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: 37Q3L

Calculation Name: 2IWG-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 2IWG

Chain ID: B

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-09-26

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2041364.727451
FMO2-HF: Nuclear repulsion 1968986.583034
FMO2-HF: Total energy -72378.144417
FMO2-MP2: Total energy -72589.034838


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:2:HIS)


Summations of interaction energy for fragment #1(B:2:HIS)
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.
-6.2990.3992.295-2.533-6.4590.015
Interaction energy analysis for fragmet #1(B:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.001
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].
3B4VAL0-0.058-0.0363.851-1.573-0.5360.002-0.406-0.6330.002
4B5HIS00.0280.0186.6230.1260.1260.0000.0000.0000.000
5B6ILE0-0.039-0.0189.348-0.017-0.0170.0000.0000.0000.000
6B7THR00.0250.01512.4920.0000.0000.0000.0000.0000.000
7B8LEU0-0.032-0.00916.2610.0060.0060.0000.0000.0000.000
8B9ASP-1-0.848-0.93118.7230.2310.2310.0000.0000.0000.000
9B10PRO0-0.004-0.01520.695-0.012-0.0120.0000.0000.0000.000
10B11ASP-1-0.853-0.91124.1060.1550.1550.0000.0000.0000.000
11B12THR0-0.052-0.02421.563-0.007-0.0070.0000.0000.0000.000
12B13ALA0-0.0110.00224.136-0.009-0.0090.0000.0000.0000.000
13B14ASN00.0530.02825.349-0.011-0.0110.0000.0000.0000.000
14B15PRO00.0370.00828.2620.0050.0050.0000.0000.0000.000
15B16TRP0-0.0340.00130.887-0.004-0.0040.0000.0000.0000.000
16B17LEU0-0.087-0.03424.4810.0020.0020.0000.0000.0000.000
17B18ILE0-0.032-0.02227.967-0.002-0.0020.0000.0000.0000.000
18B19LEU0-0.006-0.00822.7710.0070.0070.0000.0000.0000.000
19B20SER0-0.006-0.01322.038-0.010-0.0100.0000.0000.0000.000
20B21GLU-1-0.877-0.93824.0180.1850.1850.0000.0000.0000.000
21B22ASP-1-0.869-0.91220.0040.2810.2810.0000.0000.0000.000
22B23ARG10.8720.91919.738-0.184-0.1840.0000.0000.0000.000
23B24ARG10.8560.94512.046-0.465-0.4650.0000.0000.0000.000
24B25GLN00.0090.00518.4630.0150.0150.0000.0000.0000.000
25B26VAL0-0.011-0.00920.625-0.009-0.0090.0000.0000.0000.000
26B27ARG11.0191.01523.184-0.138-0.1380.0000.0000.0000.000
27B28LEU0-0.0140.00826.3490.0000.0000.0000.0000.0000.000
28B29GLY0-0.086-0.05529.075-0.003-0.0030.0000.0000.0000.000
29B30ASP-1-0.894-0.95532.2250.0960.0960.0000.0000.0000.000
30B31THR00.0060.01635.560-0.006-0.0060.0000.0000.0000.000
31B32GLN0-0.039-0.01934.7390.0070.0070.0000.0000.0000.000
32B33GLN00.0310.01031.833-0.009-0.0090.0000.0000.0000.000
33B34SER0-0.036-0.01334.7850.0000.0000.0000.0000.0000.000
34B35ILE0-0.019-0.01630.4770.0030.0030.0000.0000.0000.000
35B36PRO00.0320.01731.544-0.005-0.0050.0000.0000.0000.000
36B37GLY00.0150.00932.6160.0040.0040.0000.0000.0000.000
37B38ASN0-0.074-0.04227.667-0.009-0.0090.0000.0000.0000.000
38B39GLU-1-0.851-0.94329.5880.1090.1090.0000.0000.0000.000
