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: VK5Z1

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1944056.433745
FMO2-HF: Nuclear repulsion 1866368.800732
FMO2-HF: Total energy -77687.633013
FMO2-MP2: Total energy -77915.563263


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.
-1.1173.0570.324-1.985-2.5130.004
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 : 0.037 / q_NPA : 0.022
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].
3L5THR00.0140.0033.294-1.2761.5890.036-1.495-1.4070.006
4L6GLN00.010-0.0155.5010.0980.0980.0000.0000.0000.000
5L7PRO0-0.0130.0108.7180.0700.0700.0000.0000.0000.000
6L8PRO00.1090.06411.2520.0170.0170.0000.0000.0000.000
7L9SER0-0.0070.00012.4940.0390.0390.0000.0000.0000.000
8L10VAL0-0.026-0.00115.847-0.024-0.0240.0000.0000.0000.000
9L11SER00.000-0.00418.2940.0250.0250.0000.0000.0000.000
10L12GLY00.0150.01222.005-0.014-0.0140.0000.0000.0000.000
11L13ALA00.0080.01425.0630.0110.0110.0000.0000.0000.000
12L14PRO00.009-0.01028.541-0.007-0.0070.0000.0000.0000.000
13L15GLY00.0180.00529.4680.0030.0030.0000.0000.0000.000
14L16GLN00.0030.01626.1190.0050.0050.0000.0000.0000.000
15L17ARG10.9260.95122.0830.2240.2240.0000.0000.0000.000
16L18VAL00.0140.01820.594-0.002-0.0020.0000.0000.0000.000
17L19THR0-0.023-0.02617.5180.0090.0090.0000.0000.0000.000
18L20ILE00.0060.01512.7370.0030.0030.0000.0000.0000.000
19L21PRO00.0000.00612.758-0.016-0.0160.0000.0000.0000.000
20L22CYS0-0.038-0.0098.267-0.117-0.1170.0000.0000.0000.000
21L23THR0-0.002-0.0047.8340.1870.1870.0000.0000.0000.000
22L24GLY00.0410.0195.683-0.599-0.5990.0000.0000.0000.000
23L25GLY00.0220.0006.2870.4050.4050.0000.0000.0000.000
24L26SER0-0.010-0.0227.3670.0760.0760.0000.0000.0000.000
25L27SER00.0240.0115.7200.1210.1210.0000.0000.0000.000
26L28ASN00.0400.0003.8010.2770.4020.001-0.052-0.0740.000
27L29ILE0-0.010-0.0137.3140.3540.3540.0000.0000.0000.000
28L30GLY0-0.027-0.0199.2640.2190.2190.0000.0000.0000.000
29L31ALA0-0.042-0.00610.3400.1510.1510.0000.0000.0000.000
30L32GLY0-0.0040.00512.0740.1130.1130.0000.0000.0000.000
31L33TYR0-0.0080.0029.7460.1270.1270.0000.0000.0000.000
32L34SER0-0.013-0.00612.128-0.094-0.0940.0000.0000.0000.000
33L35VAL00.0050.01410.106-0.080-0.0800.0000.0000.0000.000
34L36HIS0-0.052-0.00511.6120.0470.0470.0000.0000.0000.000
35L37TRP00.0430.00811.864-0.076-0.0760.0000.0000.0000.000
36L38TYR0-0.025-0.03112.2510.0620.0620.0000.0000.0000.000
37L39GLN00.0320.01714.854-0.016-0.0160.0000.0000.0000.000
38L40GLN00.021-0.00615.8130.0280.0280.0000.0000.0000.000
39L41LEU00.0490.02418.091-0.010-0.0100.0000.0000.0000.000
40L42PRO00.029-0.00520.9480.0150.0150.0000.0000.0000.000
41L43GLY00.0090.02121.5700.0120.0120.0000.0000.0000.000
42L44THR0-0.062-0.01522.0690.0060.0060.0000.0000.0000.000
43L45ALA00.0290.01519.4170.0090.0090.0000.0000.0000.000
44L46PRO00.005-0.01015.089-0.022-0.0220.0000.0000.0000.000
45L47LYS10.9300.98117.7360.0560.0560.0000.0000.0000.000
46L48LEU0-0.026-0.01016.532-0.018-0.0180.0000.0000.0000.000
47L49LEU0-0.052-0.01717.4690.0030.0030.0000.0000.0000.000
48L50ILE00.011-0.00617.172-0.003-0.0030.0000.0000.0000.000
49L51TYR00.0120.01216.377-0.014-0.0140.0000.0000.0000.000
