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: 4JVLN

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063509.553442
FMO2-HF: Nuclear repulsion 1989804.079659
FMO2-HF: Total energy -73705.473784
FMO2-MP2: Total energy -73920.638512


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.
-6.274-1.7350.229-1.963-2.8070.011
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 : -0.917 / q_NPA : -0.955
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].
3A3LEU0-0.031-0.0063.635-5.800-4.003-0.012-0.831-0.9550.004
4A4ASP-1-0.755-0.8766.38922.13322.1330.0000.0000.0000.000
5A5LEU0-0.026-0.0049.856-1.280-1.2800.0000.0000.0000.000
6A6THR00.0000.00012.717-1.704-1.7040.0000.0000.0000.000
7A7GLN00.0230.01815.2810.5550.5550.0000.0000.0000.000
8A8THR0-0.032-0.01318.0150.3660.3660.0000.0000.0000.000
9A9LEU0-0.016-0.01319.042-0.517-0.5170.0000.0000.0000.000
10A10ILE00.021-0.00321.929-0.224-0.2240.0000.0000.0000.000
11A11ASN00.007-0.00425.0990.0860.0860.0000.0000.0000.000
12A12PHE0-0.026-0.01326.005-0.200-0.2000.0000.0000.0000.000
13A13PRO00.0350.02028.1250.3680.3680.0000.0000.0000.000
14A14ARG10.9640.99630.226-9.830-9.8300.0000.0000.0000.000
15A15PRO00.0540.01431.797-0.147-0.1470.0000.0000.0000.000
16A16GLY0-0.026-0.01235.295-0.039-0.0390.0000.0000.0000.000
17A17ASP-1-0.951-0.96532.0369.4889.4880.0000.0000.0000.000
18A18PRO0-0.076-0.05132.735-0.080-0.0800.0000.0000.0000.000
19A19GLU-1-0.877-0.93432.1089.0399.0390.0000.0000.0000.000
20A20LEU0-0.077-0.02626.1430.0680.0680.0000.0000.0000.000
21A21ARG10.9310.96030.112-8.744-8.7440.0000.0000.0000.000
22A22ILE00.014-0.00326.0080.1530.1530.0000.0000.0000.000
23A23ILE0-0.060-0.01330.325-0.229-0.2290.0000.0000.0000.000
24A24GLU-1-0.907-0.95229.96010.07910.0790.0000.0000.0000.000
25A25LYS10.9030.94132.726-8.442-8.4420.0000.0000.0000.000
26A26LYS10.9710.98533.967-7.946-7.9460.0000.0000.0000.000
27A27ILE0-0.014-0.02435.607-0.283-0.2830.0000.0000.0000.000
28A28ASP-1-0.908-0.95436.2028.2058.2050.0000.0000.0000.000
29A29GLY0-0.0080.00835.9780.0870.0870.0000.0000.0000.000
30A30PHE0-0.0110.00730.6590.3490.3490.0000.0000.0000.000
31A31ILE0-0.011-0.00929.865-0.313-0.3130.0000.0000.0000.000
32A32VAL00.0000.00529.7730.3200.3200.0000.0000.0000.000
33A33SER0-0.009-0.02728.201-0.092-0.0920.0000.0000.0000.000
34A34GLU-1-0.952-0.95830.2778.9748.9740.0000.0000.0000.000
35A35ILE0-0.008-0.01124.9870.0200.0200.0000.0000.0000.000
36A36ILE00.0110.01629.251-0.114-0.1140.0000.0000.0000.000
37A37MET00.033-0.00223.9030.2060.2060.0000.0000.0000.000
38A38GLY00.0520.03729.586-0.169-0.1690.0000.0000.0000.000
39A39SER0-0.040-0.03927.6870.3410.3410.0000.0000.0000.000
40A40HIS10.8680.93526.593-10.203-10.2030.0000.0000.0000.000
41A41LEU00.0060.02725.4990.1100.1100.0000.0000.0000.000
42A42CYS0-0.0200.01521.8670.4820.4820.0000.0000.0000.000
43A43THR00.0200.02517.387-0.110-0.1100.0000.0000.0000.000
