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: LJ5G9

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 OptAll
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 -2440424.776966
FMO2-HF: Nuclear repulsion 2354502.063746
FMO2-HF: Total energy -85922.71322
FMO2-MP2: Total energy -86172.54874


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.
0.5321.644-0.007-0.446-0.6590.001
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 : -0.010 / 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].
3A60PRO0-0.0040.0113.8760.0591.171-0.007-0.446-0.6590.001
4A61THR00.0300.0116.1750.3200.3200.0000.0000.0000.000
5A62VAL0-0.024-0.0139.159-0.122-0.1220.0000.0000.0000.000
6A63VAL00.0210.01412.5960.0690.0690.0000.0000.0000.000
7A64GLY00.0000.02115.910-0.032-0.0320.0000.0000.0000.000
8A65ILE00.000-0.01419.4870.0180.0180.0000.0000.0000.000
9A66PRO0-0.024-0.00322.369-0.009-0.0090.0000.0000.0000.000
10A67ASP-1-0.818-0.89025.868-0.032-0.0320.0000.0000.0000.000
11A68GLY0-0.007-0.00228.5430.0070.0070.0000.0000.0000.000
12A69THR0-0.036-0.01731.412-0.004-0.0040.0000.0000.0000.000
13A70ALA00.0160.00235.1130.0030.0030.0000.0000.0000.000
14A71VAL00.0310.01837.465-0.001-0.0010.0000.0000.0000.000
15A72VAL0-0.030-0.00541.2430.0000.0000.0000.0000.0000.000
16A73GLY00.005-0.00343.5410.0010.0010.0000.0000.0000.000
17A74ARG10.8010.89042.119-0.002-0.0020.0000.0000.0000.000
18A75SER0-0.004-0.00739.306-0.001-0.0010.0000.0000.0000.000
19A76PHE00.0150.00530.8860.0020.0020.0000.0000.0000.000
20A77ARG10.8790.90333.033-0.017-0.0170.0000.0000.0000.000
21A78VAL00.0050.02128.2020.0030.0030.0000.0000.0000.000
22A79SER0-0.011-0.00126.1890.0000.0000.0000.0000.0000.000
23A80ILE0-0.011-0.00521.311-0.003-0.0030.0000.0000.0000.000
24A81PRO00.0520.03519.3000.0040.0040.0000.0000.0000.000
25A82THR00.023-0.03218.2490.0080.0080.0000.0000.0000.000
26A83ASP-1-0.875-0.93416.8460.0910.0910.0000.0000.0000.000
27A84LEU0-0.062-0.03014.5970.0420.0420.0000.0000.0000.000
28A85ILE0-0.057-0.01813.399-0.002-0.0020.0000.0000.0000.000
29A86ALA0-0.0090.00112.866-0.061-0.0610.0000.0000.0000.000
30A87SER0-0.028-0.03610.5570.0660.0660.0000.0000.0000.000
31A88SER0-0.014-0.03612.706-0.030-0.0300.0000.0000.0000.000
32A89GLY0-0.0240.00313.694-0.007-0.0070.0000.0000.0000.000
33A90GLU-1-0.887-0.92411.112-0.154-0.1540.0000.0000.0000.000
34A91ILE0-0.017-0.00615.0540.0230.0230.0000.0000.0000.000
35A92ILE00.0290.01717.326-0.022-0.0220.0000.0000.0000.000
36A93LYS10.8050.89519.2760.0780.0780.0000.0000.0000.000
37A94VAL00.0190.01421.038-0.008-0.0080.0000.0000.0000.000
38A95SER0-0.025-0.01923.8340.0020.0020.0000.0000.0000.000
39A96ALA00.0450.02126.075-0.001-0.0010.0000.0000.0000.000
40A97ALA00.0130.00325.016-0.008-0.0080.0000.0000.0000.000
