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: L7JM9

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 OptAll
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 -2045800.522287
FMO2-HF: Nuclear repulsion 1973421.10007
FMO2-HF: Total energy -72379.422217
FMO2-MP2: Total energy -72590.356214


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.
-7.3160.382.41-2.934-7.1720.014
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 : 0.051 / q_NPA : 0.005
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].
3B4VAL0-0.023-0.0093.866-1.472-0.343-0.007-0.499-0.6240.002
4B5HIS00.0160.0096.6060.1430.1430.0000.0000.0000.000
5B6ILE0-0.027-0.0159.195-0.021-0.0210.0000.0000.0000.000
6B7THR00.0390.01912.1380.0060.0060.0000.0000.0000.000
7B8LEU0-0.044-0.01215.9770.0050.0050.0000.0000.0000.000
8B9ASP-1-0.807-0.89718.6740.2190.2190.0000.0000.0000.000
9B10PRO0-0.009-0.02820.458-0.013-0.0130.0000.0000.0000.000
10B11ASP-1-0.844-0.90523.8610.1400.1400.0000.0000.0000.000
11B12THR0-0.027-0.01021.015-0.006-0.0060.0000.0000.0000.000
12B13ALA0-0.013-0.00124.012-0.009-0.0090.0000.0000.0000.000
13B14ASN00.0400.02825.054-0.010-0.0100.0000.0000.0000.000
14B15PRO00.0300.01028.1230.0030.0030.0000.0000.0000.000
15B16TRP0-0.0250.00130.940-0.004-0.0040.0000.0000.0000.000
16B17LEU0-0.066-0.02224.3630.0000.0000.0000.0000.0000.000
17B18ILE0-0.007-0.00627.658-0.002-0.0020.0000.0000.0000.000
18B19LEU0-0.008-0.00622.6640.0040.0040.0000.0000.0000.000
19B20SER0-0.009-0.02522.060-0.008-0.0080.0000.0000.0000.000
20B21GLU-1-0.875-0.93723.7820.1630.1630.0000.0000.0000.000
21B22ASP-1-0.842-0.89920.2780.2400.2400.0000.0000.0000.000
22B23ARG10.8450.91519.597-0.161-0.1610.0000.0000.0000.000
23B24ARG10.8260.91812.037-0.400-0.4000.0000.0000.0000.000
24B25GLN00.0270.02318.1930.0090.0090.0000.0000.0000.000
25B26VAL00.0000.00220.659-0.006-0.0060.0000.0000.0000.000
26B27ARG10.8760.95423.259-0.109-0.1090.0000.0000.0000.000
27B28LEU00.0000.00726.3640.0010.0010.0000.0000.0000.000
28B29GLY0-0.018-0.01328.976-0.002-0.0020.0000.0000.0000.000
29B30ASP-1-0.883-0.94432.0660.0850.0850.0000.0000.0000.000
30B31THR0-0.022-0.01935.096-0.005-0.0050.0000.0000.0000.000
31B32GLN0-0.028-0.00334.5120.0050.0050.0000.0000.0000.000
32B33GLN00.0310.01431.701-0.008-0.0080.0000.0000.0000.000
33B34SER0-0.032-0.01834.4660.0010.0010.0000.0000.0000.000
34B35ILE00.0010.00530.0710.0020.0020.0000.0000.0000.000
35B36PRO00.0070.00431.568-0.005-0.0050.0000.0000.0000.000
36B37GLY00.0200.00332.3510.0040.0040.0000.0000.0000.000
37B38ASN0-0.066-0.03627.638-0.010-0.0100.0000.0000.0000.000
38B39GLU-1-0.889-0.96629.4850.1140.1140.0000.0000.0000.000
39B40GLU-1-0.842-0.92424.4110.1520.1520.0000.0000.0000.000
40B41ARG10.7820.88825.169-0.131-0.1310.0000.0000.0000.000
41B42PHE00.0130.00821.856-0.009-0.0090.0000.0000.0000.000
