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: YNZ72

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1942931.242126
FMO2-HF: Nuclear repulsion 1865244.589234
FMO2-HF: Total energy -77686.652892
FMO2-MP2: Total energy -77914.60581


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.
-1.0461.9650.134-1.255-1.889-0.001
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 : 0.006 / q_NPA : -0.009
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].
3L5THR00.0240.0073.204-0.9980.8460.066-0.890-1.0210.000
4L6GLN00.0310.0045.4180.3380.3380.0000.0000.0000.000
5L7PRO0-0.0170.0108.632-0.003-0.0030.0000.0000.0000.000
6L8PRO00.1130.08811.1680.0490.0490.0000.0000.0000.000
7L9SER0-0.035-0.01112.4260.0590.0590.0000.0000.0000.000
8L10VAL00.0030.01515.813-0.025-0.0250.0000.0000.0000.000
9L11SER0-0.017-0.00818.2120.0240.0240.0000.0000.0000.000
10L12GLY00.0220.00821.924-0.010-0.0100.0000.0000.0000.000
11L13ALA00.0160.02324.9780.0070.0070.0000.0000.0000.000
12L14PRO00.008-0.00428.455-0.002-0.0020.0000.0000.0000.000
13L15GLY00.0180.00229.3930.0010.0010.0000.0000.0000.000
14L16GLN0-0.0090.00426.1510.0050.0050.0000.0000.0000.000
15L17ARG10.9470.95922.4410.1160.1160.0000.0000.0000.000
16L18VAL00.0080.01320.365-0.009-0.0090.0000.0000.0000.000
17L19THR0-0.036-0.03117.2020.0150.0150.0000.0000.0000.000
18L20ILE0-0.0010.01112.642-0.017-0.0170.0000.0000.0000.000
19L21PRO00.0050.01112.6250.0240.0240.0000.0000.0000.000
20L22CYS0-0.053-0.0148.067-0.084-0.0840.0000.0000.0000.000
21L23THR0-0.014-0.0127.9590.2510.2510.0000.0000.0000.000
22L24GLY00.0460.0235.358-0.672-0.6720.0000.0000.0000.000
23L25GLY00.013-0.0045.9220.0720.0720.0000.0000.0000.000
24L26SER0-0.024-0.0287.0510.2650.2650.0000.0000.0000.000
25L27SER00.019-0.0036.023-0.170-0.1700.0000.0000.0000.000
26L28ASN00.034-0.0133.711-0.456-0.3830.000-0.021-0.0520.000
27L29ILE0-0.015-0.0087.542-0.043-0.0430.0000.0000.0000.000
28L30GLY0-0.031-0.0199.1860.0290.0290.0000.0000.0000.000
29L31ALA0-0.041-0.01110.4520.0290.0290.0000.0000.0000.000
30L32GLY0-0.0200.00312.2290.0390.0390.0000.0000.0000.000
31L33TYR0-0.021-0.00510.5960.0290.0290.0000.0000.0000.000
32L34SER0-0.058-0.03812.690-0.078-0.0780.0000.0000.0000.000
33L35VAL00.0120.00410.0970.0680.0680.0000.0000.0000.000
34L36HIS0-0.0600.00311.598-0.085-0.0850.0000.0000.0000.000
35L37TRP00.0440.00911.852-0.016-0.0160.0000.0000.0000.000
36L38TYR0-0.033-0.03312.134-0.005-0.0050.0000.0000.0000.000
37L39GLN00.0040.00314.839-0.023-0.0230.0000.0000.0000.000
38L40GLN00.018-0.00115.7600.0230.0230.0000.0000.0000.000
