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: J3499

Calculation Name: 1DUS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DUS

Chain ID: A

ChEMBL ID:

UniProt ID: Q58292

Base Structure: X-ray

Registration Date: 2023-03-13

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220382.025772
FMO2-HF: Nuclear repulsion 2145070.588331
FMO2-HF: Total energy -75311.437441
FMO2-MP2: Total energy -75535.084041


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:4:PHE)


Summations of interaction energy for fragment #1(A:4:PHE)
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.
-9.162-2.2761.054-3.547-4.392-0.015
Interaction energy analysis for fragmet #1(A:4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.034
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].
3A6GLU-1-0.883-0.9462.521-12.747-5.9611.054-3.519-4.320-0.015
4A7LYS10.9030.9414.3371.0481.1480.000-0.028-0.0720.000
5A8PRO00.0420.0347.1810.0730.0730.0000.0000.0000.000
6A9THR00.0290.0018.2300.1660.1660.0000.0000.0000.000
7A10THR0-0.038-0.00411.0880.1310.1310.0000.0000.0000.000
8A11LYS10.9710.98713.2250.3670.3670.0000.0000.0000.000
9A12SER00.004-0.00715.055-0.061-0.0610.0000.0000.0000.000
10A13ASP-1-0.840-0.87217.462-0.357-0.3570.0000.0000.0000.000
11A14VAL0-0.027-0.02320.8880.0190.0190.0000.0000.0000.000
12A15LYS10.8990.96422.9030.2460.2460.0000.0000.0000.000
13A16ILE00.0210.02226.370-0.007-0.0070.0000.0000.0000.000
14A17VAL0-0.040-0.00528.4560.0030.0030.0000.0000.0000.000
15A18GLU-1-0.817-0.89230.864-0.121-0.1210.0000.0000.0000.000
16A19ASP-1-0.816-0.89134.100-0.114-0.1140.0000.0000.0000.000
17A20ILE0-0.055-0.03036.1380.0040.0040.0000.0000.0000.000
18A21LEU0-0.029-0.02033.034-0.004-0.0040.0000.0000.0000.000
19A22ARG10.7880.84136.1180.0660.0660.0000.0000.0000.000
20A23GLY0-0.0060.00939.5730.0040.0040.0000.0000.0000.000
21A24LYS10.7710.85036.2090.0730.0730.0000.0000.0000.000
22A25LYS10.8630.92238.7550.0690.0690.0000.0000.0000.000
23A26LEU00.0250.02033.3090.0010.0010.0000.0000.0000.000
24A27LYS10.8320.89931.3160.1170.1170.0000.0000.0000.000
25A28PHE00.0200.00527.730-0.004-0.0040.0000.0000.0000.000
26A29LYS10.8630.92322.4040.2470.2470.0000.0000.0000.000
27A30THR0-0.028-0.02123.456-0.010-0.0100.0000.0000.0000.000
28A31ASP-1-0.759-0.90317.833-0.441-0.4410.0000.0000.0000.000
29A32SER0-0.022-0.04019.120-0.002-0.0020.0000.0000.0000.000
30A33GLY00.0130.02315.911-0.010-0.0100.0000.0000.0000.000
31A34VAL0-0.063-0.03316.325-0.025-0.0250.0000.0000.0000.000
32A35PHE00.0240.01119.0880.0150.0150.0000.0000.0000.000
33A36SER0-0.009-0.02522.1590.0100.0100.0000.0000.0000.000
34A37TYR00.0280.00422.6800.0170.0170.0000.0000.0000.000
35A38GLY0-0.010-0.01024.6290.0110.0110.0000.0000.0000.000
36A39LYS10.9430.97327.7730.1900.1900.0000.0000.0000.000
37A40VAL00.0810.06528.978-0.011-0.0110.0000.0000.0000.000
38A41ASP-1-0.770-0.87029.044-0.134-0.1340.0000.0000.0000.000
39A42LYS10.9790.98330.9870.1170.1170.0000.0000.0000.000
40A43GLY00.0140.00631.7910.0080.0080.0000.0000.0000.000
41A44THR00.023-0.02328.6380.0050.0050.0000.0000.0000.000
