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: 66MQZ

Calculation Name: 2XDN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XDN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9AIU0

Base Structure: X-ray

Registration Date: 2023-06-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2304708.501368
FMO2-HF: Nuclear repulsion 2222755.254225
FMO2-HF: Total energy -81953.247143
FMO2-MP2: Total energy -82191.314311


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:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
-12.031-6.5292.06-2.864-4.697-0.005
Interaction energy analysis for fragmet #1(A:5:THR)
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 : 0.016
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].
3A7GLU-1-0.906-0.9692.546-8.071-4.5090.469-1.691-2.340-0.002
4A8GLU-1-0.882-0.9302.279-1.736-0.0311.588-1.103-2.189-0.003
5A9ALA00.0030.0013.991-0.389-0.1540.003-0.070-0.1680.000
6A10GLN00.0160.0186.410-0.310-0.3100.0000.0000.0000.000
7A11GLU-1-0.886-0.9497.038-1.654-1.6540.0000.0000.0000.000
8A12THR0-0.019-0.0167.3500.2590.2590.0000.0000.0000.000
9A13ARG10.9660.9969.634-0.014-0.0140.0000.0000.0000.000
10A14ALA00.0240.01412.0330.0180.0180.0000.0000.0000.000
11A15GLN00.0340.02712.3770.0780.0780.0000.0000.0000.000
12A16ILE0-0.026-0.00912.9390.0440.0440.0000.0000.0000.000
13A17ILE00.0180.00515.7520.0040.0040.0000.0000.0000.000
14A18GLU-1-0.815-0.88917.248-0.237-0.2370.0000.0000.0000.000
15A19ALA0-0.011-0.01318.3680.0070.0070.0000.0000.0000.000
16A20ALA00.017-0.00819.8580.0210.0210.0000.0000.0000.000
17A21GLU-1-0.744-0.84021.715-0.154-0.1540.0000.0000.0000.000
18A22ARG10.8960.94017.9030.2050.2050.0000.0000.0000.000
19A23ALA0-0.001-0.00424.0150.0090.0090.0000.0000.0000.000
20A24PHE00.024-0.00824.0940.0090.0090.0000.0000.0000.000
21A25TYR00.0200.03027.4130.0040.0040.0000.0000.0000.000
22A26LYS10.9040.95228.8570.0660.0660.0000.0000.0000.000
23A27ARG10.7620.85427.7570.0180.0180.0000.0000.0000.000
24A28GLY00.0060.03030.7510.0070.0070.0000.0000.0000.000
25A29VAL00.0330.00228.0100.0030.0030.0000.0000.0000.000
26A30ALA00.0150.02529.5440.0080.0080.0000.0000.0000.000
27A31ARG10.8960.93231.6410.0170.0170.0000.0000.0000.000
28A32THR0-0.0340.01025.285-0.001-0.0010.0000.0000.0000.000
29A33THR0-0.030-0.02924.8660.0110.0110.0000.0000.0000.000
30A34LEU00.0900.03620.466-0.014-0.0140.0000.0000.0000.000
31A35ALA00.0210.00021.175-0.009-0.0090.0000.0000.0000.000
32A36ASP-1-0.771-0.86221.781-0.002-0.0020.0000.0000.0000.000
33A37ILE0-0.0080.00418.880-0.018-0.0180.0000.0000.0000.000
34A38ALA0-0.0030.00517.340-0.022-0.0220.0000.0000.0000.000
35A39GLU-1-0.769-0.86017.7370.0240.0240.0000.0000.0000.000
36A40LEU0-0.092-0.02620.281-0.021-0.0210.0000.0000.0000.000
37A41ALA0-0.048-0.03015.514-0.029-0.0290.0000.0000.0000.000
38A42GLY0-0.0130.01215.471-0.044-0.0440.0000.0000.0000.000
39A43VAL0-0.026-0.01411.840-0.026-0.0260.0000.0000.0000.000
40A44THR0-0.014-0.00612.3070.0510.0510.0000.0000.0000.000
41A45ARG10.8830.87914.409-0.037-0.0370.0000.0000.0000.000
42A46GLY0-0.014-0.01615.9610.0020.0020.0000.0000.0000.000
43A47ALA00.0170.01611.4010.0390.0390.0000.0000.0000.000
44A48ILE00.0020.00413.0810.0460.0460.0000.0000.0000.000
45A49TYR0-0.022-0.02415.516-0.025-0.0250.0000.0000.0000.000
46A50TRP0-0.054-0.00710.1110.0970.0970.0000.0000.0000.000
47A51HIS0-0.041-0.0199.270-0.066-0.0660.0000.0000.0000.000
