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: M342Z

Calculation Name: 3H4R-A-Xray372

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: 2023-06-19

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2603445.652146
FMO2-HF: Nuclear repulsion 2513894.818796
FMO2-HF: Total energy -89550.833349
FMO2-MP2: Total energy -89809.989874


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:612:PRO)


Summations of interaction energy for fragment #1(A:612:PRO)
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.
-2.473-2.238.738-4.033-4.949-0.004
Interaction energy analysis for fragmet #1(A:612:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / 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].
3A614ILE0-0.004-0.0123.169-2.9510.5330.072-2.015-1.5410.001
4A615SER0-0.0060.0015.7360.0190.0190.0000.0000.0000.000
5A616LYS10.9410.9267.215-0.103-0.1030.0000.0000.0000.000
6A617SER0-0.052-0.0478.997-0.021-0.0210.0000.0000.0000.000
7A618GLN00.0090.0333.7910.0080.154-0.001-0.019-0.1270.000
8A619LEU00.0330.0238.953-0.015-0.0150.0000.0000.0000.000
9A620ASP-1-0.768-0.85511.8560.0490.0490.0000.0000.0000.000
10A621ASP-1-0.866-0.92011.0050.0160.0160.0000.0000.0000.000
11A622ILE0-0.032-0.02510.299-0.005-0.0050.0000.0000.0000.000
12A623ALA0-0.059-0.02514.170-0.003-0.0030.0000.0000.0000.000
13A624ASP-1-0.992-0.96316.6400.0170.0170.0000.0000.0000.000
14A625THR0-0.036-0.03316.955-0.003-0.0030.0000.0000.0000.000
15A626PRO00.0230.01815.025-0.002-0.0020.0000.0000.0000.000
16A627ALA00.0510.04114.1320.0030.0030.0000.0000.0000.000
17A628LEU0-0.032-0.02014.364-0.007-0.0070.0000.0000.0000.000
18A629TYR00.0390.0066.907-0.005-0.0050.0000.0000.0000.000
19A630LEU0-0.018-0.0179.938-0.021-0.0210.0000.0000.0000.000
20A631TRP0-0.057-0.00611.002-0.022-0.0220.0000.0000.0000.000
21A632ARG10.9200.9499.180-0.011-0.0110.0000.0000.0000.000
22A633LYS10.8560.9485.531-0.010-0.0100.0000.0000.0000.000
23A634ASN00.005-0.0129.383-0.015-0.0150.0000.0000.0000.000
24A635ALA0-0.055-0.00112.6440.0010.0010.0000.0000.0000.000
25A636PRO0-0.0100.00814.221-0.011-0.0110.0000.0000.0000.000
26A637VAL00.0150.00413.8710.0100.0100.0000.0000.0000.000
27A638ASP-1-0.880-0.93916.660-0.046-0.0460.0000.0000.0000.000
28A639THR0-0.050-0.03617.5100.0050.0050.0000.0000.0000.000
29A640THR0-0.020-0.01419.3810.0030.0030.0000.0000.0000.000
30A641LYS10.8700.93017.3360.0360.0360.0000.0000.0000.000
31A642THR00.0010.00422.0490.0010.0010.0000.0000.0000.000
32A643LYS10.9210.95420.9360.0180.0180.0000.0000.0000.000
33A644THR0-0.050-0.02124.7440.0020.0020.0000.0000.0000.000
34A645LEU00.0910.02924.3390.0010.0010.0000.0000.0000.000
35A646ASP-1-0.824-0.85818.768-0.014-0.0140.0000.0000.0000.000
36A647LEU00.0690.01422.2380.0010.0010.0000.0000.0000.000
