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: 6684Z

Calculation Name: 1M4U-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1M4U

Chain ID: A

ChEMBL ID:

UniProt ID: P18075

Base Structure: X-ray

Registration Date: 2023-06-19

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1971830.815215
FMO2-HF: Nuclear repulsion 1890174.598705
FMO2-HF: Total energy -81656.21651
FMO2-MP2: Total energy -81887.747602


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(A:27:MET)


Summations of interaction energy for fragment #1(A:27: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.
-3.358-1.0233.585-2.854-3.067-0.002
Interaction energy analysis for fragmet #1(A:27:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.002
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].
3A29HIS00.0180.0133.112-3.446-1.3350.012-0.938-1.1860.002
4A30TYR00.016-0.0073.260-2.234-1.1060.033-0.649-0.512-0.005
5A31LEU00.0050.0175.3430.0330.136-0.001-0.001-0.1010.000
6A32HIS0-0.037-0.0111.7502.2081.2013.541-1.266-1.2680.001
7A33ILE00.007-0.0126.9080.0780.0780.0000.0000.0000.000
8A34ARG10.9360.9749.502-0.053-0.0530.0000.0000.0000.000
9A35PRO00.0040.0179.1010.0610.0610.0000.0000.0000.000
10A36ALA00.0540.0166.919-0.024-0.0240.0000.0000.0000.000
11A37PRO0-0.064-0.0069.039-0.098-0.0980.0000.0000.0000.000
12A38SER00.022-0.02210.6860.1760.1760.0000.0000.0000.000
13A39ASP-1-0.891-0.95212.7060.3220.3220.0000.0000.0000.000
14A40ASN0-0.084-0.02514.617-0.047-0.0470.0000.0000.0000.000
15A41LEU0-0.0340.06816.913-0.029-0.0290.0000.0000.0000.000
16A42PRO0-0.009-0.07720.5740.0110.0110.0000.0000.0000.000
17A43LEU00.034-0.01819.7430.0160.0160.0000.0000.0000.000
18A44VAL0-0.0220.01722.815-0.015-0.0150.0000.0000.0000.000
19A45ASP-1-0.772-0.84823.9770.1310.1310.0000.0000.0000.000
20A46LEU0-0.015-0.01623.4690.0050.0050.0000.0000.0000.000
21A47ILE00.0170.02025.630-0.008-0.0080.0000.0000.0000.000
22A48GLU-1-0.812-0.89127.2540.0820.0820.0000.0000.0000.000
23A49HIS00.0520.00529.654-0.004-0.0040.0000.0000.0000.000
24A50PRO00.0260.01031.592-0.003-0.0030.0000.0000.0000.000
25A51ASP-1-0.861-0.91534.6070.0350.0350.0000.0000.0000.000
26A52PRO0-0.001-0.02535.9410.0010.0010.0000.0000.0000.000
27A53ILE0-0.103-0.02135.305-0.002-0.0020.0000.0000.0000.000
28A54PHE0-0.043-0.03331.211-0.003-0.0030.0000.0000.0000.000
29A55ASP-1-0.843-0.91334.5020.0470.0470.0000.0000.0000.000
30A56PRO00.0010.00335.719-0.004-0.0040.0000.0000.0000.000
31A57LYS10.9410.94838.172-0.019-0.0190.0000.0000.0000.000
32A58GLU-1-0.889-0.96641.9590.0170.0170.0000.0000.0000.000
33A59LYS10.9260.97942.136-0.012-0.0120.0000.0000.0000.000
34A60ASP-1-0.960-0.97940.0300.0100.0100.0000.0000.0000.000
35A61LEU00.0140.01038.9770.0020.0020.0000.0000.0000.000
36A62ASN00.0480.02241.7160.0020.0020.0000.0000.0000.000
37A63GLU-1-0.858-0.95842.1260.0220.0220.0000.0000.0000.000
38A64THR0-0.0160.01442.3360.0000.0000.0000.0000.0000.000
39A65LEU00.0430.02241.357-0.001-0.0010.0000.0000.0000.000
40A66LEU00.0100.02237.385-0.001-0.0010.0000.0000.0000.000
41A67ARG10.9670.96937.924-0.020-0.0200.0000.0000.0000.000