39L41LEU00.0530.02218.078-0.023-0.0230.0000.0000.0000.000
40L42PRO00.005-0.01320.9400.0130.0130.0000.0000.0000.000
41L43GLY00.0190.02421.5280.0040.0040.0000.0000.0000.000
42L44THR0-0.062-0.01321.9130.0050.0050.0000.0000.0000.000
43L45ALA00.0300.00819.4110.0060.0060.0000.0000.0000.000
44L46PRO0-0.005-0.01415.078-0.019-0.0190.0000.0000.0000.000
45L47LYS10.9841.00617.727-0.067-0.0670.0000.0000.0000.000
46L48LEU0-0.029-0.01016.741-0.008-0.0080.0000.0000.0000.000
47L49LEU0-0.054-0.01817.455-0.021-0.0210.0000.0000.0000.000
48L50ILE00.001-0.01117.309-0.019-0.0190.0000.0000.0000.000
49L51TYR00.0090.00316.3670.0300.0300.0000.0000.0000.000
50L52GLY00.0390.01416.817-0.026-0.0260.0000.0000.0000.000
51L53SER00.013-0.00617.058-0.007-0.0070.0000.0000.0000.000
52L54ASN0-0.015-0.01018.845-0.006-0.0060.0000.0000.0000.000
53L55SER00.0000.00720.385-0.004-0.0040.0000.0000.0000.000
54L56ARG10.8800.94021.309-0.006-0.0060.0000.0000.0000.000
55L57PRO00.0180.01921.361-0.001-0.0010.0000.0000.0000.000
56L58SER00.0250.00524.281-0.013-0.0130.0000.0000.0000.000
57L59GLY00.0570.02727.0570.0060.0060.0000.0000.0000.000
58L60VAL0-0.091-0.02722.254-0.006-0.0060.0000.0000.0000.000
59L61PRO0-0.040-0.03125.273-0.003-0.0030.0000.0000.0000.000
60L62ASP-1-0.809-0.91625.8280.0070.0070.0000.0000.0000.000
61L63ARG10.7490.86825.7250.0180.0180.0000.0000.0000.000
62L64PHE0-0.0250.00520.526-0.009-0.0090.0000.0000.0000.000
63L65SER00.0240.00421.3240.0100.0100.0000.0000.0000.000
64L66GLY00.0390.03517.783-0.018-0.0180.0000.0000.0000.000
65L67SER0-0.052-0.03417.4210.0070.0070.0000.0000.0000.000
66L68LYS11.0010.97213.910-0.015-0.0150.0000.0000.0000.000
67L69SER0-0.044-0.01415.3680.0390.0390.0000.0000.0000.000
68L70GLY00.0810.04714.957-0.052-0.0520.0000.0000.0000.000
69L71THR00.0340.0159.6200.0880.0880.0000.0000.0000.000
70L72SER0-0.0240.0019.794-0.215-0.2150.0000.0000.0000.000
71L73ALA00.002-0.00311.6570.1320.1320.0000.0000.0000.000
72L74SER0-0.027-0.02213.312-0.068-0.0680.0000.0000.0000.000
73L75LEU00.0190.03715.4710.0520.0520.0000.0000.0000.000
74L76ALA0-0.047-0.03916.919-0.021-0.0210.0000.0000.0000.000
75L77ILE00.0280.01519.5010.0200.0200.0000.0000.0000.000
76L78THR0-0.017-0.01222.685-0.007-0.0070.0000.0000.0000.000
77L79GLY00.0560.02226.3240.0080.0080.0000.0000.0000.000
78L80LEU0-0.054-0.01423.3510.0080.0080.0000.0000.0000.000
79L81ARG10.9991.00026.8890.0060.0060.0000.0000.0000.000
80L82PRO00.0650.01826.873-0.002-0.0020.0000.0000.0000.000
81L83GLU-1-0.932-0.96626.8040.0050.0050.0000.0000.0000.000
82L84ASP-1-0.822-0.89123.108-0.013-0.0130.0000.0000.0000.000
