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: 82GVY

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2219135.056998
FMO2-HF: Nuclear repulsion 2143825.539578
FMO2-HF: Total energy -75309.51742
FMO2-MP2: Total energy -75533.310933


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.
-7.045-1.1220.728-3.063-3.587-0.007
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 : 0.060 / q_NPA : 0.036
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-1-0.876-0.9462.713-11.845-6.0100.728-3.040-3.523-0.007
4A7LYS10.8760.9344.2691.4341.5220.000-0.023-0.0640.000
5A8PRO00.0250.0157.8680.0560.0560.0000.0000.0000.000
6A9THR00.0300.0168.8890.1870.1870.0000.0000.0000.000
7A10THR0-0.0030.00111.1510.1570.1570.0000.0000.0000.000
8A11LYS10.9560.98413.5700.4270.4270.0000.0000.0000.000
9A12SER00.0220.00815.764-0.065-0.0650.0000.0000.0000.000
10A13ASP-1-0.859-0.88917.756-0.390-0.3900.0000.0000.0000.000
11A14VAL0-0.023-0.03221.2610.0000.0000.0000.0000.0000.000
12A15LYS10.9010.96423.3910.2470.2470.0000.0000.0000.000
13A16ILE00.0230.01626.820-0.005-0.0050.0000.0000.0000.000
14A17VAL0-0.052-0.01328.7270.0040.0040.0000.0000.0000.000
15A18GLU-1-0.889-0.94031.213-0.111-0.1110.0000.0000.0000.000
16A19ASP-1-0.867-0.94333.969-0.102-0.1020.0000.0000.0000.000
17A20ILE0-0.050-0.02435.7800.0030.0030.0000.0000.0000.000
18A21LEU0-0.042-0.02332.340-0.002-0.0020.0000.0000.0000.000
19A22ARG10.7840.85535.6040.0280.0280.0000.0000.0000.000
20A23GLY00.0030.00738.8930.0030.0030.0000.0000.0000.000
21A24LYS10.7470.82935.7320.0370.0370.0000.0000.0000.000
22A25LYS10.8940.94837.7530.0530.0530.0000.0000.0000.000
23A26LEU00.0390.02732.6050.0000.0000.0000.0000.0000.000
24A27LYS10.9660.97931.4070.1160.1160.0000.0000.0000.000
25A28PHE00.000-0.00527.256-0.001-0.0010.0000.0000.0000.000
26A29LYS10.8530.92622.3010.2780.2780.0000.0000.0000.000
27A30THR0-0.044-0.02123.739-0.008-0.0080.0000.0000.0000.000
28A31ASP-1-0.740-0.89518.183-0.512-0.5120.0000.0000.0000.000
29A32SER0-0.039-0.04119.5310.0040.0040.0000.0000.0000.000
30A33GLY0-0.0080.00916.253-0.008-0.0080.0000.0000.0000.000
31A34VAL0-0.077-0.04816.594-0.020-0.0200.0000.0000.0000.000
32A35PHE00.0120.00319.1800.0100.0100.0000.0000.0000.000
33A36SER0-0.041-0.04221.6030.0120.0120.0000.0000.0000.000
34A37TYR00.0900.03622.7890.0150.0150.0000.0000.0000.000
35A38GLY0-0.031-0.02924.7710.0110.0110.0000.0000.0000.000
36A39LYS10.9560.97628.0460.1720.1720.0000.0000.0000.000
37A40VAL00.0730.06728.830-0.008-0.0080.0000.0000.0000.000
38A41ASP-1-0.826-0.91627.789-0.109-0.1090.0000.0000.0000.000
39A42LYS10.9750.97029.9010.1060.1060.0000.0000.0000.000
40A43GLY00.0530.03230.9790.0090.0090.0000.0000.0000.000
41A44THR00.019-0.01427.9160.0100.0100.0000.0000.0000.000
42A45LYS10.8480.93430.1860.1050.1050.0000.0000.0000.000
43A46ILE0-0.052-0.01033.5550.0070.0070.0000.0000.0000.000
44A47LEU00.001-0.00129.2790.0060.0060.0000.0000.0000.000
45A48VAL00.0140.00331.1760.0060.0060.0000.0000.0000.000
