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: 167VZ

Calculation Name: 5DUR-L-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5DUR

Chain ID: L

ChEMBL ID:

UniProt ID: Q1WDM0

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1944541.516228
FMO2-HF: Nuclear repulsion 1866853.398796
FMO2-HF: Total energy -77688.117432
FMO2-MP2: Total energy -77916.108797


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(L:3:ALA)


Summations of interaction energy for fragment #1(L:3:ALA)
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.
-1.6641.9192.225-2.644-3.163-0.001
Interaction energy analysis for fragmet #1(L:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.017
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].
3L5THR0-0.008-0.0053.709-0.5241.709-0.005-1.229-0.9990.004
4L6GLN00.028-0.0166.0200.0290.0290.0000.0000.0000.000
5L7PRO0-0.0080.0189.2300.0660.0660.0000.0000.0000.000
6L8PRO00.0870.04711.2150.0280.0280.0000.0000.0000.000
7L9SER0-0.0040.00412.7140.0530.0530.0000.0000.0000.000
8L10VAL0-0.038-0.01516.166-0.028-0.0280.0000.0000.0000.000
9L11SER0-0.035-0.02418.6280.0300.0300.0000.0000.0000.000
10L12GLY00.0270.01622.436-0.015-0.0150.0000.0000.0000.000
11L13ALA00.0170.01525.7320.0110.0110.0000.0000.0000.000
12L14PRO00.0230.00128.561-0.008-0.0080.0000.0000.0000.000
13L15GLY0-0.008-0.00830.4100.0010.0010.0000.0000.0000.000
14L16GLN0-0.0120.00726.0890.0060.0060.0000.0000.0000.000
15L17ARG10.9140.94922.0800.2440.2440.0000.0000.0000.000
16L18VAL00.0140.01121.2320.0010.0010.0000.0000.0000.000
17L19THR00.000-0.01517.7430.0200.0200.0000.0000.0000.000
18L20ILE0-0.0030.01113.1810.0090.0090.0000.0000.0000.000
19L21PRO0-0.0010.00113.539-0.024-0.0240.0000.0000.0000.000
20L22CYS0-0.049-0.0198.103-0.120-0.1200.0000.0000.0000.000
21L23THR0-0.016-0.0088.2370.2590.2590.0000.0000.0000.000
22L24GLY00.0600.0255.952-0.730-0.7300.0000.0000.0000.000
23L25GLY00.015-0.0096.6500.4450.4450.0000.0000.0000.000
24L26SER00.000-0.0137.8860.0180.0180.0000.0000.0000.000
25L27SER00.0050.0025.6350.0940.0940.0000.0000.0000.000
26L28ASN00.0410.0064.0380.3010.4080.000-0.038-0.0690.000
27L29ILE00.0120.0017.1990.3420.3420.0000.0000.0000.000
28L30GLY0-0.026-0.0189.3610.2330.2330.0000.0000.0000.000
29L31ALA0-0.0290.00510.4130.1230.1230.0000.0000.0000.000
30L32GLY00.0120.00712.0900.1130.1130.0000.0000.0000.000
31L33TYR0-0.024-0.0029.5290.0860.0860.0000.0000.0000.000
32L34SER00.0370.02112.418-0.085-0.0850.0000.0000.0000.000
33L35VAL0-0.0110.00610.126-0.104-0.1040.0000.0000.0000.000
34L36HIS0-0.045-0.00511.6770.0530.0530.0000.0000.0000.000
35L37TRP00.0250.00011.794-0.100-0.1000.0000.0000.0000.000
