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

tag_button

FMODB ID: 523ZZ

Calculation Name: 2EIA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EIA

Chain ID: B

ChEMBL ID:

UniProt ID: P69732

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2123210.568737
FMO2-HF: Nuclear repulsion 2040786.328231
FMO2-HF: Total energy -82424.240506
FMO2-MP2: Total energy -82661.422175


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(B:17:PRO)


Summations of interaction energy for fragment #1(B:17: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.
-1.219-2.19710.475-5.277-4.2210.006
Interaction energy analysis for fragmet #1(B:17:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / 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].
3B19GLY00.0610.0383.8290.0841.288-0.005-0.636-0.5640.004
4B20TYR0-0.013-0.0021.962-0.436-2.89510.475-4.588-3.4280.002
5B21THR00.0470.0203.853-0.877-0.6000.005-0.053-0.2290.000
6B22THR00.0320.0125.874-0.110-0.1100.0000.0000.0000.000
7B23TRP0-0.0050.0077.109-0.157-0.1570.0000.0000.0000.000
8B24VAL0-0.0030.0037.233-0.176-0.1760.0000.0000.0000.000
9B25ASN0-0.016-0.0169.374-0.139-0.1390.0000.0000.0000.000
10B26THR00.015-0.00211.434-0.082-0.0820.0000.0000.0000.000
11B27ILE0-0.047-0.02511.984-0.062-0.0620.0000.0000.0000.000
12B28GLN0-0.053-0.02512.855-0.038-0.0380.0000.0000.0000.000
13B29THR0-0.040-0.00215.270-0.037-0.0370.0000.0000.0000.000
14B30ASN0-0.033-0.02017.166-0.008-0.0080.0000.0000.0000.000
15B31GLY00.0400.02817.459-0.020-0.0200.0000.0000.0000.000
16B32LEU00.010-0.00214.7110.0190.0190.0000.0000.0000.000
17B33LEU0-0.081-0.01317.363-0.028-0.0280.0000.0000.0000.000
18B34ASN00.0660.03019.258-0.019-0.0190.0000.0000.0000.000
19B35GLU-1-0.878-0.94919.5210.1610.1610.0000.0000.0000.000
20B36ALA0-0.0090.00717.5790.0110.0110.0000.0000.0000.000
21B37SER0-0.012-0.03615.0830.0380.0380.0000.0000.0000.000
22B38GLN00.0260.00415.3060.0420.0420.0000.0000.0000.000
23B39ASN0-0.004-0.00617.1120.0100.0100.0000.0000.0000.000
24B40LEU0-0.0030.00110.5960.0150.0150.0000.0000.0000.000
25B41PHE00.0170.01312.0510.0480.0480.0000.0000.0000.000
26B42GLY00.0160.02813.5140.0090.0090.0000.0000.0000.000
27B43ILE0-0.049-0.03913.010-0.022-0.0220.0000.0000.0000.000
28B44LEU0-0.053-0.0188.175-0.008-0.0080.0000.0000.0000.000
29B45SER0-0.011-0.01110.0040.0270.0270.0000.0000.0000.000
30B46VAL0-0.038-0.01812.059-0.056-0.0560.0000.0000.0000.000
31B47ASP-1-0.852-0.92312.6240.0940.0940.0000.0000.0000.000
32B48CYS0-0.054-0.0068.5030.0510.0510.0000.0000.0000.000
33B49THR0-0.022-0.03710.649-0.021-0.0210.0000.0000.0000.000
34B50SER00.016-0.02812.0420.0750.0750.0000.0000.0000.000
35B51GLU-1-0.828-0.86410.538-0.078-0.0780.0000.0000.0000.000
36B52GLU-1-0.797-0.8786.9450.1830.1830.0000.0000.0000.000
37B53MET0-0.047-0.0148.8490.2610.2610.0000.0000.0000.000
38B54ASN00.0310.02211.3390.0750.0750.0000.0000.0000.000
39B55ALA00.0370.0326.983-0.021-0.0210.0000.0000.0000.000
40B56PHE0-0.037-0.0096.6870.2520.2520.0000.0000.0000.000
41B57LEU00.0360.0068.848-0.086-0.0860.0000.0000.0000.000
42B58ASP-1-0.826-0.91510.8800.1220.1220.0000.0000.0000.000
43B59VAL0-0.133-0.0515.293-0.074-0.0740.0000.0000.0000.000