42A68SER0-0.099-0.03139.240-0.001-0.0010.0000.0000.0000.000
43A69LEU0-0.033-0.01834.731-0.003-0.0030.0000.0000.0000.000
44A70LEU0-0.038-0.01632.145-0.001-0.0010.0000.0000.0000.000
45A71GLY00.0390.01934.275-0.001-0.0010.0000.0000.0000.000
46A72GLY0-0.038-0.02535.2850.0030.0030.0000.0000.0000.000
47A73HIS0-0.022-0.01528.6920.0060.0060.0000.0000.0000.000
48A74TYR0-0.047-0.02432.7970.0050.0050.0000.0000.0000.000
49A75ASP-1-0.782-0.92133.1340.0370.0370.0000.0000.0000.000
50A76PRO0-0.0270.00035.3830.0040.0040.0000.0000.0000.000
51A77GLY0-0.0150.00136.8730.0010.0010.0000.0000.0000.000
52A78PHE0-0.074-0.06731.2500.0050.0050.0000.0000.0000.000
53A79MET0-0.0030.04132.0420.0040.0040.0000.0000.0000.000
54A80ALA00.006-0.00635.825-0.004-0.0040.0000.0000.0000.000
55A81THR0-0.003-0.01938.5340.0040.0040.0000.0000.0000.000
56A82SER0-0.042-0.03940.9140.0000.0000.0000.0000.0000.000
57A83PRO0-0.035-0.00139.430-0.002-0.0020.0000.0000.0000.000
58A84PRO00.0280.03840.712-0.001-0.0010.0000.0000.0000.000
59A85GLU-1-0.871-0.94438.8540.0680.0680.0000.0000.0000.000
60A86ASP-1-0.862-0.89342.6020.0440.0440.0000.0000.0000.000
61A87ARG10.8840.93845.451-0.041-0.0410.0000.0000.0000.000
62A88PRO0-0.002-0.01648.9860.0000.0000.0000.0000.0000.000
63A96GLY00.021-0.00345.2670.0010.0010.0000.0000.0000.000
64A97GLY00.0720.04143.953-0.001-0.0010.0000.0000.0000.000
65A98ALA0-0.056-0.03740.0980.0030.0030.0000.0000.0000.000
66A99GLU-1-0.963-0.98541.1350.0630.0630.0000.0000.0000.000
67A100ASP-1-0.802-0.90143.4570.0570.0570.0000.0000.0000.000
68A101LEU0-0.043-0.02036.3120.0020.0020.0000.0000.0000.000
69A102ALA0-0.028-0.01339.3200.0020.0020.0000.0000.0000.000
70A103GLU-1-0.923-0.94740.3420.0530.0530.0000.0000.0000.000
71A104LEU00.0480.00838.842-0.002-0.0020.0000.0000.0000.000
72A105ASP-1-0.817-0.90935.6990.0890.0890.0000.0000.0000.000
73A106GLN0-0.038-0.01738.3970.0010.0010.0000.0000.0000.000
74A107LEU00.0030.00040.673-0.002-0.0020.0000.0000.0000.000
75A108LEU00.010-0.00136.571-0.002-0.0020.0000.0000.0000.000
76A109ARG10.7840.89135.040-0.083-0.0830.0000.0000.0000.000
77A110GLN0-0.105-0.03137.781-0.004-0.0040.0000.0000.0000.000
78A111ARG10.8530.92839.471-0.047-0.0470.0000.0000.0000.000
79A112PRO00.0160.03634.9070.0000.0000.0000.0000.0000.000
80A113SER00.0240.01332.871-0.004-0.0040.0000.0000.0000.000
81A114GLY00.0220.00831.5410.0050.0050.0000.0000.0000.000
82A115ALA0-0.028-0.01231.241-0.005-0.0050.0000.0000.0000.000
83A116MET0-0.040-0.01531.9480.0030.0030.0000.0000.0000.000
84A117PRO00.0430.02228.710-0.004-0.0040.0000.0000.0000.000
85A118SER00.0670.02327.396-0.005-0.0050.0000.0000.0000.000
86A119GLU-1-0.913-0.94525.5340.0830.0830.0000.0000.0000.000
87A120ILE0-0.034-0.01129.787-0.001-0.0010.0000.0000.0000.000
88A121LYS10.9670.95232.989-0.036-0.0360.0000.0000.0000.000
89A122GLY0-0.053-0.02532.896-0.005-0.0050.0000.0000.0000.000
90A123LEU00.0170.01333.8470.0020.0020.0000.0000.0000.000
91A124GLU-1-0.895-0.96336.2120.0320.0320.0000.0000.0000.000
92A125PHE0-0.0270.00338.2960.0010.0010.0000.0000.0000.000
93A126SER00.015-0.03639.955-0.002-0.0020.0000.0000.0000.000
