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: N1RJQ

Calculation Name: 2E8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2E8B

Chain ID: A

ChEMBL ID:

UniProt ID: O67413

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2126024.484647
FMO2-HF: Nuclear repulsion 2052537.80156
FMO2-HF: Total energy -73486.683087
FMO2-MP2: Total energy -73705.50756


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:4:PHE)


Summations of interaction energy for fragment #1(A:4:PHE)
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.
-12.684-7.5624.51-11.045-18.5870.03
Interaction energy analysis for fragmet #1(A:4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : 0.018
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].
3A6TRP00.075-0.0082.312-8.133-1.6002.149-3.694-4.9870.017
4A7ARG10.9610.9963.822-0.2640.038-0.001-0.032-0.2690.000
5A8LYS10.9100.9784.450-0.0830.010-0.001-0.028-0.0640.000
6A9GLY00.0460.0214.4350.6650.757-0.001-0.005-0.0860.000
7A10SER0-0.120-0.0494.4700.6410.798-0.001-0.018-0.1380.000
8A11LEU00.0420.0082.176-0.871-1.5157.628-2.216-4.7670.003
9A12SER00.0590.0412.782-0.8310.2700.515-0.536-1.080-0.001
10A13LYS10.9280.9544.277-1.408-1.3900.001-0.011-0.0080.000
11A14VAL00.0150.0336.030-0.063-0.0630.0000.0000.0000.000
12A15ASN0-0.048-0.0476.023-0.862-0.8620.0000.0000.0000.000
13A16THR0-0.009-0.0028.1340.0260.0260.0000.0000.0000.000
14A17CYS0-0.035-0.0059.995-0.001-0.0010.0000.0000.0000.000
15A18TYR00.000-0.02011.8040.0440.0440.0000.0000.0000.000
16A19VAL00.0280.00415.086-0.004-0.0040.0000.0000.0000.000
17A20LEU0-0.037-0.02216.9340.0250.0250.0000.0000.0000.000
18A21ALA00.0370.00720.1180.0020.0020.0000.0000.0000.000
19A22GLY0-0.040-0.00423.1140.0090.0090.0000.0000.0000.000
20A23GLY00.0530.01525.8320.0020.0020.0000.0000.0000.000
21A24LYS10.9450.97229.4750.0530.0530.0000.0000.0000.000
22A25SER0-0.009-0.00831.161-0.004-0.0040.0000.0000.0000.000
23A26LYS11.0031.00427.8630.0910.0910.0000.0000.0000.000
24A27ARG10.9100.97031.7990.0680.0680.0000.0000.0000.000
25A28PHE00.018-0.01133.7370.0020.0020.0000.0000.0000.000
26A29GLY00.0250.00637.442-0.001-0.0010.0000.0000.0000.000
27A30GLU-1-0.896-0.94839.649-0.039-0.0390.0000.0000.0000.000
28A31ASP-1-0.893-0.93636.246-0.048-0.0480.0000.0000.0000.000
29A32LYS10.8830.94235.2340.0440.0440.0000.0000.0000.000
30A33LEU00.0890.04034.257-0.004-0.0040.0000.0000.0000.000
31A34LEU00.0400.01833.441-0.003-0.0030.0000.0000.0000.000
32A35TYR0-0.043-0.03129.718-0.004-0.0040.0000.0000.0000.000
33A36GLU-1-0.891-0.94629.489-0.065-0.0650.0000.0000.0000.000
34A37ILE0-0.028-0.01729.778-0.004-0.0040.0000.0000.0000.000
35A38LYN00.0010.00424.939-0.004-0.0040.0000.0000.0000.000
36A39GLY00.0500.01325.792-0.006-0.0060.0000.0000.0000.000
37A40LYS10.9420.98124.7780.0570.0570.0000.0000.0000.000
38A41LYS10.9300.96224.2170.0610.0610.0000.0000.0000.000
39A42VAL0-0.045-0.01220.891-0.003-0.0030.0000.0000.0000.000
