FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2J21R

Calculation Name: 3VYC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VYC

Chain ID: A

ChEMBL ID:

UniProt ID: P30822

Base Structure: X-ray

Registration Date: 2023-06-21

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 980
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -28237931.399193
FMO2-HF: Nuclear repulsion 27842112.084162
FMO2-HF: Total energy -395819.315031
FMO2-MP2: Total energy -396972.843538


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:47:ALA)


Summations of interaction energy for fragment #1(A:47:ALA)
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.
-4.574-0.7950.622-1.98-2.422-0.016
Interaction energy analysis for fragmet #1(A:47:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.021
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].
3A49GLN00.016-0.0062.649-5.424-1.8170.623-1.965-2.266-0.016
4A50LYS10.9310.9904.5302.2902.462-0.001-0.015-0.1560.000
5A51ALA00.0340.0107.6360.1800.1800.0000.0000.0000.000
6A52ASP-1-0.798-0.8969.979-0.198-0.1980.0000.0000.0000.000
7A53GLN0-0.022-0.02011.449-0.068-0.0680.0000.0000.0000.000
8A54ILE0-0.036-0.0079.8710.0470.0470.0000.0000.0000.000
9A55LEU0-0.082-0.04013.9500.0480.0480.0000.0000.0000.000
10A56GLN0-0.0030.00116.8550.0430.0430.0000.0000.0000.000
11A64LYS10.9570.96714.8700.1190.1190.0000.0000.0000.000
12A65PHE00.0470.01715.0990.0230.0230.0000.0000.0000.000
13A66ILE00.0220.00810.2170.0370.0370.0000.0000.0000.000
14A67ALA0-0.019-0.01010.4810.0130.0130.0000.0000.0000.000
15A68LEU00.0830.03510.820-0.003-0.0030.0000.0000.0000.000
16A69SER00.0020.01011.2730.0610.0610.0000.0000.0000.000
17A70ILE0-0.049-0.0215.6220.1590.1590.0000.0000.0000.000
18A71LEU00.0180.0088.0050.3680.3680.0000.0000.0000.000
19A72ASP-1-0.788-0.87310.1990.4460.4460.0000.0000.0000.000
20A73LYS10.9170.9767.634-0.552-0.5520.0000.0000.0000.000
21A74LEU0-0.032-0.0125.8140.3420.3420.0000.0000.0000.000
22A75ILE00.0250.0039.069-0.040-0.0400.0000.0000.0000.000
23A76THR0-0.006-0.01212.438-0.023-0.0230.0000.0000.0000.000
24A77ARG10.9030.9489.275-1.055-1.0550.0000.0000.0000.000
25A78LYS10.8700.9266.117-1.682-1.6820.0000.0000.0000.000
26A79TRP00.0900.05210.0830.0290.0290.0000.0000.0000.000
27A80LYS10.9260.94012.041-0.368-0.3680.0000.0000.0000.000
28A81LEU0-0.048-0.0089.774-0.009-0.0090.0000.0000.0000.000
29A82LEU0-0.0240.0007.564-0.073-0.0730.0000.0000.0000.000
30A83PRO00.0330.02311.108-0.030-0.0300.0000.0000.0000.000
31A84ASN00.049-0.01014.1030.0330.0330.0000.0000.0000.000
32A85ASP-1-0.889-0.93114.2760.0110.0110.0000.0000.0000.000
33A86HIS0-0.005-0.0219.870-0.021-0.0210.0000.0000.0000.000
34A87ARG10.7930.91112.380-0.244-0.2440.0000.0000.0000.000