36L38TYR0-0.012-0.02012.1240.0790.0790.0000.0000.0000.000
37L39GLN00.0360.01014.916-0.028-0.0280.0000.0000.0000.000
38L40GLN00.0370.02115.6550.0220.0220.0000.0000.0000.000
39L41LEU00.0520.02818.329-0.013-0.0130.0000.0000.0000.000
40L42PRO00.0370.00620.8950.0160.0160.0000.0000.0000.000
41L43GLY00.0150.03421.7170.0110.0110.0000.0000.0000.000
42L44THR0-0.077-0.04221.7720.0020.0020.0000.0000.0000.000
43L45ALA00.0540.02618.9360.0100.0100.0000.0000.0000.000
44L46PRO0-0.033-0.02114.533-0.025-0.0250.0000.0000.0000.000
45L47LYS10.9150.97617.1660.0730.0730.0000.0000.0000.000
46L48LEU0-0.016-0.00816.038-0.021-0.0210.0000.0000.0000.000
47L49LEU0-0.068-0.02917.1550.0060.0060.0000.0000.0000.000
48L50ILE00.006-0.00517.1020.0010.0010.0000.0000.0000.000
49L51TYR00.0230.00116.245-0.019-0.0190.0000.0000.0000.000
50L52GLY00.0230.01216.8670.0020.0020.0000.0000.0000.000
51L53SER0-0.001-0.00616.882-0.049-0.0490.0000.0000.0000.000
52L54ASN00.007-0.00418.8320.0180.0180.0000.0000.0000.000
53L55SER00.0080.02920.4270.0260.0260.0000.0000.0000.000
54L56ARG10.8510.90320.7420.1130.1130.0000.0000.0000.000
55L57PRO00.0090.02221.1980.0100.0100.0000.0000.0000.000
56L58SER00.017-0.00624.157-0.007-0.0070.0000.0000.0000.000
57L59GLY00.0490.02426.6630.0070.0070.0000.0000.0000.000
58L60VAL0-0.074-0.02822.030-0.001-0.0010.0000.0000.0000.000
59L61PRO0-0.005-0.00625.192-0.005-0.0050.0000.0000.0000.000
60L62ASP-1-0.772-0.89325.904-0.109-0.1090.0000.0000.0000.000
61L63ARG10.6860.83225.9710.1040.1040.0000.0000.0000.000
62L64PHE0-0.0100.00121.349-0.009-0.0090.0000.0000.0000.000
63L65SER00.0430.01521.6190.0150.0150.0000.0000.0000.000
64L66GLY00.005-0.00717.839-0.021-0.0210.0000.0000.0000.000
65L67SER0-0.071-0.03817.1310.0280.0280.0000.0000.0000.000
66L68LYS10.8520.90212.6740.5660.5660.0000.0000.0000.000
67L69SER00.0020.00815.4300.0730.0730.0000.0000.0000.000
68L70GLY00.0670.04815.302-0.064-0.0640.0000.0000.0000.000
69L71THR00.0060.00110.4430.0400.0400.0000.0000.0000.000
70L72SER0-0.047-0.02410.361-0.267-0.2670.0000.0000.0000.000
71L73ALA00.0500.01311.8440.1160.1160.0000.0000.0000.000
72L74SER0-0.003-0.00613.648-0.024-0.0240.0000.0000.0000.000
73L75LEU0-0.0040.03515.2480.0500.0500.0000.0000.0000.000
74L76ALA0-0.046-0.02416.857-0.007-0.0070.0000.0000.0000.000
75L77ILE00.0340.02519.8020.0170.0170.0000.0000.0000.000
76L78THR0-0.012-0.01123.0110.0020.0020.0000.0000.0000.000
77L79GLY00.0710.03526.7700.0080.0080.0000.0000.0000.000
78L80LEU0-0.076-0.02623.7000.0070.0070.0000.0000.0000.000
79L81ARG10.9940.99327.2740.0860.0860.0000.0000.0000.000
80L82PRO00.0630.02527.143-0.006-0.0060.0000.0000.0000.000
