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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: JLR69

Calculation Name: 4GW4-H-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4GW4

Chain ID: H

ChEMBL ID:

UniProt ID:

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2173057.637385
FMO2-HF: Nuclear repulsion 2091720.092551
FMO2-HF: Total energy -81337.544834
FMO2-MP2: Total energy -81576.561187


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:1:PCA)


Summations of interaction energy for fragment #1(H:1:PCA)
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.
-1.7580.4730.021-0.988-1.2620.001
Interaction energy analysis for fragmet #1(H:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.030
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].
3H3HIS00.0270.0163.554-0.8950.8310.013-0.792-0.9470.001
4H4LEU0-0.008-0.0115.5190.5740.5740.0000.0000.0000.000
5H5SER0-0.042-0.0049.2540.3210.3210.0000.0000.0000.000
6H6GLN00.044-0.01111.182-0.069-0.0690.0000.0000.0000.000
7H7SER00.0040.01914.9580.0800.0800.0000.0000.0000.000
8H8GLY00.0280.01118.330-0.013-0.0130.0000.0000.0000.000
9H9ALA0-0.042-0.01820.127-0.020-0.0200.0000.0000.0000.000
10H10ALA00.0270.02123.1030.0240.0240.0000.0000.0000.000
11H11VAL0-0.016-0.01625.983-0.003-0.0030.0000.0000.0000.000
12H12THR00.0030.00829.7730.0000.0000.0000.0000.0000.000
13H13LYS10.8510.91232.1230.0770.0770.0000.0000.0000.000
14H14PRO00.0460.00535.603-0.009-0.0090.0000.0000.0000.000
15H15GLY0-0.0120.00337.1980.0070.0070.0000.0000.0000.000
16H16ALA0-0.0050.00634.671-0.002-0.0020.0000.0000.0000.000
17H17SER0-0.016-0.03131.601-0.011-0.0110.0000.0000.0000.000
18H18VAL0-0.026-0.00426.2560.0140.0140.0000.0000.0000.000
19H19ARG10.8590.90522.8150.2690.2690.0000.0000.0000.000
20H20VAL0-0.0260.01019.5440.0170.0170.0000.0000.0000.000
21H21SER00.016-0.01218.164-0.005-0.0050.0000.0000.0000.000
22H22CYS0-0.061-0.02113.755-0.023-0.0230.0000.0000.0000.000
23H23GLU-1-0.788-0.84711.167-0.619-0.6190.0000.0000.0000.000
24H24ALA0-0.012-0.0159.712-0.186-0.1860.0000.0000.0000.000
25H25SER00.0440.0146.0700.2070.2070.0000.0000.0000.000
26H26GLY00.0980.0503.625-1.625-1.3760.005-0.110-0.1430.000
27H27TYR0-0.049-0.0404.051-0.388-0.1320.003-0.086-0.1720.000
28H28LYS10.8950.9476.8701.5771.5770.0000.0000.0000.000
29H29ILE00.0420.0109.2020.1550.1550.0000.0000.0000.000
30H30SER0-0.015-0.02512.0170.1160.1160.0000.0000.0000.000
31H31ASP-1-0.868-0.91314.279-0.748-0.7480.0000.0000.0000.000
32H32HIS0-0.0070.00812.078-0.076-0.0760.0000.0000.0000.000
33H33PHE00.0070.00715.212-0.033-0.0330.0000.0000.0000.000
34H34ILE00.0200.02813.094-0.074-0.0740.0000.0000.0000.000