39B40GLU-1-0.869-0.93424.7500.1470.1470.0000.0000.0000.000
40B41ARG10.8500.93725.380-0.137-0.1370.0000.0000.0000.000
41B42PHE0-0.043-0.03322.005-0.012-0.0120.0000.0000.0000.000
42B43ASP-1-0.790-0.88927.6360.0970.0970.0000.0000.0000.000
43B44SER0-0.041-0.02130.411-0.006-0.0060.0000.0000.0000.000
44B45TYR0-0.012-0.02827.294-0.008-0.0080.0000.0000.0000.000
45B46PRO00.0190.04127.0150.0060.0060.0000.0000.0000.000
46B47MET00.0020.00022.9430.0080.0080.0000.0000.0000.000
47B48VAL0-0.007-0.02520.037-0.005-0.0050.0000.0000.0000.000
48B49LEU00.0090.01218.1120.0080.0080.0000.0000.0000.000
49B50GLY00.0270.02815.022-0.001-0.0010.0000.0000.0000.000
50B51ALA00.018-0.00816.058-0.003-0.0030.0000.0000.0000.000
51B52GLN00.0130.00510.953-0.030-0.0300.0000.0000.0000.000
52B53HIS00.0150.01513.724-0.057-0.0570.0000.0000.0000.000
53B54PHE0-0.042-0.0318.8620.1030.1030.0000.0000.0000.000
54B55HIS00.008-0.01711.893-0.081-0.0810.0000.0000.0000.000
55B56SER00.0510.03410.326-0.060-0.0600.0000.0000.0000.000
56B57GLY0-0.022-0.0076.5230.2060.2060.0000.0000.0000.000
57B58LYS10.8090.8912.682-2.429-0.1711.832-1.172-2.9170.013
58B59HIS10.8070.8903.309-1.414-0.3100.068-0.260-0.912-0.001
59B60TYR0-0.030-0.0473.185-1.230-0.0360.150-0.290-1.055-0.001
60B61TRP0-0.005-0.0074.471-0.002-0.004-0.001-0.0150.0180.000
61B62GLU-1-0.790-0.8737.9840.9460.9460.0000.0000.0000.000
62B63VAL0-0.033-0.02611.068-0.015-0.0150.0000.0000.0000.000
63B64ASP-1-0.806-0.87214.6120.2570.2570.0000.0000.0000.000
64B65VAL0-0.005-0.01317.725-0.013-0.0130.0000.0000.0000.000
65B66THR0-0.013-0.04220.599-0.031-0.0310.0000.0000.0000.000
66B67GLY0-0.054-0.03222.973-0.003-0.0030.0000.0000.0000.000
67B68LYS10.7310.87723.366-0.163-0.1630.0000.0000.0000.000
68B69GLU-1-0.856-0.94926.1240.0790.0790.0000.0000.0000.000
69B70ALA0-0.007-0.01926.048-0.009-0.0090.0000.0000.0000.000
70B71TRP0-0.0120.00018.8420.0120.0120.0000.0000.0000.000
71B72ASP-1-0.837-0.90920.8110.1220.1220.0000.0000.0000.000
72B73LEU0-0.017-0.01015.4250.0220.0220.0000.0000.0000.000
73B74GLY00.0400.00114.571-0.028-0.0280.0000.0000.0000.000
74B75VAL0-0.0100.03510.7210.0360.0360.0000.0000.0000.000
75B76CYS0-0.042-0.02414.070-0.039-0.0390.0000.0000.0000.000
76B77ARG10.9690.99816.368-0.085-0.0850.0000.0000.0000.000
77B78ASP-1-0.806-0.91118.4120.2240.2240.0000.0000.0000.000
78B79SER0-0.030-0.00219.725-0.010-0.0100.0000.0000.0000.000
79B80VAL0-0.067-0.01121.076-0.016-0.0160.0000.0000.0000.000
80B81ARG10.8460.90423.672-0.084-0.0840.0000.0000.0000.000
81B82ARG10.8720.92421.803-0.180-0.1800.0000.0000.0000.000
82B83LYS10.8710.94827.497-0.115-0.1150.0000.0000.0000.000
83B84GLY00.0160.00731.213-0.005-0.0050.0000.0000.0000.000
84B85HIS00.0010.01530.8060.0020.0020.0000.0000.0000.000
85B86PHE0-0.056-0.02824.816-0.004-0.0040.0000.0000.0000.000
86B87LEU00.0210.01527.7510.0020.0020.0000.0000.0000.000
