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: 3Q2ZL

Calculation Name: 1U2C-A-Xray372

Preferred Name: Dystroglycan

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1U2C

Chain ID: A

ChEMBL ID: CHEMBL3739252

UniProt ID: Q62165

Base Structure: X-ray

Registration Date: 2023-06-21

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2438416.845565
FMO2-HF: Nuclear repulsion 2352494.741727
FMO2-HF: Total energy -85922.103838
FMO2-MP2: Total energy -86171.908183


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:58:ALA)


Summations of interaction energy for fragment #1(A:58:ALA)
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.
0.4721.822-0.014-0.54-0.7950.001
Interaction energy analysis for fragmet #1(A:58:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.023
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].
3A60PRO00.0050.0153.815-0.0421.308-0.014-0.540-0.7950.001
4A61THR00.0250.0105.9630.2650.2650.0000.0000.0000.000
5A62VAL0-0.017-0.0099.285-0.057-0.0570.0000.0000.0000.000
6A63VAL00.0270.01612.6170.0540.0540.0000.0000.0000.000
7A64GLY00.0030.02515.765-0.029-0.0290.0000.0000.0000.000
8A65ILE0-0.022-0.01819.2540.0200.0200.0000.0000.0000.000
9A66PRO0-0.0060.00222.265-0.009-0.0090.0000.0000.0000.000
10A67ASP-1-0.795-0.87825.748-0.037-0.0370.0000.0000.0000.000
11A68GLY0-0.031-0.01728.3530.0070.0070.0000.0000.0000.000
12A69THR0-0.018-0.01231.048-0.004-0.0040.0000.0000.0000.000
13A70ALA00.0210.00134.7870.0030.0030.0000.0000.0000.000
14A71VAL00.0170.02137.275-0.002-0.0020.0000.0000.0000.000
15A72VAL0-0.0030.00641.0220.0010.0010.0000.0000.0000.000
16A73GLY0-0.013-0.00843.0940.0010.0010.0000.0000.0000.000
17A74ARG10.8240.90041.778-0.003-0.0030.0000.0000.0000.000
18A75SER00.012-0.00339.286-0.001-0.0010.0000.0000.0000.000
19A76PHE00.0010.00231.0190.0010.0010.0000.0000.0000.000
20A77ARG10.9140.93732.982-0.022-0.0220.0000.0000.0000.000
21A78VAL0-0.0100.00428.1890.0020.0020.0000.0000.0000.000
22A79SER00.0110.02126.4180.0010.0010.0000.0000.0000.000
23A80ILE0-0.012-0.00821.529-0.004-0.0040.0000.0000.0000.000
24A81PRO00.0390.01919.5790.0060.0060.0000.0000.0000.000
25A82THR00.007-0.04718.5670.0080.0080.0000.0000.0000.000
26A83ASP-1-0.912-0.94317.0850.1310.1310.0000.0000.0000.000
27A84LEU0-0.067-0.02714.8570.0320.0320.0000.0000.0000.000
28A85ILE0-0.063-0.02313.3610.0030.0030.0000.0000.0000.000
29A86ALA0-0.011-0.00912.975-0.037-0.0370.0000.0000.0000.000
30A87SER0-0.021-0.03310.9170.0670.0670.0000.0000.0000.000
31A88SER00.010-0.01713.098-0.036-0.0360.0000.0000.0000.000
32A89GLY0-0.043-0.01213.883-0.024-0.0240.0000.0000.0000.000
33A90GLU-1-0.909-0.92910.568-0.010-0.0100.0000.0000.0000.000
34A91ILE0-0.035-0.02114.8430.0100.0100.0000.0000.0000.000
35A92ILE00.0370.02517.280-0.021-0.0210.0000.0000.0000.000
36A93LYS10.8610.93219.2810.0560.0560.0000.0000.0000.000