35A88ILE00.0310.02314.394-0.005-0.0050.0000.0000.0000.000
36A89GLY00.0050.00414.671-0.013-0.0130.0000.0000.0000.000
37A90ILE0-0.043-0.0359.448-0.006-0.0060.0000.0000.0000.000
38A91ARG10.8750.93713.772-0.101-0.1010.0000.0000.0000.000
39A92ASN00.0310.02117.1660.0040.0040.0000.0000.0000.000
40A93PHE00.0030.00611.171-0.014-0.0140.0000.0000.0000.000
41A94VAL0-0.041-0.02815.124-0.015-0.0150.0000.0000.0000.000
42A95VAL00.0620.03117.8130.0000.0000.0000.0000.0000.000
43A96GLY00.0090.01020.546-0.005-0.0050.0000.0000.0000.000
44A97MET0-0.023-0.01617.7610.0000.0000.0000.0000.0000.000
45A98ILE00.0170.00620.532-0.004-0.0040.0000.0000.0000.000
46A99ILE00.0310.02022.728-0.002-0.0020.0000.0000.0000.000
47A100SER0-0.066-0.03023.440-0.005-0.0050.0000.0000.0000.000
48A101MET0-0.071-0.04122.224-0.002-0.0020.0000.0000.0000.000
49A102CYS00.0030.00725.6350.0030.0030.0000.0000.0000.000
50A103GLN0-0.036-0.02128.5130.0050.0050.0000.0000.0000.000
51A104ASP-1-0.881-0.91428.854-0.042-0.0420.0000.0000.0000.000
52A105ASP-1-0.795-0.90930.671-0.012-0.0120.0000.0000.0000.000
53A106GLU-1-0.804-0.87031.635-0.014-0.0140.0000.0000.0000.000
54A107VAL0-0.047-0.02825.5640.0020.0020.0000.0000.0000.000
55A108PHE00.0150.00328.4110.0070.0070.0000.0000.0000.000
56A109LYS10.7830.87930.2480.0200.0200.0000.0000.0000.000
57A110THR0-0.098-0.06430.9920.0040.0040.0000.0000.0000.000
58A111GLN00.0300.00824.5580.0010.0010.0000.0000.0000.000
59A112LYS10.8950.96525.742-0.009-0.0090.0000.0000.0000.000
60A113ASN0-0.0080.00124.1440.0150.0150.0000.0000.0000.000
61A114LEU0-0.005-0.00918.5220.0080.0080.0000.0000.0000.000
62A115ILE00.0280.01621.2650.0060.0060.0000.0000.0000.000
63A116ASN00.0540.03823.3920.0130.0130.0000.0000.0000.000
64A117LYS10.8960.93618.591-0.060-0.0600.0000.0000.0000.000
65A118SER0-0.016-0.00418.4670.0160.0160.0000.0000.0000.000
66A119ASP-1-0.789-0.88119.5380.0650.0650.0000.0000.0000.000
67A120LEU0-0.031-0.01920.0150.0130.0130.0000.0000.0000.000
68A121THR0-0.035-0.02714.9150.0110.0110.0000.0000.0000.000
69A122LEU0-0.016-0.00817.6130.0310.0310.0000.0000.0000.000
70A123VAL00.0290.01119.9100.0120.0120.0000.0000.0000.000
71A124GLN0-0.047-0.03317.3260.0370.0370.0000.0000.0000.000
72A125ILE0-0.032-0.01515.2500.0280.0280.0000.0000.0000.000
73A126LEU00.0080.01118.2330.0080.0080.0000.0000.0000.000
74A127LYS10.8690.93820.690-0.215-0.2150.0000.0000.0000.000
75A128GLN0-0.056-0.01816.8020.0060.0060.0000.0000.0000.000
76A129GLU-1-0.863-0.92818.0810.1810.1810.0000.0000.0000.000
77A130TRP0-0.0100.01620.754-0.016-0.0160.0000.0000.0000.000
78A131PRO00.0610.02924.3410.0080.0080.0000.0000.0000.000
79A132GLN0-0.023-0.02922.623-0.018-0.0180.0000.0000.0000.000
80A133ASN0-0.042-0.03319.388-0.019-0.0190.0000.0000.0000.000