35H35HIS0-0.012-0.02316.8300.1450.1450.0000.0000.0000.000
36H36TRP0-0.016-0.01317.824-0.063-0.0630.0000.0000.0000.000
37H37TRP00.0210.00618.7560.0800.0800.0000.0000.0000.000
38H38ARG10.8050.88721.4860.2430.2430.0000.0000.0000.000
39H39GLN0-0.011-0.00422.735-0.021-0.0210.0000.0000.0000.000
40H40ALA00.0370.02725.0010.0100.0100.0000.0000.0000.000
41H41PRO0-0.001-0.01127.948-0.006-0.0060.0000.0000.0000.000
42H42GLY00.0250.01628.7570.0090.0090.0000.0000.0000.000
43H43GLN0-0.055-0.02028.7900.0040.0040.0000.0000.0000.000
44H44GLY00.0530.03126.612-0.009-0.0090.0000.0000.0000.000
45H45LEU0-0.014-0.00620.1970.0070.0070.0000.0000.0000.000
46H46GLN0-0.011-0.00424.5350.0270.0270.0000.0000.0000.000
47H47TRP00.0030.00622.6800.0140.0140.0000.0000.0000.000
48H48VAL0-0.044-0.02923.9160.0370.0370.0000.0000.0000.000
49H49GLY00.038-0.01023.6650.0370.0370.0000.0000.0000.000
50H50TRP0-0.0320.01921.311-0.043-0.0430.0000.0000.0000.000
51H51ILE0-0.010-0.01119.3680.0570.0570.0000.0000.0000.000
52H52ASN00.0160.01819.768-0.103-0.1030.0000.0000.0000.000
53H53PRO00.0230.02116.3690.0650.0650.0000.0000.0000.000
54H54LYS10.9500.98517.8990.6980.6980.0000.0000.0000.000
55H55THR00.001-0.00520.6620.0320.0320.0000.0000.0000.000
56H56GLY0-0.0050.00522.6490.0340.0340.0000.0000.0000.000
57H57GLN0-0.011-0.00923.6070.0010.0010.0000.0000.0000.000
58H58PRO00.0260.01824.479-0.041-0.0410.0000.0000.0000.000
59H59ASN0-0.029-0.02625.7230.0490.0490.0000.0000.0000.000
60H60ASN0-0.024-0.02726.117-0.014-0.0140.0000.0000.0000.000
61H61ALA00.0460.03928.2320.0160.0160.0000.0000.0000.000
62H62ARG10.9800.96730.0760.2080.2080.0000.0000.0000.000
63H63GLN00.0070.02731.8430.0000.0000.0000.0000.0000.000
64H64PHE00.003-0.01928.5320.0110.0110.0000.0000.0000.000
65H65GLN00.0850.06231.903-0.002-0.0020.0000.0000.0000.000
66H66GLY0-0.0090.00533.6090.0140.0140.0000.0000.0000.000
67H67ARG10.6980.80732.6540.1960.1960.0000.0000.0000.000
68H68VAL00.0250.01226.8880.0030.0030.0000.0000.0000.000
69H69SER0-0.100-0.04927.2150.0040.0040.0000.0000.0000.000
70H70LEU00.0030.01522.706-0.010-0.0100.0000.0000.0000.000
71H71THR00.0150.00322.8350.0140.0140.0000.0000.0000.000
72H72ARG10.8600.91218.2710.4470.4470.0000.0000.0000.000
73H73GLN0-0.060-0.03418.2600.0750.0750.0000.0000.0000.000
74H74ALA00.0170.02615.674-0.057-0.0570.0000.0000.0000.000
75H74SER0-0.002-0.02613.1180.0580.0580.0000.0000.0000.000
76H74TRP0-0.018-0.01615.653-0.032-0.0320.0000.0000.0000.000
77H74ASP-1-0.816-0.88512.855-0.433-0.4330.0000.0000.0000.000
78H75PHE0-0.086-0.04214.164-0.053-0.0530.0000.0000.0000.000
79H76ASP-1-0.898-0.9407.790-1.569-1.5690.0000.0000.0000.000
80H77THR0-0.043-0.0408.633-0.543-0.5430.0000.0000.0000.000
