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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6NR5Z

Calculation Name: 4YE4-H-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4YE4

Chain ID: H

ChEMBL ID:

UniProt ID: Q69994

Base Structure: X-ray

Registration Date: 2023-06-26

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2328226.014777
FMO2-HF: Nuclear repulsion 2241806.520342
FMO2-HF: Total energy -86419.494435
FMO2-MP2: Total energy -86669.535141


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(H:2:MET)


Summations of interaction energy for fragment #1(H:2:MET)
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.
-17.497-8.26711.484-7.175-13.54-0.039
Interaction energy analysis for fragmet #1(H:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.014
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].
3H4LEU00.0570.0273.889-0.8961.150-0.021-1.084-0.9420.003
4H5MET0-0.038-0.0237.0740.1420.1420.0000.0000.0000.000
5H6GLN00.0350.0069.947-0.027-0.0270.0000.0000.0000.000
6H7SER00.0150.01413.2550.0360.0360.0000.0000.0000.000
7H8GLY00.0100.03016.5120.0190.0190.0000.0000.0000.000
8H9GLY00.004-0.00219.0000.0130.0130.0000.0000.0000.000
9H10VAL0-0.002-0.01421.6910.0190.0190.0000.0000.0000.000
10H11MET0-0.019-0.00424.814-0.013-0.0130.0000.0000.0000.000
11H12VAL0-0.0130.00028.5490.0070.0070.0000.0000.0000.000
12H13ARG10.8630.92330.8710.0640.0640.0000.0000.0000.000
13H14PRO0-0.032-0.03133.732-0.003-0.0030.0000.0000.0000.000
14H15GLY0-0.0060.00834.3430.0070.0070.0000.0000.0000.000
15H16GLU-1-0.841-0.91232.436-0.073-0.0730.0000.0000.0000.000
16H17SER0-0.023-0.01629.366-0.008-0.0080.0000.0000.0000.000
17H18ALA0-0.006-0.00125.2370.0080.0080.0000.0000.0000.000
18H19THR0-0.033-0.03320.881-0.003-0.0030.0000.0000.0000.000
19H20LEU0-0.0270.01718.0790.0120.0120.0000.0000.0000.000
20H21SER00.013-0.00916.1740.0130.0130.0000.0000.0000.000
21H22CYS0-0.032-0.01110.792-0.060-0.0600.0000.0000.0000.000
22H23VAL00.0420.0549.960-0.018-0.0180.0000.0000.0000.000
23H24ALA00.0110.0116.372-0.117-0.1170.0000.0000.0000.000
24H25SER0-0.046-0.0314.5450.4390.623-0.001-0.056-0.1270.000
25H26GLY00.0610.0172.434-2.372-0.7964.621-3.391-2.806-0.013
26H27PHE00.0170.0142.158-6.327-3.9623.495-0.993-4.867-0.016
27H28ASP-1-0.810-0.8953.9640.1020.2360.003-0.043-0.0950.000
28H29PHE00.0190.0097.420-0.298-0.2980.0000.0000.0000.000
29H30SER0-0.031-0.0448.963-0.112-0.1120.0000.0000.0000.000
30H31ARG10.8480.9429.9160.0120.0120.0000.0000.0000.000
31H32ASN00.0240.0106.029-0.458-0.4580.0000.0000.0000.000
32H33GLY00.0140.0268.7010.1620.1620.0000.0000.0000.000
33H34PHE0-0.031-0.0196.689-0.245-0.2450.0000.0000.0000.000
34H35GLU-1-0.762-0.85410.997-0.496-0.4960.0000.0000.0000.000
35H36TRP0-0.038-0.02113.103-0.077-0.0770.0000.0000.0000.000
36H37LEU00.0170.00313.8550.0530.0530.0000.0000.0000.000
