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: 1JQ4Z

Calculation Name: 3H4R-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H4R

Chain ID: A

ChEMBL ID:

UniProt ID: P15032

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 223
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2621248.884106
FMO2-HF: Nuclear repulsion 2531356.166069
FMO2-HF: Total energy -89892.718037
FMO2-MP2: Total energy -90152.942083


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:611:ACE )


Summations of interaction energy for fragment #1(A:611: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.
0.3160.7150.002-0.287-0.1140.001
Interaction energy analysis for fragmet #1(A:611:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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].
3A613GLY 00.0790.0293.8700.1390.5380.002-0.287-0.1140.001
4A614ILE 0-0.009-0.0156.6840.2040.2040.0000.0000.0000.000
5A615SER 0-0.0030.0029.1610.0720.0720.0000.0000.0000.000
6A616LYS 10.9330.92311.7050.1720.1720.0000.0000.0000.000
7A617SER 0-0.045-0.04413.5190.0380.0380.0000.0000.0000.000
8A618GLN 00.0080.0327.2490.0420.0420.0000.0000.0000.000
9A619LEU 00.0290.02112.7040.0490.0490.0000.0000.0000.000
10A620ASP -1-0.766-0.85415.246-0.083-0.0830.0000.0000.0000.000
11A621ASP -1-0.862-0.91914.2330.0100.0100.0000.0000.0000.000
12A622ILE 0-0.033-0.02512.4540.0150.0150.0000.0000.0000.000
13A623ALA 0-0.062-0.02516.6270.0070.0070.0000.0000.0000.000
14A624ASP -1-0.993-0.96319.6370.0100.0100.0000.0000.0000.000
15A625THR 0-0.036-0.03319.4390.0070.0070.0000.0000.0000.000
16A626PRO 00.0220.01716.6380.0080.0080.0000.0000.0000.000
17A627ALA 00.0530.04215.4020.0150.0150.0000.0000.0000.000
18A628LEU 0-0.032-0.02015.5660.0290.0290.0000.0000.0000.000
19A629TYR 00.0370.0067.9880.0570.0570.0000.0000.0000.000
20A630LEU 0-0.024-0.02011.0830.0330.0330.0000.0000.0000.000
21A631TRP 0-0.049-0.00312.0870.0450.0450.0000.0000.0000.000
22A632ARG 10.9190.94912.273-0.005-0.0050.0000.0000.0000.000
23A633LYS 10.8510.9476.612-0.480-0.4800.0000.0000.0000.000
24A634ASN 00.007-0.01210.9010.1100.1100.0000.0000.0000.000
25A635ALA 0-0.055-0.00113.827-0.019-0.0190.0000.0000.0000.000
26A636PRO 0-0.0110.00716.4920.0000.0000.0000.0000.0000.000
27A637VAL 00.0170.00516.805-0.021-0.0210.0000.0000.0000.000
28A638ASP -1-0.881-0.94019.3600.0810.0810.0000.0000.0000.000
29A639THR 0-0.049-0.03519.714-0.014-0.0140.0000.0000.0000.000
30A640THR 0-0.020-0.01522.093-0.004-0.0040.0000.0000.0000.000
31A641LYS 10.8740.93321.4310.0100.0100.0000.0000.0000.000
32A642THR 00.0010.00425.571-0.004-0.0040.0000.0000.0000.000
33A643LYS 10.9220.95425.2830.0070.0070.0000.0000.0000.000
34A644THR 0-0.047-0.02028.779-0.003-0.0030.0000.0000.0000.000
35A645LEU 00.0910.02928.709-0.003-0.0030.0000.0000.0000.000