81H78TYR0-0.058-0.02810.5670.2760.2760.0000.0000.0000.000
82H78SER0-0.006-0.00513.148-0.080-0.0800.0000.0000.0000.000
83H79PHE0-0.025-0.02313.8020.0410.0410.0000.0000.0000.000
84H80TYR0-0.024-0.03017.6260.0270.0270.0000.0000.0000.000
85H81MET00.0100.00520.728-0.015-0.0150.0000.0000.0000.000
86H82ASP-1-0.807-0.85023.277-0.245-0.2450.0000.0000.0000.000
87H83LEU00.000-0.00626.752-0.007-0.0070.0000.0000.0000.000
88H84LYS10.9440.98429.2220.1860.1860.0000.0000.0000.000
89H85ALA00.0130.00732.979-0.003-0.0030.0000.0000.0000.000
90H86VAL0-0.054-0.00431.171-0.003-0.0030.0000.0000.0000.000
91H87ARG10.8850.90533.9160.1660.1660.0000.0000.0000.000
92H88SER00.0630.01933.948-0.003-0.0030.0000.0000.0000.000
93H89ASP-1-0.838-0.89433.660-0.158-0.1580.0000.0000.0000.000
94H90ASP-1-0.731-0.83430.147-0.204-0.2040.0000.0000.0000.000
95H91THR0-0.0140.01128.953-0.011-0.0110.0000.0000.0000.000
96H92ALA0-0.020-0.01425.9810.0020.0020.0000.0000.0000.000
97H93ILE00.0180.02420.3350.0070.0070.0000.0000.0000.000
98H94TYR0-0.008-0.02921.391-0.019-0.0190.0000.0000.0000.000
99H95PHE00.0340.01216.2490.0060.0060.0000.0000.0000.000
100H97ALA00.0200.00213.743-0.077-0.0770.0000.0000.0000.000
101H98ARG10.8840.9318.6922.2292.2290.0000.0000.0000.000
102H99GLN0-0.037-0.01113.3380.0340.0340.0000.0000.0000.000
103H100ARG10.7560.86511.9680.9990.9990.0000.0000.0000.000
104H101SER00.010-0.02914.7040.0280.0280.0000.0000.0000.000
105H102ASP-1-0.873-0.94218.165-0.569-0.5690.0000.0000.0000.000
106H103PHE0-0.039-0.02621.2630.0420.0420.0000.0000.0000.000
107H104TRP0-0.052-0.02220.2090.0190.0190.0000.0000.0000.000
108H105ASP-1-0.737-0.82216.587-0.813-0.8130.0000.0000.0000.000
109H106PHE00.021-0.00614.888-0.057-0.0570.0000.0000.0000.000
110H107ASP-1-0.784-0.86410.736-1.608-1.6080.0000.0000.0000.000
111H108VAL0-0.0080.0007.399-0.143-0.1430.0000.0000.0000.000
112H109TRP0-0.007-0.0199.9760.1890.1890.0000.0000.0000.000
113H110GLY00.0430.02310.476-0.158-0.1580.0000.0000.0000.000
114H111SER0-0.047-0.03512.3080.0710.0710.0000.0000.0000.000
115H112GLY0-0.0040.00813.7620.0880.0880.0000.0000.0000.000
116H113THR0-0.056-0.03917.2150.0100.0100.0000.0000.0000.000
117H114GLN00.0310.01720.021-0.021-0.0210.0000.0000.0000.000
118H115VAL00.0040.01123.4740.0130.0130.0000.0000.0000.000
119H116THR00.0280.00826.400-0.003-0.0030.0000.0000.0000.000
120H117VAL0-0.030-0.00929.9580.0120.0120.0000.0000.0000.000
121H118SER0-0.001-0.00532.9060.0080.0080.0000.0000.0000.000
122H119SER00.0460.00335.816-0.001-0.0010.0000.0000.0000.000
123H120ALA00.0030.03337.3660.0050.0050.0000.0000.0000.000
124H121SER00.0360.01537.119-0.006-0.0060.0000.0000.0000.000