94A127GLU-1-0.818-0.92739.2280.0540.0540.0000.0000.0000.000
95A128GLY00.0950.01042.4570.0020.0020.0000.0000.0000.000
96A129LEU0-0.150-0.08245.0460.0010.0010.0000.0000.0000.000
97A130ALA00.0080.00244.638-0.001-0.0010.0000.0000.0000.000
98A131GLN00.3400.39039.750-0.002-0.0020.0000.0000.0000.000
99A132GLY0-0.243-0.35642.492-0.002-0.0020.0000.0000.0000.000
100A133LYS10.8380.94444.806-0.035-0.0350.0000.0000.0000.000
101A134LYS11.0231.02546.943-0.026-0.0260.0000.0000.0000.000
102A135GLN00.037-0.02246.6660.0010.0010.0000.0000.0000.000
103A136ARG10.8591.02344.869-0.047-0.0470.0000.0000.0000.000
104A137LEU00.0580.02843.5950.0000.0000.0000.0000.0000.000
105A138SER00.0090.00246.648-0.002-0.0020.0000.0000.0000.000
106A139LYS11.0361.07645.548-0.030-0.0300.0000.0000.0000.000
107A140LYS10.9480.92345.984-0.032-0.0320.0000.0000.0000.000
108A141LEU00.0500.01444.6460.0010.0010.0000.0000.0000.000
109A142ARG10.8060.92938.062-0.038-0.0380.0000.0000.0000.000
110A143ARG10.9860.97241.249-0.035-0.0350.0000.0000.0000.000
111A144LYS10.9500.96341.956-0.036-0.0360.0000.0000.0000.000
112A145LEU00.0090.04638.9880.0010.0010.0000.0000.0000.000
113A146GLN00.1240.05237.8110.0020.0020.0000.0000.0000.000
114A147MET0-0.066-0.02037.5820.0030.0030.0000.0000.0000.000
115A148TRP00.0530.03138.5800.0030.0030.0000.0000.0000.000
116A149LEU00.022-0.00435.2480.0030.0030.0000.0000.0000.000
117A150TRP0-0.0090.00232.8160.0030.0030.0000.0000.0000.000
118A151SER00.024-0.00234.6860.0030.0030.0000.0000.0000.000
119A152GLN0-0.050-0.01435.441-0.001-0.0010.0000.0000.0000.000
120A153THR0-0.014-0.02631.0900.0040.0040.0000.0000.0000.000
121A154PHE0-0.050-0.01830.9170.0090.0090.0000.0000.0000.000
122A155CYS00.016-0.01226.6100.0110.0110.0000.0000.0000.000
123A156PRO00.0030.00830.1900.0020.0020.0000.0000.0000.000
124A157VAL0-0.0060.00328.9500.0070.0070.0000.0000.0000.000
125A158LEU0-0.046-0.01731.295-0.009-0.0090.0000.0000.0000.000
126A159TYR0-0.008-0.03030.9680.0070.0070.0000.0000.0000.000
127A160ALA00.0520.02533.857-0.003-0.0030.0000.0000.0000.000
128A161TRP0-0.032-0.00734.1020.0040.0040.0000.0000.0000.000
129A162ASN0-0.045-0.03330.1540.0000.0000.0000.0000.0000.000
130A163ASP-1-0.835-0.92834.1560.0580.0580.0000.0000.0000.000
131A164LEU00.0210.01529.4150.0030.0030.0000.0000.0000.000
132A165GLY00.0270.00331.9970.0010.0010.0000.0000.0000.000
133A166SER0-0.041-0.02934.5230.0000.0000.0000.0000.0000.000
134A167ARG10.7590.86731.221-0.061-0.0610.0000.0000.0000.000
135A168PHE00.006-0.00826.8180.0010.0010.0000.0000.0000.000
136A169TRP00.0250.03932.566-0.002-0.0020.0000.0000.0000.000
137A170PRO00.078-0.03233.901-0.002-0.0020.0000.0000.0000.000
138A171ARG10.8360.93934.381-0.052-0.0520.0000.0000.0000.000
139A172TYR00.0140.04535.1010.0040.0040.0000.0000.0000.000
140A173VAL0-0.017-0.00830.496-0.004-0.0040.0000.0000.0000.000
141A174LYS10.9120.97233.382-0.057-0.0570.0000.0000.0000.000
142A175VAL00.0090.00228.8410.0030.0030.0000.0000.0000.000
143A176GLY00.0110.00228.942-0.005-0.0050.0000.0000.0000.000
144A177SER00.026-0.00428.4200.0140.0140.0000.0000.0000.000
