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: YVGV2

Calculation Name: 2B0A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B0A

Chain ID: A

ChEMBL ID:

UniProt ID: Q58193

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptAll
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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064395.916682
FMO2-HF: Nuclear repulsion 1990689.285005
FMO2-HF: Total energy -73706.631677
FMO2-MP2: Total energy -73921.917776


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:1:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-5.76-1.2670.879-2.275-3.096-0.001
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.962
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].
3A3LEU0-0.020-0.0053.687-3.572-2.049-0.011-0.721-0.7900.003
4A4ASP-1-0.746-0.8466.86721.86521.8650.0000.0000.0000.000
5A5LEU0-0.007-0.0029.829-1.187-1.1870.0000.0000.0000.000
6A6THR0-0.013-0.02313.119-1.748-1.7480.0000.0000.0000.000
7A7GLN00.0020.01415.4370.5650.5650.0000.0000.0000.000
8A8THR0-0.045-0.02318.2750.3250.3250.0000.0000.0000.000
9A9LEU00.002-0.00719.145-0.564-0.5640.0000.0000.0000.000
10A10ILE00.013-0.00421.900-0.198-0.1980.0000.0000.0000.000
11A11ASN0-0.004-0.03325.1080.0780.0780.0000.0000.0000.000
12A12PHE0-0.011-0.00326.379-0.208-0.2080.0000.0000.0000.000
13A13PRO00.0370.01627.9210.3910.3910.0000.0000.0000.000
14A14ARG10.9030.96230.233-9.540-9.5400.0000.0000.0000.000
15A15PRO0-0.001-0.02032.041-0.167-0.1670.0000.0000.0000.000
16A16GLY00.0010.00735.622-0.133-0.1330.0000.0000.0000.000
17A17ASP-1-0.924-0.95431.2559.7569.7560.0000.0000.0000.000
18A18PRO0-0.066-0.04633.148-0.094-0.0940.0000.0000.0000.000
19A19GLU-1-0.860-0.91732.0679.1079.1070.0000.0000.0000.000
20A20LEU0-0.063-0.02026.1050.0870.0870.0000.0000.0000.000
21A21ARG10.9230.95730.095-8.741-8.7410.0000.0000.0000.000
22A22ILE00.0320.01526.0840.0720.0720.0000.0000.0000.000
23A23ILE0-0.071-0.03530.556-0.281-0.2810.0000.0000.0000.000
24A24GLU-1-0.848-0.91130.9769.5619.5610.0000.0000.0000.000
25A25LYS10.9070.94732.824-8.700-8.7000.0000.0000.0000.000
26A26LYS10.8990.94333.903-8.601-8.6010.0000.0000.0000.000
27A27ILE0-0.015-0.01835.798-0.286-0.2860.0000.0000.0000.000
28A28ASP-1-0.901-0.95436.3438.1718.1710.0000.0000.0000.000
29A29GLY0-0.0050.01036.4000.0910.0910.0000.0000.0000.000
30A30PHE0-0.0190.00131.0700.3460.3460.0000.0000.0000.000
31A31ILE0-0.013-0.01229.958-0.285-0.2850.0000.0000.0000.000
32A32VAL00.0050.00829.7860.3400.3400.0000.0000.0000.000
33A33SER0-0.034-0.04428.565-0.065-0.0650.0000.0000.0000.000
34A34GLU-1-0.927-0.93830.1498.9928.9920.0000.0000.0000.000
35A35ILE0-0.008-0.02725.5250.1310.1310.0000.0000.0000.000
36A36ILE00.0030.01429.768-0.079-0.0790.0000.0000.0000.000
37A37MET00.0280.00824.5240.2370.2370.0000.0000.0000.000
38A38GLY00.0410.03330.106-0.175-0.1750.0000.0000.0000.000
39A39SER0-0.067-0.06728.2460.3570.3570.0000.0000.0000.000