40A43ILE00.0430.02720.016-0.011-0.0110.0000.0000.0000.000
41A44GLU-1-0.885-0.94119.376-0.095-0.0950.0000.0000.0000.000
42A45ARG10.9070.95917.9880.0910.0910.0000.0000.0000.000
43A46VAL0-0.0340.00015.113-0.009-0.0090.0000.0000.0000.000
44A47TYR00.0240.00314.460-0.053-0.0530.0000.0000.0000.000
45A48GLU-1-0.914-0.95814.662-0.122-0.1220.0000.0000.0000.000
46A49THR0-0.032-0.01410.7470.0120.0120.0000.0000.0000.000
47A50ALA00.0230.02910.277-0.032-0.0320.0000.0000.0000.000
48A51LYS10.8550.9409.8630.2290.2290.0000.0000.0000.000
49A52SER0-0.041-0.0429.5600.0050.0050.0000.0000.0000.000
50A53VAL0-0.039-0.0154.4310.0820.240-0.001-0.025-0.1320.000
51A54PHE00.0100.0075.576-0.923-0.9230.0000.0000.0000.000
52A55LYS10.9030.9467.9720.6810.6810.0000.0000.0000.000
53A56GLU-1-0.918-0.95110.106-0.159-0.1590.0000.0000.0000.000
54A57VAL0-0.015-0.01111.889-0.073-0.0730.0000.0000.0000.000
55A58TYR00.0040.00914.1860.0570.0570.0000.0000.0000.000
56A59ILE00.0190.02417.231-0.015-0.0150.0000.0000.0000.000
57A60VAL0-0.0010.00319.3510.0120.0120.0000.0000.0000.000
58A61ALA0-0.009-0.01621.8160.0010.0010.0000.0000.0000.000
59A62LYS10.7990.88825.3510.0790.0790.0000.0000.0000.000
60A63ASP-1-0.888-0.94028.621-0.061-0.0610.0000.0000.0000.000
61A64ARG10.9390.95526.1860.0830.0830.0000.0000.0000.000
62A65GLU-1-0.833-0.92728.356-0.067-0.0670.0000.0000.0000.000
63A66LYS10.8600.96528.4700.0830.0830.0000.0000.0000.000
64A67PHE0-0.040-0.05524.681-0.002-0.0020.0000.0000.0000.000
65A68SER00.0710.04525.528-0.009-0.0090.0000.0000.0000.000
66A69PHE0-0.064-0.02824.859-0.001-0.0010.0000.0000.0000.000
67A70LEU0-0.0070.00621.1970.0000.0000.0000.0000.0000.000
68A71ASN0-0.038-0.00922.071-0.007-0.0070.0000.0000.0000.000
69A72ALA0-0.0020.00419.548-0.010-0.0100.0000.0000.0000.000
70A73PRO0-0.0170.00718.7560.0140.0140.0000.0000.0000.000
71A74VAL00.0280.00220.707-0.014-0.0140.0000.0000.0000.000
72A75VAL0-0.055-0.03219.9900.0080.0080.0000.0000.0000.000
73A76LEU0-0.029-0.02923.086-0.003-0.0030.0000.0000.0000.000
74A77ASP-1-0.844-0.90725.717-0.087-0.0870.0000.0000.0000.000
75A78GLU-1-0.935-1.00127.201-0.064-0.0640.0000.0000.0000.000
76A79PHE00.0010.02428.6080.0050.0050.0000.0000.0000.000
77A80GLU-1-0.865-0.92731.936-0.055-0.0550.0000.0000.0000.000
78A81GLU-1-0.877-0.89033.000-0.054-0.0540.0000.0000.0000.000
79A82SER0-0.014-0.01529.684-0.006-0.0060.0000.0000.0000.000
80A83ALA00.0150.00828.5790.0020.0020.0000.0000.0000.000
81A84SER00.016-0.00923.322-0.001-0.0010.0000.0000.0000.000
82A85ILE00.0090.02123.509-0.009-0.0090.0000.0000.0000.000
83A86ILE00.0550.03824.730-0.002-0.0020.0000.0000.0000.000
84A87GLY00.0140.02323.092-0.002-0.0020.0000.0000.0000.000
85A88LEU0-0.018-0.01118.366-0.011-0.0110.0000.0000.0000.000
86A89TYR00.0040.00120.794-0.007-0.0070.0000.0000.0000.000
87A90THR0-0.011-0.01722.9210.0020.0020.0000.0000.0000.000
88A91ALA0-0.021-0.00317.612-0.002-0.0020.0000.0000.0000.000
