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: ZY1ZN

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 OptHSide
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 -1971509.060372
FMO2-HF: Nuclear repulsion 1889848.233197
FMO2-HF: Total energy -81660.827174
FMO2-MP2: Total energy -81891.86736


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.
-4.944-0.9571.97-2.73-3.228-0.005
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 : -0.006
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].
3A29HIS00.0110.0092.983-2.979-0.9200.017-0.931-1.1450.001
4A30TYR00.019-0.0023.239-2.447-1.3380.033-0.621-0.521-0.005
5A31LEU00.0060.0145.3640.0830.184-0.001-0.002-0.0980.000
6A32HIS0-0.024-0.0042.0530.1720.8901.921-1.176-1.464-0.001
7A33ILE00.017-0.0096.9070.1400.1400.0000.0000.0000.000
8A34ARG10.9310.9729.4700.0490.0490.0000.0000.0000.000
9A35PRO00.0030.0179.0450.0240.0240.0000.0000.0000.000
10A36ALA00.0440.0116.778-0.049-0.0490.0000.0000.0000.000
11A37PRO0-0.053-0.0138.939-0.067-0.0670.0000.0000.0000.000
12A38SER00.018-0.01710.6860.1870.1870.0000.0000.0000.000
13A39ASP-1-0.900-0.95512.7060.6510.6510.0000.0000.0000.000
14A40ASN0-0.087-0.02413.748-0.106-0.1060.0000.0000.0000.000
15A41LEU0-0.0130.08316.809-0.051-0.0510.0000.0000.0000.000
16A42PRO0-0.008-0.07920.4610.0180.0180.0000.0000.0000.000
17A43LEU00.000-0.03719.1620.0180.0180.0000.0000.0000.000
18A44VAL0-0.0060.02522.873-0.020-0.0200.0000.0000.0000.000
19A45ASP-1-0.771-0.85724.0120.2000.2000.0000.0000.0000.000
20A46LEU0-0.024-0.02323.0030.0030.0030.0000.0000.0000.000
21A47ILE00.0210.02325.533-0.010-0.0100.0000.0000.0000.000
22A48GLU-1-0.797-0.86227.1660.1070.1070.0000.0000.0000.000
23A49HIS00.0230.00029.560-0.004-0.0040.0000.0000.0000.000
24A50PRO00.0430.01231.506-0.003-0.0030.0000.0000.0000.000
25A51ASP-1-0.845-0.91234.5090.0450.0450.0000.0000.0000.000
26A52PRO00.0360.00935.8460.0020.0020.0000.0000.0000.000
27A53ILE0-0.063-0.01535.104-0.003-0.0030.0000.0000.0000.000
28A54PHE0-0.036-0.03331.343-0.004-0.0040.0000.0000.0000.000
29A55ASP-1-0.759-0.81934.3890.0720.0720.0000.0000.0000.000
30A56PRO00.0250.03835.492-0.006-0.0060.0000.0000.0000.000
31A57LYS10.7910.86438.052-0.041-0.0410.0000.0000.0000.000
32A58GLU-1-0.885-0.96341.8390.0330.0330.0000.0000.0000.000
33A59LYS10.9270.97841.881-0.022-0.0220.0000.0000.0000.000
34A60ASP-1-0.922-0.97039.1980.0290.0290.0000.0000.0000.000
35A61LEU00.0100.01039.1520.0040.0040.0000.0000.0000.000
36A62ASN00.0230.01041.5840.0020.0020.0000.0000.0000.000
37A63GLU-1-0.780-0.90841.9790.0510.0510.0000.0000.0000.000
38A64THR00.0050.02442.1930.0010.0010.0000.0000.0000.000
39A65LEU00.0280.01641.262-0.001-0.0010.0000.0000.0000.000
40A66LEU0-0.0020.02137.3620.0000.0000.0000.0000.0000.000
41A67ARG10.9190.94637.780-0.048-0.0480.0000.0000.0000.000
42A68SER0-0.103-0.03739.130-0.001-0.0010.0000.0000.0000.000
43A69LEU0-0.028-0.01634.307-0.002-0.0020.0000.0000.0000.000
44A70LEU0-0.041-0.01431.720-0.001-0.0010.0000.0000.0000.000