41A98GLY0-0.0050.00624.6390.0020.0020.0000.0000.0000.000
42A99LYS10.8580.92425.9580.0820.0820.0000.0000.0000.000
43A100GLU-1-0.875-0.92426.441-0.078-0.0780.0000.0000.0000.000
44A101ALA00.0110.01227.7920.0030.0030.0000.0000.0000.000
45A102LEU00.0340.00828.146-0.005-0.0050.0000.0000.0000.000
46A103PRO00.0120.01230.7090.0000.0000.0000.0000.0000.000
47A104SER0-0.003-0.01233.8940.0010.0010.0000.0000.0000.000
48A105TRP0-0.057-0.03334.2030.0040.0040.0000.0000.0000.000
49A106LEU0-0.0070.00130.8200.0030.0030.0000.0000.0000.000
50A107HIS0-0.001-0.00432.3920.0010.0010.0000.0000.0000.000
51A108TRP00.0410.01123.3340.0010.0010.0000.0000.0000.000
52A109ASP-1-0.825-0.88028.7840.0090.0090.0000.0000.0000.000
53A110PRO0-0.060-0.04924.6990.0040.0040.0000.0000.0000.000
54A111HIS0-0.0070.00324.8690.0090.0090.0000.0000.0000.000
55A112SER0-0.069-0.05327.3820.0070.0070.0000.0000.0000.000
56A113HIS00.0250.02921.788-0.009-0.0090.0000.0000.0000.000
57A114ILE0-0.0110.00025.6830.0010.0010.0000.0000.0000.000
58A115LEU0-0.018-0.00227.073-0.006-0.0060.0000.0000.0000.000
59A116GLU-1-0.785-0.88529.3540.0090.0090.0000.0000.0000.000
60A117GLY00.020-0.01133.193-0.005-0.0050.0000.0000.0000.000
61A118LEU0-0.0260.01336.1990.0030.0030.0000.0000.0000.000
62A119PRO00.0220.02938.542-0.002-0.0020.0000.0000.0000.000
63A120LEU00.016-0.00740.3530.0030.0030.0000.0000.0000.000
64A121ASP-1-0.789-0.89642.889-0.016-0.0160.0000.0000.0000.000
65A122THR00.004-0.01043.0400.0000.0000.0000.0000.0000.000
66A123ASP-1-0.816-0.88938.704-0.024-0.0240.0000.0000.0000.000
67A124LYS10.8040.90038.8850.0160.0160.0000.0000.0000.000
68A125GLY00.0250.01838.080-0.002-0.0020.0000.0000.0000.000
69A126VAL00.0060.01031.8840.0020.0020.0000.0000.0000.000
70A127HIS0-0.030-0.02331.994-0.008-0.0080.0000.0000.0000.000
71A128TYR00.0350.00527.2810.0010.0010.0000.0000.0000.000
72A129ILE0-0.046-0.02025.119-0.003-0.0030.0000.0000.0000.000
73A130SER0-0.015-0.00121.711-0.004-0.0040.0000.0000.0000.000
74A131VAL00.0380.01018.9110.0070.0070.0000.0000.0000.000
75A132SER0-0.029-0.01516.856-0.023-0.0230.0000.0000.0000.000
76A133ALA00.0540.04813.2440.0350.0350.0000.0000.0000.000
77A134ALA00.0150.00114.350-0.057-0.0570.0000.0000.0000.000
78A135ARG10.9220.9749.5020.3910.3910.0000.0000.0000.000
79A136LEU0-0.0050.00514.082-0.020-0.0200.0000.0000.0000.000
80A137GLY00.0080.01015.045-0.014-0.0140.0000.0000.0000.000
81A138ALA0-0.005-0.02016.3400.0190.0190.0000.0000.0000.000
82A139ASN0-0.0150.00718.9830.0080.0080.0000.0000.0000.000
83A140GLY00.0190.01320.3240.0050.0050.0000.0000.0000.000
84A141SER0-0.052-0.03018.372-0.004-0.0040.0000.0000.0000.000
85A142HIS00.0580.01017.430-0.015-0.0150.0000.0000.0000.000
86A143VAL0-0.0140.00411.768-0.011-0.0110.0000.0000.0000.000
87A144PRO0-0.0050.00013.7320.0030.0030.0000.0000.0000.000