89A92LEU00.0270.00717.002-0.008-0.0080.0000.0000.0000.000
90A93LYS10.9781.00519.5900.0780.0780.0000.0000.0000.000
91A94HIS0-0.0230.00719.280-0.004-0.0040.0000.0000.0000.000
92A95ALA0-0.0010.00416.451-0.002-0.0020.0000.0000.0000.000
93A96LYS10.9340.96316.4290.1470.1470.0000.0000.0000.000
94A97GLU-1-0.826-0.90910.960-0.362-0.3620.0000.0000.0000.000
95A98GLU-1-0.822-0.92514.619-0.039-0.0390.0000.0000.0000.000
96A99ASN00.0240.01211.0190.0090.0090.0000.0000.0000.000
97A100VAL00.0030.01211.100-0.061-0.0610.0000.0000.0000.000
98A101PHE00.032-0.0017.9600.0200.0200.0000.0000.0000.000
99A102VAL0-0.028-0.01010.8200.0350.0350.0000.0000.0000.000
100A103LEU00.020-0.00511.813-0.016-0.0160.0000.0000.0000.000
101A104SER0-0.022-0.04114.7610.0220.0220.0000.0000.0000.000
102A105GLY00.0290.00817.818-0.012-0.0120.0000.0000.0000.000
103A106ASP-1-0.914-0.93219.833-0.128-0.1280.0000.0000.0000.000
104A107LEU00.0170.00216.5860.0060.0060.0000.0000.0000.000
105A108PRO0-0.056-0.03418.203-0.005-0.0050.0000.0000.0000.000
106A109LEU00.0280.00417.0760.0120.0120.0000.0000.0000.000
107A110MET0-0.0140.02612.543-0.032-0.0320.0000.0000.0000.000
108A111LYS10.9930.99610.0650.1810.1810.0000.0000.0000.000
109A112LYS10.8970.9426.238-1.366-1.3660.0000.0000.0000.000
110A113GLU-1-0.860-0.9444.919-0.186-0.1860.0000.0000.0000.000
111A114THR00.009-0.0035.795-0.418-0.4180.0000.0000.0000.000
112A115VAL0-0.021-0.0076.241-0.040-0.0400.0000.0000.0000.000
113A116LEU0-0.053-0.0341.8051.693-2.19014.142-4.218-6.0410.013
114A117TYR00.0630.0474.189-0.337-0.024-0.001-0.055-0.2570.000
115A118VAL0-0.010-0.0046.0370.3430.3430.0000.0000.0000.000
116A119LEU0-0.083-0.0512.961-0.774-0.1220.082-0.195-0.539-0.002
117A120GLU-1-0.984-0.9804.4330.0710.303-0.001-0.012-0.2190.000
118A121ASN0-0.052-0.0296.1420.1720.1720.0000.0000.0000.000
119A122PHE0-0.048-0.0208.413-0.094-0.0940.0000.0000.0000.000
120A123LYS10.9410.96910.030-0.072-0.0720.0000.0000.0000.000
121A124GLU-1-0.938-0.94613.4370.0400.0400.0000.0000.0000.000
122A125PRO0-0.002-0.00215.7140.0040.0040.0000.0000.0000.000
123A126VAL00.036-0.01315.228-0.022-0.0220.0000.0000.0000.000
124A127SER0-0.0060.02411.9960.0370.0370.0000.0000.0000.000
125A128VAL0-0.045-0.02013.148-0.045-0.0450.0000.0000.0000.000
126A129ALA00.0600.03013.4560.0110.0110.0000.0000.0000.000
127A130LYS10.8250.91514.9330.1300.1300.0000.0000.0000.000
128A131THR00.0540.04816.533-0.009-0.0090.0000.0000.0000.000
129A132GLU-1-0.817-0.90118.638-0.098-0.0980.0000.0000.0000.000
130A133LYS10.9280.96421.3640.1340.1340.0000.0000.0000.000
131A134LEU00.0030.01019.597-0.013-0.0130.0000.0000.0000.000
132A135HIS0-0.041-0.05317.2200.0090.0090.0000.0000.0000.000
133A136THR00.0070.00017.423-0.017-0.0170.0000.0000.0000.000
134A137LEU0-0.0320.00017.6720.0020.0020.0000.0000.0000.000
135A138VAL00.0450.02212.930-0.016-0.0160.0000.0000.0000.000
136A139GLY00.0400.01411.7440.0110.0110.0000.0000.0000.000
137A140VAL0-0.0550.0078.470-0.053-0.0530.0000.0000.0000.000
