0310.01133.039-0.003-0.0030.0000.0000.0000.000
168A343VAL 00.0140.00734.697-0.002-0.0020.0000.0000.0000.000
169A344ASP -1-0.921-0.96230.957-0.085-0.0850.0000.0000.0000.000
170A345SER 0-0.065-0.04730.074-0.008-0.0080.0000.0000.0000.000
171A346TYR 0-0.030-0.04030.875-0.002-0.0020.0000.0000.0000.000
172A347TYR 00.0190.00832.6590.0010.0010.0000.0000.0000.000
173A348ARG 10.9170.97226.0420.1000.1000.0000.0000.0000.000
174A349THR 0-0.0020.01228.184-0.005-0.0050.0000.0000.0000.000
175A350TRP 0-0.005-0.01929.9600.0000.0000.0000.0000.0000.000
176A351GLY 0-0.0080.00331.9490.0020.0020.0000.0000.0000.000
177A352GLY 00.024-0.00332.9570.0030.0030.0000.0000.0000.000
178A353ARG 10.9170.96534.6510.0610.0610.0000.0000.0000.000
179A354TYR 0-0.032-0.00237.9850.0030.0030.0000.0000.0000.000
180A355VAL 0-0.0030.00039.3420.0020.0020.0000.0000.0000.000
181A356GLN 0-0.022-0.00939.191-0.003-0.0030.0000.0000.0000.000
182A357PHE 00.0140.00037.5850.0030.0030.0000.0000.0000.000
183A358ALA 0-0.009-0.00441.998-0.002-0.0020.0000.0000.0000.000
184A359ILE 0-0.0070.00644.4320.0000.0000.0000.0000.0000.000
185A360GLU -1-0.888-0.96246.260-0.030-0.0300.0000.0000.0000.000
186A361LEU 0-0.039-0.01550.031-0.001-0.0010.0000.0000.0000.000
187A362LYS 00.0170.02351.9750.0000.0000.0000.0000.0000.000