44A44HIS10.8270.91820.623-12.334-12.3340.0000.0000.0000.000
45A45ILE0-0.020-0.01620.9410.2580.2580.0000.0000.0000.000
46A46ASP-1-0.825-0.92423.08811.12011.1200.0000.0000.0000.000
47A47TYR0-0.034-0.03723.0870.3430.3430.0000.0000.0000.000
48A48PRO00.022-0.00528.453-0.257-0.2570.0000.0000.0000.000
49A49LYS10.8970.96031.830-9.521-9.5210.0000.0000.0000.000
50A50HIS0-0.021-0.01330.951-0.346-0.3460.0000.0000.0000.000
51A51VAL0-0.053-0.01333.016-0.194-0.1940.0000.0000.0000.000
52A52GLY0-0.033-0.01935.649-0.239-0.2390.0000.0000.0000.000
53A53LEU0-0.073-0.03134.974-0.239-0.2390.0000.0000.0000.000
54A54GLU-1-0.905-0.94635.1748.8338.8330.0000.0000.0000.000
55A55ASN0-0.017-0.01830.2020.1340.1340.0000.0000.0000.000
56A56ARG11.0141.00130.052-10.257-10.2570.0000.0000.0000.000
57A57ILE0-0.017-0.01525.8210.2820.2820.0000.0000.0000.000
58A58PRO0-0.0140.01024.8380.0900.0900.0000.0000.0000.000
59A59PHE00.0310.01319.3410.4020.4020.0000.0000.0000.000
60A60LYS10.9390.96620.727-14.485-14.4850.0000.0000.0000.000
61A61ASP-1-0.915-0.96920.17815.29415.2940.0000.0000.0000.000
62A62GLY0-0.001-0.00221.824-0.034-0.0340.0000.0000.0000.000
63A63ILE0-0.070-0.02015.3780.3680.3680.0000.0000.0000.000
64A64ILE00.0130.01517.088-0.232-0.2320.0000.0000.0000.000
65A65LYS10.9280.96114.040-17.268-17.2680.0000.0000.0000.000
66A66GLY00.0470.02313.991-1.641-1.6410.0000.0000.0000.000
67A67LYS10.8410.93213.361-19.189-19.1890.0000.0000.0000.000
68A68GLY00.0500.02912.887-1.618-1.6180.0000.0000.0000.000
69A69TYR0-0.013-0.01913.7840.4160.4160.0000.0000.0000.000
70A70CYS0-0.0460.00314.380-0.923-0.9230.0000.0000.0000.000
71A71ILE0-0.0020.00716.1090.0490.0490.0000.0000.0000.000
72A72SER00.0270.01019.3540.2910.2910.0000.0000.0000.000
73A73LEU0-0.034-0.02721.067-0.289-0.2890.0000.0000.0000.000
74A74ASP-1-0.880-0.93524.34011.60211.6020.0000.0000.0000.000
75A75ASP-1-0.927-0.96622.48812.29912.2990.0000.0000.0000.000
76A76PHE0-0.094-0.04823.204-0.027-0.0270.0000.0000.0000.000
77A77PRO0-0.0010.01525.757-0.246-0.2460.0000.0000.0000.000
78A78GLY00.0100.00229.567-0.180-0.1800.0000.0000.0000.000
79A79ASN0-0.018-0.01624.924-0.390-0.3900.0000.0000.0000.000
80A80LYS10.9660.97226.036-11.459-11.4590.0000.0000.0000.000
81A81LEU00.0030.01723.9770.4280.4280.0000.0000.0000.000
82A82PRO00.0010.00919.316-0.108-0.1080.0000.0000.0000.000
83A83ALA0-0.022-0.00220.569-0.255-0.2550.0000.0000.0000.000
84A84CYS0-0.105-0.05517.2180.9770.9770.0000.0000.0000.000
85A85ASP-1-0.827-0.91717.48916.37216.3720.0000.0000.0000.000
86A86ILE0-0.039-0.01815.838-0.811-0.8110.0000.0000.0000.000
87A87LEU00.0500.01916.9050.8240.8240.0000.0000.0000.000
88A88LEU0-0.042-0.02013.796-0.273-0.2730.0000.0000.0000.000
89A89ILE00.0280.00017.859-0.072-0.0720.0000.0000.0000.000
90A90TYR00.0200.00217.4910.0320.0320.0000.0000.0000.000
91A91THR0-0.008-0.03219.505-0.599-0.5990.0000.0000.0000.000