81A134TRP0-0.035-0.04220.4170.0100.0100.0000.0000.0000.000
82A135PRO00.0180.00524.122-0.003-0.0030.0000.0000.0000.000
83A136GLU-1-0.939-0.97226.8540.0240.0240.0000.0000.0000.000
84A137PHE00.0540.03624.809-0.004-0.0040.0000.0000.0000.000
85A138ILE00.0280.00826.756-0.006-0.0060.0000.0000.0000.000
86A139PRO00.0160.01230.137-0.004-0.0040.0000.0000.0000.000
87A140GLU-1-0.850-0.90825.0810.0270.0270.0000.0000.0000.000
88A141LEU0-0.0120.01927.730-0.005-0.0050.0000.0000.0000.000
89A142ILE00.0180.00229.700-0.005-0.0050.0000.0000.0000.000
90A143GLY0-0.015-0.00632.244-0.004-0.0040.0000.0000.0000.000
91A144SER0-0.030-0.03628.870-0.004-0.0040.0000.0000.0000.000
92A145SER0-0.011-0.02930.956-0.002-0.0020.0000.0000.0000.000
93A146SER0-0.062-0.01633.426-0.002-0.0020.0000.0000.0000.000
94A147SER0-0.025-0.00832.905-0.003-0.0030.0000.0000.0000.000
95A148SER00.008-0.00532.620-0.003-0.0030.0000.0000.0000.000
96A149VAL00.0540.03034.4490.0040.0040.0000.0000.0000.000
97A150ASN0-0.004-0.01032.2220.0070.0070.0000.0000.0000.000
98A151VAL00.0120.00829.0380.0030.0030.0000.0000.0000.000
99A152CYS0-0.0390.00030.9430.0070.0070.0000.0000.0000.000
100A153GLU-1-0.829-0.90433.2600.0210.0210.0000.0000.0000.000
101A154ASN0-0.032-0.04526.0500.0010.0010.0000.0000.0000.000
102A155ASN00.016-0.00428.2770.0110.0110.0000.0000.0000.000
103A156MET0-0.0470.00030.0190.0090.0090.0000.0000.0000.000
104A157ILE0-0.009-0.00628.0460.0060.0060.0000.0000.0000.000
105A158VAL00.0070.00625.2520.0100.0100.0000.0000.0000.000
106A159LEU0-0.023-0.01027.7340.0110.0110.0000.0000.0000.000
107A160LYS10.8770.94230.348-0.053-0.0530.0000.0000.0000.000
108A161LEU00.0230.01325.1070.0060.0060.0000.0000.0000.000
109A162LEU0-0.002-0.00325.0330.0130.0130.0000.0000.0000.000
110A163SER0-0.009-0.01027.3490.0060.0060.0000.0000.0000.000
111A164GLU-1-0.839-0.91929.0480.0780.0780.0000.0000.0000.000
112A165GLU-1-0.837-0.87622.8670.2040.2040.0000.0000.0000.000
113A166VAL0-0.090-0.07025.3850.0100.0100.0000.0000.0000.000
114A167PHE0-0.045-0.02328.108-0.002-0.0020.0000.0000.0000.000
115A168ASP-1-0.818-0.90131.9080.0710.0710.0000.0000.0000.000
116A169PHE0-0.036-0.00329.578-0.001-0.0010.0000.0000.0000.000
117A170SER0-0.054-0.03531.318-0.004-0.0040.0000.0000.0000.000
118A171ALA00.0400.00734.8010.0000.0000.0000.0000.0000.000
119A172GLU-1-0.833-0.91737.9450.0540.0540.0000.0000.0000.000
120A173GLN0-0.069-0.03539.545-0.003-0.0030.0000.0000.0000.000
121A174MET00.0240.03037.5090.0020.0020.0000.0000.0000.000
122A175THR0-0.095-0.04840.523-0.003-0.0030.0000.0000.0000.000
123A176GLN00.0410.00140.864-0.002-0.0020.0000.0000.0000.000
124A177ALA00.024-0.00240.7510.0010.0010.0000.0000.0000.000
125A178LYS10.8780.93731.539-0.116-0.1160.0000.0000.0000.000