42A45LYS10.8270.90930.8580.1140.1140.0000.0000.0000.000
43A46ILE0-0.068-0.02434.3310.0070.0070.0000.0000.0000.000
44A47LEU00.005-0.00329.8960.0070.0070.0000.0000.0000.000
45A48VAL00.0170.01631.8230.0050.0050.0000.0000.0000.000
46A49GLU-1-0.855-0.92034.413-0.076-0.0760.0000.0000.0000.000
47A50ASN0-0.083-0.06037.3040.0080.0080.0000.0000.0000.000
48A51VAL0-0.0030.01633.6010.0040.0040.0000.0000.0000.000
49A52VAL0-0.0020.00636.6580.0000.0000.0000.0000.0000.000
50A53VAL0-0.012-0.01234.6310.0000.0000.0000.0000.0000.000
51A54ASP-1-0.796-0.89337.522-0.023-0.0230.0000.0000.0000.000
52A55LYS10.8550.90437.8340.0210.0210.0000.0000.0000.000
53A56ASP-1-0.846-0.90838.099-0.016-0.0160.0000.0000.0000.000
54A57ASP-1-0.823-0.89934.060-0.030-0.0300.0000.0000.0000.000
55A58ASP-1-0.772-0.82430.363-0.019-0.0190.0000.0000.0000.000
56A59ILE00.001-0.01028.8690.0030.0030.0000.0000.0000.000
57A60LEU0-0.014-0.00622.075-0.002-0.0020.0000.0000.0000.000
58A61ASP-1-0.811-0.91024.962-0.137-0.1370.0000.0000.0000.000
59A62LEU00.0190.00420.068-0.009-0.0090.0000.0000.0000.000
60A63GLY0-0.0140.00119.6320.0020.0020.0000.0000.0000.000
61A64CYS0-0.0300.00220.692-0.008-0.0080.0000.0000.0000.000
62A65GLY00.0350.02320.4690.0030.0030.0000.0000.0000.000
63A66TYR0-0.083-0.06421.234-0.001-0.0010.0000.0000.0000.000
64A67GLY00.0400.00023.1960.0110.0110.0000.0000.0000.000
65A68VAL0-0.044-0.01224.9200.0140.0140.0000.0000.0000.000
66A69ILE00.0350.01326.7250.0100.0100.0000.0000.0000.000
67A70GLY00.0420.00427.2340.0090.0090.0000.0000.0000.000
68A71ILE0-0.039-0.02726.7850.0080.0080.0000.0000.0000.000
69A72ALA0-0.014-0.00630.0760.0060.0060.0000.0000.0000.000
70A73LEU0-0.015-0.00431.2720.0060.0060.0000.0000.0000.000
71A74ALA00.0180.00630.6910.0060.0060.0000.0000.0000.000
72A75ASP-1-0.845-0.89532.682-0.065-0.0650.0000.0000.0000.000
73A76GLU-1-0.797-0.85836.047-0.057-0.0570.0000.0000.0000.000
74A77VAL0-0.096-0.03432.6070.0040.0040.0000.0000.0000.000
75A78LYS10.8330.91834.4250.0170.0170.0000.0000.0000.000
76A79SER0-0.032-0.04729.7810.0000.0000.0000.0000.0000.000
77A80THR00.0020.00127.042-0.003-0.0030.0000.0000.0000.000
78A81THR0-0.0080.01422.2970.0000.0000.0000.0000.0000.000
79A82MET0-0.0470.00222.090-0.008-0.0080.0000.0000.0000.000
80A83ALA00.0340.02218.485-0.002-0.0020.0000.0000.0000.000
81A84ASP-1-0.807-0.92216.492-0.314-0.3140.0000.0000.0000.000
82A85ILE00.0920.06010.319-0.012-0.0120.0000.0000.0000.000
83A86ASN0-0.031-0.02411.659-0.146-0.1460.0000.0000.0000.000
84A87ARG10.9570.9536.8510.8350.8350.0000.0000.0000.000
85A88ARG10.8580.94113.4420.4690.4690.0000.0000.0000.000
86A89ALA00.0090.00015.3740.0480.0480.0000.0000.0000.000
87A90ILE00.0050.00715.0380.0340.0340.0000.0000.0000.000
88A91LYS10.8950.95716.6860.3630.3630.0000.0000.0000.000
89A92LEU0-0.019-0.01018.4900.0310.0310.0000.0000.0000.000
90A93ALA00.0710.03921.3880.0240.0240.0000.0000.0000.000
91A94LYS10.8910.95617.5110.2170.2170.0000.0000.0000.000
92A95GLU-1-0.877-0.93921.719-0.260-0.2600.0000.0000.0000.000
93A96ASN00.012-0.01024.4740.0160.0160.0000.0000.0000.000