46A49GLU-1-0.863-0.91233.647-0.047-0.0470.0000.0000.0000.000
47A50ASN0-0.099-0.06736.6100.0070.0070.0000.0000.0000.000
48A51VAL0-0.0100.02133.1740.0050.0050.0000.0000.0000.000
49A52VAL0-0.0020.00736.088-0.003-0.0030.0000.0000.0000.000
50A53VAL0-0.043-0.03234.0900.0050.0050.0000.0000.0000.000
51A54ASP-1-0.825-0.91737.2870.0170.0170.0000.0000.0000.000
52A55LYS10.9180.96137.469-0.016-0.0160.0000.0000.0000.000
53A56ASP-1-0.923-0.96237.8830.0280.0280.0000.0000.0000.000
54A57ASP-1-0.882-0.94733.8360.0320.0320.0000.0000.0000.000
55A58ASP-1-0.781-0.85030.0690.0550.0550.0000.0000.0000.000
56A59ILE0-0.027-0.03528.6010.0060.0060.0000.0000.0000.000
57A60LEU0-0.015-0.00921.8110.0010.0010.0000.0000.0000.000
58A61ASP-1-0.835-0.92524.391-0.062-0.0620.0000.0000.0000.000
59A62LEU00.000-0.01719.624-0.003-0.0030.0000.0000.0000.000
60A63GLY0-0.034-0.00718.812-0.008-0.0080.0000.0000.0000.000
61A64CYS0-0.0050.00619.874-0.015-0.0150.0000.0000.0000.000
62A65GLY00.0210.01519.590-0.012-0.0120.0000.0000.0000.000
63A66TYR0-0.090-0.07020.4760.0010.0010.0000.0000.0000.000
64A67GLY00.0480.00522.4260.0050.0050.0000.0000.0000.000
65A68VAL0-0.044-0.00324.4810.0120.0120.0000.0000.0000.000
66A69ILE00.0380.01226.1740.0060.0060.0000.0000.0000.000
67A70GLY00.0360.00626.6430.0080.0080.0000.0000.0000.000
68A71ILE0-0.034-0.02326.4050.0050.0050.0000.0000.0000.000
69A72ALA0-0.022-0.01229.5410.0040.0040.0000.0000.0000.000
70A73LEU0-0.001-0.00830.7610.0050.0050.0000.0000.0000.000
71A74ALA00.0210.01730.3140.0070.0070.0000.0000.0000.000
72A75ASP-1-0.856-0.89532.215-0.028-0.0280.0000.0000.0000.000
73A76GLU-1-0.803-0.87135.412-0.022-0.0220.0000.0000.0000.000
74A77VAL0-0.085-0.02832.1130.0050.0050.0000.0000.0000.000
75A78LYS10.9070.98434.015-0.050-0.0500.0000.0000.0000.000
76A79SER0-0.036-0.04729.6480.0020.0020.0000.0000.0000.000
77A80THR00.0100.01026.551-0.002-0.0020.0000.0000.0000.000
78A81THR0-0.0230.00722.1090.0070.0070.0000.0000.0000.000
79A82MET0-0.0320.00321.802-0.010-0.0100.0000.0000.0000.000
80A83ALA00.0350.01717.8900.0100.0100.0000.0000.0000.000
81A84ASP-1-0.796-0.90115.816-0.221-0.2210.0000.0000.0000.000
82A85ILE00.1010.0609.9030.0000.0000.0000.0000.0000.000
83A86ASN0-0.029-0.01411.016-0.178-0.1780.0000.0000.0000.000
84A87ARG11.0320.9906.5130.8590.8590.0000.0000.0000.000
85A88ARG10.8360.92412.5770.5420.5420.0000.0000.0000.000
86A89ALA00.0210.00615.3150.0480.0480.0000.0000.0000.000
87A90ILE00.0230.02614.5920.0340.0340.0000.0000.0000.000
88A91LYS10.9070.94715.9100.4890.4890.0000.0000.0000.000
89A92LEU00.008-0.00618.3750.0270.0270.0000.0000.0000.000
90A93ALA00.0610.04320.5320.0230.0230.0000.0000.0000.000
91A94LYS10.9450.96217.2160.1450.1450.0000.0000.0000.000
92A95GLU-1-0.928-0.95521.781-0.259-0.2590.0000.0000.0000.000
93A96ASN00.0190.00024.5040.0100.0100.0000.0000.0000.000
94A97ILE00.0410.04124.7750.0090.0090.0000.0000.0000.000
95A98LYS10.9570.98224.8710.1290.1290.0000.0000.0000.000
96A99LEU0-0.097-0.04527.9120.0040.0040.0000.0000.0000.000