37A94VAL00.0210.01521.234-0.007-0.0070.0000.0000.0000.000
38A95SER0-0.062-0.03923.9230.0040.0040.0000.0000.0000.000
39A96ALA00.0290.03025.692-0.002-0.0020.0000.0000.0000.000
40A97ALA00.028-0.00724.344-0.006-0.0060.0000.0000.0000.000
41A98GLY0-0.025-0.00724.0160.0020.0020.0000.0000.0000.000
42A99LYS10.9000.95125.4270.0680.0680.0000.0000.0000.000
43A100GLU-1-0.893-0.93825.846-0.062-0.0620.0000.0000.0000.000
44A101ALA0-0.009-0.00727.2970.0050.0050.0000.0000.0000.000
45A102LEU00.0380.01427.906-0.005-0.0050.0000.0000.0000.000
46A103PRO00.0050.01330.2350.0000.0000.0000.0000.0000.000
47A104SER00.0180.00933.3420.0020.0020.0000.0000.0000.000
48A105TRP0-0.053-0.02834.2300.0040.0040.0000.0000.0000.000
49A106LEU0-0.013-0.00730.6310.0030.0030.0000.0000.0000.000
50A107HIS00.001-0.00332.3170.0010.0010.0000.0000.0000.000
51A108TRP00.0490.02023.1960.0000.0000.0000.0000.0000.000
52A109ASP-1-0.862-0.89528.9500.0210.0210.0000.0000.0000.000
53A110PRO0-0.039-0.04525.1070.0050.0050.0000.0000.0000.000
54A111HIS00.0150.00924.8890.0100.0100.0000.0000.0000.000
55A112SER0-0.072-0.04626.9940.0070.0070.0000.0000.0000.000
56A113HIS00.0510.04522.549-0.005-0.0050.0000.0000.0000.000
57A114ILE0-0.018-0.01325.8050.0000.0000.0000.0000.0000.000
58A115LEU0-0.0160.00327.172-0.005-0.0050.0000.0000.0000.000
59A116GLU-1-0.788-0.89629.4470.0140.0140.0000.0000.0000.000
60A117GLY00.024-0.00733.242-0.004-0.0040.0000.0000.0000.000
61A118LEU0-0.0410.00336.1590.0020.0020.0000.0000.0000.000
62A119PRO00.0080.02538.355-0.002-0.0020.0000.0000.0000.000
63A120LEU00.0310.00440.1580.0020.0020.0000.0000.0000.000
64A121ASP-1-0.772-0.88342.555-0.016-0.0160.0000.0000.0000.000
65A122THR0-0.007-0.01942.6340.0000.0000.0000.0000.0000.000
66A123ASP-1-0.856-0.92038.343-0.022-0.0220.0000.0000.0000.000
67A124LYS10.8070.89538.5720.0160.0160.0000.0000.0000.000
68A125GLY00.0210.01937.820-0.002-0.0020.0000.0000.0000.000
69A126VAL00.0120.01731.5840.0020.0020.0000.0000.0000.000
70A127HIS0-0.049-0.02131.617-0.006-0.0060.0000.0000.0000.000
71A128TYR00.0430.01526.4570.0010.0010.0000.0000.0000.000
72A129ILE0-0.031-0.01225.025-0.003-0.0030.0000.0000.0000.000
73A130SER0-0.013-0.00821.147-0.004-0.0040.0000.0000.0000.000
74A131VAL00.0240.00318.8400.0070.0070.0000.0000.0000.000
75A132SER0-0.038-0.01916.688-0.016-0.0160.0000.0000.0000.000
76A133ALA00.0540.04513.1100.0270.0270.0000.0000.0000.000
77A134ALA00.003-0.00813.806-0.052-0.0520.0000.0000.0000.000
78A135ARG11.0021.0149.6430.2310.2310.0000.0000.0000.000
79A136LEU00.0150.01413.948-0.021-0.0210.0000.0000.0000.000
80A137GLY00.0040.01215.5730.0030.0030.0000.0000.0000.000
81A138ALA0-0.015-0.01316.4890.0120.0120.0000.0000.0000.000
82A139ASN0-0.0010.00018.7550.0080.0080.0000.0000.0000.000
83A140GLY00.0180.01220.0100.0030.0030.0000.0000.0000.000
84A141SER0-0.073-0.03918.231-0.006-0.0060.0000.0000.0000.000