37A648GLY00.0350.03322.8160.0010.0010.0000.0000.0000.000
38A649THR00.013-0.01417.5660.0040.0040.0000.0000.0000.000
39A650ALA0-0.017-0.00420.1750.0000.0000.0000.0000.0000.000
40A651PHE0-0.028-0.02723.0340.0010.0010.0000.0000.0000.000
41A652HIS0-0.074-0.03615.961-0.008-0.0080.0000.0000.0000.000
42A653CYS00.0000.00320.2050.0000.0000.0000.0000.0000.000
43A654ARG10.8090.92921.1220.0020.0020.0000.0000.0000.000
44A655VAL0-0.041-0.05923.2490.0000.0000.0000.0000.0000.000
45A656LEU0-0.0420.00318.0660.0010.0010.0000.0000.0000.000
46A657GLU-1-0.879-0.92318.0940.0000.0000.0000.0000.0000.000
47A658LEU00.012-0.01221.648-0.003-0.0030.0000.0000.0000.000
48A659GLU-1-0.936-0.97624.304-0.010-0.0100.0000.0000.0000.000
49A660GLU-1-0.831-0.90119.140-0.030-0.0300.0000.0000.0000.000
50A661PHE00.0240.02022.918-0.002-0.0020.0000.0000.0000.000
51A662SER0-0.078-0.03224.434-0.001-0.0010.0000.0000.0000.000
52A663ASN0-0.065-0.01423.2880.0010.0010.0000.0000.0000.000
53A664ARG10.8110.87418.8190.0280.0280.0000.0000.0000.000
54A699ALA00.016-0.00131.6230.0000.0000.0000.0000.0000.000
55A700GLU-1-0.916-0.95333.288-0.011-0.0110.0000.0000.0000.000
56A701GLU-1-0.778-0.90031.346-0.006-0.0060.0000.0000.0000.000
57A702GLY0-0.0090.00031.0970.0010.0010.0000.0000.0000.000
58A703ARG10.9790.98932.1400.0060.0060.0000.0000.0000.000
59A704LYS10.7870.88631.0880.0060.0060.0000.0000.0000.000
60A705ILE00.0430.02326.6420.0010.0010.0000.0000.0000.000
61A706GLU-1-0.846-0.91330.194-0.003-0.0030.0000.0000.0000.000
62A707LEU0-0.024-0.02632.5350.0010.0010.0000.0000.0000.000
63A708MET0-0.079-0.05127.8740.0000.0000.0000.0000.0000.000
64A709TYR00.0680.04127.4440.0010.0010.0000.0000.0000.000
65A710GLN00.0070.00130.3450.0010.0010.0000.0000.0000.000
66A711SER0-0.090-0.05532.8980.0010.0010.0000.0000.0000.000
67A712VAL00.001-0.01228.3710.0010.0010.0000.0000.0000.000
68A713MET0-0.027-0.00431.0680.0010.0010.0000.0000.0000.000
69A714ALA0-0.0220.00933.1870.0000.0000.0000.0000.0000.000
70A715LEU0-0.053-0.01231.7340.0000.0000.0000.0000.0000.000
71A716PRO00.0810.02233.7300.0010.0010.0000.0000.0000.000
72A717LEU0-0.011-0.00129.1070.0000.0000.0000.0000.0000.000
73A718GLY00.0670.02229.2210.0010.0010.0000.0000.0000.000
74A719GLN00.0090.01129.2510.0000.0000.0000.0000.0000.000
75A720TRP0-0.032-0.01228.4070.0000.0000.0000.0000.0000.000
76A721LEU0-0.036-0.00325.2770.0000.0000.0000.0000.0000.000
77A722VAL0-0.010-0.01525.7750.0010.0010.0000.0000.0000.000
78A723GLU-1-0.961-0.96426.6340.0040.0040.0000.0000.0000.000
79A724SER0-0.079-0.06727.0550.0010.0010.0000.0000.0000.000
80A725ALA00.0130.00726.670-0.001-0.0010.0000.0000.0000.000
81A726GLY0-0.022-0.04422.7750.0020.0020.0000.0000.0000.000
82A727HIS0-0.0050.01617.947-0.004-0.0040.0000.0000.0000.000