88A145GLN0-0.015-0.0027.507-0.013-0.0130.0000.0000.0000.000
89A146THR0-0.001-0.01010.058-0.116-0.1160.0000.0000.0000.000
90A147SER0-0.049-0.05012.5670.0390.0390.0000.0000.0000.000
91A148SER0-0.013-0.00815.918-0.020-0.0200.0000.0000.0000.000
92A149VAL0-0.039-0.03018.3290.0060.0060.0000.0000.0000.000
93A150PHE00.0140.02021.9330.0040.0040.0000.0000.0000.000
94A151SER0-0.064-0.05325.015-0.006-0.0060.0000.0000.0000.000
95A152ILE00.0130.00228.7810.0070.0070.0000.0000.0000.000
96A153GLU-1-0.877-0.90731.841-0.022-0.0220.0000.0000.0000.000
97A154VAL0-0.064-0.01935.2260.0040.0040.0000.0000.0000.000
98A155TYR0-0.001-0.03537.505-0.001-0.0010.0000.0000.0000.000
99A156PRO00.030-0.02041.3310.0000.0000.0000.0000.0000.000
100A157GLU-1-0.814-0.86744.691-0.003-0.0030.0000.0000.0000.000
101A158ASP-1-0.845-0.91744.8160.0000.0000.0000.0000.0000.000
102A159HIS0-0.035-0.04145.6660.0010.0010.0000.0000.0000.000
103A160ASN0-0.056-0.01941.3550.0030.0030.0000.0000.0000.000
104A179ALA00.0350.01650.3850.0000.0000.0000.0000.0000.000
105A180CYS0-0.079-0.01952.1340.0000.0000.0000.0000.0000.000
106A181ALA00.0540.02255.3620.0000.0000.0000.0000.0000.000
107A182ALA00.009-0.00656.441-0.001-0.0010.0000.0000.0000.000
108A183ASP-1-0.830-0.90557.4350.0010.0010.0000.0000.0000.000
109A184GLU-1-0.914-0.95359.2410.0060.0060.0000.0000.0000.000
110A185PRO0-0.041-0.02358.7680.0000.0000.0000.0000.0000.000
111A186VAL00.0600.03054.0890.0010.0010.0000.0000.0000.000
112A187THR0-0.025-0.01857.383-0.001-0.0010.0000.0000.0000.000
113A188VAL0-0.029-0.02154.4810.0010.0010.0000.0000.0000.000
114A189LEU00.0280.02856.112-0.001-0.0010.0000.0000.0000.000
115A190THR0-0.027-0.03155.1020.0000.0000.0000.0000.0000.000
116A191VAL00.0190.00554.7300.0000.0000.0000.0000.0000.000
117A192ILE0-0.0210.00055.119-0.001-0.0010.0000.0000.0000.000
118A193LEU0-0.001-0.00551.8050.0010.0010.0000.0000.0000.000
119A194ASP-1-0.793-0.90155.310-0.007-0.0070.0000.0000.0000.000
120A195ALA00.0290.00250.4780.0000.0000.0000.0000.0000.000
121A196ASP-1-0.764-0.85449.428-0.014-0.0140.0000.0000.0000.000
122A197LEU00.0180.00345.775-0.001-0.0010.0000.0000.0000.000
123A198THR0-0.056-0.04944.869-0.001-0.0010.0000.0000.0000.000
124A199LYS10.7700.85844.8050.0120.0120.0000.0000.0000.000
125A200MET0-0.069-0.00644.4250.0010.0010.0000.0000.0000.000
126A201THR00.039-0.01038.7900.0000.0000.0000.0000.0000.000
127A202PRO00.0420.01836.3900.0020.0020.0000.0000.0000.000
128A203LYS10.8730.92934.3540.0000.0000.0000.0000.0000.000
129A204GLN00.0440.04438.6630.0010.0010.0000.0000.0000.000
130A205ARG10.7920.90140.2450.0160.0160.0000.0000.0000.000
131A206ILE00.0200.01537.6530.0010.0010.0000.0000.0000.000
132A207ASP-1-0.797-0.89441.0810.0060.0060.0000.0000.0000.000