85A142HIS00.0460.00817.373-0.010-0.0100.0000.0000.0000.000
86A143VAL0-0.025-0.01311.656-0.014-0.0140.0000.0000.0000.000
87A144PRO00.000-0.00213.3010.0060.0060.0000.0000.0000.000
88A145GLN0-0.0110.0007.2890.0090.0090.0000.0000.0000.000
89A146THR00.001-0.00310.052-0.102-0.1020.0000.0000.0000.000
90A147SER0-0.032-0.04512.4840.0310.0310.0000.0000.0000.000
91A148SER0-0.022-0.00416.044-0.022-0.0220.0000.0000.0000.000
92A149VAL0-0.038-0.03818.2230.0070.0070.0000.0000.0000.000
93A150PHE00.0020.02421.8010.0020.0020.0000.0000.0000.000
94A151SER0-0.070-0.05724.859-0.003-0.0030.0000.0000.0000.000
95A152ILE00.011-0.00228.5670.0060.0060.0000.0000.0000.000
96A153GLU-1-0.874-0.90831.624-0.025-0.0250.0000.0000.0000.000
97A154VAL0-0.073-0.03234.9800.0040.0040.0000.0000.0000.000
98A155TYR0-0.029-0.05637.156-0.001-0.0010.0000.0000.0000.000
99A156PRO00.015-0.02541.1170.0010.0010.0000.0000.0000.000
100A157GLU-1-0.851-0.92544.652-0.003-0.0030.0000.0000.0000.000
101A158ASP-1-0.874-0.90844.697-0.003-0.0030.0000.0000.0000.000
102A159HIS0-0.038-0.03845.0010.0020.0020.0000.0000.0000.000
103A160ASN0-0.0100.01741.1710.0020.0020.0000.0000.0000.000
104A179ALA0-0.011-0.01950.1540.0000.0000.0000.0000.0000.000
105A180CYS0-0.087-0.02752.0260.0000.0000.0000.0000.0000.000
106A181ALA00.0590.04055.2340.0000.0000.0000.0000.0000.000
107A182ALA00.0810.03656.3790.0000.0000.0000.0000.0000.000
108A183ASP-1-0.894-0.96357.3030.0000.0000.0000.0000.0000.000
109A184GLU-1-0.985-1.00159.2930.0050.0050.0000.0000.0000.000
110A185PRO0-0.029-0.01558.5300.0000.0000.0000.0000.0000.000
111A186VAL00.0200.00954.1070.0010.0010.0000.0000.0000.000
112A187THR0-0.010-0.01157.448-0.001-0.0010.0000.0000.0000.000
113A188VAL0-0.034-0.02554.3130.0010.0010.0000.0000.0000.000
114A189LEU00.0380.03155.9210.0000.0000.0000.0000.0000.000
115A190THR0-0.034-0.03855.1140.0000.0000.0000.0000.0000.000
116A191VAL00.0210.00454.4580.0000.0000.0000.0000.0000.000
117A192ILE0-0.024-0.00854.875-0.001-0.0010.0000.0000.0000.000
118A193LEU00.0100.00551.4610.0010.0010.0000.0000.0000.000
119A194ASP-1-0.794-0.89055.054-0.004-0.0040.0000.0000.0000.000
120A195ALA00.015-0.00450.4290.0000.0000.0000.0000.0000.000
121A196ASP-1-0.780-0.87949.357-0.011-0.0110.0000.0000.0000.000
122A197LEU00.0360.00845.6370.0000.0000.0000.0000.0000.000
123A198THR0-0.077-0.05744.832-0.001-0.0010.0000.0000.0000.000
124A199LYS10.7830.89044.8300.0090.0090.0000.0000.0000.000
125A200MET0-0.073-0.01444.0760.0010.0010.0000.0000.0000.000
126A201THR00.017-0.01838.626-0.001-0.0010.0000.0000.0000.000
127A202PRO00.0620.01736.1650.0020.0020.0000.0000.0000.000
128A203LYS10.8640.92834.724-0.008-0.0080.0000.0000.0000.000
129A204GLN00.0510.04138.5000.0010.0010.0000.0000.0000.000
130A205ARG10.8540.93640.3240.0110.0110.0000.0000.0000.000
131A206ILE0-0.0030.00437.6740.0010.0010.0000.0000.0000.000
