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: J2369

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2040529.154725
FMO2-HF: Nuclear repulsion 1968153.356064
FMO2-HF: Total energy -72375.798661
FMO2-MP2: Total energy -72586.914618


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.
-3.8953.043.723-2.824-7.8340.018
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 : 0.027 / 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].
3B4VAL0-0.049-0.0323.851-0.1200.8950.002-0.393-0.6240.002
4B5HIS00.0240.0106.580-0.098-0.0980.0000.0000.0000.000
5B6ILE0-0.036-0.0159.290-0.055-0.0550.0000.0000.0000.000
6B7THR00.0320.02812.4920.0170.0170.0000.0000.0000.000
7B8LEU0-0.021-0.02016.261-0.010-0.0100.0000.0000.0000.000
8B9ASP-1-0.869-0.95418.7190.2720.2720.0000.0000.0000.000
9B10PRO0-0.017-0.00720.662-0.023-0.0230.0000.0000.0000.000
10B11ASP-1-0.870-0.92524.0960.1800.1800.0000.0000.0000.000
11B12THR0-0.033-0.02821.405-0.018-0.0180.0000.0000.0000.000
12B13ALA00.0020.00224.114-0.016-0.0160.0000.0000.0000.000
13B14ASN00.0250.02625.351-0.006-0.0060.0000.0000.0000.000
14B15PRO00.0570.01828.2790.0070.0070.0000.0000.0000.000
15B16TRP0-0.0340.00730.9090.0000.0000.0000.0000.0000.000
16B17LEU0-0.081-0.03424.5720.0010.0010.0000.0000.0000.000
17B18ILE0-0.042-0.02427.9930.0030.0030.0000.0000.0000.000
18B19LEU00.000-0.01022.8420.0040.0040.0000.0000.0000.000
19B20SER0-0.022-0.02522.100-0.012-0.0120.0000.0000.0000.000
20B21GLU-1-0.885-0.95024.0180.2300.2300.0000.0000.0000.000
21B22ASP-1-0.868-0.91219.9230.3650.3650.0000.0000.0000.000
22B23ARG10.8800.93319.738-0.229-0.2290.0000.0000.0000.000
23B24ARG10.8920.96011.958-0.662-0.6620.0000.0000.0000.000
24B25GLN00.0210.02518.463-0.005-0.0050.0000.0000.0000.000
25B26VAL0-0.015-0.01420.653-0.002-0.0020.0000.0000.0000.000
26B27ARG11.0231.02023.244-0.143-0.1430.0000.0000.0000.000
27B28LEU0-0.0090.01326.4230.0030.0030.0000.0000.0000.000
28B29GLY0-0.081-0.05629.147-0.002-0.0020.0000.0000.0000.000
29B30ASP-1-0.904-0.96932.2910.0810.0810.0000.0000.0000.000
30B31THR00.0130.03235.629-0.005-0.0050.0000.0000.0000.000
31B32GLN0-0.049-0.02134.7810.0060.0060.0000.0000.0000.000
32B33GLN00.0420.01131.870-0.010-0.0100.0000.0000.0000.000
33B34SER0-0.037-0.01434.799-0.002-0.0020.0000.0000.0000.000
34B35ILE0-0.007-0.01730.5430.0070.0070.0000.0000.0000.000
35B36PRO00.0260.01831.663-0.008-0.0080.0000.0000.0000.000
36B37GLY00.0020.00832.5870.0020.0020.0000.0000.0000.000
37B38ASN0-0.047-0.03427.934-0.013-0.0130.0000.0000.0000.000
38B39GLU-1-0.864-0.94329.4110.0990.0990.0000.0000.0000.000
39B40GLU-1-0.921-0.96524.6970.1440.1440.0000.0000.0000.000
40B41ARG10.8710.95025.348-0.143-0.1430.0000.0000.0000.000
41B42PHE0-0.046-0.03522.153-0.014-0.0140.0000.0000.0000.000
42B43ASP-1-0.805-0.90627.6400.0710.0710.0000.0000.0000.000
