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

tag_button

FMODB ID: J38Y9

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2438082.36989
FMO2-HF: Nuclear repulsion 2352161.523307
FMO2-HF: Total energy -85920.846583
FMO2-MP2: Total energy -86170.79212


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.
0.5341.906-0.015-0.547-0.810.001
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 : -0.019 / q_NPA : -0.020
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].
3A60PRO00.0090.0103.8150.0691.441-0.015-0.547-0.8100.001
4A61THR0-0.0040.0005.9600.2600.2600.0000.0000.0000.000
5A62VAL00.0210.0099.292-0.059-0.0590.0000.0000.0000.000
6A63VAL00.0380.02012.6160.0540.0540.0000.0000.0000.000
7A64GLY0-0.0070.00915.768-0.029-0.0290.0000.0000.0000.000
8A65ILE0-0.025-0.02119.2560.0210.0210.0000.0000.0000.000
9A66PRO0-0.022-0.00522.266-0.009-0.0090.0000.0000.0000.000
10A67ASP-1-0.817-0.91625.750-0.039-0.0390.0000.0000.0000.000
11A68GLY0-0.043-0.02628.3500.0070.0070.0000.0000.0000.000
12A69THR0-0.018-0.00731.046-0.004-0.0040.0000.0000.0000.000
13A70ALA00.0260.00034.7840.0030.0030.0000.0000.0000.000
14A71VAL00.0040.02137.270-0.002-0.0020.0000.0000.0000.000
15A72VAL00.003-0.00141.0170.0010.0010.0000.0000.0000.000
16A73GLY0-0.020-0.01343.0850.0010.0010.0000.0000.0000.000
17A74ARG10.8220.89241.745-0.003-0.0030.0000.0000.0000.000
18A75SER00.0230.00139.242-0.002-0.0020.0000.0000.0000.000
19A76PHE00.0090.00831.1320.0010.0010.0000.0000.0000.000
20A77ARG10.9640.97433.001-0.025-0.0250.0000.0000.0000.000
21A78VAL0-0.0090.00328.2690.0020.0020.0000.0000.0000.000
22A79SER00.0210.01626.551-0.002-0.0020.0000.0000.0000.000
23A80ILE0-0.0070.00221.440-0.004-0.0040.0000.0000.0000.000
24A81PRO00.0200.01119.5480.0070.0070.0000.0000.0000.000
25A82THR00.018-0.04918.5720.0080.0080.0000.0000.0000.000
26A83ASP-1-0.909-0.94317.0880.1400.1400.0000.0000.0000.000
27A84LEU0-0.075-0.03214.8710.0330.0330.0000.0000.0000.000
28A85ILE0-0.065-0.01713.3680.0040.0040.0000.0000.0000.000
29A86ALA00.005-0.00112.971-0.036-0.0360.0000.0000.0000.000
30A87SER0-0.0070.00210.7040.0610.0610.0000.0000.0000.000
31A88SER0-0.035-0.03613.102-0.050-0.0500.0000.0000.0000.000
32A89GLY0-0.0050.00413.885-0.025-0.0250.0000.0000.0000.000
33A90GLU-1-0.925-0.97110.138-0.013-0.0130.0000.0000.0000.000
34A91ILE0-0.033-0.01814.8310.0090.0090.0000.0000.0000.000
35A92ILE00.0380.02617.087-0.022-0.0220.0000.0000.0000.000
36A93LYS10.8850.95019.2670.0520.0520.0000.0000.0000.000
37A94VAL00.0310.02321.216-0.008-0.0080.0000.0000.0000.000
38A95SER0-0.089-0.07823.9060.0040.0040.0000.0000.0000.000
39A96ALA00.0550.03925.628-0.002-0.0020.0000.0000.0000.000
40A97ALA00.045-0.00424.262-0.006-0.0060.0000.0000.0000.000
41A98GLY0-0.060-0.02423.9490.0020.0020.0000.0000.0000.000