92A92GLY00.0140.01420.862-0.458-0.4580.0000.0000.0000.000
93A93PHE0-0.006-0.03321.847-0.288-0.2880.0000.0000.0000.000
94A94SER0-0.007-0.02019.110-0.195-0.1950.0000.0000.0000.000
95A95LYS10.8970.96321.134-11.197-11.1970.0000.0000.0000.000
96A96TYR0-0.106-0.07722.162-0.309-0.3090.0000.0000.0000.000
97A97TRP00.0980.04921.576-0.419-0.4190.0000.0000.0000.000
98A98GLY0-0.030-0.00923.7530.0440.0440.0000.0000.0000.000
99A99ARG10.8610.94426.093-10.581-10.5810.0000.0000.0000.000
100A100ASP-1-0.809-0.91228.9459.3199.3190.0000.0000.0000.000
101A101GLU-1-0.891-0.96630.3799.3529.3520.0000.0000.0000.000
102A102TYR0-0.093-0.06023.4940.1930.1930.0000.0000.0000.000
103A103PHE0-0.035-0.04828.2820.2050.2050.0000.0000.0000.000
104A104GLU-1-0.908-0.94530.7368.5928.5920.0000.0000.0000.000
105A105LYS10.8370.93528.253-10.044-10.0440.0000.0000.0000.000
106A106ILE0-0.025-0.01729.0320.3700.3700.0000.0000.0000.000
107A107PRO0-0.049-0.01826.490-0.139-0.1390.0000.0000.0000.000
108A108GLU-1-0.910-0.94728.9418.8248.8240.0000.0000.0000.000
109A109ILE0-0.014-0.01926.2660.2230.2230.0000.0000.0000.000
110A110PRO00.0090.01428.991-0.162-0.1620.0000.0000.0000.000
111A111PHE00.0550.02024.747-0.146-0.1460.0000.0000.0000.000
112A112LEU00.0330.00728.8320.2450.2450.0000.0000.0000.000
113A113ASP-1-0.852-0.93230.4569.0819.0810.0000.0000.0000.000
114A114ASP-1-0.921-0.96529.21910.09110.0910.0000.0000.0000.000
115A115ILE0-0.047-0.02525.4610.2570.2570.0000.0000.0000.000
116A116ILE0-0.0240.00227.7910.1360.1360.0000.0000.0000.000
117A117LYS10.9270.97030.599-9.096-9.0960.0000.0000.0000.000
118A118SER0-0.062-0.01625.8690.2100.2100.0000.0000.0000.000
119A119ASN0-0.018-0.02225.097-0.439-0.4390.0000.0000.0000.000
120A120ILE0-0.015-0.00821.6080.5230.5230.0000.0000.0000.000
121A121LYS10.9430.97221.202-14.501-14.5010.0000.0000.0000.000
122A122CYS0-0.084-0.03219.876-0.370-0.3700.0000.0000.0000.000
123A123VAL00.0400.02920.7800.5230.5230.0000.0000.0000.000
124A124GLY00.0280.01318.999-0.179-0.1790.0000.0000.0000.000
125A125ILE0-0.016-0.00820.0320.0800.0800.0000.0000.0000.000
126A126ASP-1-0.724-0.81518.35914.46214.4620.0000.0000.0000.000
127A127ALA00.0200.00920.234-0.478-0.4780.0000.0000.0000.000
128A128CYS0-0.0110.00623.9250.1180.1180.0000.0000.0000.000
129A129THR0-0.018-0.00926.543-0.128-0.1280.0000.0000.0000.000
130A130ILE00.0260.01425.3440.2160.2160.0000.0000.0000.000
131A131GLY00.0300.01727.827-0.184-0.1840.0000.0000.0000.000
132A132GLY00.0320.01431.6020.0730.0730.0000.0000.0000.000
133A133PHE00.0210.00433.9120.2630.2630.0000.0000.0000.000
134A134GLU-1-0.874-0.94535.4988.2338.2330.0000.0000.0000.000
135A135GLU-1-0.852-0.92531.7089.1529.1520.0000.0000.0000.000
136A136HIS10.7640.86728.793-10.268-10.2680.0000.0000.0000.000
137A137LYS11.0031.00631.791-8.063-8.0630.0000.0000.0000.000
138A138ARG10.8900.97033.645-9.057-9.0570.0000.0000.0000.000
139A139LEU00.0320.02626.9880.0450.0450.0000.0000.0000.000