40A40HIS10.8390.90626.988-10.198-10.1980.0000.0000.0000.000
41A41LEU0-0.0160.01325.7600.1820.1820.0000.0000.0000.000
42A42CYS0-0.0450.01221.8750.4340.4340.0000.0000.0000.000
43A43THR00.0210.00417.552-0.093-0.0930.0000.0000.0000.000
44A44HIS10.8300.93020.801-12.082-12.0820.0000.0000.0000.000
45A45ILE0-0.009-0.01221.1270.2930.2930.0000.0000.0000.000
46A46ASP-1-0.786-0.89223.34210.78710.7870.0000.0000.0000.000
47A47TYR0-0.043-0.03524.0640.5670.5670.0000.0000.0000.000
48A48PRO00.011-0.00528.782-0.252-0.2520.0000.0000.0000.000
49A49LYS10.8320.91632.198-9.324-9.3240.0000.0000.0000.000
50A50HIS0-0.007-0.00131.126-0.377-0.3770.0000.0000.0000.000
51A51VAL0-0.026-0.00233.266-0.187-0.1870.0000.0000.0000.000
52A52GLY0-0.0170.00035.786-0.270-0.2700.0000.0000.0000.000
53A53LEU0-0.073-0.04035.310-0.235-0.2350.0000.0000.0000.000
54A54GLU-1-0.906-0.95035.1798.7408.7400.0000.0000.0000.000
55A55ASN0-0.017-0.01330.4870.1930.1930.0000.0000.0000.000
56A56ARG10.9010.93929.726-9.937-9.9370.0000.0000.0000.000
57A57ILE0-0.023-0.01425.4450.2980.2980.0000.0000.0000.000
58A58PRO00.0050.00924.4530.0460.0460.0000.0000.0000.000
59A59PHE00.0450.02219.4100.4250.4250.0000.0000.0000.000
60A60LYS10.8960.91721.215-14.174-14.1740.0000.0000.0000.000
61A61ASP-1-0.873-0.92620.24914.98114.9810.0000.0000.0000.000
62A62GLY00.0720.03521.727-0.011-0.0110.0000.0000.0000.000
63A63ILE0-0.070-0.01915.2750.3060.3060.0000.0000.0000.000
64A64ILE00.0260.02317.3180.0140.0140.0000.0000.0000.000
65A65LYS10.9370.97214.109-17.018-17.0180.0000.0000.0000.000
66A66GLY00.0240.00914.068-1.550-1.5500.0000.0000.0000.000
67A67LYS10.8520.93512.868-18.292-18.2920.0000.0000.0000.000
68A68GLY00.0360.01512.410-1.402-1.4020.0000.0000.0000.000
69A69TYR0-0.029-0.03513.063-0.014-0.0140.0000.0000.0000.000
70A70CYS0-0.070-0.01813.454-0.626-0.6260.0000.0000.0000.000
71A71ILE0-0.0010.00915.152-0.009-0.0090.0000.0000.0000.000
72A72SER00.021-0.01118.3640.3550.3550.0000.0000.0000.000
73A73LEU0-0.065-0.03920.379-0.238-0.2380.0000.0000.0000.000
74A74ASP-1-0.845-0.89923.54611.41511.4150.0000.0000.0000.000
75A75ASP-1-0.921-0.96120.95812.29912.2990.0000.0000.0000.000
76A76PHE0-0.072-0.05121.8550.0520.0520.0000.0000.0000.000
77A77PRO00.0030.00925.096-0.183-0.1830.0000.0000.0000.000
78A78GLY00.012-0.00828.411-0.275-0.2750.0000.0000.0000.000
79A79ASN0-0.0370.00323.856-0.457-0.4570.0000.0000.0000.000
80A80LYS10.9600.97125.037-11.268-11.2680.0000.0000.0000.000
81A81LEU00.0110.01723.1660.4000.4000.0000.0000.0000.000
82A82PRO00.0020.00517.999-0.069-0.0690.0000.0000.0000.000
83A83ALA0-0.0060.00519.436-0.144-0.1440.0000.0000.0000.000
84A84CYS0-0.101-0.04816.6750.8690.8690.0000.0000.0000.000
85A85ASP-1-0.786-0.87117.30915.88715.8870.0000.0000.0000.000
86A86ILE0-0.030-0.01415.512-0.745-0.7450.0000.0000.0000.000
87A87LEU00.0300.01216.3440.6650.6650.0000.0000.0000.000
88A88LEU0-0.028-0.01312.981-0.321-0.3210.0000.0000.0000.000
89A89ILE00.020-0.00217.032-0.200-0.2000.0000.0000.0000.000