37H38ARG10.8190.91016.9360.2600.2600.0000.0000.0000.000
38H39GLN00.0450.02119.227-0.012-0.0120.0000.0000.0000.000
39H40GLY00.0350.01521.1180.0140.0140.0000.0000.0000.000
40H41PRO00.0140.00524.769-0.011-0.0110.0000.0000.0000.000
41H42GLY00.007-0.00226.9990.0090.0090.0000.0000.0000.000
42H43LYS10.8590.97024.7330.2180.2180.0000.0000.0000.000
43H44GLY00.0210.00722.436-0.001-0.0010.0000.0000.0000.000
44H45LEU0-0.011-0.01915.7840.0070.0070.0000.0000.0000.000
45H46GLN00.0200.00020.1330.0200.0200.0000.0000.0000.000
46H47TRP00.0350.01216.6130.0240.0240.0000.0000.0000.000
47H48LEU0-0.047-0.02318.7460.0510.0510.0000.0000.0000.000
48H49ALA00.0160.00218.4700.0470.0470.0000.0000.0000.000
49H50THR00.0220.00314.686-0.047-0.0470.0000.0000.0000.000
50H51VAL0-0.035-0.01514.1640.0730.0730.0000.0000.0000.000
51H52THR00.0840.04313.670-0.062-0.0620.0000.0000.0000.000
52H53PHE00.0540.00712.0900.0330.0330.0000.0000.0000.000
53H54GLU-1-0.843-0.90813.735-0.146-0.1460.0000.0000.0000.000
54H55SER0-0.041-0.02816.5710.0310.0310.0000.0000.0000.000
55H56LYS10.8380.92818.2230.1970.1970.0000.0000.0000.000
56H57THR00.0020.00418.383-0.035-0.0350.0000.0000.0000.000
57H58HIS0-0.0020.00019.6270.0030.0030.0000.0000.0000.000
58H59VAL00.0230.00620.450-0.026-0.0260.0000.0000.0000.000
59H60THR00.0260.02122.8710.0270.0270.0000.0000.0000.000
60H61ALA00.024-0.00424.4940.0140.0140.0000.0000.0000.000
61H62SER0-0.0020.00427.0690.0090.0090.0000.0000.0000.000
62H63ALA00.009-0.00125.3720.0070.0070.0000.0000.0000.000
63H64ARG10.8750.94125.5930.2030.2030.0000.0000.0000.000
64H65GLY00.0310.02227.8250.0100.0100.0000.0000.0000.000
65H66ARG10.7640.86528.3990.1730.1730.0000.0000.0000.000
66H67PHE0-0.011-0.01323.5310.0010.0010.0000.0000.0000.000
67H68THR0-0.020-0.01723.2960.0060.0060.0000.0000.0000.000
68H69ILE0-0.0290.01315.2970.0070.0070.0000.0000.0000.000
69H70SER00.006-0.00318.4050.0310.0310.0000.0000.0000.000
70H71ARG10.8080.88811.3240.3110.3110.0000.0000.0000.000
71H72ASP-1-0.757-0.84315.5750.0970.0970.0000.0000.0000.000
72H73ASN00.0610.00914.029-0.021-0.0210.0000.0000.0000.000
73H74SER0-0.072-0.03414.2170.0620.0620.0000.0000.0000.000
74H75ARG10.9100.94014.444-0.041-0.0410.0000.0000.0000.000
75H76ARG10.8960.9617.672-0.709-0.7090.0000.0000.0000.000
76H77THR0-0.005-0.00710.422-0.019-0.0190.0000.0000.0000.000
77H78VAL0-0.0110.00411.390-0.003-0.0030.0000.0000.0000.000
78H79TYR0-0.006-0.03114.2490.0290.0290.0000.0000.0000.000
79H80LEU0-0.010-0.00217.520-0.028-0.0280.0000.0000.0000.000
80H81GLN00.0260.02219.9810.0110.0110.0000.0000.0000.000
81H82MET0-0.043-0.02122.356-0.022-0.0220.0000.0000.0000.000
82H83THR00.0720.01726.1100.0180.0180.0000.0000.0000.000
83H84ASN00.0080.01129.951-0.006-0.0060.0000.0000.0000.000
84H85LEU00.0120.01826.589-0.009-0.0090.0000.0000.0000.000