44B60VAL00.0150.0168.588-0.003-0.0030.0000.0000.0000.000
45B61PRO0-0.006-0.00711.401-0.064-0.0640.0000.0000.0000.000
46B62GLY0-0.024-0.01913.107-0.041-0.0410.0000.0000.0000.000
47B63GLN00.0320.01315.8930.0010.0010.0000.0000.0000.000
48B64ALA0-0.001-0.01318.693-0.012-0.0120.0000.0000.0000.000
49B65GLY00.0740.05620.5390.0030.0030.0000.0000.0000.000
50B66GLN00.008-0.01519.319-0.013-0.0130.0000.0000.0000.000
51B67LYS10.8360.90213.575-0.214-0.2140.0000.0000.0000.000
52B68GLN0-0.028-0.01318.7360.0010.0010.0000.0000.0000.000
53B69ILE0-0.0060.01522.019-0.003-0.0030.0000.0000.0000.000
54B70LEU0-0.013-0.01216.901-0.001-0.0010.0000.0000.0000.000
55B71LEU00.0250.00017.6440.0020.0020.0000.0000.0000.000
56B72ASP-1-0.809-0.89321.1730.0830.0830.0000.0000.0000.000
57B73ALA0-0.063-0.02623.295-0.007-0.0070.0000.0000.0000.000
58B74ILE00.013-0.01618.452-0.004-0.0040.0000.0000.0000.000
59B75ASP-1-0.804-0.88222.8940.0850.0850.0000.0000.0000.000
60B76LYS10.8710.94525.506-0.090-0.0900.0000.0000.0000.000
61B77ILE0-0.053-0.02224.834-0.007-0.0070.0000.0000.0000.000
62B78ALA0-0.014-0.01824.320-0.006-0.0060.0000.0000.0000.000
63B79ASP-1-0.873-0.94426.3520.0510.0510.0000.0000.0000.000
64B80ASP-1-0.856-0.88829.7420.0530.0530.0000.0000.0000.000
65B81TRP00.002-0.01127.983-0.003-0.0030.0000.0000.0000.000
66B82ASP-1-0.760-0.89728.7630.0420.0420.0000.0000.0000.000
67B83ASN0-0.101-0.04031.113-0.006-0.0060.0000.0000.0000.000
68B84ARG10.7820.85733.186-0.057-0.0570.0000.0000.0000.000
69B85HIS10.7830.89831.272-0.048-0.0480.0000.0000.0000.000
70B86PRO00.0520.05332.5480.0000.0000.0000.0000.0000.000
71B87LEU0-0.012-0.02830.393-0.003-0.0030.0000.0000.0000.000
72B88PRO0-0.018-0.02034.0740.0000.0000.0000.0000.0000.000
73B89ASN0-0.0250.00034.321-0.001-0.0010.0000.0000.0000.000
74B90ALA00.0300.03130.061-0.003-0.0030.0000.0000.0000.000
75B91PRO00.0010.00228.5050.0000.0000.0000.0000.0000.000
76B92LEU00.0210.00526.6850.0030.0030.0000.0000.0000.000
77B93VAL0-0.014-0.01023.0620.0020.0020.0000.0000.0000.000
78B94ALA00.0120.01822.5720.0020.0020.0000.0000.0000.000
79B95PRO00.007-0.00524.574-0.007-0.0070.0000.0000.0000.000
80B96PRO00.0320.01824.2720.0010.0010.0000.0000.0000.000
81B97GLN00.0360.00424.869-0.002-0.0020.0000.0000.0000.000
82B98GLY00.0220.02426.6130.0030.0030.0000.0000.0000.000
83B99PRO0-0.007-0.01827.2230.0010.0010.0000.0000.0000.000
84B100ILE00.0080.02422.273-0.001-0.0010.0000.0000.0000.000
85B101PRO00.0150.00126.5670.0050.0050.0000.0000.0000.000
86B102MET00.0180.00724.4440.0000.0000.0000.0000.0000.000
87B103THR00.0380.03026.3860.0040.0040.0000.0000.0000.000
88B104ALA00.0480.01425.0210.0050.0050.0000.0000.0000.000
89B105ARG10.8560.92223.104-0.011-0.0110.0000.0000.0000.000
90B106PHE0-0.012-0.02921.5660.0030.0030.0000.0000.0000.000
91B107ILE00.0240.04420.7210.0020.0020.0000.0000.0000.000
92B108ARG10.8080.89918.605-0.085-0.0850.0000.0000.0000.000
93B109GLY0-0.016-0.03417.1870.0120.0120.0000.0000.0000.000
94B110LEU00.0220.01017.427-0.016-0.0160.0000.0000.0000.000
95B111GLY0-0.050-0.00318.474-0.013-0.0130.0000.0000.0000.000
96B112VAL0-0.073-0.03618.568-0.008-0.0080.0000.0000.0000.000
97B113PRO00.0450.04217.2670.0040.0040.0000.0000.0000.000
98B114ARG10.8870.8949.6320.2760.2760.0000.0000.0000.000