48A52PHE0-0.020-0.01914.130-0.060-0.0600.0000.0000.0000.000
49A53ASN0-0.036-0.01617.9480.0230.0230.0000.0000.0000.000
50A54ASN0-0.012-0.02320.772-0.012-0.0120.0000.0000.0000.000
51A55LYS10.8270.90822.269-0.026-0.0260.0000.0000.0000.000
52A56ALA00.0460.01324.425-0.015-0.0150.0000.0000.0000.000
53A57GLU-1-0.785-0.87319.7830.1470.1470.0000.0000.0000.000
54A58LEU0-0.043-0.02718.769-0.015-0.0150.0000.0000.0000.000
55A59VAL0-0.043-0.03021.708-0.023-0.0230.0000.0000.0000.000
56A60GLN0-0.013-0.00924.207-0.011-0.0110.0000.0000.0000.000
57A61ALA00.0100.01219.663-0.012-0.0120.0000.0000.0000.000
58A62LEU0-0.050-0.02821.764-0.022-0.0220.0000.0000.0000.000
59A63LEU00.002-0.00223.505-0.013-0.0130.0000.0000.0000.000
60A64ASP-1-0.862-0.92823.009-0.040-0.0400.0000.0000.0000.000
61A65SER0-0.053-0.02921.364-0.014-0.0140.0000.0000.0000.000
62A66LEU0-0.049-0.02022.979-0.015-0.0150.0000.0000.0000.000
63A67ALA0-0.021-0.01325.962-0.001-0.0010.0000.0000.0000.000
64A68GLU-1-0.939-0.96919.912-0.238-0.2380.0000.0000.0000.000
65A69THR0-0.040-0.03924.101-0.009-0.0090.0000.0000.0000.000
66A70HIS0-0.039-0.02925.9870.0040.0040.0000.0000.0000.000
67A71ASP-1-0.827-0.88826.364-0.112-0.1120.0000.0000.0000.000
68A72HIS00.0240.01828.2560.0050.0050.0000.0000.0000.000
69A73LEU0-0.002-0.00829.8200.0090.0090.0000.0000.0000.000
70A74ALA00.0130.00731.3560.0090.0090.0000.0000.0000.000
71A75ARG10.8160.89329.3800.0970.0970.0000.0000.0000.000
72A76ALA00.0000.00632.6860.0060.0060.0000.0000.0000.000
73A77SER0-0.092-0.06235.2410.0080.0080.0000.0000.0000.000
74A78GLU-1-0.847-0.94334.586-0.056-0.0560.0000.0000.0000.000
75A79SER0-0.0080.01436.0750.0070.0070.0000.0000.0000.000
76A80GLU-1-0.836-0.93937.920-0.040-0.0400.0000.0000.0000.000
77A81ASP-1-0.925-0.95439.100-0.054-0.0540.0000.0000.0000.000
78A82GLU-1-0.873-0.92438.305-0.080-0.0800.0000.0000.0000.000
79A83VAL0-0.047-0.03140.4710.0050.0050.0000.0000.0000.000
80A84ASP-1-0.862-0.94841.959-0.065-0.0650.0000.0000.0000.000
81A85PRO00.0430.04140.612-0.004-0.0040.0000.0000.0000.000
82A86LEU00.020-0.00840.898-0.002-0.0020.0000.0000.0000.000
83A87GLY00.0370.01542.302-0.001-0.0010.0000.0000.0000.000
84A88CYS0-0.116-0.05436.959-0.007-0.0070.0000.0000.0000.000
85A89MET00.0450.02237.687-0.003-0.0030.0000.0000.0000.000
86A90ARG10.7670.85038.8520.0670.0670.0000.0000.0000.000
87A91LYS10.8870.94336.7830.0830.0830.0000.0000.0000.000
88A92LEU00.0030.02233.573-0.006-0.0060.0000.0000.0000.000
89A93LEU00.000-0.00435.140-0.004-0.0040.0000.0000.0000.000
90A94LEU00.0240.01137.106-0.002-0.0020.0000.0000.0000.000
91A95GLN0-0.0200.00129.689-0.005-0.0050.0000.0000.0000.000
92A96VAL00.0140.00832.599-0.006-0.0060.0000.0000.0000.000
93A97PHE0-0.013-0.02433.7060.0000.0000.0000.0000.0000.000
94A98ASN0-0.038-0.04033.966-0.003-0.0030.0000.0000.0000.000
95A99GLU-1-0.788-0.87127.181-0.158-0.1580.0000.0000.0000.000
96A100LEU00.0000.02030.935-0.004-0.0040.0000.0000.0000.000
97A101VAL00.002-0.00732.8370.0000.0000.0000.0000.0000.000
98A102LEU0-0.047-0.01531.424-0.002-0.0020.0000.0000.0000.000
99A103ASP-1-0.804-0.88826.127-0.200-0.2000.0000.0000.0000.000
100A104ALA0-0.046-0.02627.0320.0120.0120.0000.0000.0000.000
101A105ARG10.8060.88518.4120.2540.2540.0000.0000.0000.000
102A106THR00.0650.00425.6900.0180.0180.0000.0000.0000.000
103A107ARG10.8600.95127.8840.1370.1370.0000.0000.0000.000
104A108ARG10.7550.85922.9000.1850.1850.0000.0000.0000.000