90A90TYR00.012-0.00417.0970.0670.0670.0000.0000.0000.000
91A91THR00.008-0.03119.106-0.622-0.6220.0000.0000.0000.000
92A92GLY00.0060.01620.809-0.446-0.4460.0000.0000.0000.000
93A93PHE0-0.025-0.03221.975-0.231-0.2310.0000.0000.0000.000
94A94SER00.041-0.01119.659-0.191-0.1910.0000.0000.0000.000
95A95LYS10.8230.92021.608-11.286-11.2860.0000.0000.0000.000
96A96TYR0-0.054-0.03523.174-0.498-0.4980.0000.0000.0000.000
97A97TRP00.0580.02821.896-0.435-0.4350.0000.0000.0000.000
98A98GLY0-0.0110.00224.5750.0600.0600.0000.0000.0000.000
99A99ARG10.8180.88526.766-10.336-10.3360.0000.0000.0000.000
100A100ASP-1-0.840-0.92529.8649.3119.3110.0000.0000.0000.000
101A101GLU-1-0.842-0.91331.0499.5809.5800.0000.0000.0000.000
102A102TYR0-0.057-0.05023.7900.1000.1000.0000.0000.0000.000
103A103PHE0-0.001-0.01328.7770.1550.1550.0000.0000.0000.000
104A104GLU-1-0.869-0.94330.9758.7188.7180.0000.0000.0000.000
105A105LYS10.8390.94228.075-9.830-9.8300.0000.0000.0000.000
106A106ILE00.0050.00028.7310.3740.3740.0000.0000.0000.000
107A107PRO0-0.040-0.01326.313-0.117-0.1170.0000.0000.0000.000
108A108GLU-1-0.915-0.95228.7588.6018.6010.0000.0000.0000.000
109A109ILE0-0.008-0.01325.5390.2560.2560.0000.0000.0000.000
110A110PRO00.0310.02128.534-0.134-0.1340.0000.0000.0000.000
111A111PHE00.0280.01123.979-0.156-0.1560.0000.0000.0000.000
112A112LEU00.0270.01028.3580.2540.2540.0000.0000.0000.000
113A113ASP-1-0.784-0.87929.4498.9248.9240.0000.0000.0000.000
114A114ASP-1-0.870-0.93228.5779.5579.5570.0000.0000.0000.000
115A115ILE0-0.0030.00024.4090.2340.2340.0000.0000.0000.000
116A116ILE00.0030.01626.9280.1800.1800.0000.0000.0000.000
117A117LYS10.7850.90229.977-9.386-9.3860.0000.0000.0000.000
118A118SER0-0.059-0.03425.5140.2270.2270.0000.0000.0000.000
119A119ASN00.001-0.01124.522-0.252-0.2520.0000.0000.0000.000
120A120ILE0-0.0090.00521.0290.5690.5690.0000.0000.0000.000
121A121LYS10.8380.89921.290-14.751-14.7510.0000.0000.0000.000
122A122CYS0-0.070-0.02919.708-0.195-0.1950.0000.0000.0000.000
123A123VAL00.0310.02920.3290.4410.4410.0000.0000.0000.000
124A124GLY00.0210.00518.4440.0200.0200.0000.0000.0000.000
125A125ILE00.0080.00319.3700.0860.0860.0000.0000.0000.000
126A126ASP-1-0.738-0.82218.26714.12214.1220.0000.0000.0000.000
127A127ALA00.0160.01320.069-0.394-0.3940.0000.0000.0000.000
128A128CYS0-0.0310.00123.8880.1310.1310.0000.0000.0000.000
129A129THR0-0.009-0.00426.532-0.144-0.1440.0000.0000.0000.000
130A130ILE00.0080.00524.6160.1940.1940.0000.0000.0000.000
131A131GLY00.0100.00727.207-0.167-0.1670.0000.0000.0000.000
132A132GLY00.0450.02331.0490.0220.0220.0000.0000.0000.000
133A133PHE0-0.017-0.00333.3900.2720.2720.0000.0000.0000.000
134A134GLU-1-0.838-0.93134.9118.2258.2250.0000.0000.0000.000
135A135GLU-1-0.874-0.92931.0589.0069.0060.0000.0000.0000.000
136A136HIS10.7800.86928.534-10.127-10.1270.0000.0000.0000.000
137A137LYS10.9330.96631.418-8.057-8.0570.0000.0000.0000.000
138A138ARG10.8550.91133.192-8.811-8.8110.0000.0000.0000.000