99B115GLU-1-0.883-0.96714.568-0.070-0.0700.0000.0000.0000.000
100B116ARG10.7570.85816.5430.0290.0290.0000.0000.0000.000
101B117GLN0-0.065-0.04215.0370.0400.0400.0000.0000.0000.000
102B118MET0-0.046-0.03111.4860.0040.0040.0000.0000.0000.000
103B119GLU-1-0.812-0.84915.782-0.033-0.0330.0000.0000.0000.000
104B120PRO00.0870.04019.4500.0120.0120.0000.0000.0000.000
105B121ALA0-0.118-0.04821.1360.0010.0010.0000.0000.0000.000
106B122PHE00.017-0.02016.6830.0050.0050.0000.0000.0000.000
107B123ASP-1-0.803-0.88219.1840.0410.0410.0000.0000.0000.000
108B124GLN00.010-0.01120.2430.0140.0140.0000.0000.0000.000
109B125PHE0-0.0260.00420.2800.0070.0070.0000.0000.0000.000
110B126ARG10.8540.91314.800-0.056-0.0560.0000.0000.0000.000
111B127GLN0-0.051-0.02717.7480.0220.0220.0000.0000.0000.000
112B128THR0-0.024-0.01419.5030.0080.0080.0000.0000.0000.000
113B129TYR0-0.016-0.01815.6420.0000.0000.0000.0000.0000.000
114B130ARG10.9050.95115.378-0.211-0.2110.0000.0000.0000.000
115B131GLN0-0.026-0.01317.6410.0250.0250.0000.0000.0000.000
116B132TRP00.0900.05221.006-0.001-0.0010.0000.0000.0000.000
117B133ILE00.0370.02315.0030.0010.0010.0000.0000.0000.000
118B134ILE0-0.079-0.03617.8110.0050.0050.0000.0000.0000.000
119B135GLU-1-0.920-0.97520.0030.1100.1100.0000.0000.0000.000
120B136ALA0-0.0100.00020.705-0.009-0.0090.0000.0000.0000.000
121B137MET0-0.013-0.01816.4930.0070.0070.0000.0000.0000.000
122B138SER00.0000.02521.105-0.014-0.0140.0000.0000.0000.000
123B139GLU-1-0.839-0.91424.2520.0850.0850.0000.0000.0000.000
124B140GLY00.0470.01023.534-0.009-0.0090.0000.0000.0000.000
125B141ILE0-0.032-0.02721.153-0.008-0.0080.0000.0000.0000.000
126B142LYS10.8600.91425.141-0.106-0.1060.0000.0000.0000.000
127B143VAL0-0.043-0.00327.662-0.009-0.0090.0000.0000.0000.000
128B144MET0-0.023-0.01624.310-0.009-0.0090.0000.0000.0000.000
129B145ILE00.0110.01527.792-0.005-0.0050.0000.0000.0000.000
130B146GLY0-0.040-0.01930.116-0.005-0.0050.0000.0000.0000.000
131B147LYS10.9010.97729.981-0.085-0.0850.0000.0000.0000.000
132B148PRO0-0.034-0.01431.9050.0020.0020.0000.0000.0000.000
133B149LYS10.8920.93429.118-0.076-0.0760.0000.0000.0000.000
134B150ALA00.1290.08231.400-0.001-0.0010.0000.0000.0000.000
135B151GLN00.009-0.00432.982-0.007-0.0070.0000.0000.0000.000
136B152ASN0-0.033-0.02534.8150.0010.0010.0000.0000.0000.000
137B153ILE0-0.0200.01234.897-0.003-0.0030.0000.0000.0000.000
138B154ARG10.8630.94137.572-0.041-0.0410.0000.0000.0000.000
139B155GLN00.0350.02941.2980.0010.0010.0000.0000.0000.000
140B156GLY00.0180.00343.9110.0000.0000.0000.0000.0000.000
141B157ALA00.016-0.01546.534-0.001-0.0010.0000.0000.0000.000
142B158LYS10.9430.96749.804-0.027-0.0270.0000.0000.0000.000
143B159GLU-1-0.810-0.86642.7370.0370.0370.0000.0000.0000.000
144B160PRO00.0690.05145.9390.0000.0000.0000.0000.0000.000
145B161TYR00.0440.00043.2500.0010.0010.0000.0000.0000.000
146B162PRO00.022-0.00243.2490.0020.0020.0000.0000.0000.000
147B163GLU-1-0.862-0.93541.3470.0320.0320.0000.0000.0000.000
148B164PHE0-0.086-0.03140.0600.0030.0030.0000.0000.0000.000
149B165VAL0-0.002-0.00938.8190.0030.0030.0000.0000.0000.000
150B166ASP-1-0.933-0.94736.8080.0440.0440.0000.0000.0000.000