36A646ASP -1-0.827-0.86123.155-0.028-0.0280.0000.0000.0000.000
37A647LEU 00.0670.01226.698-0.006-0.0060.0000.0000.0000.000
38A648GLY 00.0370.03427.536-0.003-0.0030.0000.0000.0000.000
39A649THR 00.011-0.01422.008-0.007-0.0070.0000.0000.0000.000
40A650ALA 0-0.018-0.00524.668-0.005-0.0050.0000.0000.0000.000
41A651PHE 0-0.027-0.02727.337-0.004-0.0040.0000.0000.0000.000
42A652HIS 0-0.077-0.03721.0340.0120.0120.0000.0000.0000.000
43A653CYS 00.0010.00324.588-0.007-0.0070.0000.0000.0000.000
44A654ARG 10.8040.92725.7680.0510.0510.0000.0000.0000.000
45A655VAL 0-0.051-0.06228.5060.0000.0000.0000.0000.0000.000
46A656LEU 0-0.0290.00923.4150.0000.0000.0000.0000.0000.000
47A657GLU -1-0.878-0.92422.479-0.127-0.1270.0000.0000.0000.000
48A658LEU 00.013-0.01126.1890.0100.0100.0000.0000.0000.000
49A659GLU -1-0.935-0.97728.389-0.070-0.0700.0000.0000.0000.000
50A660GLU -1-0.832-0.90222.976-0.066-0.0660.0000.0000.0000.000
51A661PHE 00.0210.02026.7860.0070.0070.0000.0000.0000.000
52A662SER 0-0.075-0.03328.4490.0060.0060.0000.0000.0000.000
53A663ASN 0-0.053-0.01526.7000.0090.0090.0000.0000.0000.000
54A664ARG 10.8260.87522.5120.0660.0660.0000.0000.0000.000
55A665NME 0-0.035-0.00326.4090.0060.0060.0000.0000.0000.000
56A698ACE 00.024-0.00133.293-0.001-0.0010.0000.0000.0000.000
57A699ALA 00.002-0.00533.9590.0030.0030.0000.0000.0000.000
58A700GLU -1-0.912-0.94237.173-0.011-0.0110.0000.0000.0000.000
59A701GLU -1-0.775-0.89835.664-0.020-0.0200.0000.0000.0000.000
60A702GLY 0-0.032-0.01135.230-0.003-0.0030.0000.0000.0000.000
61A703ARG 10.9850.99236.2500.0180.0180.0000.0000.0000.000
62A704LYS 10.7890.88635.5680.0200.0200.0000.0000.0000.000
63A705ILE 00.0390.02231.006-0.002-0.0020.0000.0000.0000.000
64A706GLU -1-0.841-0.91134.827-0.043-0.0430.0000.0000.0000.000
65A707LEU 0-0.025-0.02737.2030.0000.0000.0000.0000.0000.000
66A708MET 0-0.078-0.05132.9020.0000.0000.0000.0000.0000.000
67A709TYR 00.0650.04032.543-0.002-0.0020.0000.0000.0000.000
68A710GLN 00.0130.00335.483-0.002-0.0020.0000.0000.0000.000
69A711SER 0-0.089-0.05538.2350.0010.0010.0000.0000.0000.000
70A712VAL 0-0.003-0.01533.8480.0000.0000.0000.0000.0000.000
71A713MET 0-0.030-0.00436.421-0.003-0.0030.0000.0000.0000.000
72A714ALA 0-0.0180.01138.6670.0010.0010.0000.0000.0000.000
73A715LEU 0-0.052-0.01237.4360.0000.0000.0000.0000.0000.000
74A716PRO 00.0800.02139.454-0.003-0.0030.0000.0000.0000.000
75A717LEU 0-0.011-0.00134.852-0.002-0.0020.0000.0000.0000.000
76A718GLY 00.0670.02134.988-0.005-0.0050.0000.0000.0000.000
77A719GLN 00.0090.01234.916-0.001-0.0010.0000.0000.0000.000
78A720TRP 0-0.032-0.01233.853-0.002-0.0020.0000.0000.0000.000
79A721LEU 0-0.034-0.00131.013-0.004-0.0040.0000.0000.0000.000
80A722VAL 0-0.017-0.01831.250-0.006-0.0060.0000.0000.0000.000