87B88LEU00.0450.03322.0980.0040.0040.0000.0000.0000.000
88B89SER00.0330.01223.695-0.008-0.0080.0000.0000.0000.000
89B90SER00.0840.04120.3500.0060.0060.0000.0000.0000.000
90B91LYS10.8910.95121.622-0.020-0.0200.0000.0000.0000.000
91B92SER0-0.054-0.04123.783-0.005-0.0050.0000.0000.0000.000
92B93GLY0-0.097-0.03920.6630.0060.0060.0000.0000.0000.000
93B94PHE00.0710.02819.0190.0220.0220.0000.0000.0000.000
94B95TRP00.0230.00115.243-0.005-0.0050.0000.0000.0000.000
95B96THR00.0340.01415.5340.0270.0270.0000.0000.0000.000
96B97ILE0-0.017-0.00516.865-0.026-0.0260.0000.0000.0000.000
97B98TRP0-0.0050.01719.2950.0210.0210.0000.0000.0000.000
98B99LEU0-0.032-0.00121.770-0.015-0.0150.0000.0000.0000.000
99B100TRP0-0.033-0.03624.4400.0060.0060.0000.0000.0000.000
100B101ASN0-0.017-0.01228.007-0.006-0.0060.0000.0000.0000.000
101B102LYS10.9951.02028.968-0.077-0.0770.0000.0000.0000.000
102B103GLN0-0.060-0.04827.774-0.008-0.0080.0000.0000.0000.000
103B104LYS10.9600.99428.207-0.050-0.0500.0000.0000.0000.000
104B105TYR00.0690.02721.9180.0030.0030.0000.0000.0000.000
105B106GLU-1-0.848-0.89823.5420.0400.0400.0000.0000.0000.000
106B107ALA00.0620.02520.4710.0140.0140.0000.0000.0000.000
107B108GLY00.0300.00820.643-0.008-0.0080.0000.0000.0000.000
108B109THR0-0.052-0.02721.9790.0030.0030.0000.0000.0000.000
109B110TYR0-0.044-0.01323.6770.0060.0060.0000.0000.0000.000
110B111PRO00.004-0.02727.187-0.006-0.0060.0000.0000.0000.000
111B112GLN0-0.026-0.00126.112-0.002-0.0020.0000.0000.0000.000
112B113THR00.001-0.00923.684-0.012-0.0120.0000.0000.0000.000
113B114PRO0-0.032-0.01224.7080.0080.0080.0000.0000.0000.000
114B115LEU00.0010.00819.897-0.009-0.0090.0000.0000.0000.000
115B116HIS0-0.039-0.01724.1110.0090.0090.0000.0000.0000.000
116B117LEU00.0110.00519.635-0.007-0.0070.0000.0000.0000.000
117B118GLN0-0.014-0.01323.6580.0060.0060.0000.0000.0000.000
118B119VAL00.0330.02821.7760.0010.0010.0000.0000.0000.000
119B120PRO0-0.025-0.01721.7980.0060.0060.0000.0000.0000.000
120B121PRO00.0080.02118.0850.0050.0050.0000.0000.0000.000
121B122CYS0-0.058-0.02819.527-0.011-0.0110.0000.0000.0000.000
122B123GLN00.010-0.01614.7320.0070.0070.0000.0000.0000.000
123B124VAL0-0.0090.00213.610-0.028-0.0280.0000.0000.0000.000
124B125GLY00.0440.0349.7930.0660.0660.0000.0000.0000.000
125B126ILE0-0.062-0.0309.292-0.105-0.1050.0000.0000.0000.000
126B127PHE0-0.025-0.0252.890-1.0420.0650.244-0.390-0.9600.002
127B128LEU00.0000.0035.725-0.106-0.1060.0000.0000.0000.000
128B129ASP-1-0.780-0.8835.7610.2710.2710.0000.0000.0000.000
129B130TYR0-0.029-0.0297.866-0.267-0.2670.0000.0000.0000.000
130B131GLU-1-0.777-0.9108.5640.4250.4250.0000.0000.0000.000
131B132ALA0-0.0380.00310.073-0.095-0.0950.0000.0000.0000.000
132B133GLY0-0.0060.01612.010-0.030-0.0300.0000.0000.0000.000
133B134MET0-0.025-0.02710.998-0.072-0.0720.0000.0000.0000.000
134B135VAL0-0.005-0.00410.3550.1190.1190.0000.0000.0000.000