151B167ARG10.8320.88335.467-0.040-0.0400.0000.0000.0000.000
152B168LEU0-0.044-0.02734.6750.0050.0050.0000.0000.0000.000
153B169LEU0-0.003-0.00133.5360.0050.0050.0000.0000.0000.000
154B170SER0-0.0050.00331.4070.0060.0060.0000.0000.0000.000
155B171GLN00.0320.00829.8450.0020.0020.0000.0000.0000.000
156B172ILE00.0350.03828.8720.0070.0070.0000.0000.0000.000
157B173LYS10.9210.97625.115-0.067-0.0670.0000.0000.0000.000
158B174SER0-0.129-0.08725.4340.0070.0070.0000.0000.0000.000
159B175GLU-1-0.861-0.93824.3770.0960.0960.0000.0000.0000.000
160B176GLY0-0.051-0.00722.0060.0090.0090.0000.0000.0000.000
161B177HIS0-0.022-0.01721.9730.0120.0120.0000.0000.0000.000
162B178PRO00.011-0.00922.530-0.006-0.0060.0000.0000.0000.000
163B179GLN00.016-0.00223.948-0.004-0.0040.0000.0000.0000.000
164B180GLU-1-0.909-0.94526.7310.0480.0480.0000.0000.0000.000
165B181ILE00.0290.00726.390-0.004-0.0040.0000.0000.0000.000
166B182SER00.0070.00727.227-0.001-0.0010.0000.0000.0000.000
167B183LYS10.8880.91329.182-0.041-0.0410.0000.0000.0000.000
168B184PHE00.0240.01832.182-0.002-0.0020.0000.0000.0000.000
169B185LEU00.0160.00429.732-0.003-0.0030.0000.0000.0000.000
170B186THR00.0000.00932.854-0.002-0.0020.0000.0000.0000.000
171B187ASP-1-0.860-0.90235.1800.0370.0370.0000.0000.0000.000
172B188THR0-0.037-0.02536.857-0.003-0.0030.0000.0000.0000.000
173B189LEU00.001-0.01034.605-0.002-0.0020.0000.0000.0000.000
174B190THR0-0.032-0.02538.091-0.002-0.0020.0000.0000.0000.000
175B191ILE00.0660.02740.350-0.002-0.0020.0000.0000.0000.000
176B192GLN0-0.039-0.01440.6910.0010.0010.0000.0000.0000.000
177B193ASN0-0.038-0.03738.357-0.002-0.0020.0000.0000.0000.000
178B194ALA00.0650.05342.1790.0000.0000.0000.0000.0000.000
179B195ASN0-0.055-0.03744.870-0.001-0.0010.0000.0000.0000.000
180B196GLU-1-0.818-0.93147.9360.0290.0290.0000.0000.0000.000
181B197GLU-1-0.926-0.96150.8920.0230.0230.0000.0000.0000.000
182B198CYS0-0.078-0.01447.899-0.001-0.0010.0000.0000.0000.000
183B199ARG10.7970.91245.754-0.033-0.0330.0000.0000.0000.000
184B200ASN0-0.092-0.04748.970-0.001-0.0010.0000.0000.0000.000
185B201ALA00.0450.03151.760-0.001-0.0010.0000.0000.0000.000
186B202MET00.0380.01745.4600.0000.0000.0000.0000.0000.000
187B203ARG10.8250.93349.493-0.026-0.0260.0000.0000.0000.000
188B204HIS0-0.013-0.02051.8570.0000.0000.0000.0000.0000.000
189B205LEU0-0.050-0.00447.1890.0000.0000.0000.0000.0000.000
190B206ARG10.9000.94245.241-0.024-0.0240.0000.0000.0000.000
191B207PRO0-0.001-0.00540.4720.0000.0000.0000.0000.0000.000
192B208GLU-1-0.871-0.93740.3480.0320.0320.0000.0000.0000.000
193B209ASP-1-0.846-0.89941.4360.0240.0240.0000.0000.0000.000
194B210THR0-0.007-0.02441.7640.0020.0020.0000.0000.0000.000
195B211LEU00.0250.01538.2480.0000.0000.0000.0000.0000.000
196B212GLU-1-0.841-0.93541.8090.0250.0250.0000.0000.0000.000
197B213GLU-1-0.911-0.94744.7860.0200.0200.0000.0000.0000.000
198B214LYS10.8200.90340.653-0.034-0.0340.0000.0000.0000.000
199B215MET0-0.040-0.04742.8260.0000.0000.0000.0000.0000.000
200B216TYR0-0.036-0.01646.198-0.001-0.0010.0000.0000.0000.000
201B217ALA00.0050.00749.189-0.001-0.0010.0000.0000.0000.000
202B219ARG10.8970.95550.350-0.018-0.0180.0000.0000.0000.000
203B220ASP-1-0.978-0.97551.6140.0200.0200.0000.0000.0000.000