132A207ASP-1-0.813-0.90641.0560.0110.0110.0000.0000.0000.000
133A208LEU0-0.0190.00242.8470.0010.0010.0000.0000.0000.000
134A209LEU00.0260.00242.8840.0010.0010.0000.0000.0000.000
135A210ASN0-0.029-0.02342.4140.0020.0020.0000.0000.0000.000
136A211ARG10.7890.88744.543-0.007-0.0070.0000.0000.0000.000
137A212MET0-0.0030.00247.7350.0000.0000.0000.0000.0000.000
138A213GLN00.0160.01143.7610.0010.0010.0000.0000.0000.000
139A214SER0-0.032-0.00349.0330.0000.0000.0000.0000.0000.000
140A215PHE0-0.011-0.00951.6330.0000.0000.0000.0000.0000.000
141A216SER00.005-0.03650.0300.0000.0000.0000.0000.0000.000
142A217GLU-1-0.982-0.98051.1690.0140.0140.0000.0000.0000.000
143A218VAL0-0.053-0.02348.0060.0010.0010.0000.0000.0000.000
144A219GLU-1-0.853-0.93843.1800.0200.0200.0000.0000.0000.000
145A220LEU00.0330.01340.459-0.002-0.0020.0000.0000.0000.000
146A221HIS0-0.041-0.01140.045-0.002-0.0020.0000.0000.0000.000
147A222ASN0-0.078-0.03942.095-0.002-0.0020.0000.0000.0000.000
148A223MET0-0.0500.03545.415-0.001-0.0010.0000.0000.0000.000
149A224LYS10.8210.90645.6680.0010.0010.0000.0000.0000.000
150A225LEU0-0.029-0.03145.1160.0000.0000.0000.0000.0000.000
151A226VAL00.0290.01546.427-0.001-0.0010.0000.0000.0000.000
152A227PRO00.0090.00247.6960.0010.0010.0000.0000.0000.000
153A228VAL0-0.0130.02450.7350.0000.0000.0000.0000.0000.000
154A229VAL00.0400.01353.034-0.001-0.0010.0000.0000.0000.000
155A230ASN0-0.063-0.04555.6780.0010.0010.0000.0000.0000.000
156A231ASN00.0180.00858.0690.0000.0000.0000.0000.0000.000
157A232ARG10.9621.00059.2400.0060.0060.0000.0000.0000.000
158A233LEU00.0080.00358.4470.0000.0000.0000.0000.0000.000
159A234PHE00.0230.00160.8720.0010.0010.0000.0000.0000.000
160A235ASP-1-0.771-0.83961.065-0.002-0.0020.0000.0000.0000.000
161A236MET0-0.020-0.01763.1110.0000.0000.0000.0000.0000.000
162A237SER0-0.088-0.06863.7040.0000.0000.0000.0000.0000.000
163A238ALA0-0.042-0.01963.4890.0000.0000.0000.0000.0000.000
164A239PHE0-0.0070.00163.7510.0000.0000.0000.0000.0000.000
165A240MET0-0.0080.00264.9720.0000.0000.0000.0000.0000.000
166A241ALA00.0290.01164.2420.0000.0000.0000.0000.0000.000
167A242GLY00.0020.01164.2730.0000.0000.0000.0000.0000.000
168A243PRO0-0.041-0.01064.1850.0000.0000.0000.0000.0000.000
169A244GLY00.0360.02361.7090.0010.0010.0000.0000.0000.000
170A245ASN00.0780.02959.6350.0000.0000.0000.0000.0000.000
171A246ALA0-0.042-0.01460.3640.0000.0000.0000.0000.0000.000
172A247LYS10.9200.94862.468-0.001-0.0010.0000.0000.0000.000
173A248LYS10.9010.94263.4940.0030.0030.0000.0000.0000.000
174A249VAL00.0100.02058.8310.0000.0000.0000.0000.0000.000
175A250VAL0-0.050-0.03557.4320.0000.0000.0000.0000.0000.000
176A251GLU-1-0.825-0.89853.102-0.009-0.0090.0000.0000.0000.000
177A252ASN0-0.088-0.04253.1260.0000.0000.0000.0000.0000.000
178A253GLY00.0120.01354.0710.0000.0000.0000.0000.0000.000