133A208LEU0-0.024-0.00643.0030.0010.0010.0000.0000.0000.000
134A209LEU00.0110.00043.0350.0010.0010.0000.0000.0000.000
135A210ASN0-0.051-0.03742.5030.0030.0030.0000.0000.0000.000
136A211ARG10.7900.89244.544-0.002-0.0020.0000.0000.0000.000
137A212MET00.0200.02047.9010.0000.0000.0000.0000.0000.000
138A213GLN00.0230.01143.9160.0010.0010.0000.0000.0000.000
139A214SER0-0.034-0.00549.1190.0010.0010.0000.0000.0000.000
140A215PHE0-0.016-0.01351.8540.0000.0000.0000.0000.0000.000
141A216SER0-0.009-0.05250.0980.0000.0000.0000.0000.0000.000
142A217GLU-1-0.980-0.97051.5720.0120.0120.0000.0000.0000.000
143A218VAL0-0.051-0.02148.1710.0010.0010.0000.0000.0000.000
144A219GLU-1-0.803-0.91443.3620.0180.0180.0000.0000.0000.000
145A220LEU0-0.003-0.01340.444-0.001-0.0010.0000.0000.0000.000
146A221HIS0-0.017-0.00240.265-0.003-0.0030.0000.0000.0000.000
147A222ASN0-0.085-0.04242.352-0.002-0.0020.0000.0000.0000.000
148A223MET0-0.0790.02345.751-0.001-0.0010.0000.0000.0000.000
149A224LYS10.8130.90345.8440.0020.0020.0000.0000.0000.000
150A225LEU0-0.027-0.02045.2820.0000.0000.0000.0000.0000.000
151A226VAL00.0310.02546.529-0.001-0.0010.0000.0000.0000.000
152A227PRO00.007-0.00747.9810.0010.0010.0000.0000.0000.000
153A228VAL0-0.0280.01251.0110.0010.0010.0000.0000.0000.000
154A229VAL00.0480.02553.167-0.001-0.0010.0000.0000.0000.000
155A230ASN0-0.026-0.02655.8160.0010.0010.0000.0000.0000.000
156A231ASN00.0410.02058.1870.0000.0000.0000.0000.0000.000
157A232ARG10.9240.96959.3710.0070.0070.0000.0000.0000.000
158A233LEU00.006-0.00158.6710.0000.0000.0000.0000.0000.000
159A234PHE00.000-0.00360.7770.0010.0010.0000.0000.0000.000
160A235ASP-1-0.755-0.84761.031-0.002-0.0020.0000.0000.0000.000
161A236MET0-0.014-0.01363.1310.0000.0000.0000.0000.0000.000
162A237SER0-0.074-0.05263.5510.0000.0000.0000.0000.0000.000
163A238ALA0-0.041-0.02063.6930.0000.0000.0000.0000.0000.000
164A239PHE0-0.011-0.00563.5170.0000.0000.0000.0000.0000.000
165A240MET0-0.0190.00564.8910.0000.0000.0000.0000.0000.000
166A241ALA00.015-0.00464.3740.0000.0000.0000.0000.0000.000
167A242GLY00.0010.00664.4630.0000.0000.0000.0000.0000.000
168A243PRO0-0.026-0.00264.1250.0000.0000.0000.0000.0000.000
169A244GLY00.0460.02361.7070.0010.0010.0000.0000.0000.000
170A245ASN00.0840.04359.5120.0000.0000.0000.0000.0000.000
171A246ALA0-0.0050.02860.8740.0000.0000.0000.0000.0000.000
172A247LYS10.8560.89562.8110.0010.0010.0000.0000.0000.000
173A248LYS10.8780.93863.7080.0050.0050.0000.0000.0000.000
174A249VAL00.0230.01758.8020.0010.0010.0000.0000.0000.000
175A250VAL0-0.047-0.02457.3840.0000.0000.0000.0000.0000.000
176A251GLU-1-0.829-0.89652.980-0.013-0.0130.0000.0000.0000.000
177A252ASN0-0.106-0.05753.3270.0000.0000.0000.0000.0000.000
178A253GLY00.0200.02154.5210.0010.0010.0000.0000.0000.000