45A71GLY00.0590.02834.3500.0020.0020.0000.0000.0000.000
46A72GLY0-0.034-0.02535.9420.0030.0030.0000.0000.0000.000
47A73HIS0-0.028-0.01328.9520.0110.0110.0000.0000.0000.000
48A74TYR0-0.032-0.02633.2370.0080.0080.0000.0000.0000.000
49A75ASP-1-0.768-0.90533.4440.0910.0910.0000.0000.0000.000
50A76PRO0-0.022-0.00435.7580.0050.0050.0000.0000.0000.000
51A77GLY0-0.0100.00737.2460.0000.0000.0000.0000.0000.000
52A78PHE0-0.055-0.06031.5180.0080.0080.0000.0000.0000.000
53A79MET00.0100.04531.6280.0050.0050.0000.0000.0000.000
54A80ALA00.0160.00635.882-0.006-0.0060.0000.0000.0000.000
55A81THR0-0.036-0.04738.4850.0050.0050.0000.0000.0000.000
56A82SER0-0.022-0.01940.830-0.001-0.0010.0000.0000.0000.000
57A83PRO0-0.019-0.00539.213-0.002-0.0020.0000.0000.0000.000
58A84PRO0-0.0040.01640.666-0.002-0.0020.0000.0000.0000.000
59A85GLU-1-0.883-0.95538.5660.1110.1110.0000.0000.0000.000
60A86ASP-1-0.825-0.88142.4290.0720.0720.0000.0000.0000.000
61A87ARG10.8910.95445.367-0.066-0.0660.0000.0000.0000.000
62A88PRO0-0.029-0.02948.8660.0000.0000.0000.0000.0000.000
63A96GLY00.025-0.00145.2460.0010.0010.0000.0000.0000.000
64A97GLY00.0680.04143.889-0.002-0.0020.0000.0000.0000.000
65A98ALA0-0.049-0.03840.0690.0060.0060.0000.0000.0000.000
66A99GLU-1-0.947-0.97641.0910.0970.0970.0000.0000.0000.000
67A100ASP-1-0.822-0.90743.3140.0920.0920.0000.0000.0000.000
68A101LEU0-0.063-0.02736.4630.0030.0030.0000.0000.0000.000
69A102ALA0-0.002-0.00539.2580.0040.0040.0000.0000.0000.000
70A103GLU-1-0.927-0.95440.2780.0880.0880.0000.0000.0000.000
71A104LEU00.0440.01038.866-0.001-0.0010.0000.0000.0000.000
72A105ASP-1-0.816-0.90535.6600.1470.1470.0000.0000.0000.000
73A106GLN00.0100.00638.2890.0070.0070.0000.0000.0000.000
74A107LEU00.0000.00740.570-0.002-0.0020.0000.0000.0000.000
75A108LEU00.0110.00536.734-0.002-0.0020.0000.0000.0000.000
76A109ARG10.7640.88034.990-0.134-0.1340.0000.0000.0000.000
77A110GLN0-0.107-0.05338.152-0.004-0.0040.0000.0000.0000.000
78A111ARG10.8360.91740.106-0.089-0.0890.0000.0000.0000.000
79A112PRO0-0.0120.03135.3250.0010.0010.0000.0000.0000.000
80A113SER00.0370.01233.531-0.005-0.0050.0000.0000.0000.000
81A114GLY00.0350.01232.2030.0080.0080.0000.0000.0000.000
82A115ALA0-0.033-0.01231.853-0.010-0.0100.0000.0000.0000.000
83A116MET0-0.0290.00032.5230.0040.0040.0000.0000.0000.000
84A117PRO00.0490.02828.857-0.004-0.0040.0000.0000.0000.000
85A118SER00.0530.01727.964-0.011-0.0110.0000.0000.0000.000
86A119GLU-1-0.889-0.93325.9020.1610.1610.0000.0000.0000.000
87A120ILE0-0.018-0.00829.761-0.005-0.0050.0000.0000.0000.000
88A121LYS10.9700.95433.116-0.090-0.0900.0000.0000.0000.000
89A122GLY0-0.043-0.02032.875-0.009-0.0090.0000.0000.0000.000
90A123LEU0-0.0140.00733.0610.0000.0000.0000.0000.0000.000
91A124GLU-1-0.804-0.86736.0230.0650.0650.0000.0000.0000.000
92A125PHE0-0.006-0.00737.761-0.001-0.0010.0000.0000.0000.000
93A126SER0-0.020-0.04139.543-0.004-0.0040.0000.0000.0000.000
94A127GLU-1-0.792-0.89538.5920.0840.0840.0000.0000.0000.000
95A128GLY00.0540.00941.8310.0030.0030.0000.0000.0000.000