94A97ILE00.0220.02725.2550.0090.0090.0000.0000.0000.000
95A98LYS10.8800.93026.6320.1230.1230.0000.0000.0000.000
96A99LEU0-0.085-0.03627.8520.0060.0060.0000.0000.0000.000
97A100ASN0-0.033-0.03030.4250.0080.0080.0000.0000.0000.000
98A101ASN0-0.030-0.01032.9110.0070.0070.0000.0000.0000.000
99A102LEU00.0400.01930.9370.0060.0060.0000.0000.0000.000
100A103ASP-1-0.830-0.91729.647-0.096-0.0960.0000.0000.0000.000
101A104ASN0-0.035-0.00931.7130.0020.0020.0000.0000.0000.000
102A105TYR00.0310.03232.5580.0050.0050.0000.0000.0000.000
103A106ASP-1-0.823-0.89928.654-0.038-0.0380.0000.0000.0000.000
104A107ILE00.0090.00426.260-0.004-0.0040.0000.0000.0000.000
105A108ARG10.7550.83522.9650.0240.0240.0000.0000.0000.000
106A109VAL0-0.003-0.00919.299-0.006-0.0060.0000.0000.0000.000
107A110VAL0-0.013-0.01916.542-0.012-0.0120.0000.0000.0000.000
108A111HIS0-0.038-0.0208.6740.0310.0310.0000.0000.0000.000
109A112SER00.022-0.01913.5800.0580.0580.0000.0000.0000.000
110A113ASP-1-0.886-0.93111.470-0.220-0.2200.0000.0000.0000.000
111A114LEU00.024-0.00713.4240.0510.0510.0000.0000.0000.000
112A115TYR0-0.009-0.02417.233-0.012-0.0120.0000.0000.0000.000
113A116GLU-1-0.854-0.89413.5640.0810.0810.0000.0000.0000.000
114A117ASN0-0.073-0.04214.2520.0630.0630.0000.0000.0000.000
115A118VAL0-0.019-0.01016.363-0.011-0.0110.0000.0000.0000.000
116A119LYS10.8200.88719.834-0.051-0.0510.0000.0000.0000.000
117A120ASP-1-0.794-0.84821.6830.0130.0130.0000.0000.0000.000
118A121ARG10.8280.91523.4130.0220.0220.0000.0000.0000.000
119A122LYS10.9620.98326.101-0.036-0.0360.0000.0000.0000.000
120A123TYR0-0.026-0.02323.506-0.007-0.0070.0000.0000.0000.000
121A124ASN0-0.0110.00529.9340.0070.0070.0000.0000.0000.000
122A125LYS10.8220.89731.4410.0350.0350.0000.0000.0000.000
123A126ILE00.0050.01625.753-0.002-0.0020.0000.0000.0000.000
124A127ILE00.0130.00527.3050.0020.0020.0000.0000.0000.000
125A128THR0-0.008-0.02023.760-0.010-0.0100.0000.0000.0000.000
126A129ASN0-0.014-0.02825.4990.0140.0140.0000.0000.0000.000
127A130PRO00.0120.03523.447-0.015-0.0150.0000.0000.0000.000
128A131PRO00.0420.00719.4400.0000.0000.0000.0000.0000.000
129A132ILE00.020-0.00622.3800.0030.0030.0000.0000.0000.000
130A133ARG10.9110.93820.1320.2710.2710.0000.0000.0000.000
131A134ALA00.0060.02118.891-0.009-0.0090.0000.0000.0000.000
132A135GLY00.0750.05720.4600.0120.0120.0000.0000.0000.000
133A136LYS10.8990.91923.2830.0650.0650.0000.0000.0000.000
134A137GLU-1-0.843-0.92522.181-0.063-0.0630.0000.0000.0000.000
135A138VAL00.0530.03318.7660.0100.0100.0000.0000.0000.000
136A139LEU0-0.025-0.01821.4230.0060.0060.0000.0000.0000.000
137A140HIS10.8410.92524.7340.0400.0400.0000.0000.0000.000
138A141ARG10.8250.87415.608-0.007-0.0070.0000.0000.0000.000
139A142ILE00.0070.00321.1540.0050.0050.0000.0000.0000.000
140A143ILE0-0.024-0.00823.6580.0040.0040.0000.0000.0000.000
141A144GLU-1-0.869-0.91525.7240.0160.0160.0000.0000.0000.000
142A145GLU-1-0.730-0.83520.3370.0210.0210.0000.0000.0000.000
143A146GLY00.0300.01824.7150.0020.0020.0000.0000.0000.000