42B43ASP-1-0.817-0.89327.5030.0960.0960.0000.0000.0000.000
43B44SER0-0.021-0.03230.755-0.005-0.0050.0000.0000.0000.000
44B45TYR0-0.017-0.03227.240-0.008-0.0080.0000.0000.0000.000
45B46PRO00.0080.02626.8430.0060.0060.0000.0000.0000.000
46B47MET0-0.014-0.00822.9680.0080.0080.0000.0000.0000.000
47B48VAL00.002-0.00720.086-0.004-0.0040.0000.0000.0000.000
48B49LEU00.0210.02017.5930.0050.0050.0000.0000.0000.000
49B50GLY00.0250.01414.608-0.004-0.0040.0000.0000.0000.000
50B51ALA00.0190.00615.6900.0010.0010.0000.0000.0000.000
51B52GLN00.0110.00810.989-0.012-0.0120.0000.0000.0000.000
52B53HIS0-0.001-0.00213.211-0.048-0.0480.0000.0000.0000.000
53B54PHE0-0.043-0.0308.4410.1000.1000.0000.0000.0000.000
54B55HIS00.027-0.00711.672-0.094-0.0940.0000.0000.0000.000
55B56SER00.0440.03410.782-0.055-0.0550.0000.0000.0000.000
56B57GLY00.0020.0016.9720.1240.1240.0000.0000.0000.000
57B58LYS10.7910.8812.768-3.574-1.4141.345-1.036-2.4680.013
58B59HIS10.7980.8862.965-1.660-0.1010.204-0.465-1.298-0.003
59B60TYR0-0.026-0.0362.986-1.0270.2590.207-0.315-1.178-0.001
60B61TRP00.007-0.0064.484-0.072-0.045-0.001-0.015-0.0110.000
61B62GLU-1-0.797-0.8867.8970.6460.6460.0000.0000.0000.000
62B63VAL0-0.046-0.02410.9710.0030.0030.0000.0000.0000.000
63B64ASP-1-0.774-0.85014.7360.1770.1770.0000.0000.0000.000
64B65VAL0-0.013-0.02017.625-0.004-0.0040.0000.0000.0000.000
65B66THR00.002-0.03520.530-0.024-0.0240.0000.0000.0000.000
66B67GLY0-0.058-0.02322.916-0.001-0.0010.0000.0000.0000.000
67B68LYS10.7170.86423.080-0.127-0.1270.0000.0000.0000.000
68B69GLU-1-0.816-0.90725.8630.0530.0530.0000.0000.0000.000
69B70ALA0-0.026-0.02926.201-0.008-0.0080.0000.0000.0000.000
70B71TRP00.0220.01619.0810.0090.0090.0000.0000.0000.000
71B72ASP-1-0.824-0.89421.0640.1050.1050.0000.0000.0000.000
72B73LEU0-0.006-0.00515.6080.0180.0180.0000.0000.0000.000
73B74GLY00.025-0.00413.792-0.022-0.0220.0000.0000.0000.000
74B75VAL0-0.0100.01110.8420.0320.0320.0000.0000.0000.000
75B76CYS0-0.058-0.02214.172-0.036-0.0360.0000.0000.0000.000
76B77ARG10.9290.97416.034-0.109-0.1090.0000.0000.0000.000
77B78ASP-1-0.809-0.90418.2180.2250.2250.0000.0000.0000.000
78B79SER0-0.017-0.00419.534-0.012-0.0120.0000.0000.0000.000
79B80VAL0-0.052-0.00120.947-0.018-0.0180.0000.0000.0000.000
80B81ARG10.8140.86623.457-0.091-0.0910.0000.0000.0000.000
81B82ARG10.8370.92121.696-0.194-0.1940.0000.0000.0000.000
82B83LYS10.8650.95926.947-0.117-0.1170.0000.0000.0000.000
83B84GLY00.0340.02130.761-0.003-0.0030.0000.0000.0000.000
84B85HIS0-0.006-0.00630.5480.0020.0020.0000.0000.0000.000
85B86PHE0-0.029-0.00124.619-0.002-0.0020.0000.0000.0000.000
86B87LEU00.0210.01927.380-0.002-0.0020.0000.0000.0000.000
87B88LEU00.0210.02121.5960.0050.0050.0000.0000.0000.000
88B89SER00.0370.00923.136-0.009-0.0090.0000.0000.0000.000