139A139LEU00.0220.03126.6510.0510.0510.0000.0000.0000.000
140A140LEU00.009-0.00128.2380.0610.0610.0000.0000.0000.000
141A141SER0-0.070-0.05730.798-0.026-0.0260.0000.0000.0000.000
142A142ASN0-0.055-0.03431.599-0.234-0.2340.0000.0000.0000.000
143A143ASN0-0.027-0.01127.613-0.092-0.0920.0000.0000.0000.000
144A144ILE0-0.0120.01424.6330.4790.4790.0000.0000.0000.000
145A145LEU0-0.027-0.01623.300-0.259-0.2590.0000.0000.0000.000
146A146ILE00.0350.01223.6480.2240.2240.0000.0000.0000.000
147A147ILE00.008-0.00418.3160.0130.0130.0000.0000.0000.000
148A148GLU-1-0.760-0.85721.56911.41811.4180.0000.0000.0000.000
149A149ASN00.0130.00722.0890.0280.0280.0000.0000.0000.000
150A150LEU0-0.0010.02115.6870.5750.5750.0000.0000.0000.000
151A151ASN0-0.050-0.03213.058-0.543-0.5430.0000.0000.0000.000
152A152GLU-1-0.809-0.93315.57417.31617.3160.0000.0000.0000.000
153A153ASN0-0.034-0.02810.6270.6870.6870.0000.0000.0000.000
154A154LEU00.0320.01211.6391.0371.0370.0000.0000.0000.000
155A155LYS10.9931.01113.792-15.503-15.5030.0000.0000.0000.000
156A156ASN0-0.079-0.0409.695-1.254-1.2540.0000.0000.0000.000
157A157LEU00.0100.0127.7611.5281.5280.0000.0000.0000.000
158A158VAL00.0100.01110.884-0.294-0.2940.0000.0000.0000.000
159A159GLY00.0000.00413.8790.1790.1790.0000.0000.0000.000
160A160LYS10.8160.9168.885-22.517-22.5170.0000.0000.0000.000
161A161SER00.004-0.00410.977-1.004-1.0040.0000.0000.0000.000
162A162PHE00.0270.0257.5701.4071.4070.0000.0000.0000.000
163A163TYR00.0080.0188.131-3.190-3.1900.0000.0000.0000.000
164A164PHE00.0440.0059.1331.9671.9670.0000.0000.0000.000
165A165LEU0-0.024-0.0198.920-0.882-0.8820.0000.0000.0000.000
166A166GLY00.0490.01912.2410.4090.4090.0000.0000.0000.000
167A167LEU0-0.045-0.03212.318-0.772-0.7720.0000.0000.0000.000
168A168PRO00.0060.00516.356-0.067-0.0670.0000.0000.0000.000
169A169LEU00.0210.01619.9720.1910.1910.0000.0000.0000.000
170A170LYS10.8570.92621.497-14.506-14.5060.0000.0000.0000.000
171A171ILE00.0240.01823.430-0.440-0.4400.0000.0000.0000.000
172A172PHE0-0.029-0.02924.3140.3210.3210.0000.0000.0000.000
173A173ASP-1-0.846-0.92128.9708.8988.8980.0000.0000.0000.000
174A174ILE00.0270.04128.174-0.334-0.3340.0000.0000.0000.000
175A175ASP-1-0.779-0.88030.85210.22810.2280.0000.0000.0000.000
176A176ALA00.0360.00926.9870.1570.1570.0000.0000.0000.000
177A177SER0-0.031-0.02023.729-0.116-0.1160.0000.0000.0000.000
178A178PRO00.0340.02721.7000.3540.3540.0000.0000.0000.000
179A179ILE0-0.019-0.02017.3040.2690.2690.0000.0000.0000.000
180A180ARG10.8650.93611.999-21.643-21.6430.0000.0000.0000.000
181A181CYS0-0.024-0.00813.616-0.057-0.0570.0000.0000.0000.000
182A182ILE0-0.0020.0017.1170.4310.4310.0000.0000.0000.000
183A183ALA00.0160.0137.581-1.511-1.5110.0000.0000.0000.000
184A184ILE0-0.012-0.0133.9312.1992.6090.002-0.163-0.2480.001
185A185LEU0-0.041-0.0282.212-7.190-6.1360.798-0.639-1.2140.002
186A186GLU-1-0.925-0.9603.07228.02229.5280.090-0.752-0.844-0.007