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: 1JQVZ

Calculation Name: 1M4U-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1978792.18609
FMO2-HF: Nuclear repulsion 1896965.377876
FMO2-HF: Total energy -81826.808214
FMO2-MP2: Total energy -82058.868943


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.
-3.193-0.8343.571-2.873-3.057-0.002
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 : 0.016 / q_NPA : -0.001
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].
3A29HIS 00.0180.0123.091-3.423-1.3400.018-0.932-1.1680.002
4A30TYR 00.016-0.0073.255-2.304-1.1540.035-0.667-0.518-0.005
5A31LEU 00.0030.0165.3430.0450.1540.000-0.003-0.1060.000
6A32HIS 0-0.035-0.0091.7522.1731.1903.518-1.271-1.2650.001
7A33ILE 00.006-0.0136.9090.0850.0850.0000.0000.0000.000
8A34ARG 10.9340.9739.497-0.045-0.0450.0000.0000.0000.000
9A35PRO 00.0060.0189.0960.0620.0620.0000.0000.0000.000
10A36ALA 00.0530.0156.909-0.021-0.0210.0000.0000.0000.000
11A37PRO 0-0.066-0.0079.029-0.102-0.1020.0000.0000.0000.000
12A38SER 00.022-0.02210.6860.1780.1780.0000.0000.0000.000
13A39ASP -1-0.894-0.95512.7060.3120.3120.0000.0000.0000.000
14A40ASN 0-0.076-0.02114.616-0.049-0.0490.0000.0000.0000.000
15A41LEU 0-0.0370.06416.913-0.031-0.0310.0000.0000.0000.000
16A42PRO 0-0.004-0.07520.5740.0100.0100.0000.0000.0000.000
17A43LEU 00.032-0.01519.7420.0160.0160.0000.0000.0000.000
18A44VAL 0-0.0210.01522.823-0.015-0.0150.0000.0000.0000.000
19A45ASP -1-0.773-0.84923.9850.1290.1290.0000.0000.0000.000
20A46LEU 0-0.016-0.01723.4580.0050.0050.0000.0000.0000.000
21A47ILE 00.0180.02125.622-0.008-0.0080.0000.0000.0000.000
22A48GLU -1-0.812-0.89227.2460.0800.0800.0000.0000.0000.000
23A49HIS 00.0530.00529.645-0.004-0.0040.0000.0000.0000.000
24A50PRO 00.0220.00931.584-0.003-0.0030.0000.0000.0000.000
25A51ASP -1-0.860-0.91534.5980.0340.0340.0000.0000.0000.000
26A52PRO 00.001-0.02435.9310.0010.0010.0000.0000.0000.000
27A53ILE 0-0.106-0.02235.295-0.003-0.0030.0000.0000.0000.000
28A54PHE 0-0.041-0.03331.201-0.003-0.0030.0000.0000.0000.000
29A55ASP -1-0.839-0.91134.4890.0470.0470.0000.0000.0000.000
30A56PRO 0-0.0060.00135.705-0.004-0.0040.0000.0000.0000.000
31A57LYS 10.9450.94938.159-0.018-0.0180.0000.0000.0000.000
32A58GLU -1-0.893-0.96741.9460.0170.0170.0000.0000.0000.000
33A59LYS 10.9270.97942.121-0.012-0.0120.0000.0000.0000.000
34A60ASP -1-0.958-0.97940.0140.0090.0090.0000.0000.0000.000
35A61LEU 00.0080.00938.9620.0020.0020.0000.0000.0000.000
36A62ASN 00.0530.02341.7010.0020.0020.0000.0000.0000.000
37A63GLU -1-0.859-0.95942.1100.0220.0220.0000.0000.0000.000
38A64THR 0-0.0180.01342.3190.0000.0000.0000.0000.0000.000
39A65LEU 00.0410.02141.339-0.001-0.0010.0000.0000.0000.000
40A66LEU 00.0060.01837.369-0.001-0.0010.0000.0000.0000.000
41A67ARG 10.9650.96937.907-0.019-0.0190.0000.0000.0000.000
42A68SER 0-0.081-0.02339.240-0.001-0.0010.0000.0000.0000.000
43A69LEU 0-0.041-0.02034.712-0.003-0.0030.0000.0000.0000.000
44A70LEU 0-0.042-0.01632.129-0.001-0.0010.0000.0000.0000.000
45A71GLY 00.0430.02134.275-0.001-0.0010.0000.0000.0000.000