126A179ALA00.0580.02935.8910.0030.0030.0000.0000.0000.000
127A180LEU0-0.003-0.01337.123-0.002-0.0020.0000.0000.0000.000
128A181HIS00.0050.01932.460-0.007-0.0070.0000.0000.0000.000
129A182LEU00.0310.03431.129-0.002-0.0020.0000.0000.0000.000
130A183LYS10.7980.90434.914-0.052-0.0520.0000.0000.0000.000
131A184ASN0-0.009-0.02137.7870.0000.0000.0000.0000.0000.000
132A185SER0-0.020-0.01335.122-0.002-0.0020.0000.0000.0000.000
133A186MET0-0.028-0.00529.5460.0010.0010.0000.0000.0000.000
134A187SER0-0.0050.00434.756-0.002-0.0020.0000.0000.0000.000
135A188LYS10.8780.93034.345-0.059-0.0590.0000.0000.0000.000
136A189GLU-1-0.829-0.93431.7350.0610.0610.0000.0000.0000.000
137A190PHE00.0310.01933.6990.0000.0000.0000.0000.0000.000
138A191GLU-1-0.879-0.93236.7340.0340.0340.0000.0000.0000.000
139A192GLN0-0.041-0.01535.207-0.005-0.0050.0000.0000.0000.000
140A193ILE00.0290.02332.076-0.003-0.0030.0000.0000.0000.000
141A194PHE00.0240.01335.996-0.003-0.0030.0000.0000.0000.000
142A195LYS10.9420.97539.648-0.027-0.0270.0000.0000.0000.000
143A196LEU0-0.0030.00934.185-0.003-0.0030.0000.0000.0000.000
144A197CYS0-0.009-0.01037.882-0.002-0.0020.0000.0000.0000.000
145A198PHE00.005-0.01039.650-0.002-0.0020.0000.0000.0000.000
146A199GLN0-0.012-0.02541.525-0.001-0.0010.0000.0000.0000.000
147A200VAL0-0.030-0.01737.981-0.003-0.0030.0000.0000.0000.000
148A201LEU0-0.029-0.01041.444-0.002-0.0020.0000.0000.0000.000
149A202GLU-1-0.889-0.94244.3250.0140.0140.0000.0000.0000.000
150A203GLN0-0.098-0.04443.437-0.002-0.0020.0000.0000.0000.000
151A204GLY00.0240.03542.959-0.001-0.0010.0000.0000.0000.000
152A205SER0-0.082-0.04642.830-0.001-0.0010.0000.0000.0000.000
153A206SER00.0270.00538.9870.0010.0010.0000.0000.0000.000
154A207SER00.025-0.00241.7700.0030.0030.0000.0000.0000.000
155A208SER00.009-0.02636.9990.0010.0010.0000.0000.0000.000
156A209LEU00.0010.00937.1130.0030.0030.0000.0000.0000.000
157A210ILE00.0170.02038.2290.0030.0030.0000.0000.0000.000
158A211VAL00.0230.00838.2500.0030.0030.0000.0000.0000.000
159A212ALA00.0120.01134.5230.0030.0030.0000.0000.0000.000
160A213THR0-0.019-0.04036.2360.0040.0040.0000.0000.0000.000
161A214LEU0-0.030-0.01938.1850.0030.0030.0000.0000.0000.000
162A215GLU-1-0.851-0.91335.3160.0480.0480.0000.0000.0000.000
163A216SER0-0.028-0.01534.3490.0030.0030.0000.0000.0000.000
164A217LEU00.005-0.00435.9630.0030.0030.0000.0000.0000.000
165A218LEU00.008-0.00739.1820.0020.0020.0000.0000.0000.000
166A219ARG10.7710.88033.606-0.071-0.0710.0000.0000.0000.000
167A220TYR0-0.009-0.02531.0610.0050.0050.0000.0000.0000.000
168A221LEU0-0.0260.00237.661-0.001-0.0010.0000.0000.0000.000
169A222HIS0-0.012-0.02139.905-0.001-0.0010.0000.0000.0000.000
170A223TRP0-0.063-0.02535.2690.0000.0000.0000.0000.0000.000