85H86GLN00.031-0.01230.7810.0140.0140.0000.0000.0000.000
86H87PRO00.0450.01431.056-0.012-0.0120.0000.0000.0000.000
87H88ASP-1-0.876-0.93429.013-0.199-0.1990.0000.0000.0000.000
88H89ASP-1-0.759-0.83126.996-0.191-0.1910.0000.0000.0000.000
89H90THR0-0.0160.00726.050-0.011-0.0110.0000.0000.0000.000
90H91ALA0-0.017-0.00923.113-0.004-0.0040.0000.0000.0000.000
91H92MET0-0.0190.01218.1050.0120.0120.0000.0000.0000.000
92H93TYR0-0.010-0.02518.403-0.027-0.0270.0000.0000.0000.000
93H94PHE0-0.010-0.00913.2390.0150.0150.0000.0000.0000.000
94H96VAL00.0240.0038.747-0.148-0.1480.0000.0000.0000.000
95H97LYS10.8100.9052.8973.2643.7580.148-0.089-0.5530.000
96H98ASP-1-0.847-0.9127.370-0.984-0.9840.0000.0000.0000.000
97H99GLN0-0.041-0.0485.962-0.544-0.5440.0000.0000.0000.000
98H100THR00.005-0.0028.9530.2400.2400.0000.0000.0000.000
99H101ILE0-0.020-0.0039.769-0.028-0.0280.0000.0000.0000.000
100H102PHE00.0300.00311.2300.0580.0580.0000.0000.0000.000
101H103HIS00.0260.01515.2320.0520.0520.0000.0000.0000.000
102H104LYS10.9140.93918.4410.0300.0300.0000.0000.0000.000
103H105ASN0-0.032-0.03421.0730.0070.0070.0000.0000.0000.000
104H106GLY00.0220.02420.9910.0030.0030.0000.0000.0000.000
105H107ALA0-0.0090.01320.852-0.011-0.0110.0000.0000.0000.000
106H108VAL0-0.035-0.03615.3560.0070.0070.0000.0000.0000.000
107H109ASP-1-0.857-0.88815.113-0.263-0.2630.0000.0000.0000.000
108H110PHE0-0.006-0.03113.543-0.034-0.0340.0000.0000.0000.000
109H111PHE00.0020.00312.1180.0530.0530.0000.0000.0000.000
110H112SER0-0.019-0.02811.535-0.144-0.1440.0000.0000.0000.000
111H113TYR0-0.015-0.0089.2950.0970.0970.0000.0000.0000.000
112H114PHE0-0.0010.0008.175-0.122-0.1220.0000.0000.0000.000
113H115ASP-1-0.790-0.8762.551-8.368-7.2981.025-0.818-1.277-0.011
114H116LEU0-0.052-0.0152.414-1.551-0.2922.215-0.693-2.780-0.002
115H117TRP00.021-0.0124.7090.6440.746-0.001-0.008-0.0930.000
116H118GLY00.0090.0087.439-0.184-0.1840.0000.0000.0000.000
117H119ARG10.7700.8649.7770.2580.2580.0000.0000.0000.000
118H120GLY00.0340.03712.4880.0610.0610.0000.0000.0000.000
119H121ALA0-0.061-0.04615.2430.0540.0540.0000.0000.0000.000
120H122PRO0-0.0010.01018.154-0.008-0.0080.0000.0000.0000.000
121H123VAL00.0100.00521.7220.0200.0200.0000.0000.0000.000
122H124ILE0-0.020-0.01024.308-0.006-0.0060.0000.0000.0000.000
123H125VAL00.0110.01828.0170.0100.0100.0000.0000.0000.000
124H126SER00.003-0.00431.0470.0010.0010.0000.0000.0000.000
125H127ALA00.0520.02134.5780.0040.0040.0000.0000.0000.000
126H128ALA0-0.0100.01436.3680.0070.0070.0000.0000.0000.000
127H129SER00.0330.02537.2160.0000.0000.0000.0000.0000.000
128H130THR0-0.022-0.02534.502-0.004-0.0040.0000.0000.0000.000
129H131LYS10.7970.89736.6810.0580.0580.0000.0000.0000.000
130H132GLY00.0860.04937.419-0.005-0.0050.0000.0000.0000.000
131H133PRO0-0.046-0.01837.0820.0000.0000.0000.0000.0000.000