89B90SER00.0680.03819.9890.0080.0080.0000.0000.0000.000
90B91LYS10.9150.96321.063-0.036-0.0360.0000.0000.0000.000
91B92SER0-0.002-0.00424.2120.0010.0010.0000.0000.0000.000
92B93GLY0-0.057-0.02020.5020.0050.0050.0000.0000.0000.000
93B94PHE00.0210.00618.7160.0240.0240.0000.0000.0000.000
94B95TRP00.012-0.00415.155-0.007-0.0070.0000.0000.0000.000
95B96THR00.0340.01115.3850.0250.0250.0000.0000.0000.000
96B97ILE0-0.015-0.00516.361-0.024-0.0240.0000.0000.0000.000
97B98TRP0-0.030-0.01319.0330.0210.0210.0000.0000.0000.000
98B99LEU0-0.0200.00521.856-0.013-0.0130.0000.0000.0000.000
99B100TRP00.009-0.01924.4050.0050.0050.0000.0000.0000.000
100B101ASN0-0.063-0.05028.111-0.006-0.0060.0000.0000.0000.000
101B102LYS10.9320.98029.016-0.056-0.0560.0000.0000.0000.000
102B103GLN0-0.013-0.01727.369-0.005-0.0050.0000.0000.0000.000
103B104LYS10.9250.98527.636-0.037-0.0370.0000.0000.0000.000
104B105TYR00.0720.03421.8820.0050.0050.0000.0000.0000.000
105B106GLU-1-0.838-0.89223.2770.0310.0310.0000.0000.0000.000
106B107ALA00.0320.01820.1480.0120.0120.0000.0000.0000.000
107B108GLY00.0500.02620.459-0.007-0.0070.0000.0000.0000.000
108B109THR0-0.048-0.04221.7310.0110.0110.0000.0000.0000.000
109B110TYR0-0.046-0.02123.4450.0040.0040.0000.0000.0000.000
110B111PRO0-0.008-0.02726.935-0.002-0.0020.0000.0000.0000.000
111B112GLN0-0.015-0.00525.716-0.001-0.0010.0000.0000.0000.000
112B113THR0-0.030-0.01023.692-0.010-0.0100.0000.0000.0000.000
113B114PRO00.0130.00524.4800.0050.0050.0000.0000.0000.000
114B115LEU0-0.0060.00519.602-0.009-0.0090.0000.0000.0000.000
115B116HIS0-0.006-0.00623.9430.0080.0080.0000.0000.0000.000
116B117LEU0-0.0090.00019.492-0.010-0.0100.0000.0000.0000.000
117B118GLN0-0.015-0.01523.2480.0090.0090.0000.0000.0000.000
118B119VAL00.0180.02921.7290.0030.0030.0000.0000.0000.000
119B120PRO00.002-0.00821.7940.0040.0040.0000.0000.0000.000
120B121PRO0-0.0150.01518.1900.0050.0050.0000.0000.0000.000
121B122CYS0-0.028-0.01419.8420.0000.0000.0000.0000.0000.000
122B123GLN0-0.016-0.03114.8370.0050.0050.0000.0000.0000.000
123B124VAL0-0.0070.00413.656-0.027-0.0270.0000.0000.0000.000
124B125GLY00.0310.0169.9840.0550.0550.0000.0000.0000.000
125B126ILE0-0.046-0.0288.953-0.078-0.0780.0000.0000.0000.000
126B127PHE00.000-0.0032.682-1.585-0.0500.662-0.604-1.5930.003
127B128LEU0-0.0020.0105.862-0.094-0.0940.0000.0000.0000.000
128B129ASP-1-0.794-0.9065.6221.1031.1030.0000.0000.0000.000
129B130TYR0-0.009-0.0097.767-0.321-0.3210.0000.0000.0000.000
130B131GLU-1-0.793-0.9058.4110.9060.9060.0000.0000.0000.000
131B132ALA0-0.0260.00110.151-0.154-0.1540.0000.0000.0000.000
132B133GLY00.0100.02511.801-0.069-0.0690.0000.0000.0000.000
133B134MET0-0.037-0.02611.016-0.093-0.0930.0000.0000.0000.000
134B135VAL0-0.017-0.01610.0340.1500.1500.0000.0000.0000.000
135B136SER0-0.028-0.0119.968-0.066-0.0660.0000.0000.0000.000