81A723GLU -1-0.954-0.96131.949-0.060-0.0600.0000.0000.0000.000
82A724SER 0-0.081-0.06732.425-0.006-0.0060.0000.0000.0000.000
83A725ALA 00.0130.00731.6990.0000.0000.0000.0000.0000.000
84A726GLY 0-0.024-0.04427.929-0.003-0.0030.0000.0000.0000.000
85A727HIS 0-0.0010.01622.4110.0110.0110.0000.0000.0000.000
86A728ALA 00.0900.03822.4460.0010.0010.0000.0000.0000.000
87A729GLU -1-0.843-0.92517.694-0.188-0.1880.0000.0000.0000.000
88A730SER 0-0.092-0.04116.851-0.039-0.0390.0000.0000.0000.000
89A731SER 0-0.037-0.03812.701-0.034-0.0340.0000.0000.0000.000
90A732ILE 00.0490.02914.2180.0160.0160.0000.0000.0000.000
91A733TYR 0-0.038-0.0467.778-0.204-0.2040.0000.0000.0000.000
92A734TRP 00.0420.04612.9050.0400.0400.0000.0000.0000.000
93A735GLU -1-0.900-0.94212.901-0.435-0.4350.0000.0000.0000.000
94A736ASP -1-0.867-0.95214.582-0.164-0.1640.0000.0000.0000.000
95A737PRO 0-0.025-0.01616.6530.0200.0200.0000.0000.0000.000
96A738GLU -1-0.892-0.93019.751-0.101-0.1010.0000.0000.0000.000
97A739THR 0-0.047-0.02415.698-0.001-0.0010.0000.0000.0000.000
98A740GLY 00.0220.01715.5500.0100.0100.0000.0000.0000.000
99A741ILE 0-0.019-0.00310.313-0.055-0.0550.0000.0000.0000.000
100A742LEU 0-0.0060.0166.985-0.047-0.0470.0000.0000.0000.000
101A743CYS 0-0.054-0.0259.649-0.061-0.0610.0000.0000.0000.000
102A744ARG 10.9110.9376.9290.9260.9260.0000.0000.0000.000
103A745CYS 0-0.069-0.02011.6580.0800.0800.0000.0000.0000.000
104A746ARG 10.8930.95113.6880.2590.2590.0000.0000.0000.000
105A747PRO 00.0170.01016.2030.0260.0260.0000.0000.0000.000
106A748ASP -1-0.783-0.88520.025-0.154-0.1540.0000.0000.0000.000
107A749LYS 10.9170.97022.0060.1150.1150.0000.0000.0000.000
108A750ILE 0-0.048-0.00721.9680.0000.0000.0000.0000.0000.000
109A751ILE 0-0.003-0.02125.0170.0020.0020.0000.0000.0000.000
110A752PRO 0-0.026-0.01426.2900.0030.0030.0000.0000.0000.000
111A753GLU -1-0.889-0.94928.438-0.085-0.0850.0000.0000.0000.000
112A754PHE 0-0.0240.00231.8790.0030.0030.0000.0000.0000.000
113A755HIS 0-0.063-0.02128.2860.0010.0010.0000.0000.0000.000
114A756TRP 00.0390.00629.0590.0030.0030.0000.0000.0000.000
115A757ILE 00.0010.01222.149-0.009-0.0090.0000.0000.0000.000
116A758MET 0-0.0250.00025.8900.0130.0130.0000.0000.0000.000
117A759ASP -1-0.860-0.94022.407-0.150-0.1500.0000.0000.0000.000
118A760VAL 0-0.0060.00825.0230.0140.0140.0000.0000.0000.000
119A761LYS 10.8930.94321.6520.1210.1210.0000.0000.0000.000
120A762THR 0-0.0140.00127.2800.0050.0050.0000.0000.0000.000
121A763THR 0-0.044-0.02829.2740.0010.0010.0000.0000.0000.000
122A764ALA 0-0.0100.00631.9760.0010.0010.0000.0000.0000.000
123A765ASP -1-0.842-0.92235.108-0.025-0.0250.0000.0000.0000.000
124A766ILE 00.0390.00534.891-0.002-0.0020.0000.0000.0000.000
125A767GLN 00.014-0.01036.542-0.004-0.0040.0000.0000.0000.000