83L85GLU-1-0.836-0.92321.974-0.048-0.0480.0000.0000.0000.000
84L86ALA0-0.050-0.01819.7270.0140.0140.0000.0000.0000.000
85L87ASP-1-0.835-0.90814.573-0.046-0.0460.0000.0000.0000.000
86L88TYR0-0.039-0.03914.4580.0410.0410.0000.0000.0000.000
87L89TYR00.0070.0149.432-0.058-0.0580.0000.0000.0000.000
88L91GLN00.0690.0297.648-0.064-0.0640.0000.0000.0000.000
89L92SER0-0.012-0.0107.359-0.238-0.2380.0000.0000.0000.000
90L93TYR00.0000.0127.8280.4330.4330.0000.0000.0000.000
91L94ASP-1-0.749-0.8285.1221.7521.770-0.001-0.001-0.0150.000
92L95SER0-0.005-0.0147.567-0.042-0.0420.0000.0000.0000.000
93L96SER0-0.016-0.0117.303-0.421-0.4210.0000.0000.0000.000
94L97LEU0-0.010-0.0019.4060.1350.1350.0000.0000.0000.000
95L98SER0-0.069-0.03312.2620.0220.0220.0000.0000.0000.000
96L99GLY00.0120.01910.914-0.062-0.0620.0000.0000.0000.000
97L100SER00.010-0.0027.478-0.127-0.1270.0000.0000.0000.000
98L101GLN0-0.038-0.0188.6430.1110.1110.0000.0000.0000.000
99L102VAL00.0080.0133.323-0.1300.4410.063-0.179-0.4550.000
100L103PHE00.025-0.0074.234-1.072-1.010-0.001-0.013-0.0470.000
101L104GLY00.0220.0183.714-0.2920.1510.007-0.151-0.299-0.001
102L105ALA0-0.024-0.0225.4890.3150.3150.0000.0000.0000.000
103L106GLY0-0.0040.0046.7360.0700.0700.0000.0000.0000.000
104L107THR0-0.087-0.08710.051-0.083-0.0830.0000.0000.0000.000
105L108ARG10.9380.96912.7160.0800.0800.0000.0000.0000.000
106L109VAL0-0.048-0.02416.233-0.023-0.0230.0000.0000.0000.000
107L110THR0-0.019-0.01319.1180.0210.0210.0000.0000.0000.000
108L111VAL0-0.028-0.03622.232-0.008-0.0080.0000.0000.0000.000
109L112LEU00.034-0.01025.2400.0060.0060.0000.0000.0000.000
110L113GLY0-0.063-0.00728.0600.0020.0020.0000.0000.0000.000
111L114GLN0-0.065-0.04227.6630.0120.0120.0000.0000.0000.000
112L115PRO00.0060.01832.184-0.003-0.0030.0000.0000.0000.000
113L116LYS10.9750.98734.6920.0300.0300.0000.0000.0000.000
114L117ALA0-0.0140.00235.1610.0030.0030.0000.0000.0000.000
115L118ASN0-0.021-0.03236.141-0.004-0.0040.0000.0000.0000.000
116L119PRO00.0210.01136.3610.0020.0020.0000.0000.0000.000
117L120THR00.0180.02938.0050.0000.0000.0000.0000.0000.000
118L121VAL0-0.027-0.02639.1100.0010.0010.0000.0000.0000.000
119L122THR0-0.011-0.00640.7180.0000.0000.0000.0000.0000.000
120L123LEU0-0.036-0.01041.5400.0000.0000.0000.0000.0000.000
121L124PHE0-0.007-0.00142.4330.0000.0000.0000.0000.0000.000
122L125PRO00.007-0.00345.095-0.001-0.0010.0000.0000.0000.000
123L126PRO00.0340.02946.5400.0010.0010.0000.0000.0000.000
124L127SER00.0500.02046.864-0.001-0.0010.0000.0000.0000.000
125L128SER0-0.005-0.02749.0880.0000.0000.0000.0000.0000.000