50L52GLY00.0410.01416.7890.0070.0070.0000.0000.0000.000
51L53SER0-0.002-0.01117.066-0.048-0.0480.0000.0000.0000.000
52L54ASN0-0.004-0.00618.8560.0220.0220.0000.0000.0000.000
53L55SER00.0030.01120.3920.0230.0230.0000.0000.0000.000
54L56ARG10.8440.92321.3190.1170.1170.0000.0000.0000.000
55L57PRO00.0210.02221.3070.0090.0090.0000.0000.0000.000
56L58SER00.0340.00324.290-0.005-0.0050.0000.0000.0000.000
57L59GLY00.0370.02027.0670.0070.0070.0000.0000.0000.000
58L60VAL0-0.080-0.02422.2180.0010.0010.0000.0000.0000.000
59L61PRO0-0.031-0.02025.354-0.003-0.0030.0000.0000.0000.000
60L62ASP-1-0.778-0.90225.843-0.104-0.1040.0000.0000.0000.000
61L63ARG10.6810.82525.7380.0950.0950.0000.0000.0000.000
62L64PHE0-0.0180.00520.816-0.010-0.0100.0000.0000.0000.000
63L65SER00.0640.02121.3220.0110.0110.0000.0000.0000.000
64L66GLY0-0.0090.00617.801-0.020-0.0200.0000.0000.0000.000
65L67SER0-0.063-0.03917.3970.0240.0240.0000.0000.0000.000
66L68LYS10.9240.93213.0800.5190.5190.0000.0000.0000.000
67L69SER0-0.033-0.00615.4450.0630.0630.0000.0000.0000.000
68L70GLY00.0770.04415.202-0.041-0.0410.0000.0000.0000.000
69L71THR00.0260.01210.0910.0310.0310.0000.0000.0000.000
70L72SER0-0.0240.00510.130-0.280-0.2800.0000.0000.0000.000
71L73ALA00.005-0.00511.6600.1500.1500.0000.0000.0000.000
72L74SER0-0.036-0.02413.312-0.014-0.0140.0000.0000.0000.000
73L75LEU00.0240.03715.4880.0390.0390.0000.0000.0000.000
74L76ALA0-0.061-0.04616.9370.0050.0050.0000.0000.0000.000
75L77ILE00.0350.01619.3960.0170.0170.0000.0000.0000.000
76L78THR00.0050.00422.7730.0070.0070.0000.0000.0000.000
77L79GLY00.0590.02626.4130.0070.0070.0000.0000.0000.000
78L80LEU0-0.065-0.02323.1020.0070.0070.0000.0000.0000.000
79L81ARG11.0181.00326.9750.0770.0770.0000.0000.0000.000
80L82PRO00.0630.01626.954-0.004-0.0040.0000.0000.0000.000
81L83GLU-1-0.915-0.95726.880-0.028-0.0280.0000.0000.0000.000
82L84ASP-1-0.788-0.85423.207-0.092-0.0920.0000.0000.0000.000
83L85GLU-1-0.767-0.85422.051-0.062-0.0620.0000.0000.0000.000
84L86ALA0-0.041-0.01719.7590.0170.0170.0000.0000.0000.000
85L87ASP-1-0.781-0.85114.649-0.034-0.0340.0000.0000.0000.000
86L88TYR0-0.039-0.04014.5330.0120.0120.0000.0000.0000.000
87L89TYR00.0150.0159.584-0.047-0.0470.0000.0000.0000.000
88L91GLN00.0380.0197.671-0.024-0.0240.0000.0000.0000.000
89L92SER0-0.012-0.0357.030-0.135-0.1350.0000.0000.0000.000
90L93TYR00.0050.0187.6450.2290.2290.0000.0000.0000.000
91L94ASP-1-0.743-0.8304.570-1.642-1.616-0.001-0.007-0.0170.000
92L95SER0-0.037-0.0266.6840.3260.3260.0000.0000.0000.000
93L96SER0-0.028-0.0326.9190.0260.0260.0000.0000.0000.000
94L97LEU0-0.013-0.0059.2790.1060.1060.0000.0000.0000.000
95L98SER0-0.057-0.02611.9430.0480.0480.0000.0000.0000.000
96L99GLY00.0160.02010.099-0.056-0.0560.0000.0000.0000.000
97L100SER00.0130.0006.8730.1620.1620.0000.0000.0000.000
98L101GLN0-0.029-0.0127.811-0.332-0.3320.0000.0000.0000.000
99L102VAL00.0020.0052.754-0.2300.4310.283-0.270-0.673-0.001
100L103PHE00.021-0.0064.232-0.754-0.686-0.001-0.013-0.0540.000
101L104GLY00.0180.0183.727-0.2510.1780.006-0.148-0.288-0.001
102L105ALA0-0.024-0.0205.4830.3580.3580.0000.0000.0000.000
103L106GLY00.0000.0056.7910.0770.0770.0000.0000.0000.000
104L107THR0-0.076-0.05110.120-0.050-0.0500.0000.0000.0000.000