145A178CYS0-0.0620.01624.7940.0160.0160.0000.0000.0000.000
146A179PHE00.0720.03429.4300.0000.0000.0000.0000.0000.000
147A180SER0-0.031-0.04329.228-0.002-0.0020.0000.0000.0000.000
148A181LYS10.9530.99831.211-0.119-0.1190.0000.0000.0000.000
149A182ARG10.9280.96633.445-0.100-0.1000.0000.0000.0000.000
150A183SER0-0.002-0.03731.4930.0070.0070.0000.0000.0000.000
151A184CYS0-0.0190.01325.5390.0060.0060.0000.0000.0000.000
152A185SER0-0.031-0.03930.4420.0000.0000.0000.0000.0000.000
153A186VAL0-0.0700.02632.514-0.005-0.0050.0000.0000.0000.000
154A187PRO00.051-0.03133.0050.0000.0000.0000.0000.0000.000
155A188GLU-1-0.899-0.94633.2770.1080.1080.0000.0000.0000.000
156A189GLY0-0.009-0.01630.4390.0010.0010.0000.0000.0000.000
157A190MET0-0.0340.00425.9540.0060.0060.0000.0000.0000.000
158A191VAL00.0250.03826.139-0.014-0.0140.0000.0000.0000.000
159A193LYS10.8500.93421.622-0.250-0.2500.0000.0000.0000.000
160A194PRO00.1080.02221.511-0.013-0.0130.0000.0000.0000.000
161A195SER0-0.097-0.04420.5580.0130.0130.0000.0000.0000.000
162A196LYS10.9410.96720.221-0.087-0.0870.0000.0000.0000.000
163A197SER0-0.015-0.00220.011-0.004-0.0040.0000.0000.0000.000
164A198VAL00.0440.04421.963-0.013-0.0130.0000.0000.0000.000
165A199HIS00.0200.00018.9250.0060.0060.0000.0000.0000.000
166A200LEU00.0500.03724.352-0.014-0.0140.0000.0000.0000.000
167A201THR0-0.053-0.03126.7460.0090.0090.0000.0000.0000.000
168A202VAL00.0290.01528.476-0.006-0.0060.0000.0000.0000.000
169A203LEU0-0.0200.00429.530-0.003-0.0030.0000.0000.0000.000
170A204ARG10.7780.87927.301-0.072-0.0720.0000.0000.0000.000
171A205TRP00.0030.02330.068-0.009-0.0090.0000.0000.0000.000
172A206ARG10.9520.97024.938-0.018-0.0180.0000.0000.0000.000
173A207CYS00.0030.04730.005-0.005-0.0050.0000.0000.0000.000
174A208GLN0-0.067-0.03028.7100.0010.0010.0000.0000.0000.000
175A209ARG10.8990.96029.2350.0090.0090.0000.0000.0000.000
176A210ARG11.0681.01431.089-0.003-0.0030.0000.0000.0000.000
177A211GLY00.0270.00432.030-0.003-0.0030.0000.0000.0000.000
178A212GLY00.0760.02333.1980.0000.0000.0000.0000.0000.000
179A213GLN0-0.019-0.01134.285-0.001-0.0010.0000.0000.0000.000
180A214ARG10.8920.92733.8490.0100.0100.0000.0000.0000.000
181A216GLY00.0300.01433.205-0.005-0.0050.0000.0000.0000.000
182A217TRP0-0.0030.02132.2330.0060.0060.0000.0000.0000.000
183A218ILE0-0.059-0.03326.390-0.007-0.0070.0000.0000.0000.000
184A219PRO00.0880.03227.3000.0080.0080.0000.0000.0000.000
185A220ILE0-0.075-0.02424.5430.0020.0020.0000.0000.0000.000
186A221GLN0-0.017-0.00920.668-0.019-0.0190.0000.0000.0000.000
187A222TYR0-0.016-0.05222.9820.0160.0160.0000.0000.0000.000
188A223PRO0-0.0060.02221.224-0.011-0.0110.0000.0000.0000.000
189A224ILE00.000-0.00723.4040.0010.0010.0000.0000.0000.000
190A225ILE0-0.010-0.01423.9060.0030.0030.0000.0000.0000.000
191A226SER00.025-0.00424.661-0.009-0.0090.0000.0000.0000.000
192A227GLU-1-0.944-0.96724.7950.0790.0790.0000.0000.0000.000
193A229LYS10.9570.97022.537-0.160-0.1600.0000.0000.0000.000
194A231SER0-0.005-0.01222.0630.0160.0160.0000.0000.0000.000
195A232CYS00.0580.04622.390-0.009-0.0090.0000.0000.0000.000