42A99LYS10.9130.95525.3580.0650.0650.0000.0000.0000.000
43A100GLU-1-0.898-0.93225.792-0.059-0.0590.0000.0000.0000.000
44A101ALA0-0.029-0.02127.2510.0050.0050.0000.0000.0000.000
45A102LEU00.0160.01727.372-0.005-0.0050.0000.0000.0000.000
46A103PRO00.0030.01130.1290.0000.0000.0000.0000.0000.000
47A104SER00.0250.00933.2800.0020.0020.0000.0000.0000.000
48A105TRP0-0.045-0.01734.0180.0040.0040.0000.0000.0000.000
49A106LEU0-0.004-0.00530.4360.0030.0030.0000.0000.0000.000
50A107HIS0-0.040-0.03432.2920.0010.0010.0000.0000.0000.000
51A108TRP00.0360.01923.2140.0000.0000.0000.0000.0000.000
52A109ASP-1-0.838-0.87328.9690.0240.0240.0000.0000.0000.000
53A110PRO0-0.057-0.05525.2280.0050.0050.0000.0000.0000.000
54A111HIS00.0150.00524.8860.0110.0110.0000.0000.0000.000
55A112SER0-0.069-0.04826.9960.0070.0070.0000.0000.0000.000
56A113HIS00.0500.04922.438-0.006-0.0060.0000.0000.0000.000
57A114ILE0-0.008-0.00625.8050.0000.0000.0000.0000.0000.000
58A115LEU0-0.027-0.00427.120-0.005-0.0050.0000.0000.0000.000
59A116GLU-1-0.867-0.95829.4410.0130.0130.0000.0000.0000.000
60A117GLY00.024-0.00933.236-0.004-0.0040.0000.0000.0000.000
61A118LEU0-0.0500.00136.1500.0020.0020.0000.0000.0000.000
62A119PRO0-0.0220.01138.240-0.002-0.0020.0000.0000.0000.000
63A120LEU00.0390.00040.1470.0020.0020.0000.0000.0000.000
64A121ASP-1-0.841-0.94142.542-0.017-0.0170.0000.0000.0000.000
65A122THR0-0.017-0.02442.474-0.001-0.0010.0000.0000.0000.000
66A123ASP-1-0.860-0.91138.309-0.022-0.0220.0000.0000.0000.000
67A124LYS10.8850.95538.5320.0180.0180.0000.0000.0000.000
68A125GLY00.0130.01537.734-0.002-0.0020.0000.0000.0000.000
69A126VAL00.0200.02231.4790.0020.0020.0000.0000.0000.000
70A127HIS0-0.058-0.02731.556-0.006-0.0060.0000.0000.0000.000
71A128TYR00.0400.01226.2720.0010.0010.0000.0000.0000.000
72A129ILE0-0.032-0.01125.022-0.002-0.0020.0000.0000.0000.000
73A130SER00.0120.00221.310-0.004-0.0040.0000.0000.0000.000
74A131VAL00.0070.00118.7990.0080.0080.0000.0000.0000.000
75A132SER0-0.033-0.01216.597-0.016-0.0160.0000.0000.0000.000
76A133ALA00.0620.04313.0270.0290.0290.0000.0000.0000.000
77A134ALA00.009-0.00113.773-0.054-0.0540.0000.0000.0000.000
78A135ARG11.0221.0239.9270.1900.1900.0000.0000.0000.000
79A136LEU00.0120.01213.923-0.023-0.0230.0000.0000.0000.000
80A137GLY0-0.0080.00515.6230.0060.0060.0000.0000.0000.000
81A138ALA0-0.017-0.01216.5330.0120.0120.0000.0000.0000.000
82A139ASN00.0240.01918.1870.0140.0140.0000.0000.0000.000
83A140GLY00.0200.01220.0450.0020.0020.0000.0000.0000.000
84A141SER0-0.091-0.05618.293-0.006-0.0060.0000.0000.0000.000
85A142HIS00.0390.00417.385-0.010-0.0100.0000.0000.0000.000
86A143VAL0-0.019-0.01111.742-0.014-0.0140.0000.0000.0000.000
87A144PRO0-0.024-0.00713.2210.0090.0090.0000.0000.0000.000
88A145GLN00.0110.0136.7330.0170.0170.0000.0000.0000.000