97A100ASN0-0.032-0.02829.9320.0060.0060.0000.0000.0000.000
98A101ASN0-0.0110.01132.8120.0040.0040.0000.0000.0000.000
99A102LEU00.0190.00430.4860.0070.0070.0000.0000.0000.000
100A103ASP-1-0.914-0.97829.918-0.062-0.0620.0000.0000.0000.000
101A104ASN0-0.048-0.00931.7880.0030.0030.0000.0000.0000.000
102A105TYR00.0070.01632.0940.0060.0060.0000.0000.0000.000
103A106ASP-1-0.908-0.94029.1470.0350.0350.0000.0000.0000.000
104A107ILE00.0180.00325.7010.0010.0010.0000.0000.0000.000
105A108ARG10.7650.86522.286-0.112-0.1120.0000.0000.0000.000
106A109VAL0-0.029-0.01818.718-0.006-0.0060.0000.0000.0000.000
107A110VAL0-0.044-0.02916.667-0.003-0.0030.0000.0000.0000.000
108A111HIS0-0.095-0.0458.4370.0400.0400.0000.0000.0000.000
109A112SER00.013-0.03113.6120.1060.1060.0000.0000.0000.000
110A113ASP-1-0.876-0.90711.1950.2490.2490.0000.0000.0000.000
111A114LEU00.035-0.01213.1870.0330.0330.0000.0000.0000.000
112A115TYR0-0.058-0.05516.902-0.024-0.0240.0000.0000.0000.000
113A116GLU-1-0.932-0.97012.7610.5920.5920.0000.0000.0000.000
114A117ASN0-0.044-0.01714.4870.0660.0660.0000.0000.0000.000
115A118VAL0-0.0200.00116.592-0.033-0.0330.0000.0000.0000.000
116A119LYS10.9610.98319.590-0.320-0.3200.0000.0000.0000.000
117A120ASP-1-0.787-0.86722.0960.1770.1770.0000.0000.0000.000
118A121ARG10.9290.96623.700-0.105-0.1050.0000.0000.0000.000
119A122LYS10.9640.99326.140-0.123-0.1230.0000.0000.0000.000
120A123TYR0-0.007-0.02323.361-0.015-0.0150.0000.0000.0000.000
121A124ASN00.0240.02429.7250.0050.0050.0000.0000.0000.000
122A125LYS10.9090.96331.098-0.027-0.0270.0000.0000.0000.000
123A126ILE00.0070.02725.4810.0020.0020.0000.0000.0000.000
124A127ILE00.002-0.00627.203-0.003-0.0030.0000.0000.0000.000
125A128THR00.001-0.01223.406-0.004-0.0040.0000.0000.0000.000
126A129ASN0-0.002-0.00725.1080.0090.0090.0000.0000.0000.000
127A130PRO0-0.028-0.00123.055-0.012-0.0120.0000.0000.0000.000
128A131PRO00.0380.01719.151-0.014-0.0140.0000.0000.0000.000
129A132ILE00.031-0.00522.0280.0170.0170.0000.0000.0000.000
130A133ARG10.9370.94820.6960.2410.2410.0000.0000.0000.000
131A134ALA00.0070.02118.738-0.004-0.0040.0000.0000.0000.000
132A135GLY00.0670.04820.1150.0220.0220.0000.0000.0000.000
133A136LYS10.9190.92623.0870.0020.0020.0000.0000.0000.000
134A137GLU-1-0.847-0.91621.7620.0570.0570.0000.0000.0000.000
135A138VAL00.0380.02118.4890.0180.0180.0000.0000.0000.000
136A139LEU0-0.023-0.01121.1140.0040.0040.0000.0000.0000.000
137A140HIS10.8680.91624.345-0.055-0.0550.0000.0000.0000.000
138A141ARG11.0031.03415.840-0.307-0.3070.0000.0000.0000.000
139A142ILE00.0040.01021.1870.0070.0070.0000.0000.0000.000
140A143ILE0-0.042-0.00423.5590.0000.0000.0000.0000.0000.000
141A144GLU-1-0.940-0.97925.9800.1420.1420.0000.0000.0000.000
142A145GLU-1-0.840-0.92920.5200.2570.2570.0000.0000.0000.000
143A146GLY00.0260.01224.7550.0010.0010.0000.0000.0000.000
144A147LYS10.8920.94726.334-0.093-0.0930.0000.0000.0000.000
145A148GLU-1-0.946-0.97125.3960.1890.1890.0000.0000.0000.000