43B44SER0-0.019-0.00130.404-0.004-0.0040.0000.0000.0000.000
44B45TYR00.0020.00627.242-0.008-0.0080.0000.0000.0000.000
45B46PRO00.0490.04726.8900.0090.0090.0000.0000.0000.000
46B47MET0-0.0150.00322.9090.0040.0040.0000.0000.0000.000
47B48VAL0-0.005-0.01220.1470.0050.0050.0000.0000.0000.000
48B49LEU0-0.006-0.00518.076-0.009-0.0090.0000.0000.0000.000
49B50GLY00.0310.02615.0470.0150.0150.0000.0000.0000.000
50B51ALA00.016-0.02015.983-0.011-0.0110.0000.0000.0000.000
51B52GLN00.0020.00310.956-0.072-0.0720.0000.0000.0000.000
52B53HIS00.0190.01613.637-0.103-0.1030.0000.0000.0000.000
53B54PHE0-0.039-0.0308.5530.1010.1010.0000.0000.0000.000
54B55HIS00.018-0.00811.781-0.070-0.0700.0000.0000.0000.000
55B56SER00.0420.02710.344-0.032-0.0320.0000.0000.0000.000
56B57GLY00.0080.0276.2740.2600.2600.0000.0000.0000.000
57B58LYS10.8920.9522.5990.0582.5573.231-1.433-4.2970.017
58B59HIS10.8090.8813.231-0.9890.2280.107-0.332-0.992-0.002
59B60TYR0-0.029-0.0333.205-1.350-0.2440.087-0.261-0.933-0.001
60B61TRP0-0.0130.0014.5810.3830.374-0.001-0.0130.0240.000
61B62GLU-1-0.803-0.8918.0900.2310.2310.0000.0000.0000.000
62B63VAL0-0.040-0.02911.2300.0760.0760.0000.0000.0000.000
63B64ASP-1-0.853-0.91714.7640.1400.1400.0000.0000.0000.000
64B65VAL0-0.024-0.02117.8970.0040.0040.0000.0000.0000.000
65B66THR0-0.007-0.02520.758-0.030-0.0300.0000.0000.0000.000
66B67GLY0-0.056-0.03223.1530.0080.0080.0000.0000.0000.000
67B68LYS10.7760.92223.247-0.105-0.1050.0000.0000.0000.000
68B69GLU-1-0.935-0.98526.2740.0190.0190.0000.0000.0000.000
69B70ALA0-0.002-0.01726.171-0.011-0.0110.0000.0000.0000.000
70B71TRP0-0.037-0.02018.9520.0140.0140.0000.0000.0000.000
71B72ASP-1-0.863-0.93220.9490.0160.0160.0000.0000.0000.000
72B73LEU0-0.019-0.01715.4000.0280.0280.0000.0000.0000.000
73B74GLY00.030-0.00314.667-0.039-0.0390.0000.0000.0000.000
74B75VAL0-0.0030.03710.8950.0380.0380.0000.0000.0000.000
75B76CYS0-0.051-0.03414.099-0.029-0.0290.0000.0000.0000.000
76B77ARG10.9811.01316.3430.0220.0220.0000.0000.0000.000
77B78ASP-1-0.820-0.92518.3150.1820.1820.0000.0000.0000.000
78B79SER0-0.0040.01519.667-0.003-0.0030.0000.0000.0000.000
79B80VAL0-0.079-0.01921.204-0.013-0.0130.0000.0000.0000.000
80B81ARG10.8840.94023.649-0.026-0.0260.0000.0000.0000.000
81B82ARG10.8470.90921.940-0.141-0.1410.0000.0000.0000.000
82B83LYS10.9150.95727.485-0.092-0.0920.0000.0000.0000.000
83B84GLY0-0.034-0.01931.205-0.007-0.0070.0000.0000.0000.000
84B85HIS00.0310.02730.8280.0040.0040.0000.0000.0000.000
85B86PHE0-0.082-0.05324.780-0.003-0.0030.0000.0000.0000.000
86B87LEU00.0320.01927.7840.0010.0010.0000.0000.0000.000
87B88LEU00.0530.03322.1670.0030.0030.0000.0000.0000.000
88B89SER00.0300.01523.748-0.016-0.0160.0000.0000.0000.000
89B90SER00.0980.04420.3430.0140.0140.0000.0000.0000.000