140A140LEU0-0.011-0.00528.3290.0620.0620.0000.0000.0000.000
141A141SER0-0.114-0.08431.000-0.043-0.0430.0000.0000.0000.000
142A142ASN0-0.067-0.03831.804-0.333-0.3330.0000.0000.0000.000
143A143ASN0-0.100-0.05428.2690.2520.2520.0000.0000.0000.000
144A144ILE00.0080.02424.9860.4170.4170.0000.0000.0000.000
145A145LEU0-0.043-0.02823.204-0.257-0.2570.0000.0000.0000.000
146A146ILE00.0570.02323.9030.2750.2750.0000.0000.0000.000
147A147ILE00.001-0.00318.0420.0340.0340.0000.0000.0000.000
148A148GLU-1-0.770-0.86821.71111.74611.7460.0000.0000.0000.000
149A149ASN0-0.010-0.01821.5940.2100.2100.0000.0000.0000.000
150A150LEU0-0.0060.01115.6270.5590.5590.0000.0000.0000.000
151A151ASN00.014-0.00612.702-0.493-0.4930.0000.0000.0000.000
152A152GLU-1-0.841-0.94014.49917.33417.3340.0000.0000.0000.000
153A153ASN0-0.053-0.03510.242-0.464-0.4640.0000.0000.0000.000
154A154LEU0-0.002-0.01011.5751.3261.3260.0000.0000.0000.000
155A155LYS10.9901.01213.965-15.453-15.4530.0000.0000.0000.000
156A156ASN0-0.046-0.0259.052-1.653-1.6530.0000.0000.0000.000
157A157LEU00.013-0.0038.3441.5951.5950.0000.0000.0000.000
158A158VAL00.0330.02911.633-0.178-0.1780.0000.0000.0000.000
159A159GLY0-0.036-0.00814.6030.2390.2390.0000.0000.0000.000
160A160LYS10.8280.9208.959-24.652-24.6520.0000.0000.0000.000
161A161SER00.011-0.00912.042-1.439-1.4390.0000.0000.0000.000
162A162PHE00.0060.0178.2451.8101.8100.0000.0000.0000.000
163A163TYR00.0160.0108.178-4.399-4.3990.0000.0000.0000.000
164A164PHE00.0380.0129.0212.5912.5910.0000.0000.0000.000
165A165LEU0-0.007-0.0168.990-1.114-1.1140.0000.0000.0000.000
166A166GLY00.0470.01512.3220.3580.3580.0000.0000.0000.000
167A167LEU0-0.018-0.02012.710-0.841-0.8410.0000.0000.0000.000
168A168PRO00.0010.00316.0730.0140.0140.0000.0000.0000.000
169A169LEU00.0280.01319.5120.1880.1880.0000.0000.0000.000
170A170LYS10.9370.98621.893-14.102-14.1020.0000.0000.0000.000
171A171ILE0-0.005-0.00923.388-0.500-0.5000.0000.0000.0000.000
172A172PHE0-0.020-0.02124.6760.3070.3070.0000.0000.0000.000
173A173ASP-1-0.883-0.94628.7609.0569.0560.0000.0000.0000.000
174A174ILE00.0110.02927.718-0.339-0.3390.0000.0000.0000.000
175A175ASP-1-0.828-0.91930.03910.30510.3050.0000.0000.0000.000
176A176ALA00.0550.01726.8170.1790.1790.0000.0000.0000.000
177A177SER0-0.012-0.00522.447-0.316-0.3160.0000.0000.0000.000
178A178PRO00.0130.03021.3440.3860.3860.0000.0000.0000.000
179A179ILE0-0.025-0.02116.9570.2530.2530.0000.0000.0000.000
180A180ARG10.8530.92412.179-21.339-21.3390.0000.0000.0000.000
181A181CYS0-0.034-0.01213.1990.2240.2240.0000.0000.0000.000
182A182ILE00.0090.0096.7480.3190.3190.0000.0000.0000.000
183A183ALA0-0.010-0.0077.965-1.661-1.6610.0000.0000.0000.000
184A184ILE00.0080.0023.9881.3831.8030.006-0.166-0.2600.001
185A185LEU0-0.048-0.0323.232-10.791-9.2120.226-0.744-1.0620.007
186A186GLU-1-0.946-0.9613.56536.65137.3940.009-0.222-0.530-0.001