126L129GLU-1-0.900-0.95248.3780.0200.0200.0000.0000.0000.000
127L130GLU-1-0.834-0.90943.9990.0120.0120.0000.0000.0000.000
128L131LEU0-0.022-0.01348.269-0.001-0.0010.0000.0000.0000.000
129L132GLN0-0.084-0.02751.0780.0000.0000.0000.0000.0000.000
130L133ALA0-0.0020.00848.4290.0000.0000.0000.0000.0000.000
131L134ASN0-0.078-0.05149.096-0.001-0.0010.0000.0000.0000.000
132L135LYS10.9390.95943.754-0.010-0.0100.0000.0000.0000.000
133L136ALA00.013-0.01045.6340.0000.0000.0000.0000.0000.000
134L137THR00.0170.01240.402-0.001-0.0010.0000.0000.0000.000
135L138LEU0-0.0610.00143.0730.0010.0010.0000.0000.0000.000
136L139VAL00.0310.01538.705-0.001-0.0010.0000.0000.0000.000
137L140CYS0-0.106-0.02538.840-0.002-0.0020.0000.0000.0000.000
138L141LEU00.006-0.00536.5840.0000.0000.0000.0000.0000.000
139L142ILE0-0.018-0.01034.764-0.001-0.0010.0000.0000.0000.000
140L143SER00.0310.00434.5930.0010.0010.0000.0000.0000.000
141L144ASP-1-0.799-0.89934.123-0.001-0.0010.0000.0000.0000.000
142L145PHE0-0.058-0.01530.932-0.002-0.0020.0000.0000.0000.000
143L146TYR00.0450.01927.301-0.001-0.0010.0000.0000.0000.000
144L147PRO00.0640.01629.0380.0020.0020.0000.0000.0000.000
145L148GLY00.036-0.00227.9040.0040.0040.0000.0000.0000.000
146L149ALA0-0.008-0.00327.723-0.003-0.0030.0000.0000.0000.000
147L150VAL0-0.012-0.00930.0320.0020.0020.0000.0000.0000.000
148L151THR0-0.0010.00732.181-0.001-0.0010.0000.0000.0000.000
149L152VAL00.0240.00634.7550.0020.0020.0000.0000.0000.000
150L153ALA0-0.046-0.02537.021-0.001-0.0010.0000.0000.0000.000
151L154TRP00.0660.02238.2770.0010.0010.0000.0000.0000.000
152L155LYS10.8430.92242.4200.0170.0170.0000.0000.0000.000
153L156ALA00.0890.04546.0990.0020.0020.0000.0000.0000.000
154L157ASP-1-0.812-0.91549.017-0.008-0.0080.0000.0000.0000.000
155L158GLY0-0.025-0.01349.826-0.001-0.0010.0000.0000.0000.000
156L159SER0-0.041-0.00649.168-0.002-0.0020.0000.0000.0000.000
157L160PRO0-0.027-0.03643.8820.0010.0010.0000.0000.0000.000
158L161VAL00.0330.03142.6630.0000.0000.0000.0000.0000.000
159L162LYS10.9090.93940.5380.0240.0240.0000.0000.0000.000
160L163ALA00.0290.01039.234-0.001-0.0010.0000.0000.0000.000
161L164GLY00.0700.04038.9630.0010.0010.0000.0000.0000.000
162L165VAL0-0.049-0.01135.7350.0020.0020.0000.0000.0000.000
163L166GLU-1-0.872-0.92932.407-0.002-0.0020.0000.0000.0000.000
164L167THR0-0.048-0.03131.6780.0020.0020.0000.0000.0000.000
165L168THR00.0370.03428.7580.0000.0000.0000.0000.0000.000
166L169THR0-0.005-0.00424.670-0.004-0.0040.0000.0000.0000.000
167L170PRO0-0.043-0.03026.8290.0060.0060.0000.0000.0000.000