90B91LYS10.8930.95121.6680.0730.0730.0000.0000.0000.000
91B92SER0-0.061-0.04223.8290.0060.0060.0000.0000.0000.000
92B93GLY0-0.094-0.04820.6620.0140.0140.0000.0000.0000.000
93B94PHE00.0670.03119.0760.0200.0200.0000.0000.0000.000
94B95TRP00.0240.00515.206-0.003-0.0030.0000.0000.0000.000
95B96THR00.0350.01215.6080.0060.0060.0000.0000.0000.000
96B97ILE0-0.035-0.00916.793-0.020-0.0200.0000.0000.0000.000
97B98TRP0-0.0020.02119.4150.0200.0200.0000.0000.0000.000
98B99LEU0-0.0170.01121.896-0.017-0.0170.0000.0000.0000.000
99B100TRP0-0.044-0.03924.5360.0180.0180.0000.0000.0000.000
100B101ASN0-0.011-0.01228.120-0.003-0.0030.0000.0000.0000.000
101B102LYS11.0111.03329.132-0.018-0.0180.0000.0000.0000.000
102B103GLN0-0.043-0.03627.926-0.005-0.0050.0000.0000.0000.000
103B104LYS10.9330.97228.3030.0250.0250.0000.0000.0000.000
104B105TYR00.0530.02021.9280.0060.0060.0000.0000.0000.000
105B106GLU-1-0.883-0.93623.628-0.058-0.0580.0000.0000.0000.000
106B107ALA00.0580.01220.4020.0030.0030.0000.0000.0000.000
107B108GLY00.0290.00920.7600.0060.0060.0000.0000.0000.000
108B109THR0-0.0420.00322.144-0.002-0.0020.0000.0000.0000.000
109B110TYR0-0.049-0.01623.7630.0140.0140.0000.0000.0000.000
110B111PRO0-0.011-0.03527.263-0.005-0.0050.0000.0000.0000.000
111B112GLN00.0200.03126.217-0.005-0.0050.0000.0000.0000.000
112B113THR0-0.006-0.03123.789-0.006-0.0060.0000.0000.0000.000
113B114PRO0-0.0080.00624.7760.0010.0010.0000.0000.0000.000
114B115LEU00.0020.00520.276-0.017-0.0170.0000.0000.0000.000
115B116HIS0-0.042-0.02324.1780.0200.0200.0000.0000.0000.000
116B117LEU00.0050.00619.923-0.015-0.0150.0000.0000.0000.000
117B118GLN0-0.006-0.01123.7760.0240.0240.0000.0000.0000.000
118B119VAL00.0330.02421.9020.0140.0140.0000.0000.0000.000
119B120PRO0-0.029-0.01121.949-0.012-0.0120.0000.0000.0000.000
120B121PRO00.0070.01618.1800.0090.0090.0000.0000.0000.000
121B122CYS0-0.046-0.02519.6890.0100.0100.0000.0000.0000.000
122B123GLN00.0670.02414.767-0.009-0.0090.0000.0000.0000.000
123B124VAL0-0.020-0.00213.656-0.044-0.0440.0000.0000.0000.000
124B125GLY00.0400.0309.9410.0810.0810.0000.0000.0000.000
125B126ILE0-0.055-0.0199.402-0.078-0.0780.0000.0000.0000.000
126B127PHE0-0.007-0.0292.866-1.266-0.1590.297-0.392-1.0120.002
127B128LEU0-0.0050.0005.7910.0440.0440.0000.0000.0000.000
128B129ASP-1-0.862-0.9465.755-0.594-0.5940.0000.0000.0000.000
129B130TYR0-0.030-0.0367.852-0.157-0.1570.0000.0000.0000.000
130B131GLU-1-0.798-0.9298.482-0.069-0.0690.0000.0000.0000.000
131B132ALA0-0.0390.0069.786-0.037-0.0370.0000.0000.0000.000
132B133GLY0-0.0170.01311.6340.0060.0060.0000.0000.0000.000
133B134MET0-0.017-0.02310.847-0.035-0.0350.0000.0000.0000.000
134B135VAL0-0.008-0.00110.3970.0620.0620.0000.0000.0000.000
135B136SER0-0.0080.01010.0900.0010.0010.0000.0000.0000.000