83A728ALA00.0920.03917.4920.0030.0030.0000.0000.0000.000
84A729GLU-1-0.843-0.92512.7030.0400.0400.0000.0000.0000.000
85A730SER0-0.092-0.04111.7360.0160.0160.0000.0000.0000.000
86A731SER0-0.041-0.0397.8300.0470.0470.0000.0000.0000.000
87A732ILE00.0520.0309.162-0.025-0.0250.0000.0000.0000.000
88A733TYR0-0.040-0.0473.770-0.1120.1730.002-0.040-0.2470.000
89A734TRP00.0410.0469.247-0.002-0.0020.0000.0000.0000.000
90A735GLU-1-0.902-0.94210.7030.1570.1570.0000.0000.0000.000
91A736ASP-1-0.865-0.95212.4670.0710.0710.0000.0000.0000.000
92A737PRO0-0.025-0.01714.8090.0060.0060.0000.0000.0000.000
93A738GLU-1-0.891-0.93018.1250.0670.0670.0000.0000.0000.000
94A739THR0-0.045-0.02214.7060.0070.0070.0000.0000.0000.000
95A740GLY00.0190.01614.8860.0120.0120.0000.0000.0000.000
96A741ILE0-0.015-0.0029.5200.0320.0320.0000.0000.0000.000
97A742LEU0-0.0140.0134.866-0.053-0.0530.0000.0000.0000.000
98A743CYS0-0.049-0.0247.674-0.050-0.0500.0000.0000.0000.000
99A744ARG10.9100.9362.1470.170-3.5028.665-1.959-3.034-0.005
100A745CYS0-0.069-0.0196.8730.0320.0320.0000.0000.0000.000
101A746ARG10.8940.9508.037-0.095-0.0950.0000.0000.0000.000
102A747PRO00.0230.01310.535-0.007-0.0070.0000.0000.0000.000
103A748ASP-1-0.787-0.88814.3230.0470.0470.0000.0000.0000.000
104A749LYS10.9200.97116.345-0.024-0.0240.0000.0000.0000.000
105A750ILE0-0.051-0.00816.8940.0030.0030.0000.0000.0000.000
106A751ILE0-0.001-0.02019.615-0.003-0.0030.0000.0000.0000.000
107A752PRO0-0.023-0.01321.4670.0010.0010.0000.0000.0000.000
108A753GLU-1-0.892-0.95123.5600.0140.0140.0000.0000.0000.000
109A754PHE0-0.0260.00226.7870.0000.0000.0000.0000.0000.000
110A755HIS0-0.063-0.02123.2570.0010.0010.0000.0000.0000.000
111A756TRP00.0400.00723.6710.0010.0010.0000.0000.0000.000
112A757ILE0-0.0040.01116.6540.0010.0010.0000.0000.0000.000
113A758MET0-0.0230.00020.203-0.003-0.0030.0000.0000.0000.000
114A759ASP-1-0.862-0.94016.6510.0540.0540.0000.0000.0000.000
115A760VAL0-0.0020.00919.339-0.005-0.0050.0000.0000.0000.000
116A761LYS10.8910.94216.289-0.045-0.0450.0000.0000.0000.000
117A762THR0-0.0160.00021.844-0.003-0.0030.0000.0000.0000.000
118A763THR0-0.043-0.02724.2520.0010.0010.0000.0000.0000.000
119A764ALA0-0.0080.00626.976-0.002-0.0020.0000.0000.0000.000
120A765ASP-1-0.843-0.92130.2540.0060.0060.0000.0000.0000.000
121A766ILE00.0450.00729.5550.0010.0010.0000.0000.0000.000
122A767GLN00.009-0.01231.3880.0020.0020.0000.0000.0000.000
123A768ARG10.9440.98326.664-0.009-0.0090.0000.0000.0000.000
124A769PHE00.0850.02123.6640.0010.0010.0000.0000.0000.000
125A770LYS10.9780.98228.194-0.012-0.0120.0000.0000.0000.000
126A771THR0-0.069-0.02829.9130.0000.0000.0000.0000.0000.000
127A772ALA0-0.052-0.00426.7690.0010.0010.0000.0000.0000.000