89A146THR0-0.018-0.01510.040-0.106-0.1060.0000.0000.0000.000
90A147SER0-0.029-0.05012.4190.0390.0390.0000.0000.0000.000
91A148SER0-0.0250.00715.971-0.023-0.0230.0000.0000.0000.000
92A149VAL0-0.033-0.03118.2110.0080.0080.0000.0000.0000.000
93A150PHE00.0200.03521.7510.0010.0010.0000.0000.0000.000
94A151SER0-0.042-0.01524.849-0.003-0.0030.0000.0000.0000.000
95A152ILE00.005-0.00228.5570.0070.0070.0000.0000.0000.000
96A153GLU-1-0.928-0.96031.615-0.028-0.0280.0000.0000.0000.000
97A154VAL0-0.059-0.02834.9710.0040.0040.0000.0000.0000.000
98A155TYR00.018-0.00937.139-0.001-0.0010.0000.0000.0000.000
99A156PRO00.012-0.02641.1090.0010.0010.0000.0000.0000.000
100A157GLU-1-0.830-0.90844.643-0.004-0.0040.0000.0000.0000.000
101A158ASP-1-0.866-0.90944.635-0.003-0.0030.0000.0000.0000.000
102A159HIS0-0.038-0.04144.9530.0020.0020.0000.0000.0000.000
103A160ASN0-0.0120.01941.1030.0020.0020.0000.0000.0000.000
104A179ALA00.000-0.01750.1850.0000.0000.0000.0000.0000.000
105A180CYS0-0.098-0.02852.0330.0000.0000.0000.0000.0000.000
106A181ALA00.0630.03855.2390.0000.0000.0000.0000.0000.000
107A182ALA00.0890.03956.3730.0000.0000.0000.0000.0000.000
108A183ASP-1-0.952-0.98857.3070.0000.0000.0000.0000.0000.000
109A184GLU-1-0.995-1.00459.4090.0050.0050.0000.0000.0000.000
110A185PRO0-0.048-0.03458.5330.0000.0000.0000.0000.0000.000
111A186VAL00.0240.01854.1390.0010.0010.0000.0000.0000.000
112A187THR0-0.009-0.00657.450-0.001-0.0010.0000.0000.0000.000
113A188VAL0-0.035-0.02354.5350.0010.0010.0000.0000.0000.000
114A189LEU00.0380.02555.915-0.001-0.0010.0000.0000.0000.000
115A190THR0-0.026-0.03355.2330.0000.0000.0000.0000.0000.000
116A191VAL00.0180.00354.4040.0000.0000.0000.0000.0000.000
117A192ILE0-0.031-0.01254.868-0.001-0.0010.0000.0000.0000.000
118A193LEU00.010-0.00151.3510.0010.0010.0000.0000.0000.000
119A194ASP-1-0.791-0.87455.042-0.004-0.0040.0000.0000.0000.000
120A195ALA00.0290.00050.3920.0000.0000.0000.0000.0000.000
121A196ASP-1-0.783-0.88549.533-0.011-0.0110.0000.0000.0000.000
122A197LEU00.0380.01145.6420.0000.0000.0000.0000.0000.000
123A198THR0-0.070-0.05044.817-0.001-0.0010.0000.0000.0000.000
124A199LYS10.8120.92044.8000.0090.0090.0000.0000.0000.000
125A200MET0-0.054-0.00744.0390.0010.0010.0000.0000.0000.000
126A201THR00.006-0.01038.627-0.001-0.0010.0000.0000.0000.000
127A202PRO00.0720.02535.9910.0020.0020.0000.0000.0000.000
128A203LYS10.9340.98535.703-0.008-0.0080.0000.0000.0000.000
129A204GLN00.0350.02038.4900.0010.0010.0000.0000.0000.000
130A205ARG10.8770.95240.2630.0110.0110.0000.0000.0000.000
131A206ILE0-0.0080.00237.6300.0010.0010.0000.0000.0000.000
132A207ASP-1-0.872-0.93741.0510.0110.0110.0000.0000.0000.000
133A208LEU00.0070.01242.8420.0010.0010.0000.0000.0000.000
134A209LEU00.022-0.00142.7420.0010.0010.0000.0000.0000.000