136B137PHE00.0150.01010.7220.0200.0200.0000.0000.0000.000
137B138TYR0-0.015-0.0048.809-0.081-0.0810.0000.0000.0000.000
138B139ASN00.033-0.01512.8050.0920.0920.0000.0000.0000.000
139B140ILE00.011-0.00511.092-0.028-0.0280.0000.0000.0000.000
140B141THR00.0110.01114.7020.0150.0150.0000.0000.0000.000
141B142ASP-1-0.870-0.90217.714-0.155-0.1550.0000.0000.0000.000
142B143HIS00.009-0.00116.237-0.031-0.0310.0000.0000.0000.000
143B144GLY00.0150.02512.832-0.047-0.0470.0000.0000.0000.000
144B145SER0-0.069-0.05013.123-0.105-0.1050.0000.0000.0000.000
145B146LEU0-0.044-0.02512.5090.0160.0160.0000.0000.0000.000
146B147ILE0-0.057-0.02314.9930.0420.0420.0000.0000.0000.000
147B148TYR00.021-0.02515.6610.0170.0170.0000.0000.0000.000
148B149SER0-0.007-0.00612.865-0.017-0.0170.0000.0000.0000.000
149B150PHE0-0.0270.00714.9480.0260.0260.0000.0000.0000.000
150B151SER00.007-0.02814.724-0.044-0.0440.0000.0000.0000.000
151B152GLU-1-0.902-0.95516.328-0.204-0.2040.0000.0000.0000.000
152B153CYS0-0.052-0.00415.4900.0370.0370.0000.0000.0000.000
153B154ALA0-0.050-0.00717.5290.0420.0420.0000.0000.0000.000
154B155PHE0-0.043-0.03312.2410.0070.0070.0000.0000.0000.000
155B156THR0-0.006-0.00116.882-0.005-0.0050.0000.0000.0000.000
156B157GLY00.0230.01318.6090.0140.0140.0000.0000.0000.000
157B158PRO00.0200.01815.6230.0070.0070.0000.0000.0000.000
158B159LEU0-0.041-0.00311.785-0.035-0.0350.0000.0000.0000.000
159B160ARG10.8680.94213.628-0.209-0.2090.0000.0000.0000.000
160B161PRO0-0.0190.00711.768-0.049-0.0490.0000.0000.0000.000
161B162PHE0-0.002-0.01513.7250.0090.0090.0000.0000.0000.000
162B163PHE00.041-0.00413.632-0.005-0.0050.0000.0000.0000.000
163B164SER00.001-0.01218.778-0.002-0.0020.0000.0000.0000.000
164B165PRO0-0.024-0.01622.211-0.011-0.0110.0000.0000.0000.000
165B166GLY00.0980.06123.993-0.006-0.0060.0000.0000.0000.000
166B167PHE00.0710.03826.5410.0090.0090.0000.0000.0000.000
167B168ASN00.0080.01230.1120.0000.0000.0000.0000.0000.000
168B169ASP-1-0.876-0.93932.5230.0320.0320.0000.0000.0000.000
169B170GLY0-0.010-0.00633.9030.0000.0000.0000.0000.0000.000
170B171GLY0-0.031-0.02035.5770.0000.0000.0000.0000.0000.000
171B172LYS10.9070.94633.137-0.034-0.0340.0000.0000.0000.000
172B173ASN0-0.004-0.02027.2790.0010.0010.0000.0000.0000.000
173B174THR0-0.011-0.00529.1880.0060.0060.0000.0000.0000.000
174B175ALA00.0130.02326.2550.0100.0100.0000.0000.0000.000
175B176PRO0-0.029-0.02823.650-0.008-0.0080.0000.0000.0000.000
176B177LEU0-0.0040.02119.043-0.005-0.0050.0000.0000.0000.000
177B178THR00.019-0.01118.0920.0040.0040.0000.0000.0000.000
178B179LEU0-0.033-0.00912.855-0.013-0.0130.0000.0000.0000.000
179B180CYS0-0.0180.00412.4680.0030.0030.0000.0000.0000.000
180B181PRO00.000-0.02312.1740.0910.0910.0000.0000.0000.000
181B182LEU0-0.0050.0166.6510.3230.3230.0000.0000.0000.000