138A141TYR0-0.007-0.03711.6140.0650.0650.0000.0000.0000.000
139A142SER00.0460.02814.330-0.016-0.0160.0000.0000.0000.000
140A143LYS10.8560.91516.2460.0970.0970.0000.0000.0000.000
141A144LYS10.9230.96918.595-0.017-0.0170.0000.0000.0000.000
142A145LEU0-0.027-0.00518.4270.0050.0050.0000.0000.0000.000
143A146LEU0-0.033-0.01521.896-0.002-0.0020.0000.0000.0000.000
144A147GLU-1-0.879-0.93423.589-0.024-0.0240.0000.0000.0000.000
145A148LYS10.9040.95025.2240.0300.0300.0000.0000.0000.000
146A149ILE0-0.025-0.02821.418-0.001-0.0010.0000.0000.0000.000
147A150GLU-1-0.915-0.95926.032-0.049-0.0490.0000.0000.0000.000
148A151GLU-1-0.904-0.95128.624-0.026-0.0260.0000.0000.0000.000
149A152ARG10.8080.87927.8740.0450.0450.0000.0000.0000.000
150A153ILE00.0080.01026.7530.0010.0010.0000.0000.0000.000
151A154LYS10.9560.99731.0240.0350.0350.0000.0000.0000.000
152A155LYS10.8370.90633.7150.0310.0310.0000.0000.0000.000
153A156GLY00.0430.03834.3540.0020.0020.0000.0000.0000.000
154A157ASP-1-0.804-0.85531.876-0.050-0.0500.0000.0000.0000.000
155A158TYR0-0.052-0.09829.681-0.004-0.0040.0000.0000.0000.000
156A159ARG10.8120.88028.3330.0410.0410.0000.0000.0000.000
157A160ILE00.0640.01821.8770.0020.0020.0000.0000.0000.000
158A161TRP00.0040.00224.5090.0040.0040.0000.0000.0000.000
159A162ALA0-0.010-0.00626.1430.0040.0040.0000.0000.0000.000
160A163LEU00.0140.01022.6500.0040.0040.0000.0000.0000.000
161A164LEU00.0140.00019.9140.0040.0040.0000.0000.0000.000
162A165LYS10.9250.96623.4860.0520.0520.0000.0000.0000.000
163A166ASP-1-0.904-0.93126.347-0.026-0.0260.0000.0000.0000.000
164A167VAL0-0.020-0.01121.6490.0040.0040.0000.0000.0000.000
165A168GLY00.0320.03522.8710.0080.0080.0000.0000.0000.000
166A169TYR0-0.084-0.07018.831-0.005-0.0050.0000.0000.0000.000
167A170ASN0-0.028-0.00515.6750.0130.0130.0000.0000.0000.000
168A171GLU-1-0.841-0.92516.395-0.115-0.1150.0000.0000.0000.000
169A172VAL0-0.0040.00210.7720.0110.0110.0000.0000.0000.000
170A173GLU-1-0.940-0.97414.170-0.174-0.1740.0000.0000.0000.000
171A174ILE0-0.057-0.03611.372-0.044-0.0440.0000.0000.0000.000
172A175PRO00.0430.0209.4580.0440.0440.0000.0000.0000.000
173A176GLU-1-0.812-0.93112.710-0.179-0.1790.0000.0000.0000.000
174A177GLU-1-0.923-0.96012.750-0.249-0.2490.0000.0000.0000.000
175A178LEU0-0.027-0.0247.854-0.004-0.0040.0000.0000.0000.000
176A179ARG10.8410.95612.5570.1800.1800.0000.0000.0000.000
177A180TYR00.0180.00414.0660.0270.0270.0000.0000.0000.000
178A181THR0-0.049-0.03812.1010.0050.0050.0000.0000.0000.000
179A182LEU0-0.017-0.01714.197-0.001-0.0010.0000.0000.0000.000
180A183LEU0-0.0290.01117.0640.0160.0160.0000.0000.0000.000
181A184ASN00.014-0.00120.378-0.003-0.0030.0000.0000.0000.000
182A185MET00.0160.00023.0800.0060.0060.0000.0000.0000.000
183A186ASN0-0.104-0.10425.6720.0080.0080.0000.0000.0000.000
184A187THR0-0.059-0.06328.8160.0040.0040.0000.0000.0000.000
185A188LYS11.0961.14531.4140.0540.0540.0000.0000.0000.000