128A773TYR00.0130.00823.4850.0020.0020.0000.0000.0000.000
129A774TYR00.0150.01722.7810.0040.0040.0000.0000.0000.000
130A775ASP-1-0.905-0.96222.9620.0220.0220.0000.0000.0000.000
131A776TYR0-0.079-0.02319.895-0.002-0.0020.0000.0000.0000.000
132A777ARG10.7600.82815.196-0.047-0.0470.0000.0000.0000.000
133A778TYR00.002-0.01317.8880.0060.0060.0000.0000.0000.000
134A779HIS00.0740.02819.8980.0020.0020.0000.0000.0000.000
135A780VAL00.006-0.00415.9060.0010.0010.0000.0000.0000.000
136A781GLN0-0.044-0.02314.7340.0060.0060.0000.0000.0000.000
137A782ASP-1-0.819-0.88616.3640.0430.0430.0000.0000.0000.000
138A783ALA0-0.001-0.00418.1420.0030.0030.0000.0000.0000.000
139A784PHE00.0190.0029.6080.0020.0020.0000.0000.0000.000
140A785TYR00.006-0.00912.0550.0180.0180.0000.0000.0000.000
141A786SER0-0.032-0.03114.955-0.002-0.0020.0000.0000.0000.000
142A787ASP-1-0.730-0.82216.7390.0530.0530.0000.0000.0000.000
143A788GLY0-0.001-0.01513.505-0.001-0.0010.0000.0000.0000.000
144A789TYR0-0.040-0.03414.480-0.002-0.0020.0000.0000.0000.000
145A790GLU-1-0.874-0.93316.6190.0400.0400.0000.0000.0000.000
146A791ALA0-0.0590.00716.431-0.003-0.0030.0000.0000.0000.000
147A792GLN0-0.096-0.07714.0340.0040.0040.0000.0000.0000.000
148A793PHE0-0.026-0.01517.045-0.005-0.0050.0000.0000.0000.000
149A794GLY0-0.059-0.01120.016-0.004-0.0040.0000.0000.0000.000
150A795VAL0-0.001-0.01022.7150.0000.0000.0000.0000.0000.000
151A796GLN0-0.011-0.01821.1490.0030.0030.0000.0000.0000.000
152A797PRO00.0000.02019.500-0.003-0.0030.0000.0000.0000.000
153A798THR0-0.033-0.00222.763-0.001-0.0010.0000.0000.0000.000
154A799PHE0-0.007-0.00116.8430.0010.0010.0000.0000.0000.000
155A800VAL0-0.038-0.02922.259-0.003-0.0030.0000.0000.0000.000
156A801PHE0-0.010-0.01619.3230.0010.0010.0000.0000.0000.000
157A802LEU00.0190.02023.141-0.003-0.0030.0000.0000.0000.000
158A803VAL0-0.043-0.03024.2830.0000.0000.0000.0000.0000.000
159A804ALA00.0570.02526.298-0.002-0.0020.0000.0000.0000.000
160A805SER0-0.028-0.01027.7410.0000.0000.0000.0000.0000.000
161A806THR0-0.047-0.02727.503-0.001-0.0010.0000.0000.0000.000
162A807THR00.005-0.02530.627-0.001-0.0010.0000.0000.0000.000
163A808ILE0-0.065-0.01134.0340.0010.0010.0000.0000.0000.000
164A809GLU-1-0.932-0.95536.8400.0040.0040.0000.0000.0000.000
165A810CYS0-0.009-0.02039.1270.0000.0000.0000.0000.0000.000
166A811GLY00.005-0.00441.7490.0000.0000.0000.0000.0000.000
167A812ARG10.9460.97038.316-0.003-0.0030.0000.0000.0000.000
168A813TYR00.0470.03133.1050.0000.0000.0000.0000.0000.000
169A814PRO0-0.0030.02633.7960.0000.0000.0000.0000.0000.000
170A815VAL00.008-0.01529.1770.0000.0000.0000.0000.0000.000
171A816GLU-1-0.929-0.96729.7340.0110.0110.0000.0000.0000.000
172A817ILE0-0.0010.01927.7140.0010.0010.0000.0000.0000.000
173A818PHE0-0.062-0.03826.365-0.001-0.0010.0000.0000.0000.000