46A72GLY 0-0.036-0.02535.2850.0030.0030.0000.0000.0000.000
47A73HIS 0-0.024-0.01628.6920.0060.0060.0000.0000.0000.000
48A74TYR 0-0.046-0.02332.7970.0050.0050.0000.0000.0000.000
49A75ASP -1-0.781-0.92133.1340.0360.0360.0000.0000.0000.000
50A76PRO 0-0.031-0.00235.3830.0040.0040.0000.0000.0000.000
51A77GLY 0-0.0120.00236.8730.0010.0010.0000.0000.0000.000
52A78PHE 0-0.076-0.06631.2500.0050.0050.0000.0000.0000.000
53A79MET 0-0.0020.04232.0420.0040.0040.0000.0000.0000.000
54A80ALA 00.004-0.00835.825-0.004-0.0040.0000.0000.0000.000
55A81THR 0-0.003-0.02138.5340.0040.0040.0000.0000.0000.000
56A82SER 0-0.041-0.03940.9140.0000.0000.0000.0000.0000.000
57A83PRO 0-0.035-0.00239.430-0.002-0.0020.0000.0000.0000.000
58A84PRO 00.0280.03840.712-0.001-0.0010.0000.0000.0000.000
59A85GLU -1-0.871-0.94338.8540.0670.0670.0000.0000.0000.000
60A86ASP -1-0.864-0.89442.6020.0430.0430.0000.0000.0000.000
61A87ARG 10.8870.93445.451-0.040-0.0400.0000.0000.0000.000
62A88PRO 0-0.050-0.05748.986-0.001-0.0010.0000.0000.0000.000
63A89NME 00.0450.04551.1710.0010.0010.0000.0000.0000.000
64A95ACE 00.009-0.01043.5940.0010.0010.0000.0000.0000.000
65A96GLY 00.0260.00044.657-0.002-0.0020.0000.0000.0000.000
66A97GLY 00.0620.04943.953-0.001-0.0010.0000.0000.0000.000
67A98ALA 0-0.067-0.04040.0890.0030.0030.0000.0000.0000.000
68A99GLU -1-0.964-0.98541.1350.0620.0620.0000.0000.0000.000
69A100ASP -1-0.799-0.90043.4570.0560.0560.0000.0000.0000.000
70A101LEU 0-0.043-0.01936.3120.0020.0020.0000.0000.0000.000
71A102ALA 0-0.023-0.01039.3200.0010.0010.0000.0000.0000.000
72A103GLU -1-0.925-0.94840.3420.0520.0520.0000.0000.0000.000
73A104LEU 00.0460.00738.842-0.002-0.0020.0000.0000.0000.000
74A105ASP -1-0.818-0.90935.6990.0870.0870.0000.0000.0000.000
75A106GLN 0-0.033-0.01438.3970.0010.0010.0000.0000.0000.000
76A107LEU 00.000-0.00240.673-0.002-0.0020.0000.0000.0000.000
77A108LEU 00.007-0.00236.571-0.002-0.0020.0000.0000.0000.000
78A109ARG 10.7920.89635.040-0.081-0.0810.0000.0000.0000.000
79A110GLN 0-0.106-0.03137.781-0.004-0.0040.0000.0000.0000.000
80A111ARG 10.8480.92539.471-0.046-0.0460.0000.0000.0000.000
81A112PRO 00.0170.03834.9070.0000.0000.0000.0000.0000.000
82A113SER 00.0220.01232.879-0.004-0.0040.0000.0000.0000.000
83A114GLY 00.0250.00931.5410.0040.0040.0000.0000.0000.000
84A115ALA 0-0.031-0.01431.241-0.005-0.0050.0000.0000.0000.000
85A116MET 0-0.043-0.01631.9480.0030.0030.0000.0000.0000.000
86A117PRO 00.0430.02328.710-0.004-0.0040.0000.0000.0000.000
87A118SER 00.0690.02327.396-0.005-0.0050.0000.0000.0000.000
88A119GLU -1-0.910-0.94225.5340.0800.0800.0000.0000.0000.000
89A120ILE 0-0.030-0.01029.787-0.001-0.0010.0000.0000.0000.000
90A121LYS 10.9660.95132.989-0.035-0.0350.0000.0000.0000.000
91A122GLY 0-0.054-0.02432.896-0.005-0.0050.0000.0000.0000.000
92A123LEU 00.0190.01333.8470.0020.0020.0000.0000.0000.000
93A124GLU -1-0.900-0.96636.2120.0310.0310.0000.0000.0000.000
94A125PHE 0-0.0220.00638.2960.0010.0010.0000.0000.0000.000
95A126SER 00.009-0.03839.955-0.002-0.0020.0000.0000.0000.000
96A127GLU -1-0.820-0.92839.2290.0530.0530.0000.0000.0000.000