135B136SER0-0.0040.0239.992-0.042-0.0420.0000.0000.0000.000
136B137PHE00.0220.01510.6410.0860.0860.0000.0000.0000.000
137B138TYR0-0.006-0.0048.338-0.084-0.0840.0000.0000.0000.000
138B139ASN00.034-0.01512.6860.0810.0810.0000.0000.0000.000
139B140ILE00.013-0.00510.733-0.031-0.0310.0000.0000.0000.000
140B141THR00.0140.01114.516-0.003-0.0030.0000.0000.0000.000
141B142ASP-1-0.869-0.88517.5420.0140.0140.0000.0000.0000.000
142B143HIS00.001-0.00416.167-0.002-0.0020.0000.0000.0000.000
143B144GLY00.0210.02912.670-0.003-0.0030.0000.0000.0000.000
144B145SER0-0.091-0.07512.992-0.057-0.0570.0000.0000.0000.000
145B146LEU0-0.034-0.02012.4890.0400.0400.0000.0000.0000.000
146B147ILE0-0.056-0.02114.9040.0000.0000.0000.0000.0000.000
147B148TYR00.022-0.02915.605-0.013-0.0130.0000.0000.0000.000
148B149SER0-0.020-0.02812.8870.0110.0110.0000.0000.0000.000
149B150PHE0-0.0230.00914.867-0.011-0.0110.0000.0000.0000.000
150B151SER00.007-0.03814.649-0.005-0.0050.0000.0000.0000.000
151B152GLU-1-0.877-0.92616.509-0.083-0.0830.0000.0000.0000.000
152B153CYS0-0.0530.00015.4290.0220.0220.0000.0000.0000.000
153B154ALA0-0.055-0.02517.5230.0220.0220.0000.0000.0000.000
154B155PHE0-0.045-0.02712.0730.0150.0150.0000.0000.0000.000
155B156THR00.0020.00216.938-0.009-0.0090.0000.0000.0000.000
156B157GLY00.0250.01718.7070.0060.0060.0000.0000.0000.000
157B158PRO00.0150.01415.7100.0280.0280.0000.0000.0000.000
158B159LEU0-0.042-0.00312.110-0.038-0.0380.0000.0000.0000.000
159B160ARG10.8210.89613.697-0.242-0.2420.0000.0000.0000.000
160B161PRO00.0060.00611.462-0.016-0.0160.0000.0000.0000.000
161B162PHE0-0.021-0.01313.717-0.021-0.0210.0000.0000.0000.000
162B163PHE00.042-0.01013.4780.0110.0110.0000.0000.0000.000
163B164SER00.015-0.01018.717-0.015-0.0150.0000.0000.0000.000
164B165PRO00.0020.00322.1290.0010.0010.0000.0000.0000.000
165B166GLY00.0640.05023.901-0.007-0.0070.0000.0000.0000.000
166B167PHE00.0680.03226.4430.0020.0020.0000.0000.0000.000
167B168ASN0-0.004-0.01430.0040.0040.0040.0000.0000.0000.000
168B169ASP-1-0.847-0.92232.4170.0760.0760.0000.0000.0000.000
169B170GLY0-0.024-0.01433.7820.0020.0020.0000.0000.0000.000
170B171GLY0-0.032-0.01535.459-0.002-0.0020.0000.0000.0000.000
171B172LYS10.8080.89433.076-0.081-0.0810.0000.0000.0000.000
172B173ASN00.0150.00727.0490.0080.0080.0000.0000.0000.000
173B174THR00.004-0.00129.0770.0070.0070.0000.0000.0000.000
174B175ALA00.0150.03125.9810.0050.0050.0000.0000.0000.000
175B176PRO0-0.018-0.01023.418-0.006-0.0060.0000.0000.0000.000
176B177LEU00.0070.02218.9190.0040.0040.0000.0000.0000.000
177B178THR00.014-0.00918.118-0.009-0.0090.0000.0000.0000.000
178B179LEU0-0.0220.00112.7720.0200.0200.0000.0000.0000.000
179B180CYS00.0060.01112.592-0.029-0.0290.0000.0000.0000.000
180B181PRO00.0340.00812.1480.0640.0640.0000.0000.0000.000
181B182LEU0-0.056-0.0167.2850.1590.1590.0000.0000.0000.000