168L171SER00.0230.01424.999-0.002-0.0020.0000.0000.0000.000
169L172LYS10.8320.93123.3000.0260.0260.0000.0000.0000.000
170L173GLN0-0.024-0.01725.8490.0090.0090.0000.0000.0000.000
171L174SER0-0.006-0.01127.220-0.003-0.0030.0000.0000.0000.000
172L175ASN00.0120.00728.937-0.001-0.0010.0000.0000.0000.000
173L176ASN0-0.021-0.00926.879-0.005-0.0050.0000.0000.0000.000
174L177LYS10.9280.98428.7500.0020.0020.0000.0000.0000.000
175L178TYR0-0.016-0.00624.4650.0010.0010.0000.0000.0000.000
176L179ALA00.0340.02429.6310.0010.0010.0000.0000.0000.000
177L180ALA0-0.029-0.02829.926-0.002-0.0020.0000.0000.0000.000
178L181SER00.0020.00531.9280.0020.0020.0000.0000.0000.000
179L182SER0-0.0060.00733.368-0.001-0.0010.0000.0000.0000.000
180L183TYR00.0410.01833.9860.0020.0020.0000.0000.0000.000
181L184LEU00.0000.00637.851-0.002-0.0020.0000.0000.0000.000
182L185SER0-0.013-0.00939.5090.0020.0020.0000.0000.0000.000
183L186LEU0-0.016-0.02142.011-0.002-0.0020.0000.0000.0000.000
184L187THR0-0.0020.00245.7340.0020.0020.0000.0000.0000.000
185L188PRO00.0360.01248.602-0.001-0.0010.0000.0000.0000.000
186L189GLU-1-0.909-0.94851.3780.0000.0000.0000.0000.0000.000
187L190GLN00.0230.01947.8040.0000.0000.0000.0000.0000.000
188L191TRP00.009-0.00449.426-0.001-0.0010.0000.0000.0000.000
189L192LYS10.9130.94251.274-0.005-0.0050.0000.0000.0000.000
190L193SER0-0.012-0.00254.4750.0000.0000.0000.0000.0000.000
191L194HIS0-0.075-0.01752.0550.0000.0000.0000.0000.0000.000
192L195ARG10.9420.97454.5950.0080.0080.0000.0000.0000.000
193L196SER0-0.066-0.03052.1000.0000.0000.0000.0000.0000.000
194L197TYR00.0340.01146.397-0.001-0.0010.0000.0000.0000.000
195L198SER00.0160.01246.6120.0010.0010.0000.0000.0000.000
196L200GLN00.007-0.00742.107-0.002-0.0020.0000.0000.0000.000
197L201VAL00.0170.01336.819-0.001-0.0010.0000.0000.0000.000
198L202THR00.0180.02137.4870.0010.0010.0000.0000.0000.000
199L203HIS10.8610.91733.1080.0290.0290.0000.0000.0000.000
200L204GLU-1-0.951-0.97533.223-0.046-0.0460.0000.0000.0000.000
201L205GLY00.0180.01136.5770.0010.0010.0000.0000.0000.000
202L206SER0-0.034-0.00439.6790.0020.0020.0000.0000.0000.000
203L207THR0-0.008-0.01440.476-0.001-0.0010.0000.0000.0000.000
204L208VAL0-0.026-0.00841.8590.0010.0010.0000.0000.0000.000
205L209GLU-1-0.887-0.95843.010-0.013-0.0130.0000.0000.0000.000
206L210LYS10.8860.95744.1320.0070.0070.0000.0000.0000.000
207L211THR00.038-0.00346.451-0.001-0.0010.0000.0000.0000.000
208L212VAL0-0.028-0.00247.6690.0010.0010.0000.0000.0000.000
209L213ALA00.0530.00050.191-0.001-0.0010.0000.0000.0000.000
210L214PRO0-0.0170.01753.1000.0010.0010.0000.0000.0000.000