97A128GLY 00.1000.01142.4580.0020.0020.0000.0000.0000.000
98A129LEU 0-0.153-0.08345.0460.0010.0010.0000.0000.0000.000
99A130ALA 00.0070.00244.639-0.001-0.0010.0000.0000.0000.000
100A131GLN 00.3430.39339.751-0.002-0.0020.0000.0000.0000.000
101A132GLY 0-0.246-0.36042.493-0.002-0.0020.0000.0000.0000.000
102A133LYS 10.8400.94644.806-0.034-0.0340.0000.0000.0000.000
103A134LYS 11.0211.02446.943-0.025-0.0250.0000.0000.0000.000
104A135GLN 00.037-0.02246.6660.0010.0010.0000.0000.0000.000
105A136ARG 10.8621.02444.869-0.046-0.0460.0000.0000.0000.000
106A137LEU 00.0550.02843.5950.0000.0000.0000.0000.0000.000
107A138SER 00.007-0.00146.648-0.002-0.0020.0000.0000.0000.000
108A139LYS 11.0351.07545.550-0.029-0.0290.0000.0000.0000.000
109A140LYS 10.9440.92145.984-0.031-0.0310.0000.0000.0000.000
110A141LEU 00.0540.01444.6460.0010.0010.0000.0000.0000.000
111A142ARG 10.8070.93238.062-0.037-0.0370.0000.0000.0000.000
112A143ARG 10.9880.97241.248-0.033-0.0330.0000.0000.0000.000
113A144LYS 10.9500.96441.956-0.035-0.0350.0000.0000.0000.000
114A145LEU 00.0060.04538.9880.0010.0010.0000.0000.0000.000
115A146GLN 00.1240.05237.8110.0020.0020.0000.0000.0000.000
116A147MET 0-0.074-0.02237.5820.0030.0030.0000.0000.0000.000
117A148TRP 00.0600.03338.5800.0030.0030.0000.0000.0000.000
118A149LEU 00.024-0.00435.2480.0030.0030.0000.0000.0000.000
119A150TRP 0-0.0110.00232.8150.0030.0030.0000.0000.0000.000
120A151SER 00.020-0.00534.6860.0030.0030.0000.0000.0000.000
121A152GLN 0-0.048-0.01435.441-0.001-0.0010.0000.0000.0000.000
122A153THR 0-0.008-0.02331.0900.0040.0040.0000.0000.0000.000
123A154PHE 0-0.053-0.01930.9170.0080.0080.0000.0000.0000.000
124A192CYS 00.007-0.01426.6100.0100.0100.0000.0000.0000.000
125A156PRO 0-0.0030.00430.1900.0020.0020.0000.0000.0000.000
126A157VAL 0-0.0050.00428.9500.0070.0070.0000.0000.0000.000
127A158LEU 0-0.050-0.01931.295-0.009-0.0090.0000.0000.0000.000
128A159TYR 0-0.006-0.02930.9670.0060.0060.0000.0000.0000.000
129A160ALA 00.0540.02533.857-0.003-0.0030.0000.0000.0000.000
130A161TRP 0-0.036-0.00834.1020.0040.0040.0000.0000.0000.000
131A162ASN 0-0.042-0.03230.1530.0000.0000.0000.0000.0000.000
132A163ASP -1-0.835-0.92934.1560.0570.0570.0000.0000.0000.000
133A164LEU 00.0200.01529.4150.0040.0040.0000.0000.0000.000
134A165GLY 00.0290.00331.9850.0010.0010.0000.0000.0000.000
135A166SER 0-0.043-0.02934.5100.0000.0000.0000.0000.0000.000
136A167ARG 10.7580.86631.210-0.060-0.0600.0000.0000.0000.000
137A168PHE 00.006-0.00726.8040.0010.0010.0000.0000.0000.000
138A169TRP 00.0240.03732.552-0.002-0.0020.0000.0000.0000.000
139A170PRO 00.075-0.03433.885-0.002-0.0020.0000.0000.0000.000
140A171ARG 10.8360.93934.377-0.051-0.0510.0000.0000.0000.000
141A172TYR 00.0150.04735.1010.0040.0040.0000.0000.0000.000
142A173VAL 0-0.022-0.00930.496-0.004-0.0040.0000.0000.0000.000
143A174LYS 10.9150.97333.382-0.056-0.0560.0000.0000.0000.000
144A175VAL 00.0070.00128.8410.0030.0030.0000.0000.0000.000
145A176GLY 00.0120.00228.942-0.005-0.0050.0000.0000.0000.000
146A177SER 00.027-0.00428.4200.0140.0140.0000.0000.0000.000
147A228CYS 0-0.0660.01724.7940.0160.0160.0000.0000.0000.000