81L83GLU-1-0.863-0.93726.774-0.041-0.0410.0000.0000.0000.000
82L84ASP-1-0.759-0.83323.338-0.106-0.1060.0000.0000.0000.000
83L85GLU-1-0.744-0.82722.103-0.085-0.0850.0000.0000.0000.000
84L86ALA0-0.034-0.01419.6840.0180.0180.0000.0000.0000.000
85L87ASP-1-0.779-0.86015.005-0.073-0.0730.0000.0000.0000.000
86L88TYR0-0.045-0.04614.5630.0240.0240.0000.0000.0000.000
87L89TYR0-0.005-0.0029.573-0.052-0.0520.0000.0000.0000.000
88L91GLN00.0440.0257.590-0.026-0.0260.0000.0000.0000.000
89L92SER0-0.017-0.0336.804-0.114-0.1140.0000.0000.0000.000
90L93TYR0-0.0180.0027.7360.2220.2220.0000.0000.0000.000
91L94ASP-1-0.766-0.8384.278-1.639-1.595-0.001-0.011-0.0320.000
92L95SER00.003-0.0056.4110.3460.3460.0000.0000.0000.000
93L96SER0-0.048-0.0436.8490.0090.0090.0000.0000.0000.000
94L97LEU0-0.010-0.0069.0680.1650.1650.0000.0000.0000.000
95L98SER0-0.039-0.01211.8950.0510.0510.0000.0000.0000.000
96L99GLY00.0320.0229.171-0.123-0.1230.0000.0000.0000.000
97L100SER0-0.030-0.0256.3890.1270.1270.0000.0000.0000.000
98L101GLN00.0030.0047.323-0.379-0.3790.0000.0000.0000.000
99L102VAL0-0.0020.0112.2790.0280.2042.147-0.862-1.461-0.001
100L103PHE00.0370.0043.683-0.998-0.8450.001-0.041-0.1120.000
101L104GLY00.0180.0133.211-1.396-0.5260.083-0.463-0.490-0.004
102L105ALA0-0.026-0.0245.5290.4460.4460.0000.0000.0000.000
103L106GLY00.0150.0216.7160.1390.1390.0000.0000.0000.000
104L107THR0-0.079-0.05210.287-0.087-0.0870.0000.0000.0000.000
105L108ARG10.7840.86313.3050.0890.0890.0000.0000.0000.000
106L109VAL0-0.027-0.01016.775-0.028-0.0280.0000.0000.0000.000
107L110THR0-0.020-0.01319.6280.0280.0280.0000.0000.0000.000
108L111VAL0-0.029-0.03122.789-0.012-0.0120.0000.0000.0000.000
109L112LEU00.0350.00425.1690.0110.0110.0000.0000.0000.000
110L113GLY0-0.042-0.00628.6140.0050.0050.0000.0000.0000.000
111L114GLN0-0.080-0.06027.7150.0110.0110.0000.0000.0000.000
112L115PRO00.0110.01332.655-0.001-0.0010.0000.0000.0000.000
113L116LYS10.8790.93834.8600.0250.0250.0000.0000.0000.000
114L117ALA0-0.024-0.00335.3290.0020.0020.0000.0000.0000.000
115L118ASN00.012-0.01036.309-0.001-0.0010.0000.0000.0000.000
116L119PRO00.0210.01236.1960.0000.0000.0000.0000.0000.000
117L120THR0-0.0010.02038.1090.0000.0000.0000.0000.0000.000
118L121VAL00.000-0.00538.9910.0020.0020.0000.0000.0000.000
119L122THR0-0.024-0.00940.847-0.002-0.0020.0000.0000.0000.000
120L123LEU0-0.027-0.01341.5230.0010.0010.0000.0000.0000.000
121L124PHE0-0.0030.00541.764-0.001-0.0010.0000.0000.0000.000
122L125PRO00.0050.00545.2310.0010.0010.0000.0000.0000.000
123L126PRO00.0250.03546.3840.0010.0010.0000.0000.0000.000