179A254ALA0-0.049-0.04050.462-0.001-0.0010.0000.0000.0000.000
180A255LEU0-0.018-0.01251.7290.0010.0010.0000.0000.0000.000
181A256LEU00.0290.01848.9210.0000.0000.0000.0000.0000.000
182A257SER0-0.026-0.01550.8160.0000.0000.0000.0000.0000.000
183A258TRP00.0870.03850.4820.0000.0000.0000.0000.0000.000
184A259LYS10.9080.96351.617-0.008-0.0080.0000.0000.0000.000
185A260LEU00.0060.00653.5470.0010.0010.0000.0000.0000.000
186A261GLY00.015-0.00956.4190.0010.0010.0000.0000.0000.000
187A263SER00.0130.00959.0390.0000.0000.0000.0000.0000.000
188A264LEU0-0.0120.00260.0890.0000.0000.0000.0000.0000.000
189A265ASN00.0210.00363.598-0.001-0.0010.0000.0000.0000.000
190A266GLN00.038-0.01066.1080.0000.0000.0000.0000.0000.000
191A267ASN0-0.044-0.02167.8110.0000.0000.0000.0000.0000.000
192A268SER0-0.0070.01064.3360.0000.0000.0000.0000.0000.000
193A269VAL0-0.038-0.00462.0910.0000.0000.0000.0000.0000.000
194A270PRO00.0470.03358.9200.0000.0000.0000.0000.0000.000
195A271ASP-1-0.795-0.88562.0820.0080.0080.0000.0000.0000.000
196A272ILE00.0450.02359.7040.0000.0000.0000.0000.0000.000
197A273ARG10.9050.91861.657-0.009-0.0090.0000.0000.0000.000
198A274GLY00.0030.01159.4550.0000.0000.0000.0000.0000.000
199A275VAL0-0.013-0.01056.8880.0000.0000.0000.0000.0000.000
200A276GLU-1-0.850-0.92159.2680.0050.0050.0000.0000.0000.000
201A277THR0-0.001-0.00962.7110.0000.0000.0000.0000.0000.000
202A278PRO00.0500.01858.7860.0000.0000.0000.0000.0000.000
203A279ALA0-0.0100.00159.8110.0000.0000.0000.0000.0000.000
204A280ARG10.7920.89260.710-0.005-0.0050.0000.0000.0000.000
205A281GLU-1-0.955-0.98163.1620.0060.0060.0000.0000.0000.000
206A282GLY0-0.034-0.00560.7540.0000.0000.0000.0000.0000.000
207A283ALA00.0070.00458.8110.0000.0000.0000.0000.0000.000
208A284MET00.0030.01255.2950.0000.0000.0000.0000.0000.000
209A285SER0-0.004-0.00454.7820.0000.0000.0000.0000.0000.000
210A286ALA0-0.065-0.03154.4850.0000.0000.0000.0000.0000.000
211A287GLN0-0.045-0.02150.7300.0000.0000.0000.0000.0000.000
212A288LEU0-0.010-0.02050.2700.0000.0000.0000.0000.0000.000
213A289GLY00.0010.01049.6410.0000.0000.0000.0000.0000.000
214A290TYR0-0.011-0.01646.783-0.002-0.0020.0000.0000.0000.000
215A291PRO0-0.032-0.00653.3790.0010.0010.0000.0000.0000.000
216A292VAL00.0320.01656.2750.0000.0000.0000.0000.0000.000
217A293VAL0-0.019-0.03258.1760.0000.0000.0000.0000.0000.000
218A294GLY00.0020.00659.8000.0000.0000.0000.0000.0000.000
219A295TRP00.0010.02359.4820.0000.0000.0000.0000.0000.000
220A296HIS00.0310.00159.2990.0000.0000.0000.0000.0000.000
221A297ILE00.0020.00459.9160.0000.0000.0000.0000.0000.000
222A298ALA00.0200.00960.4120.0000.0000.0000.0000.0000.000
223A299ASN00.0100.01959.9790.0010.0010.0000.0000.0000.000
224A300LYS10.8320.90057.0350.0000.0000.0000.0000.0000.000
225A301LYS10.9200.95958.9400.0010.0010.0000.0000.0000.000
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