146A149LEU0-0.027-0.00522.7350.0050.0050.0000.0000.0000.000
147A150LEU0-0.051-0.00927.380-0.009-0.0090.0000.0000.0000.000
148A151LYS10.7960.88230.653-0.061-0.0610.0000.0000.0000.000
149A152ASP-1-0.850-0.92833.6140.0780.0780.0000.0000.0000.000
150A153ASN0-0.071-0.04636.915-0.005-0.0050.0000.0000.0000.000
151A154GLY00.0140.01933.885-0.006-0.0060.0000.0000.0000.000
152A155GLU-1-0.839-0.94833.5940.0210.0210.0000.0000.0000.000
153A156ILE0-0.0100.00927.0420.0000.0000.0000.0000.0000.000
154A157TRP0-0.007-0.01530.396-0.007-0.0070.0000.0000.0000.000
155A158VAL00.0230.00528.324-0.003-0.0030.0000.0000.0000.000
156A159VAL0-0.038-0.00129.201-0.001-0.0010.0000.0000.0000.000
157A160ILE00.0220.00429.047-0.004-0.0040.0000.0000.0000.000
158A161GLN0-0.027-0.01030.430-0.003-0.0030.0000.0000.0000.000
159A162THR0-0.113-0.12132.9830.0060.0060.0000.0000.0000.000
160A163LYS10.9750.98535.5960.0470.0470.0000.0000.0000.000
161A164GLN00.0770.00136.3400.0070.0070.0000.0000.0000.000
162A165GLY00.0310.04132.7080.0060.0060.0000.0000.0000.000
163A166ALA00.0620.02532.7070.0070.0070.0000.0000.0000.000
164A167LYS10.9370.97634.3200.0190.0190.0000.0000.0000.000
165A168SER0-0.049-0.02032.8090.0060.0060.0000.0000.0000.000
166A169LEU00.0380.02228.8810.0070.0070.0000.0000.0000.000
167A170ALA00.0490.02132.1730.0060.0060.0000.0000.0000.000
168A171LYS10.8990.94035.285-0.009-0.0090.0000.0000.0000.000
169A172TYR00.0660.04728.0100.0000.0000.0000.0000.0000.000
170A173MET00.003-0.00231.3570.0040.0040.0000.0000.0000.000
171A174LYS10.9270.96933.321-0.026-0.0260.0000.0000.0000.000
172A175ASP-1-0.898-0.94934.1060.0530.0530.0000.0000.0000.000
173A176VAL0-0.0120.00730.2010.0040.0040.0000.0000.0000.000
174A177PHE0-0.031-0.03930.4230.0060.0060.0000.0000.0000.000
175A178GLY00.0130.02835.438-0.001-0.0010.0000.0000.0000.000
176A179ASN0-0.062-0.04437.856-0.009-0.0090.0000.0000.0000.000
177A180VAL0-0.0170.00935.8720.0020.0020.0000.0000.0000.000
178A181GLU-1-0.891-0.93037.9400.0070.0070.0000.0000.0000.000
179A182THR0-0.084-0.05438.086-0.003-0.0030.0000.0000.0000.000
180A183VAL00.0350.02237.964-0.001-0.0010.0000.0000.0000.000
181A184THR00.0310.01338.090-0.003-0.0030.0000.0000.0000.000
182A185ILE0-0.025-0.02438.700-0.001-0.0010.0000.0000.0000.000
183A186LYS11.0001.00538.8420.0470.0470.0000.0000.0000.000
184A187GLY00.0470.02138.244-0.004-0.0040.0000.0000.0000.000
185A188GLY00.0590.03737.611-0.005-0.0050.0000.0000.0000.000
186A189TYR0-0.0090.05931.2970.0000.0000.0000.0000.0000.000
187A190ARG10.9280.94634.6900.0250.0250.0000.0000.0000.000
188A191VAL00.0460.03734.037-0.003-0.0030.0000.0000.0000.000
189A192LEU0-0.067-0.03032.8710.0020.0020.0000.0000.0000.000
190A193LYS10.9690.99533.654-0.015-0.0150.0000.0000.0000.000
191A194SER00.000-0.02233.623-0.002-0.0020.0000.0000.0000.000
192A195LYS10.8970.96234.627-0.034-0.0340.0000.0000.0000.000
193A196LYS10.8500.93831.486-0.103-0.1030.0000.0000.0000.000
194A197LEU00.0100.00935.834-0.001-0.0010.0000.0000.0000.000