105L108ARG10.8540.89212.7940.0470.0470.0000.0000.0000.000
106L109VAL0-0.046-0.02316.306-0.018-0.0180.0000.0000.0000.000
107L110THR0-0.030-0.01319.1970.0250.0250.0000.0000.0000.000
108L111VAL0-0.023-0.03222.308-0.013-0.0130.0000.0000.0000.000
109L112LEU00.033-0.00424.9350.0100.0100.0000.0000.0000.000
110L113GLY0-0.055-0.00328.1390.0040.0040.0000.0000.0000.000
111L114GLN0-0.091-0.06627.4230.0100.0100.0000.0000.0000.000
112L115PRO00.0090.01532.2580.0000.0000.0000.0000.0000.000
113L116LYS10.9080.95134.7600.0180.0180.0000.0000.0000.000
114L117ALA0-0.0030.01035.2010.0010.0010.0000.0000.0000.000
115L118ASN00.018-0.00236.1980.0000.0000.0000.0000.0000.000
116L119PRO00.0170.00936.4990.0010.0010.0000.0000.0000.000
117L120THR0-0.0090.01538.053-0.001-0.0010.0000.0000.0000.000
118L121VAL0-0.002-0.01539.1520.0020.0020.0000.0000.0000.000
119L122THR0-0.018-0.01040.751-0.002-0.0020.0000.0000.0000.000
120L123LEU0-0.032-0.01041.5700.0020.0020.0000.0000.0000.000
121L124PHE0-0.008-0.00142.155-0.001-0.0010.0000.0000.0000.000
122L125PRO00.0070.00345.1130.0010.0010.0000.0000.0000.000
123L126PRO00.0370.03446.5550.0010.0010.0000.0000.0000.000
124L127SER00.0430.01647.286-0.002-0.0020.0000.0000.0000.000
125L128SER00.024-0.01249.0970.0000.0000.0000.0000.0000.000
126L129GLU-1-0.937-0.96348.4090.0420.0420.0000.0000.0000.000
127L130GLU-1-0.800-0.88144.2390.0440.0440.0000.0000.0000.000
128L131LEU0-0.003-0.00648.2670.0000.0000.0000.0000.0000.000
129L132GLN0-0.086-0.03151.0770.0000.0000.0000.0000.0000.000
130L133ALA0-0.0060.00448.4590.0000.0000.0000.0000.0000.000
131L134ASN0-0.087-0.05449.1410.0010.0010.0000.0000.0000.000
132L135LYS10.9380.96244.068-0.049-0.0490.0000.0000.0000.000
133L136ALA0-0.001-0.00845.633-0.002-0.0020.0000.0000.0000.000
134L137THR0-0.002-0.01640.3560.0020.0020.0000.0000.0000.000
135L138LEU0-0.061-0.00143.110-0.002-0.0020.0000.0000.0000.000
136L139VAL00.0230.01038.6470.0020.0020.0000.0000.0000.000
137L140CYS0-0.092-0.02038.980-0.003-0.0030.0000.0000.0000.000
138L141LEU00.0240.00836.6020.0020.0020.0000.0000.0000.000
139L142ILE0-0.024-0.01434.830-0.004-0.0040.0000.0000.0000.000
140L143SER00.0640.01634.6320.0030.0030.0000.0000.0000.000
141L144ASP-1-0.763-0.87134.1670.0000.0000.0000.0000.0000.000
142L145PHE0-0.045-0.00330.987-0.003-0.0030.0000.0000.0000.000
143L146TYR00.0270.01127.8050.0010.0010.0000.0000.0000.000
144L147PRO00.0770.02429.0210.0000.0000.0000.0000.0000.000
145L148GLY00.0350.00527.9570.0040.0040.0000.0000.0000.000
146L149ALA0-0.012-0.00427.7700.0030.0030.0000.0000.0000.000
147L150VAL0-0.015-0.01030.077-0.003-0.0030.0000.0000.0000.000
148L151THR0-0.0060.01132.2160.0020.0020.0000.0000.0000.000
149L152VAL00.019-0.00334.787-0.002-0.0020.0000.0000.0000.000
150L153ALA0-0.041-0.02037.0490.0020.0020.0000.0000.0000.000
151L154TRP00.0610.02138.322-0.003-0.0030.0000.0000.0000.000
152L155LYS10.8190.90342.439-0.015-0.0150.0000.0000.0000.000
153L156ALA00.0980.05046.1180.0010.0010.0000.0000.0000.000
154L157ASP-1-0.742-0.85449.0320.0160.0160.0000.0000.0000.000
155L158GLY0-0.017-0.00349.848-0.001-0.0010.0000.0000.0000.000
156L159SER0-0.039-0.01049.204-0.001-0.0010.0000.0000.0000.000
157L160PRO0-0.039-0.04143.8620.0010.0010.0000.0000.0000.000