174A819MET00.0590.03025.7800.0020.0020.0000.0000.0000.000
175A820MET0-0.0430.01222.253-0.002-0.0020.0000.0000.0000.000
176A821GLY00.0110.00926.0810.0000.0000.0000.0000.0000.000
177A822GLU-1-0.895-0.95928.0270.0240.0240.0000.0000.0000.000
178A823GLU-1-0.951-0.96428.2010.0230.0230.0000.0000.0000.000
179A824ALA00.007-0.00826.0070.0010.0010.0000.0000.0000.000
180A825LYS10.9070.95622.474-0.036-0.0360.0000.0000.0000.000
181A826LEU00.0080.01522.9790.0040.0040.0000.0000.0000.000
182A827ALA00.0360.01023.9750.0030.0030.0000.0000.0000.000
183A828GLY0-0.003-0.01521.1990.0020.0020.0000.0000.0000.000
184A829GLN00.0710.01519.6840.0060.0060.0000.0000.0000.000
185A830GLN0-0.0070.00520.2330.0030.0030.0000.0000.0000.000
186A831GLU-1-0.951-0.99318.6530.0470.0470.0000.0000.0000.000
187A832TYR0-0.016-0.05614.9740.0040.0040.0000.0000.0000.000
188A833HIS10.8630.94915.705-0.058-0.0580.0000.0000.0000.000
189A834ARG10.8870.95617.858-0.040-0.0400.0000.0000.0000.000
190A835ASN00.0240.01914.4370.0020.0020.0000.0000.0000.000
191A836LEU00.0320.00111.4190.0040.0040.0000.0000.0000.000
192A837ARG10.8840.94814.424-0.049-0.0490.0000.0000.0000.000
193A838THR0-0.0200.01416.4130.0050.0050.0000.0000.0000.000
194A839LEU0-0.008-0.0119.7730.0010.0010.0000.0000.0000.000
195A840SER0-0.001-0.02813.6320.0220.0220.0000.0000.0000.000
196A841ASP-1-0.921-0.94515.0400.0800.0800.0000.0000.0000.000
197A842CYS0-0.037-0.01914.158-0.003-0.0030.0000.0000.0000.000
198A843LEU0-0.044-0.0019.9960.0100.0100.0000.0000.0000.000
199A844ASN0-0.033-0.01313.8740.0060.0060.0000.0000.0000.000
200A845THR0-0.092-0.05717.117-0.011-0.0110.0000.0000.0000.000
201A846ASP-1-0.923-0.97515.4090.0790.0790.0000.0000.0000.000
202A847GLU-1-0.920-0.93316.9720.0330.0330.0000.0000.0000.000
203A848TRP0-0.046-0.03510.8410.0050.0050.0000.0000.0000.000
204A849PRO00.0210.01317.463-0.009-0.0090.0000.0000.0000.000
205A850ALA00.063-0.02119.2640.0000.0000.0000.0000.0000.000
206A851ILE0-0.049-0.02120.845-0.003-0.0030.0000.0000.0000.000
207A852LYS10.9931.01121.968-0.021-0.0210.0000.0000.0000.000
208A853THR0-0.031-0.01724.856-0.002-0.0020.0000.0000.0000.000
209A854LEU0-0.015-0.00928.3550.0010.0010.0000.0000.0000.000
210A855SER0-0.010-0.01530.6680.0000.0000.0000.0000.0000.000
211A856LEU00.0130.01133.4190.0000.0000.0000.0000.0000.000
212A857PRO00.0250.02635.4820.0010.0010.0000.0000.0000.000
213A858ARG10.9920.97735.862-0.011-0.0110.0000.0000.0000.000
214A859TRP00.003-0.00536.1030.0000.0000.0000.0000.0000.000
215A860ALA0-0.0030.01739.743-0.001-0.0010.0000.0000.0000.000
216A861LYS11.0200.99241.609-0.005-0.0050.0000.0000.0000.000
217A862GLU-1-1.013-1.00542.6890.0070.0070.0000.0000.0000.000
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