96A129LEU0-0.146-0.08044.4100.0010.0010.0000.0000.0000.000
97A130ALA00.0250.00743.906-0.002-0.0020.0000.0000.0000.000
98A131GLN00.009-0.01138.993-0.005-0.0050.0000.0000.0000.000
99A132GLY00.0200.01341.851-0.002-0.0020.0000.0000.0000.000
100A133LYS10.8760.96044.211-0.054-0.0540.0000.0000.0000.000
101A134LYS11.0241.02146.408-0.043-0.0430.0000.0000.0000.000
102A135GLN00.034-0.02446.3570.0010.0010.0000.0000.0000.000
103A136ARG10.8991.01644.430-0.073-0.0730.0000.0000.0000.000
104A137LEU00.0430.01443.5030.0000.0000.0000.0000.0000.000
105A138SER0-0.013-0.00946.418-0.003-0.0030.0000.0000.0000.000
106A139LYS11.0451.03345.343-0.059-0.0590.0000.0000.0000.000
107A140LYS10.9570.97645.970-0.053-0.0530.0000.0000.0000.000
108A141LEU00.012-0.01245.7220.0020.0020.0000.0000.0000.000
109A142ARG10.7630.86737.758-0.075-0.0750.0000.0000.0000.000
110A143ARG11.0070.99441.252-0.072-0.0720.0000.0000.0000.000
111A144LYS10.9420.96042.165-0.063-0.0630.0000.0000.0000.000
112A145LEU00.0110.02639.4970.0020.0020.0000.0000.0000.000
113A146GLN00.0740.02837.5080.0000.0000.0000.0000.0000.000
114A147MET0-0.065-0.02237.8040.0050.0050.0000.0000.0000.000
115A148TRP00.0520.03338.9090.0050.0050.0000.0000.0000.000
116A149LEU00.0220.00035.3270.0050.0050.0000.0000.0000.000
117A150TRP00.001-0.00733.3250.0040.0040.0000.0000.0000.000
118A151SER00.0260.00935.1280.0060.0060.0000.0000.0000.000
119A152GLN0-0.0300.00935.353-0.002-0.0020.0000.0000.0000.000
120A153THR0-0.009-0.01931.3370.0070.0070.0000.0000.0000.000
121A154PHE0-0.059-0.02631.3670.0150.0150.0000.0000.0000.000
122A155CYS00.027-0.00626.5800.0150.0150.0000.0000.0000.000
123A156PRO00.0000.00730.4310.0070.0070.0000.0000.0000.000
124A157VAL0-0.011-0.00628.6280.0090.0090.0000.0000.0000.000
125A158LEU0-0.045-0.00931.268-0.014-0.0140.0000.0000.0000.000
126A159TYR0-0.016-0.03830.6500.0120.0120.0000.0000.0000.000
127A160ALA00.0730.04533.695-0.006-0.0060.0000.0000.0000.000
128A161TRP0-0.053-0.02833.9280.0070.0070.0000.0000.0000.000
129A162ASN0-0.043-0.02630.136-0.006-0.0060.0000.0000.0000.000
130A163ASP-1-0.807-0.90334.1560.0900.0900.0000.0000.0000.000
131A164LEU00.0210.01429.4380.0040.0040.0000.0000.0000.000
132A165GLY00.0290.01031.8810.0000.0000.0000.0000.0000.000
133A166SER0-0.040-0.05034.4020.0010.0010.0000.0000.0000.000
134A167ARG10.6750.80431.354-0.085-0.0850.0000.0000.0000.000
135A168PHE00.012-0.01226.6070.0020.0020.0000.0000.0000.000
136A169TRP00.0140.03832.438-0.003-0.0030.0000.0000.0000.000
137A170PRO00.062-0.02833.762-0.001-0.0010.0000.0000.0000.000
138A171ARG10.8110.92134.259-0.082-0.0820.0000.0000.0000.000
139A172TYR00.0130.02935.0180.0050.0050.0000.0000.0000.000
140A173VAL0-0.0010.00030.229-0.004-0.0040.0000.0000.0000.000
141A174LYS10.8360.93633.346-0.111-0.1110.0000.0000.0000.000
142A175VAL00.002-0.00728.2160.0070.0070.0000.0000.0000.000
143A176GLY00.0030.00428.787-0.008-0.0080.0000.0000.0000.000
144A177SER00.013-0.00928.2940.0200.0200.0000.0000.0000.000
145A178CYS0-0.0170.03324.8670.0230.0230.0000.0000.0000.000