125H122THR0-0.038-0.02934.515-0.003-0.0030.0000.0000.0000.000
126H123LYS10.8640.93136.6150.0110.0110.0000.0000.0000.000
127H124GLY00.0400.03037.195-0.001-0.0010.0000.0000.0000.000
128H125PRO0-0.049-0.02136.624-0.004-0.0040.0000.0000.0000.000
129H126SER00.0130.01239.2280.0040.0040.0000.0000.0000.000
130H127VAL00.0100.00639.976-0.004-0.0040.0000.0000.0000.000
131H128PHE0-0.003-0.00942.7110.0030.0030.0000.0000.0000.000
132H129PRO00.0450.03044.409-0.001-0.0010.0000.0000.0000.000
133H130LEU0-0.032-0.01442.995-0.003-0.0030.0000.0000.0000.000
134H131ALA00.0550.02146.4790.0030.0030.0000.0000.0000.000
135H132PRO0-0.034-0.00848.586-0.004-0.0040.0000.0000.0000.000
136H141THR0-0.061-0.04545.5880.0000.0000.0000.0000.0000.000
137H142ALA0-0.0080.00947.470-0.003-0.0030.0000.0000.0000.000
138H143ALA00.009-0.00344.2450.0010.0010.0000.0000.0000.000
139H144LEU0-0.0080.01942.9530.0000.0000.0000.0000.0000.000
140H145GLY00.042-0.00541.6740.0000.0000.0000.0000.0000.000
141H146CYS0-0.037-0.01140.2210.0020.0020.0000.0000.0000.000
142H147LEU00.0230.03540.126-0.003-0.0030.0000.0000.0000.000
143H148VAL0-0.036-0.02536.3750.0050.0050.0000.0000.0000.000
144H149LYS10.9000.91238.4260.0190.0190.0000.0000.0000.000
145H150ASP-1-0.777-0.86840.282-0.020-0.0200.0000.0000.0000.000
146H151TYR00.0030.01432.8700.0060.0060.0000.0000.0000.000
147H152PHE00.0410.01533.676-0.009-0.0090.0000.0000.0000.000
148H153PRO00.0340.01530.3790.0100.0100.0000.0000.0000.000
149H154GLU-1-0.855-0.90728.672-0.073-0.0730.0000.0000.0000.000
150H155PRO0-0.003-0.00525.894-0.001-0.0010.0000.0000.0000.000
151H156VAL0-0.037-0.04028.8370.0090.0090.0000.0000.0000.000
152H157THR0-0.0420.00327.282-0.002-0.0020.0000.0000.0000.000
153H158VAL00.019-0.01130.3230.0030.0030.0000.0000.0000.000
154H159SER0-0.0130.00631.8900.0050.0050.0000.0000.0000.000
155H160TRP00.0660.02633.820-0.004-0.0040.0000.0000.0000.000
156H161ASN00.000-0.01936.4420.0040.0040.0000.0000.0000.000
157H162SER0-0.011-0.01434.7400.0070.0070.0000.0000.0000.000
158H163GLY0-0.020-0.00232.7710.0120.0120.0000.0000.0000.000
159H164ALA0-0.036-0.01133.5440.0020.0020.0000.0000.0000.000
160H165LEU0-0.023-0.00736.034-0.004-0.0040.0000.0000.0000.000
161H166THR00.007-0.00831.352-0.003-0.0030.0000.0000.0000.000
162H167SER00.0410.01234.109-0.009-0.0090.0000.0000.0000.000
163H168GLY00.0330.01735.6330.0000.0000.0000.0000.0000.000
164H169VAL0-0.047-0.01534.409-0.005-0.0050.0000.0000.0000.000
165H170HIS00.0010.01034.164-0.006-0.0060.0000.0000.0000.000
166H171THR0-0.039-0.03231.9950.0050.0050.0000.0000.0000.000
167H172PHE0-0.0130.00432.384-0.005-0.0050.0000.0000.0000.000
168H173PRO00.0210.00630.2080.0050.0050.0000.0000.0000.000