135A210ASN0-0.007-0.01942.4470.0020.0020.0000.0000.0000.000
136A211ARG10.8110.90044.542-0.009-0.0090.0000.0000.0000.000
137A212MET00.0130.01447.7330.0000.0000.0000.0000.0000.000
138A213GLN00.0340.02143.8060.0000.0000.0000.0000.0000.000
139A214SER0-0.041-0.00949.0350.0000.0000.0000.0000.0000.000
140A215PHE0-0.008-0.00651.6360.0000.0000.0000.0000.0000.000
141A216SER00.011-0.02250.0540.0000.0000.0000.0000.0000.000
142A217GLU-1-0.970-0.97751.2220.0140.0140.0000.0000.0000.000
143A218VAL0-0.067-0.02347.8790.0010.0010.0000.0000.0000.000
144A219GLU-1-0.899-0.96842.9030.0220.0220.0000.0000.0000.000
145A220LEU00.0240.00840.815-0.002-0.0020.0000.0000.0000.000
146A221HIS0-0.0180.00240.108-0.002-0.0020.0000.0000.0000.000
147A222ASN0-0.061-0.01142.097-0.003-0.0030.0000.0000.0000.000
148A223MET0-0.0700.01545.417-0.001-0.0010.0000.0000.0000.000
149A224LYS10.7790.87845.6660.0020.0020.0000.0000.0000.000
150A225LEU0-0.022-0.02545.3600.0000.0000.0000.0000.0000.000
151A226VAL00.0350.01446.419-0.001-0.0010.0000.0000.0000.000
152A227PRO00.005-0.00347.6590.0010.0010.0000.0000.0000.000
153A228VAL00.0000.03750.7230.0000.0000.0000.0000.0000.000
154A229VAL00.0420.01653.172-0.001-0.0010.0000.0000.0000.000
155A230ASN0-0.084-0.05255.6640.0010.0010.0000.0000.0000.000
156A231ASN00.0330.01358.0580.0000.0000.0000.0000.0000.000
157A232ARG10.9600.99859.2340.0060.0060.0000.0000.0000.000
158A233LEU00.0090.00458.4210.0000.0000.0000.0000.0000.000
159A234PHE00.019-0.00560.8610.0010.0010.0000.0000.0000.000
160A235ASP-1-0.792-0.84461.094-0.002-0.0020.0000.0000.0000.000
161A236MET0-0.020-0.02763.1040.0010.0010.0000.0000.0000.000
162A237SER0-0.103-0.08063.6630.0000.0000.0000.0000.0000.000
163A238ALA0-0.028-0.01763.4400.0000.0000.0000.0000.0000.000
164A239PHE0-0.015-0.00263.6040.0000.0000.0000.0000.0000.000
165A240MET0-0.0090.00264.8660.0000.0000.0000.0000.0000.000
166A241ALA00.0320.01064.2390.0000.0000.0000.0000.0000.000
167A242GLY00.0020.00164.2690.0000.0000.0000.0000.0000.000
168A243PRO0-0.048-0.01564.1800.0000.0000.0000.0000.0000.000
169A244GLY00.0400.02861.6980.0010.0010.0000.0000.0000.000
170A245ASN00.0740.02759.5080.0000.0000.0000.0000.0000.000
171A246ALA0-0.059-0.02560.3480.0000.0000.0000.0000.0000.000
172A247LYS10.9430.96062.457-0.001-0.0010.0000.0000.0000.000
173A248LYS10.9110.94663.3360.0030.0030.0000.0000.0000.000
174A249VAL00.0040.01758.8070.0000.0000.0000.0000.0000.000
175A250VAL0-0.065-0.04157.0830.0000.0000.0000.0000.0000.000
176A251GLU-1-0.886-0.94253.119-0.008-0.0080.0000.0000.0000.000
177A252ASN0-0.068-0.04452.5850.0000.0000.0000.0000.0000.000
178A253GLY00.0130.01354.0530.0000.0000.0000.0000.0000.000
179A254ALA0-0.047-0.03650.480-0.001-0.0010.0000.0000.0000.000
180A255LEU0-0.028-0.02051.7270.0010.0010.0000.0000.0000.000