136B137PHE0-0.0070.00110.4350.0660.0660.0000.0000.0000.000
137B138TYR00.0100.0018.741-0.096-0.0960.0000.0000.0000.000
138B139ASN00.0470.00112.6380.0800.0800.0000.0000.0000.000
139B140ILE00.0050.00710.533-0.038-0.0380.0000.0000.0000.000
140B141THR0-0.020-0.00114.438-0.006-0.0060.0000.0000.0000.000
141B142ASP-1-0.872-0.90917.278-0.049-0.0490.0000.0000.0000.000
142B143HIS0-0.015-0.01316.141-0.024-0.0240.0000.0000.0000.000
143B144GLY00.0180.02312.551-0.019-0.0190.0000.0000.0000.000
144B145SER0-0.076-0.06412.854-0.056-0.0560.0000.0000.0000.000
145B146LEU0-0.016-0.01712.6850.0350.0350.0000.0000.0000.000
146B147ILE0-0.030-0.00314.9150.0060.0060.0000.0000.0000.000
147B148TYR00.022-0.01515.424-0.002-0.0020.0000.0000.0000.000
148B149SER00.012-0.00114.1230.0010.0010.0000.0000.0000.000
149B150PHE0-0.0300.00514.621-0.013-0.0130.0000.0000.0000.000
150B151SER0-0.013-0.04614.3150.0100.0100.0000.0000.0000.000
151B152GLU-1-0.847-0.90616.316-0.034-0.0340.0000.0000.0000.000
152B153CYS0-0.092-0.03115.2230.0070.0070.0000.0000.0000.000
153B154ALA0-0.036-0.01717.3230.0190.0190.0000.0000.0000.000
154B155PHE0-0.041-0.02211.7730.0250.0250.0000.0000.0000.000
155B156THR00.007-0.00116.666-0.008-0.0080.0000.0000.0000.000
156B157GLY00.0310.01917.430-0.020-0.0200.0000.0000.0000.000
157B158PRO0-0.0060.02215.8400.0450.0450.0000.0000.0000.000
158B159LEU0-0.0210.00411.920-0.044-0.0440.0000.0000.0000.000
159B160ARG10.8000.86613.935-0.251-0.2510.0000.0000.0000.000
160B161PRO00.0000.00711.104-0.015-0.0150.0000.0000.0000.000
161B162PHE00.003-0.00713.367-0.017-0.0170.0000.0000.0000.000
162B163PHE00.015-0.01213.3260.0050.0050.0000.0000.0000.000
163B164SER00.036-0.00718.655-0.008-0.0080.0000.0000.0000.000
164B165PRO0-0.0150.00522.178-0.001-0.0010.0000.0000.0000.000
165B166GLY00.0710.04023.890-0.008-0.0080.0000.0000.0000.000
166B167PHE00.0380.01226.4220.0020.0020.0000.0000.0000.000
167B168ASN00.002-0.00729.9150.0030.0030.0000.0000.0000.000
168B169ASP-1-0.854-0.92332.5410.0630.0630.0000.0000.0000.000
169B170GLY0-0.026-0.01533.5520.0010.0010.0000.0000.0000.000
170B171GLY0-0.029-0.01635.384-0.002-0.0020.0000.0000.0000.000
171B172LYS10.8120.89133.117-0.058-0.0580.0000.0000.0000.000
172B173ASN00.0500.02726.8690.0020.0020.0000.0000.0000.000
173B174THR0-0.001-0.00328.6230.0080.0080.0000.0000.0000.000
174B175ALA00.0210.02725.9750.0050.0050.0000.0000.0000.000
175B176PRO0-0.016-0.01423.155-0.003-0.0030.0000.0000.0000.000
176B177LEU00.0020.02418.953-0.002-0.0020.0000.0000.0000.000
177B178THR00.009-0.02718.339-0.004-0.0040.0000.0000.0000.000
178B179LEU0-0.0270.00212.9330.0130.0130.0000.0000.0000.000
179B180CYS00.0190.02212.362-0.018-0.0180.0000.0000.0000.000
180B181PRO00.012-0.00312.5360.0560.0560.0000.0000.0000.000
181B182LEU0-0.050-0.0077.5080.1550.1550.0000.0000.0000.000