179A254ALA0-0.034-0.02650.809-0.001-0.0010.0000.0000.0000.000
180A255LEU0-0.014-0.00751.9650.0010.0010.0000.0000.0000.000
181A256LEU00.0230.01548.9650.0000.0000.0000.0000.0000.000
182A257SER0-0.032-0.02250.7970.0000.0000.0000.0000.0000.000
183A258TRP00.0830.03250.5700.0000.0000.0000.0000.0000.000
184A259LYS10.8700.93351.796-0.009-0.0090.0000.0000.0000.000
185A260LEU0-0.002-0.00453.7120.0010.0010.0000.0000.0000.000
186A261GLY00.016-0.00756.6300.0010.0010.0000.0000.0000.000
187A263SER00.008-0.00359.2160.0000.0000.0000.0000.0000.000
188A264LEU0-0.0100.01960.0580.0000.0000.0000.0000.0000.000
189A265ASN00.0310.01563.733-0.001-0.0010.0000.0000.0000.000
190A266GLN00.0450.00066.2490.0000.0000.0000.0000.0000.000
191A267ASN0-0.063-0.03068.1750.0000.0000.0000.0000.0000.000
192A268SER0-0.019-0.01264.9020.0000.0000.0000.0000.0000.000
193A269VAL0-0.0120.00562.0210.0000.0000.0000.0000.0000.000
194A270PRO00.0260.02358.8230.0000.0000.0000.0000.0000.000
195A271ASP-1-0.801-0.89262.0060.0070.0070.0000.0000.0000.000
196A272ILE00.0530.02959.6880.0000.0000.0000.0000.0000.000
197A273ARG10.8550.90061.629-0.008-0.0080.0000.0000.0000.000
198A274GLY00.0290.02159.0730.0000.0000.0000.0000.0000.000
199A275VAL00.0140.00356.7610.0000.0000.0000.0000.0000.000
200A276GLU-1-0.848-0.90559.1660.0030.0030.0000.0000.0000.000
201A277THR0-0.018-0.01962.7860.0000.0000.0000.0000.0000.000
202A278PRO00.0660.02058.777-0.001-0.0010.0000.0000.0000.000
203A279ALA0-0.0150.01260.057-0.001-0.0010.0000.0000.0000.000
204A280ARG10.7810.87660.949-0.003-0.0030.0000.0000.0000.000
205A281GLU-1-0.938-0.97462.9100.0040.0040.0000.0000.0000.000
206A282GLY0-0.043-0.01760.3120.0000.0000.0000.0000.0000.000
207A283ALA00.0180.02058.6720.0000.0000.0000.0000.0000.000
208A284MET00.0110.01654.9230.0000.0000.0000.0000.0000.000
209A285SER0-0.029-0.02854.5690.0000.0000.0000.0000.0000.000
210A286ALA0-0.046-0.01854.320-0.001-0.0010.0000.0000.0000.000
211A287GLN0-0.044-0.02550.5640.0000.0000.0000.0000.0000.000
212A288LEU0-0.018-0.02550.2410.0000.0000.0000.0000.0000.000
213A289GLY0-0.0010.00749.605-0.001-0.0010.0000.0000.0000.000
214A290TYR0-0.005-0.01246.659-0.002-0.0020.0000.0000.0000.000
215A291PRO0-0.035-0.01553.3180.0010.0010.0000.0000.0000.000
216A292VAL00.0460.02656.3500.0000.0000.0000.0000.0000.000
217A293VAL0-0.027-0.03058.2620.0000.0000.0000.0000.0000.000
218A294GLY0-0.008-0.01060.0210.0000.0000.0000.0000.0000.000
219A295TRP00.0070.02259.5450.0000.0000.0000.0000.0000.000
220A296HIS00.015-0.00459.1830.0000.0000.0000.0000.0000.000
221A297ILE00.0330.02259.9260.0000.0000.0000.0000.0000.000
222A298ALA00.0210.01160.5120.0000.0000.0000.0000.0000.000
223A299ASN00.0010.01360.3380.0010.0010.0000.0000.0000.000
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