132H134SER0-0.0110.00739.7330.0040.0040.0000.0000.0000.000
133H135VAL0-0.006-0.00740.999-0.004-0.0040.0000.0000.0000.000
134H136PHE00.009-0.00143.6690.0040.0040.0000.0000.0000.000
135H137PRO0-0.019-0.00545.420-0.002-0.0020.0000.0000.0000.000
136H138LEU0-0.015-0.00743.3330.0000.0000.0000.0000.0000.000
137H139ALA00.0260.00947.3300.0000.0000.0000.0000.0000.000
138H140PRO00.0330.04249.392-0.002-0.0020.0000.0000.0000.000
139H141SER00.039-0.00451.1860.0020.0020.0000.0000.0000.000
140H142SER00.0170.00454.059-0.001-0.0010.0000.0000.0000.000
141H143LYS10.9300.95754.3890.0400.0400.0000.0000.0000.000
142H144SER0-0.0060.01249.583-0.002-0.0020.0000.0000.0000.000
143H145THR0-0.027-0.02849.9910.0000.0000.0000.0000.0000.000
144H146SER0-0.020-0.00450.5860.0010.0010.0000.0000.0000.000
145H147GLY00.0590.03251.7110.0000.0000.0000.0000.0000.000
146H148GLY00.0340.02952.1290.0010.0010.0000.0000.0000.000
147H149THR0-0.0130.00346.2510.0020.0020.0000.0000.0000.000
148H150ALA00.0010.00348.9020.0000.0000.0000.0000.0000.000
149H151ALA00.0000.00245.347-0.002-0.0020.0000.0000.0000.000
150H152LEU0-0.0060.01044.5540.0020.0020.0000.0000.0000.000
151H153GLY00.045-0.00542.992-0.003-0.0030.0000.0000.0000.000
152H154CYS0-0.0710.00740.1480.0040.0040.0000.0000.0000.000
153H155LEU00.0410.04440.883-0.005-0.0050.0000.0000.0000.000
154H156VAL0-0.031-0.02637.4740.0050.0050.0000.0000.0000.000
155H157LYS10.8940.93338.8060.0560.0560.0000.0000.0000.000
156H158ASP-1-0.789-0.87840.247-0.059-0.0590.0000.0000.0000.000
157H159TYR0-0.009-0.02232.4780.0070.0070.0000.0000.0000.000
158H160PHE00.0630.02432.527-0.009-0.0090.0000.0000.0000.000
159H161PRO00.0340.02229.8260.0080.0080.0000.0000.0000.000
160H162GLU-1-0.777-0.87428.353-0.113-0.1130.0000.0000.0000.000
161H163PRO0-0.059-0.02726.5160.0000.0000.0000.0000.0000.000
162H164VAL00.0080.00029.2580.0120.0120.0000.0000.0000.000
163H165THR0-0.044-0.02128.972-0.006-0.0060.0000.0000.0000.000
164H166VAL00.015-0.01231.9060.0060.0060.0000.0000.0000.000
165H167SER0-0.0250.00033.707-0.003-0.0030.0000.0000.0000.000
166H168TRP00.0250.00935.7600.0030.0030.0000.0000.0000.000
167H169ASN00.011-0.00838.7790.0010.0010.0000.0000.0000.000
168H170SER0-0.018-0.01838.5010.0020.0020.0000.0000.0000.000
169H171GLY00.0040.00735.5590.0030.0030.0000.0000.0000.000
170H172ALA0-0.032-0.00536.115-0.002-0.0020.0000.0000.0000.000
171H173LEU0-0.040-0.01038.4340.0000.0000.0000.0000.0000.000
172H174THR00.015-0.00333.480-0.003-0.0030.0000.0000.0000.000
173H175SER00.0310.00436.240-0.006-0.0060.0000.0000.0000.000
174H176GLY00.0440.03137.5910.0030.0030.0000.0000.0000.000
175H177VAL0-0.044-0.01534.8200.0000.0000.0000.0000.0000.000
176H178HIS00.0090.00635.161-0.010-0.0100.0000.0000.0000.000
177H179THR00.005-0.00133.1010.0080.0080.0000.0000.0000.000
178H180PHE0-0.0080.00732.816-0.007-0.0070.0000.0000.0000.000