124L127SER00.0470.01847.264-0.002-0.0020.0000.0000.0000.000
125L128SER00.020-0.01149.1200.0000.0000.0000.0000.0000.000
126L129GLU-1-0.926-0.95647.9250.0400.0400.0000.0000.0000.000
127L130GLU-1-0.779-0.87844.1760.0410.0410.0000.0000.0000.000
128L131LEU0-0.019-0.01848.1610.0000.0000.0000.0000.0000.000
129L132GLN0-0.063-0.02551.162-0.001-0.0010.0000.0000.0000.000
130L133ALA0-0.0180.00248.0460.0000.0000.0000.0000.0000.000
131L134ASN0-0.084-0.04448.8390.0010.0010.0000.0000.0000.000
132L135LYS10.9120.95044.175-0.045-0.0450.0000.0000.0000.000
133L136ALA00.031-0.00245.786-0.002-0.0020.0000.0000.0000.000
134L137THR0-0.024-0.02240.1010.0010.0010.0000.0000.0000.000
135L138LEU0-0.051-0.00443.081-0.001-0.0010.0000.0000.0000.000
136L139VAL00.0320.01638.8610.0020.0020.0000.0000.0000.000
137L140CYS0-0.079-0.02339.030-0.003-0.0030.0000.0000.0000.000
138L141LEU00.0270.01236.3280.0020.0020.0000.0000.0000.000
139L142ILE00.0010.00134.881-0.004-0.0040.0000.0000.0000.000
140L143SER00.0580.00834.4960.0020.0020.0000.0000.0000.000
141L144ASP-1-0.758-0.85734.328-0.008-0.0080.0000.0000.0000.000
142L145PHE0-0.0170.00930.806-0.004-0.0040.0000.0000.0000.000
143L146TYR00.0460.01427.9590.0000.0000.0000.0000.0000.000
144L147PRO00.0780.03429.2800.0010.0010.0000.0000.0000.000
145L148GLY00.0220.00127.8000.0050.0050.0000.0000.0000.000
146L149ALA0-0.018-0.00527.9690.0040.0040.0000.0000.0000.000
147L150VAL0-0.019-0.02130.145-0.001-0.0010.0000.0000.0000.000
148L151THR00.0060.01532.1260.0010.0010.0000.0000.0000.000
149L152VAL0-0.001-0.00634.750-0.002-0.0020.0000.0000.0000.000
150L153ALA0-0.020-0.01237.1550.0010.0010.0000.0000.0000.000
151L154TRP00.0480.00738.283-0.002-0.0020.0000.0000.0000.000
152L155LYS10.8010.89942.381-0.009-0.0090.0000.0000.0000.000
153L156ALA00.0870.04946.1270.0010.0010.0000.0000.0000.000
154L157ASP-1-0.757-0.85049.1490.0120.0120.0000.0000.0000.000
155L158GLY0-0.0120.00649.861-0.001-0.0010.0000.0000.0000.000
156L159SER0-0.044-0.02349.148-0.001-0.0010.0000.0000.0000.000
157L160PRO0-0.016-0.02844.1530.0010.0010.0000.0000.0000.000
158L161VAL00.0380.03142.9990.0010.0010.0000.0000.0000.000
159L162LYS10.9160.94240.666-0.014-0.0140.0000.0000.0000.000
160L163ALA00.0260.01839.5630.0020.0020.0000.0000.0000.000
161L164GLY00.0480.01939.442-0.002-0.0020.0000.0000.0000.000
162L165VAL0-0.038-0.01135.8350.0010.0010.0000.0000.0000.000
163L166GLU-1-0.855-0.91031.9430.0620.0620.0000.0000.0000.000
164L167THR0-0.063-0.04531.591-0.007-0.0070.0000.0000.0000.000
165L168THR00.0190.03128.5300.0020.0020.0000.0000.0000.000
166L169THR00.0380.01424.198-0.004-0.0040.0000.0000.0000.000
167L170PRO0-0.048-0.03126.8750.0040.0040.0000.0000.0000.000