148A179PHE 00.0560.02729.430-0.001-0.0010.0000.0000.0000.000
149A180SER 0-0.013-0.03429.228-0.002-0.0020.0000.0000.0000.000
150A181LYS 10.9480.99631.211-0.118-0.1180.0000.0000.0000.000
151A182ARG 10.9180.96033.445-0.098-0.0980.0000.0000.0000.000
152A183SER 00.003-0.03431.4910.0070.0070.0000.0000.0000.000
153A230CYS 0-0.044-0.00325.5390.0050.0050.0000.0000.0000.000
154A185SER 0-0.020-0.03230.442-0.001-0.0010.0000.0000.0000.000
155A186VAL 0-0.0860.01632.514-0.005-0.0050.0000.0000.0000.000
156A187PRO 00.049-0.03433.0050.0000.0000.0000.0000.0000.000
157A188GLU -1-0.906-0.94933.2770.1070.1070.0000.0000.0000.000
158A189GLY 0-0.017-0.02030.4370.0010.0010.0000.0000.0000.000
159A190MET 0-0.0080.02025.9540.0040.0040.0000.0000.0000.000
160A191VAL 00.0260.03726.138-0.016-0.0160.0000.0000.0000.000
161A193LYS 10.8260.92021.611-0.249-0.2490.0000.0000.0000.000
162A194PRO 00.0910.01421.511-0.014-0.0140.0000.0000.0000.000
163A195SER 0-0.090-0.03920.5580.0130.0130.0000.0000.0000.000
164A196LYS 10.9390.96420.221-0.085-0.0850.0000.0000.0000.000
165A197SER 0-0.016-0.00120.020-0.004-0.0040.0000.0000.0000.000
166A198VAL 00.0460.04221.963-0.015-0.0150.0000.0000.0000.000
167A199HIS 00.019-0.00118.9240.0060.0060.0000.0000.0000.000
168A200LEU 00.0460.03524.352-0.014-0.0140.0000.0000.0000.000
169A201THR 0-0.053-0.03126.7460.0090.0090.0000.0000.0000.000
170A202VAL 00.0290.01628.476-0.006-0.0060.0000.0000.0000.000
171A203LEU 0-0.0210.00429.513-0.003-0.0030.0000.0000.0000.000
172A204ARG 10.7810.88027.287-0.071-0.0710.0000.0000.0000.000
173A205TRP 00.0010.02230.053-0.009-0.0090.0000.0000.0000.000
174A206ARG 10.9560.97224.925-0.017-0.0170.0000.0000.0000.000
175A215CYS 0-0.0110.04429.991-0.005-0.0050.0000.0000.0000.000
176A208GLN 0-0.061-0.02928.6970.0010.0010.0000.0000.0000.000
177A209ARG 10.8990.95929.2240.0100.0100.0000.0000.0000.000
178A210ARG 11.0711.01531.080-0.003-0.0030.0000.0000.0000.000
179A211GLY 00.0270.00332.021-0.003-0.0030.0000.0000.0000.000
180A212GLY 00.0760.02433.1880.0000.0000.0000.0000.0000.000
181A213GLN 0-0.019-0.01134.274-0.001-0.0010.0000.0000.0000.000
182A214ARG 10.8920.92733.8350.0100.0100.0000.0000.0000.000
183A216GLY 00.0310.01333.190-0.005-0.0050.0000.0000.0000.000
184A217TRP 0-0.0050.02032.2180.0060.0060.0000.0000.0000.000
185A218ILE 0-0.062-0.03526.373-0.007-0.0070.0000.0000.0000.000
186A219PRO 00.0890.03327.2820.0080.0080.0000.0000.0000.000
187A220ILE 0-0.074-0.02424.5270.0020.0020.0000.0000.0000.000
188A221GLN 0-0.018-0.01020.668-0.019-0.0190.0000.0000.0000.000
189A222TYR 0-0.016-0.05322.9820.0170.0170.0000.0000.0000.000
190A223PRO 0-0.0060.02321.224-0.011-0.0110.0000.0000.0000.000
191A224ILE 0-0.002-0.00823.4040.0010.0010.0000.0000.0000.000
192A225ILE 0-0.004-0.01123.9060.0030.0030.0000.0000.0000.000
193A226SER 00.022-0.00524.661-0.009-0.0090.0000.0000.0000.000
194A227GLU -1-0.950-0.97124.7950.0760.0760.0000.0000.0000.000
195A229LYS 10.9580.96922.537-0.157-0.1570.0000.0000.0000.000
196A231SER 0-0.044-0.02822.0630.0140.0140.0000.0000.0000.000
197A232CYS -1-0.793-0.88022.3900.2350.2350.0000.0000.0000.000