169H174ALA0-0.023-0.01231.2620.0050.0050.0000.0000.0000.000
170H175VAL00.0050.00733.097-0.011-0.0110.0000.0000.0000.000
171H176LEU0-0.022-0.00934.6470.0070.0070.0000.0000.0000.000
172H177GLN0-0.027-0.02536.6820.0020.0020.0000.0000.0000.000
173H178SER00.0360.00840.383-0.002-0.0020.0000.0000.0000.000
174H179SER00.0030.00542.407-0.002-0.0020.0000.0000.0000.000
175H180GLY00.0040.00439.0930.0010.0010.0000.0000.0000.000
176H181LEU0-0.048-0.01737.9510.0000.0000.0000.0000.0000.000
177H182TYR0-0.016-0.01430.724-0.003-0.0030.0000.0000.0000.000
178H183SER0-0.029-0.01736.6790.0100.0100.0000.0000.0000.000
179H184LEU00.0230.03132.824-0.007-0.0070.0000.0000.0000.000
180H185SER00.002-0.02436.5230.0040.0040.0000.0000.0000.000
181H186SER00.0110.02435.885-0.004-0.0040.0000.0000.0000.000
182H187VAL00.0270.00337.3720.0010.0010.0000.0000.0000.000
183H188VAL00.0240.01138.1170.0020.0020.0000.0000.0000.000
184H189THR0-0.0160.00540.192-0.003-0.0030.0000.0000.0000.000
185H190VAL00.0170.00441.9340.0040.0040.0000.0000.0000.000
186H191PRO00.0560.02944.629-0.004-0.0040.0000.0000.0000.000
187H192SER00.0560.01447.7050.0020.0020.0000.0000.0000.000
188H193SER00.0180.01550.7730.0000.0000.0000.0000.0000.000
189H194SER0-0.013-0.01547.4160.0020.0020.0000.0000.0000.000
190H195LEU0-0.010-0.01048.1010.0020.0020.0000.0000.0000.000
191H196GLY00.0200.02250.3180.0000.0000.0000.0000.0000.000
192H197THR0-0.059-0.02649.7570.0010.0010.0000.0000.0000.000
193H198GLN00.0000.00744.1020.0050.0050.0000.0000.0000.000
194H199THR0-0.0070.01344.128-0.005-0.0050.0000.0000.0000.000
195H200TYR00.0350.00042.5050.0040.0040.0000.0000.0000.000
196H201ILE0-0.032-0.02641.014-0.004-0.0040.0000.0000.0000.000
197H202CYM-1-0.796-0.87038.7820.0360.0360.0000.0000.0000.000
198H203ASN00.015-0.00136.0710.0050.0050.0000.0000.0000.000
199H204VAL00.0340.01634.9910.0040.0040.0000.0000.0000.000
200H205ASN0-0.047-0.02631.9220.0120.0120.0000.0000.0000.000
201H206HIS10.8430.89032.221-0.009-0.0090.0000.0000.0000.000
202H207LYS11.0160.99225.059-0.126-0.1260.0000.0000.0000.000
203H208PRO00.0230.02229.4720.0070.0070.0000.0000.0000.000
204H209SER00.0070.00031.478-0.008-0.0080.0000.0000.0000.000
205H210ASN0-0.025-0.01933.7820.0060.0060.0000.0000.0000.000
206H211THR00.0130.03634.939-0.001-0.0010.0000.0000.0000.000
207H212LYS10.9520.96932.216-0.104-0.1040.0000.0000.0000.000
208H213VAL0-0.0060.00637.361-0.002-0.0020.0000.0000.0000.000
209H214ASP-1-0.845-0.90639.1630.0570.0570.0000.0000.0000.000
210H215LYS10.8700.92641.452-0.025-0.0250.0000.0000.0000.000
211H216ARG10.8840.93843.266-0.051-0.0510.0000.0000.0000.000
212H217VAL0-0.0150.00444.001-0.004-0.0040.0000.0000.0000.000