168L171SER0-0.0080.00825.1010.0020.0020.0000.0000.0000.000
169L172LYS10.7400.84323.6540.0390.0390.0000.0000.0000.000
170L173GLN0-0.032-0.03926.0560.0110.0110.0000.0000.0000.000
171L174SER00.001-0.01027.744-0.006-0.0060.0000.0000.0000.000
172L175ASN00.0120.00329.116-0.003-0.0030.0000.0000.0000.000
173L176ASN00.0280.02326.500-0.003-0.0030.0000.0000.0000.000
174L177LYS10.8230.93128.7190.0080.0080.0000.0000.0000.000
175L178TYR00.0000.00724.393-0.001-0.0010.0000.0000.0000.000
176L179ALA0-0.0080.00029.695-0.001-0.0010.0000.0000.0000.000
177L180ALA0-0.011-0.01029.8260.0010.0010.0000.0000.0000.000
178L181SER0-0.0130.00131.7860.0000.0000.0000.0000.0000.000
179L182SER0-0.001-0.01233.2200.0010.0010.0000.0000.0000.000
180L183TYR00.0180.00133.625-0.001-0.0010.0000.0000.0000.000
181L184LEU0-0.003-0.00138.1250.0000.0000.0000.0000.0000.000
182L185SER0-0.0100.00339.4100.0000.0000.0000.0000.0000.000
183L186LEU0-0.036-0.02442.045-0.002-0.0020.0000.0000.0000.000
184L187THR00.013-0.00645.8460.0020.0020.0000.0000.0000.000
185L188PRO00.0240.00248.766-0.002-0.0020.0000.0000.0000.000
186L189GLU-1-0.915-0.95551.5280.0250.0250.0000.0000.0000.000
187L190GLN00.0780.06247.5500.0000.0000.0000.0000.0000.000
188L191TRP00.0170.01549.291-0.002-0.0020.0000.0000.0000.000
189L192LYS10.9220.94551.317-0.026-0.0260.0000.0000.0000.000
190L193SER0-0.008-0.00454.578-0.001-0.0010.0000.0000.0000.000
191L194HIS0-0.099-0.04351.8040.0000.0000.0000.0000.0000.000
192L195ARG10.8620.91554.501-0.009-0.0090.0000.0000.0000.000
193L196SER0-0.042-0.02752.0980.0000.0000.0000.0000.0000.000
194L197TYR00.003-0.01646.9070.0010.0010.0000.0000.0000.000
195L198SER0-0.026-0.02246.4770.0000.0000.0000.0000.0000.000
196L200GLN00.003-0.00242.559-0.002-0.0020.0000.0000.0000.000
197L201VAL00.014-0.00237.0290.0020.0020.0000.0000.0000.000
198L202THR0-0.030-0.01937.895-0.001-0.0010.0000.0000.0000.000
199L203HIS10.8840.92733.1800.0190.0190.0000.0000.0000.000
200L204GLU-1-0.907-0.95733.639-0.034-0.0340.0000.0000.0000.000
201L205GLY00.0230.01036.7550.0000.0000.0000.0000.0000.000
202L206SER0-0.028-0.00539.6690.0000.0000.0000.0000.0000.000
203L207THR00.0200.00740.3170.0000.0000.0000.0000.0000.000
204L208VAL0-0.0130.00841.972-0.001-0.0010.0000.0000.0000.000
205L209GLU-1-0.815-0.89143.2020.0070.0070.0000.0000.0000.000
206L210LYS10.8560.93943.913-0.008-0.0080.0000.0000.0000.000
207L211THR00.019-0.01346.3860.0000.0000.0000.0000.0000.000
208L212VAL0-0.011-0.00247.6410.0000.0000.0000.0000.0000.000
209L213ALA00.0450.00950.3220.0000.0000.0000.0000.0000.000
210L214PRO0-0.0150.02053.1320.0000.0000.0000.0000.0000.000