179H181PRO00.018-0.00529.9250.0030.0030.0000.0000.0000.000
180H182ALA0-0.0040.01431.3290.0070.0070.0000.0000.0000.000
181H183VAL0-0.023-0.01132.455-0.009-0.0090.0000.0000.0000.000
182H184LEU0-0.026-0.01332.8080.0070.0070.0000.0000.0000.000
183H185GLN0-0.039-0.03735.2860.0020.0020.0000.0000.0000.000
184H186SER00.0340.00738.771-0.002-0.0020.0000.0000.0000.000
185H187SER0-0.0020.00141.1980.0000.0000.0000.0000.0000.000
186H188GLY00.0220.01737.3940.0020.0020.0000.0000.0000.000
187H189LEU0-0.047-0.01836.587-0.002-0.0020.0000.0000.0000.000
188H190TYR00.019-0.00129.944-0.001-0.0010.0000.0000.0000.000
189H191SER0-0.022-0.00835.9750.0090.0090.0000.0000.0000.000
190H192LEU00.0620.04333.352-0.007-0.0070.0000.0000.0000.000
191H193SER0-0.006-0.02236.8700.0090.0090.0000.0000.0000.000
192H194SER0-0.0150.00036.592-0.004-0.0040.0000.0000.0000.000
193H195VAL00.017-0.00538.4130.0050.0050.0000.0000.0000.000
194H196VAL00.0160.00739.393-0.003-0.0030.0000.0000.0000.000
195H197THR0-0.027-0.00441.5440.0010.0010.0000.0000.0000.000
196H198VAL00.0080.00343.3520.0010.0010.0000.0000.0000.000
197H199PRO00.0740.03146.064-0.001-0.0010.0000.0000.0000.000
198H200SER0-0.034-0.01649.2370.0020.0020.0000.0000.0000.000
199H201SER00.0190.00452.1930.0000.0000.0000.0000.0000.000
200H202SER0-0.020-0.02449.5190.0010.0010.0000.0000.0000.000
201H203LEU0-0.010-0.01350.2380.0010.0010.0000.0000.0000.000
202H204GLY0-0.0030.00752.5490.0000.0000.0000.0000.0000.000
203H205THR0-0.038-0.02552.8690.0020.0020.0000.0000.0000.000
204H206GLN0-0.033-0.00346.7660.0030.0030.0000.0000.0000.000
205H207THR0-0.0050.01447.129-0.001-0.0010.0000.0000.0000.000
206H208TYR00.0430.00844.528-0.001-0.0010.0000.0000.0000.000
207H209ILE00.015-0.00242.8520.0000.0000.0000.0000.0000.000
208H211ASN00.010-0.01437.4630.0010.0010.0000.0000.0000.000
209H212VAL0-0.0060.00136.696-0.005-0.0050.0000.0000.0000.000
210H213ASN0-0.009-0.01833.1970.0110.0110.0000.0000.0000.000
211H214HIS00.0160.02133.0960.0000.0000.0000.0000.0000.000
212H215LYS11.0170.99626.7010.0330.0330.0000.0000.0000.000
213H216PRO0-0.0060.00729.4840.0070.0070.0000.0000.0000.000
214H217SER0-0.003-0.01631.7220.0030.0030.0000.0000.0000.000
215H218ASN0-0.050-0.02234.1370.0060.0060.0000.0000.0000.000
216H219THR00.0080.00235.5130.0030.0030.0000.0000.0000.000
217H220LYS10.8480.90936.6000.0210.0210.0000.0000.0000.000
218H221VAL0-0.0030.00538.8290.0020.0020.0000.0000.0000.000
219H222ASP-1-0.785-0.87740.525-0.026-0.0260.0000.0000.0000.000
220H223LYS10.8910.93643.0180.0340.0340.0000.0000.0000.000
221H224ARG10.8610.91245.0480.0200.0200.0000.0000.0000.000
222H225VAL0-0.066-0.03045.497-0.001-0.0010.0000.0000.0000.000
223H226GLU-1-0.789-0.88148.423-0.023-0.0230.0000.0000.0000.000
224H227PRO00.0160.00851.798-0.002-0.0020.0000.0000.0000.000
225H228LYS10.9510.98454.1130.0290.0290.0000.0000.0000.000