171A224ILE0-0.0090.00939.071-0.001-0.0010.0000.0000.0000.000
172A225PRO0-0.013-0.00340.592-0.001-0.0010.0000.0000.0000.000
173A226TYR00.0700.02143.745-0.002-0.0020.0000.0000.0000.000
174A227ARG10.7610.85646.780-0.027-0.0270.0000.0000.0000.000
175A228TYR0-0.009-0.02943.390-0.003-0.0030.0000.0000.0000.000
176A229ILE0-0.0160.01643.786-0.001-0.0010.0000.0000.0000.000
177A230TYR0-0.004-0.02347.511-0.001-0.0010.0000.0000.0000.000
178A231GLU-1-0.841-0.89750.4140.0230.0230.0000.0000.0000.000
179A232THR0-0.060-0.02846.919-0.002-0.0020.0000.0000.0000.000
180A233ASN0-0.017-0.02350.0260.0010.0010.0000.0000.0000.000
181A234ILE00.0330.01845.454-0.001-0.0010.0000.0000.0000.000
182A235LEU00.0180.02348.8440.0000.0000.0000.0000.0000.000
183A236GLU-1-0.875-0.90651.1250.0160.0160.0000.0000.0000.000
184A237LEU0-0.0340.00547.416-0.001-0.0010.0000.0000.0000.000
185A238LEU00.000-0.01545.513-0.001-0.0010.0000.0000.0000.000
186A239SER0-0.005-0.03249.543-0.001-0.0010.0000.0000.0000.000
187A240THR0-0.034-0.03152.765-0.001-0.0010.0000.0000.0000.000
188A241LYS10.9360.98647.963-0.014-0.0140.0000.0000.0000.000
189A242PHE0-0.006-0.02546.323-0.001-0.0010.0000.0000.0000.000
190A243MET00.0240.03549.1110.0010.0010.0000.0000.0000.000
191A244THR0-0.039-0.01751.6450.0000.0000.0000.0000.0000.000
192A245SER0-0.050-0.03147.719-0.001-0.0010.0000.0000.0000.000
193A246PRO00.019-0.00749.3330.0010.0010.0000.0000.0000.000
194A247ASP-1-0.852-0.90844.6270.0160.0160.0000.0000.0000.000
195A248THR0-0.033-0.02044.1160.0010.0010.0000.0000.0000.000
196A249ARG10.9441.01145.786-0.016-0.0160.0000.0000.0000.000
197A250ALA00.0620.02544.6550.0010.0010.0000.0000.0000.000
198A251ILE00.0260.00839.9880.0010.0010.0000.0000.0000.000
199A252THR00.012-0.00943.6590.0020.0020.0000.0000.0000.000
200A253LEU00.0390.02446.3690.0000.0000.0000.0000.0000.000
201A254LYS10.8520.92641.749-0.037-0.0370.0000.0000.0000.000
202A255CYS0-0.050-0.01343.1520.0020.0020.0000.0000.0000.000
203A256LEU0-0.039-0.02044.9100.0010.0010.0000.0000.0000.000
204A257THR0-0.001-0.02346.958-0.001-0.0010.0000.0000.0000.000
205A258GLU-1-0.820-0.89342.4000.0480.0480.0000.0000.0000.000
206A259VAL0-0.020-0.00845.8550.0010.0010.0000.0000.0000.000
207A260SER0-0.045-0.01747.986-0.001-0.0010.0000.0000.0000.000
208A261ASN0-0.0080.00245.690-0.002-0.0020.0000.0000.0000.000
209A262LEU0-0.0130.01644.4670.0020.0020.0000.0000.0000.000
210A263LYS10.9210.95643.774-0.054-0.0540.0000.0000.0000.000
211A264ILE00.0520.03248.8400.0000.0000.0000.0000.0000.000
212A265PRO0-0.035-0.01451.0790.0000.0000.0000.0000.0000.000
213A266GLN00.006-0.01154.2660.0000.0000.0000.0000.0000.000
214A267ASP-1-0.866-0.92157.1100.0240.0240.0000.0000.0000.000
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