146A179PHE00.0710.03829.325-0.003-0.0030.0000.0000.0000.000
147A180SER0-0.017-0.03329.126-0.003-0.0030.0000.0000.0000.000
148A181LYS10.9420.98631.183-0.185-0.1850.0000.0000.0000.000
149A182ARG10.9170.96133.449-0.160-0.1600.0000.0000.0000.000
150A183SER00.017-0.00831.6440.0100.0100.0000.0000.0000.000
151A184CYS00.0110.01825.5370.0060.0060.0000.0000.0000.000
152A185SER0-0.034-0.05530.4790.0020.0020.0000.0000.0000.000
153A186VAL0-0.0780.02232.583-0.008-0.0080.0000.0000.0000.000
154A187PRO00.055-0.02632.7670.0020.0020.0000.0000.0000.000
155A188GLU-1-0.918-0.95533.2150.1650.1650.0000.0000.0000.000
156A189GLY00.004-0.00430.5130.0000.0000.0000.0000.0000.000
157A190MET0-0.065-0.01025.5620.0090.0090.0000.0000.0000.000
158A191VAL00.0250.02426.258-0.020-0.0200.0000.0000.0000.000
159A193LYS10.8450.93121.559-0.395-0.3950.0000.0000.0000.000
160A194PRO00.1060.02021.456-0.017-0.0170.0000.0000.0000.000
161A195SER0-0.055-0.03220.7430.0260.0260.0000.0000.0000.000
162A196LYS10.7800.87720.859-0.213-0.2130.0000.0000.0000.000
163A197SER00.0040.00919.489-0.011-0.0110.0000.0000.0000.000
164A198VAL00.0270.02922.353-0.010-0.0100.0000.0000.0000.000
165A199HIS00.021-0.00719.336-0.005-0.0050.0000.0000.0000.000
166A200LEU00.0360.03524.642-0.018-0.0180.0000.0000.0000.000
167A201THR0-0.054-0.02726.8280.0130.0130.0000.0000.0000.000
168A202VAL00.0390.01128.353-0.009-0.0090.0000.0000.0000.000
169A203LEU0-0.0050.01029.387-0.003-0.0030.0000.0000.0000.000
170A204ARG10.7580.85027.028-0.101-0.1010.0000.0000.0000.000
171A205TRP00.0240.01929.936-0.011-0.0110.0000.0000.0000.000
172A206ARG10.9140.94925.690-0.031-0.0310.0000.0000.0000.000
173A207CYS0-0.0230.02429.884-0.007-0.0070.0000.0000.0000.000
174A208GLN0-0.0060.00328.2450.0000.0000.0000.0000.0000.000
175A209ARG10.8820.95429.1360.0080.0080.0000.0000.0000.000
176A210ARG11.0751.02531.1320.0010.0010.0000.0000.0000.000
177A211GLY00.0460.00731.944-0.003-0.0030.0000.0000.0000.000
178A212GLY00.0560.01733.0950.0010.0010.0000.0000.0000.000
179A213GLN0-0.026-0.01534.184-0.001-0.0010.0000.0000.0000.000
180A214ARG10.8980.93133.8290.0090.0090.0000.0000.0000.000
181A216GLY00.0410.02333.084-0.006-0.0060.0000.0000.0000.000
182A217TRP00.0030.02032.1040.0080.0080.0000.0000.0000.000
183A218ILE0-0.044-0.02326.032-0.009-0.0090.0000.0000.0000.000
184A219PRO00.0830.02527.2570.0090.0090.0000.0000.0000.000
185A220ILE0-0.073-0.02324.4810.0000.0000.0000.0000.0000.000
186A221GLN0-0.027-0.01520.884-0.023-0.0230.0000.0000.0000.000
187A222TYR0-0.033-0.03822.8860.0200.0200.0000.0000.0000.000
188A223PRO0-0.0030.01520.960-0.011-0.0110.0000.0000.0000.000
189A224ILE00.0120.00023.363-0.004-0.0040.0000.0000.0000.000
190A225ILE0-0.009-0.01523.7170.0110.0110.0000.0000.0000.000
191A226SER00.024-0.00424.828-0.014-0.0140.0000.0000.0000.000
192A227GLU-1-0.848-0.89924.8220.1930.1930.0000.0000.0000.000
193A229LYS10.9290.97022.963-0.288-0.2880.0000.0000.0000.000
194A231SER00.003-0.01022.0250.0280.0280.0000.0000.0000.000
195A232CYS00.0640.04922.4220.0070.0070.0000.0000.0000.000