158L161VAL00.0360.02942.9720.0000.0000.0000.0000.0000.000
159L162LYS10.9150.94440.550-0.021-0.0210.0000.0000.0000.000
160L163ALA00.0270.01239.2380.0020.0020.0000.0000.0000.000
161L164GLY00.0670.03738.967-0.002-0.0020.0000.0000.0000.000
162L165VAL0-0.056-0.01235.665-0.001-0.0010.0000.0000.0000.000
163L166GLU-1-0.877-0.92632.3430.0700.0700.0000.0000.0000.000
164L167THR0-0.030-0.01531.882-0.005-0.0050.0000.0000.0000.000
165L168THR00.0270.04028.7860.0030.0030.0000.0000.0000.000
166L169THR00.0220.00724.679-0.004-0.0040.0000.0000.0000.000
167L170PRO0-0.038-0.03326.9400.0040.0040.0000.0000.0000.000
168L171SER0-0.0090.00925.0490.0050.0050.0000.0000.0000.000
169L172LYS10.7390.86023.6660.0220.0220.0000.0000.0000.000
170L173GLN0-0.018-0.01825.8960.0110.0110.0000.0000.0000.000
171L174SER0-0.002-0.00927.275-0.004-0.0040.0000.0000.0000.000
172L175ASN00.003-0.00728.992-0.005-0.0050.0000.0000.0000.000
173L176ASN00.0170.01526.511-0.003-0.0030.0000.0000.0000.000
174L177LYS10.8750.95328.8130.0010.0010.0000.0000.0000.000
175L178TYR0-0.005-0.00624.5090.0010.0010.0000.0000.0000.000
176L179ALA00.0130.01529.675-0.002-0.0020.0000.0000.0000.000
177L180ALA0-0.017-0.02629.9640.0030.0030.0000.0000.0000.000
178L181SER0-0.0040.00231.961-0.001-0.0010.0000.0000.0000.000
179L182SER0-0.008-0.01533.3890.0020.0020.0000.0000.0000.000
180L183TYR00.0200.00833.751-0.002-0.0020.0000.0000.0000.000
181L184LEU00.0080.00637.8620.0010.0010.0000.0000.0000.000
182L185SER0-0.014-0.00739.5050.0010.0010.0000.0000.0000.000
183L186LEU0-0.029-0.02542.012-0.002-0.0020.0000.0000.0000.000
184L187THR0-0.011-0.01745.7340.0010.0010.0000.0000.0000.000
185L188PRO00.0540.01548.598-0.002-0.0020.0000.0000.0000.000
186L189GLU-1-0.920-0.95951.3760.0280.0280.0000.0000.0000.000
187L190GLN00.0660.05947.5920.0000.0000.0000.0000.0000.000
188L191TRP00.0140.00249.344-0.001-0.0010.0000.0000.0000.000
189L192LYS10.9130.94051.280-0.028-0.0280.0000.0000.0000.000
190L193SER0-0.016-0.00554.463-0.001-0.0010.0000.0000.0000.000
191L194HIS0-0.102-0.03552.1090.0000.0000.0000.0000.0000.000
192L195ARG10.8670.91954.606-0.013-0.0130.0000.0000.0000.000
193L196SER0-0.035-0.02052.0120.0000.0000.0000.0000.0000.000
194L197TYR00.002-0.00546.7150.0010.0010.0000.0000.0000.000
195L198SER00.0050.00446.7480.0000.0000.0000.0000.0000.000
196L200GLN0-0.011-0.02342.137-0.002-0.0020.0000.0000.0000.000
197L201VAL00.0290.01636.8550.0020.0020.0000.0000.0000.000
198L202THR0-0.0060.00237.827-0.002-0.0020.0000.0000.0000.000
199L203HIS10.8770.93133.1010.0080.0080.0000.0000.0000.000
200L204GLU-1-0.926-0.97233.240-0.023-0.0230.0000.0000.0000.000
201L205GLY00.0240.00936.631-0.001-0.0010.0000.0000.0000.000
202L206SER0-0.043-0.00839.7260.0000.0000.0000.0000.0000.000
203L207THR0-0.009-0.02040.5220.0010.0010.0000.0000.0000.000
204L208VAL0-0.022-0.00741.892-0.001-0.0010.0000.0000.0000.000
205L209GLU-1-0.841-0.91743.0470.0130.0130.0000.0000.0000.000
206L210LYS10.8850.96043.966-0.012-0.0120.0000.0000.0000.000
207L211THR00.018-0.01446.4840.0010.0010.0000.0000.0000.000
208L212VAL0-0.020-0.00147.5250.0000.0000.0000.0000.0000.000
209L213ALA00.0490.00250.2140.0000.0000.0000.0000.0000.000
210L214PRO0-0.0060.02353.1190.0000.0000.0000.0000.0000.000