126A768ARG 10.9450.98331.0490.0300.0300.0000.0000.0000.000
127A769PHE 00.0870.02328.8390.0000.0000.0000.0000.0000.000
128A770LYS 10.9800.98432.9770.0420.0420.0000.0000.0000.000
129A771THR 0-0.071-0.02934.3890.0000.0000.0000.0000.0000.000
130A772ALA 0-0.051-0.00531.2230.0000.0000.0000.0000.0000.000
131A773TYR 00.0100.00628.119-0.003-0.0030.0000.0000.0000.000
132A774TYR 00.0140.01727.191-0.007-0.0070.0000.0000.0000.000
133A775ASP -1-0.901-0.96127.114-0.039-0.0390.0000.0000.0000.000
134A776TYR 0-0.076-0.02324.3860.0040.0040.0000.0000.0000.000
135A777ARG 10.7570.82718.7820.0820.0820.0000.0000.0000.000
136A778TYR 00.000-0.01422.781-0.015-0.0150.0000.0000.0000.000
137A779HIS 00.0750.02724.667-0.011-0.0110.0000.0000.0000.000
138A780VAL 00.007-0.00219.845-0.007-0.0070.0000.0000.0000.000
139A781GLN 0-0.043-0.02219.990-0.019-0.0190.0000.0000.0000.000
140A782ASP -1-0.820-0.88721.270-0.131-0.1310.0000.0000.0000.000
141A783ALA 00.004-0.00222.884-0.013-0.0130.0000.0000.0000.000
142A784PHE 00.0110.00013.730-0.009-0.0090.0000.0000.0000.000
143A785TYR 00.007-0.01017.317-0.041-0.0410.0000.0000.0000.000
144A786SER 0-0.030-0.03120.084-0.008-0.0080.0000.0000.0000.000
145A787ASP -1-0.731-0.82220.767-0.164-0.1640.0000.0000.0000.000
146A788GLY 0-0.005-0.01617.943-0.007-0.0070.0000.0000.0000.000
147A789TYR 0-0.038-0.03418.781-0.010-0.0100.0000.0000.0000.000
148A790GLU -1-0.874-0.93221.240-0.146-0.1460.0000.0000.0000.000
149A791ALA 0-0.0550.01019.9980.0060.0060.0000.0000.0000.000
150A792GLN 0-0.094-0.07617.814-0.022-0.0220.0000.0000.0000.000
151A793PHE 0-0.028-0.01620.8310.0040.0040.0000.0000.0000.000
152A794GLY 0-0.062-0.01223.9680.0160.0160.0000.0000.0000.000
153A795VAL 00.000-0.01126.7290.0080.0080.0000.0000.0000.000
154A796GLN 0-0.013-0.01925.291-0.009-0.0090.0000.0000.0000.000
155A797PRO 0-0.0020.01924.6230.0090.0090.0000.0000.0000.000
156A798THR 0-0.033-0.00227.8090.0080.0080.0000.0000.0000.000
157A799PHE 0-0.0060.00022.404-0.006-0.0060.0000.0000.0000.000
158A800VAL 0-0.039-0.02927.7670.0110.0110.0000.0000.0000.000
159A801PHE 0-0.012-0.01724.749-0.004-0.0040.0000.0000.0000.000
160A802LEU 00.0210.02128.9130.0080.0080.0000.0000.0000.000
161A803VAL 0-0.037-0.02829.925-0.001-0.0010.0000.0000.0000.000
162A804ALA 00.0530.02331.7900.0040.0040.0000.0000.0000.000
163A805SER 0-0.027-0.01032.9580.0010.0010.0000.0000.0000.000
164A806THR 0-0.051-0.02932.2220.0010.0010.0000.0000.0000.000
165A807THR 00.003-0.02635.4130.0020.0020.0000.0000.0000.000
166A808ILE 0-0.065-0.01238.8250.0000.0000.0000.0000.0000.000
167A809GLU -1-0.928-0.95341.750-0.025-0.0250.0000.0000.0000.000
168A810CYS 0-0.009-0.02044.1930.0000.0000.0000.0000.0000.000
169A811GLY 00.002-0.00446.7670.0000.0000.0000.0000.0000.000
170A812ARG 10.9490.97143.5980.0260.0260.0000.0000.0000.000