181A256LEU00.0380.02248.8700.0000.0000.0000.0000.0000.000
182A257SER0-0.050-0.01850.8080.0000.0000.0000.0000.0000.000
183A258TRP00.0890.03450.4800.0000.0000.0000.0000.0000.000
184A259LYS10.9230.97151.619-0.008-0.0080.0000.0000.0000.000
185A260LEU0-0.0010.00153.5490.0010.0010.0000.0000.0000.000
186A261GLY00.015-0.00456.4230.0010.0010.0000.0000.0000.000
187A263SER00.0060.00459.0440.0000.0000.0000.0000.0000.000
188A264LEU00.0040.01060.0970.0000.0000.0000.0000.0000.000
189A265ASN0-0.0130.00363.6020.0000.0000.0000.0000.0000.000
190A266GLN00.064-0.00966.1110.0000.0000.0000.0000.0000.000
191A267ASN0-0.040-0.02967.8150.0000.0000.0000.0000.0000.000
192A268SER0-0.0140.01764.5940.0000.0000.0000.0000.0000.000
193A269VAL0-0.044-0.01061.8390.0000.0000.0000.0000.0000.000
194A270PRO00.0360.03058.9400.0000.0000.0000.0000.0000.000
195A271ASP-1-0.791-0.89162.0880.0090.0090.0000.0000.0000.000
196A272ILE00.0470.02759.8400.0000.0000.0000.0000.0000.000
197A273ARG10.9180.92961.660-0.010-0.0100.0000.0000.0000.000
198A274GLY00.0040.01059.4580.0000.0000.0000.0000.0000.000
199A275VAL0-0.010-0.00556.7700.0000.0000.0000.0000.0000.000
200A276GLU-1-0.908-0.98659.2690.0050.0050.0000.0000.0000.000
201A277THR00.0010.00862.7100.0000.0000.0000.0000.0000.000
202A278PRO00.0310.00258.7500.0000.0000.0000.0000.0000.000
203A279ALA00.0020.00759.8000.0000.0000.0000.0000.0000.000
204A280ARG10.8600.95160.707-0.005-0.0050.0000.0000.0000.000
205A281GLU-1-0.975-0.99263.3000.0070.0070.0000.0000.0000.000
206A282GLY0-0.0250.00060.7500.0000.0000.0000.0000.0000.000
207A283ALA00.0170.01058.8120.0000.0000.0000.0000.0000.000
208A284MET00.0000.01455.3620.0000.0000.0000.0000.0000.000
209A285SER0-0.059-0.02654.7780.0000.0000.0000.0000.0000.000
210A286ALA0-0.020-0.01454.4780.0000.0000.0000.0000.0000.000
211A287GLN0-0.060-0.02850.7560.0000.0000.0000.0000.0000.000
212A288LEU0-0.013-0.02950.2540.0000.0000.0000.0000.0000.000
213A289GLY00.0080.01749.6340.0000.0000.0000.0000.0000.000
214A290TYR0-0.014-0.01947.246-0.001-0.0010.0000.0000.0000.000
215A291PRO0-0.027-0.00153.3700.0010.0010.0000.0000.0000.000
216A292VAL00.0390.01956.2940.0000.0000.0000.0000.0000.000
217A293VAL0-0.021-0.03158.1680.0000.0000.0000.0000.0000.000
218A294GLY0-0.0010.00159.7930.0000.0000.0000.0000.0000.000
219A295TRP00.0060.03559.4760.0000.0000.0000.0000.0000.000
220A296HIS00.030-0.00359.2160.0000.0000.0000.0000.0000.000
221A297ILE00.0140.01059.9140.0000.0000.0000.0000.0000.000
222A298ALA00.0130.00460.4110.0000.0000.0000.0000.0000.000
223A299ASN00.0400.03859.9780.0010.0010.0000.0000.0000.000
224A300LYS10.8490.92056.8820.0000.0000.0000.0000.0000.000
225A301LYS10.9800.98658.9390.0020.0020.0000.0000.0000.000
226A302PRO0-0.0060.01055.3940.0000.0000.0000.0000.0000.000
227A303THR00.0190.01550.818-0.001-0.0010.0000.0000.0000.000