144A147LYS10.8750.93226.735-0.008-0.0080.0000.0000.0000.000
145A148GLU-1-0.871-0.92324.1570.0500.0500.0000.0000.0000.000
146A149LEU0-0.008-0.00122.7150.0030.0030.0000.0000.0000.000
147A150LEU0-0.034-0.00127.340-0.002-0.0020.0000.0000.0000.000
148A151LYS10.8330.90830.5980.0150.0150.0000.0000.0000.000
149A152ASP-1-0.837-0.93133.5650.0090.0090.0000.0000.0000.000
150A153ASN0-0.007-0.00936.706-0.004-0.0040.0000.0000.0000.000
151A154GLY00.0360.04534.421-0.004-0.0040.0000.0000.0000.000
152A155GLU-1-0.844-0.93734.021-0.032-0.0320.0000.0000.0000.000
153A156ILE00.0090.01727.551-0.004-0.0040.0000.0000.0000.000
154A157TRP0-0.002-0.01630.662-0.001-0.0010.0000.0000.0000.000
155A158VAL00.004-0.00328.524-0.007-0.0070.0000.0000.0000.000
156A159VAL0-0.023-0.00429.8170.0050.0050.0000.0000.0000.000
157A160ILE00.0220.01229.351-0.007-0.0070.0000.0000.0000.000
158A161GLN00.0050.01031.3410.0030.0030.0000.0000.0000.000
159A162THR0-0.008-0.03733.6500.0070.0070.0000.0000.0000.000
160A163LYS10.9490.96836.4050.0720.0720.0000.0000.0000.000
161A164GLN00.0930.03036.6630.0020.0020.0000.0000.0000.000
162A165GLY00.0290.02933.0850.0030.0030.0000.0000.0000.000
163A166ALA00.0640.02933.3600.0040.0040.0000.0000.0000.000
164A167LYS10.9070.94834.9130.0520.0520.0000.0000.0000.000
165A168SER0-0.048-0.01632.8330.0040.0040.0000.0000.0000.000
166A169LEU00.0210.02528.5700.0040.0040.0000.0000.0000.000
167A170ALA00.0500.02032.3590.0050.0050.0000.0000.0000.000
168A171LYS10.9230.96035.5160.0340.0340.0000.0000.0000.000
169A172TYR00.033-0.00928.3860.0010.0010.0000.0000.0000.000
170A173MET0-0.020-0.00131.6120.0020.0020.0000.0000.0000.000
171A174LYS10.8670.92033.4580.0180.0180.0000.0000.0000.000
172A175ASP-1-0.888-0.93034.334-0.009-0.0090.0000.0000.0000.000
173A176VAL00.0100.02329.9980.0040.0040.0000.0000.0000.000
174A177PHE0-0.021-0.02330.4780.0050.0050.0000.0000.0000.000
175A178GLY00.0160.03035.5050.0010.0010.0000.0000.0000.000
176A179ASN0-0.057-0.03537.878-0.004-0.0040.0000.0000.0000.000
177A180VAL0-0.0250.00236.145-0.002-0.0020.0000.0000.0000.000
178A181GLU-1-0.812-0.89338.198-0.033-0.0330.0000.0000.0000.000
179A182THR0-0.074-0.06038.350-0.005-0.0050.0000.0000.0000.000
180A183VAL00.0320.03037.8530.0000.0000.0000.0000.0000.000
181A184THR00.0110.01438.5520.0000.0000.0000.0000.0000.000
182A185ILE0-0.021-0.02339.343-0.002-0.0020.0000.0000.0000.000
183A186LYS10.9991.00039.5420.0730.0730.0000.0000.0000.000
184A187GLY00.0280.01338.831-0.004-0.0040.0000.0000.0000.000
185A188GLY00.0190.01638.044-0.005-0.0050.0000.0000.0000.000
186A189TYR0-0.069-0.01931.4130.0000.0000.0000.0000.0000.000
187A190ARG10.9210.95935.3330.0610.0610.0000.0000.0000.000
188A191VAL00.0280.02934.578-0.006-0.0060.0000.0000.0000.000
189A192LEU0-0.082-0.04333.3480.0050.0050.0000.0000.0000.000
190A193LYS10.8540.94033.8400.0310.0310.0000.0000.0000.000
191A194SER00.014-0.02033.9210.0010.0010.0000.0000.0000.000
192A195LYS10.8460.92134.7460.0160.0160.0000.0000.0000.000
193A196LYS10.8170.91331.499-0.011-0.0110.0000.0000.0000.000
194A197LEU00.0130.01335.8170.0020.0020.0000.0000.0000.000