171A813TYR 00.0480.03238.2450.0020.0020.0000.0000.0000.000
172A814PRO 0-0.0040.02639.123-0.002-0.0020.0000.0000.0000.000
173A815VAL 00.014-0.01234.764-0.001-0.0010.0000.0000.0000.000
174A816GLU -1-0.933-0.96935.376-0.044-0.0440.0000.0000.0000.000
175A817ILE 0-0.0010.01933.461-0.004-0.0040.0000.0000.0000.000
176A818PHE 0-0.064-0.03931.8590.0050.0050.0000.0000.0000.000
177A819MET 00.0610.03131.223-0.007-0.0070.0000.0000.0000.000
178A820MET 0-0.0500.01027.2380.0080.0080.0000.0000.0000.000
179A821GLY 00.0160.01131.119-0.001-0.0010.0000.0000.0000.000
180A822GLU -1-0.895-0.95932.560-0.067-0.0670.0000.0000.0000.000
181A823GLU -1-0.950-0.96332.381-0.051-0.0510.0000.0000.0000.000
182A824ALA 00.007-0.00930.356-0.001-0.0010.0000.0000.0000.000
183A825LYS 10.9080.95727.1010.1130.1130.0000.0000.0000.000
184A826LEU 00.0090.01527.103-0.010-0.0100.0000.0000.0000.000
185A827ALA 00.0370.01027.472-0.004-0.0040.0000.0000.0000.000
186A828GLY 0-0.004-0.01524.930-0.001-0.0010.0000.0000.0000.000
187A829GLN 00.0740.01423.220-0.016-0.0160.0000.0000.0000.000
188A830GLN 0-0.0090.00523.233-0.004-0.0040.0000.0000.0000.000
189A831GLU -1-0.953-0.99422.068-0.068-0.0680.0000.0000.0000.000
190A832TYR 0-0.014-0.05517.990-0.002-0.0020.0000.0000.0000.000
191A833HIS 10.8630.94918.4220.1470.1470.0000.0000.0000.000
192A834ARG 10.8840.95519.9300.0750.0750.0000.0000.0000.000
193A835ASN 00.0270.02017.225-0.003-0.0030.0000.0000.0000.000
194A836LEU 00.0300.00013.8420.0080.0080.0000.0000.0000.000
195A837ARG 10.8890.94915.9440.1000.1000.0000.0000.0000.000
196A838THR 0-0.0230.01218.0970.0130.0130.0000.0000.0000.000
197A839LEU 0-0.012-0.01210.7820.0150.0150.0000.0000.0000.000
198A840SER 00.009-0.02513.9810.0200.0200.0000.0000.0000.000
199A841ASP -1-0.926-0.94715.266-0.011-0.0110.0000.0000.0000.000
200A842CYS 0-0.040-0.02014.3740.0160.0160.0000.0000.0000.000
201A843LEU 0-0.0450.0009.6890.0320.0320.0000.0000.0000.000
202A844ASN 0-0.030-0.01113.3500.0340.0340.0000.0000.0000.000
203A845THR 0-0.093-0.05816.2570.0090.0090.0000.0000.0000.000
204A846ASP -1-0.926-0.97514.8030.2110.2110.0000.0000.0000.000
205A847GLU -1-0.919-0.93316.3800.1190.1190.0000.0000.0000.000
206A848TRP 0-0.047-0.03611.002-0.028-0.0280.0000.0000.0000.000
207A849PRO 00.0200.01317.8530.0060.0060.0000.0000.0000.000
208A850ALA 00.067-0.02020.290-0.001-0.0010.0000.0000.0000.000
209A851ILE 0-0.051-0.02121.901-0.005-0.0050.0000.0000.0000.000
210A852LYS 10.9921.01024.432-0.004-0.0040.0000.0000.0000.000
211A853THR 0-0.030-0.01626.7080.0010.0010.0000.0000.0000.000
212A854LEU 0-0.015-0.00930.156-0.004-0.0040.0000.0000.0000.000
213A855SER 0-0.008-0.01532.8460.0010.0010.0000.0000.0000.000
214A856LEU 00.0110.01035.770-0.001-0.0010.0000.0000.0000.000
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