105A109ILE00.0170.01023.8500.0160.0160.0000.0000.0000.000
106A110ASN0-0.001-0.00628.0960.0190.0190.0000.0000.0000.000
107A111GLU-1-0.782-0.88431.651-0.051-0.0510.0000.0000.0000.000
108A112ILE0-0.102-0.05026.6300.0100.0100.0000.0000.0000.000
109A113LEU0-0.034-0.01828.2260.0120.0120.0000.0000.0000.000
110A114HIS0-0.034-0.02731.7560.0060.0060.0000.0000.0000.000
111A115HIS0-0.094-0.06234.7570.0110.0110.0000.0000.0000.000
112A116LYS10.8410.92431.8100.0590.0590.0000.0000.0000.000
113A117CYS0-0.0070.01531.0170.0050.0050.0000.0000.0000.000
114A118GLU-1-0.876-0.92532.785-0.006-0.0060.0000.0000.0000.000
115A119PHE0-0.016-0.01233.9060.0030.0030.0000.0000.0000.000
116A120THR0-0.007-0.02334.598-0.001-0.0010.0000.0000.0000.000
117A121ASP-1-0.921-0.96236.0570.0200.0200.0000.0000.0000.000
118A122ASP-1-0.903-0.94433.9350.0390.0390.0000.0000.0000.000
119A123MET0-0.0320.00028.9920.0060.0060.0000.0000.0000.000
120A124CYS00.010-0.00532.752-0.004-0.0040.0000.0000.0000.000
121A125GLU-1-0.838-0.92027.3460.0720.0720.0000.0000.0000.000
122A126ILE0-0.0020.00629.494-0.007-0.0070.0000.0000.0000.000
123A127ARG10.9230.95931.293-0.009-0.0090.0000.0000.0000.000
124A128GLN00.000-0.00232.706-0.002-0.0020.0000.0000.0000.000
125A129GLN00.0650.03227.608-0.005-0.0050.0000.0000.0000.000
126A130ARG10.8800.93330.8670.0170.0170.0000.0000.0000.000
127A131GLN0-0.019-0.02033.038-0.003-0.0030.0000.0000.0000.000
128A132SER00.0140.00831.586-0.001-0.0010.0000.0000.0000.000
129A133ALA00.0710.05030.452-0.004-0.0040.0000.0000.0000.000
130A134VAL0-0.041-0.03232.207-0.006-0.0060.0000.0000.0000.000
131A135LEU0-0.035-0.02535.692-0.002-0.0020.0000.0000.0000.000
132A136ASP-1-0.903-0.94031.465-0.019-0.0190.0000.0000.0000.000
133A137CYS0-0.034-0.03133.879-0.006-0.0060.0000.0000.0000.000
134A138HIS0-0.069-0.02935.066-0.005-0.0050.0000.0000.0000.000
135A139LYS10.8900.93936.9130.0180.0180.0000.0000.0000.000
136A140GLY00.0560.04135.856-0.001-0.0010.0000.0000.0000.000
137A141ILE0-0.010-0.01336.753-0.001-0.0010.0000.0000.0000.000
138A142THR0-0.046-0.03239.4280.0010.0010.0000.0000.0000.000
139A143LEU0-0.013-0.00338.0000.0020.0020.0000.0000.0000.000
140A144ALA00.0710.04538.8960.0010.0010.0000.0000.0000.000
141A145LEU0-0.030-0.01540.8950.0000.0000.0000.0000.0000.000
142A146ALA0-0.006-0.01144.0270.0010.0010.0000.0000.0000.000
143A147ASN0-0.017-0.00640.3010.0060.0060.0000.0000.0000.000
144A148ALA00.0030.00844.3980.0000.0000.0000.0000.0000.000
145A149VAL0-0.055-0.01146.0810.0010.0010.0000.0000.0000.000
146A150ARG10.8500.93744.1460.0370.0370.0000.0000.0000.000
147A151ARG10.7600.87843.9650.0500.0500.0000.0000.0000.000
148A152GLY0-0.030-0.00648.884-0.001-0.0010.0000.0000.0000.000
149A153GLN0-0.030-0.02545.5700.0000.0000.0000.0000.0000.000
150A154LEU0-0.035-0.00946.3980.0000.0000.0000.0000.0000.000
151A155PRO0-0.042-0.01950.5760.0010.0010.0000.0000.0000.000
152A156GLY00.0660.03052.6900.0000.0000.0000.0000.0000.000
153A157GLU-1-0.893-0.95954.217-0.019-0.0190.0000.0000.0000.000
154A158LEU0-0.029-0.01048.8160.0010.0010.0000.0000.0000.000
155A159ASP-1-0.815-0.88950.572-0.019-0.0190.0000.0000.0000.000
156A160ALA00.0260.00446.197-0.001-0.0010.0000.0000.0000.000
157A161GLU-1-0.760-0.86644.296-0.021-0.0210.0000.0000.0000.000
158A162ARG10.8150.87746.0620.0190.0190.0000.0000.0000.000
159A163ALA0-0.011-0.00647.694-0.001-0.0010.0000.0000.0000.000
160A164ALA00.0780.04042.380-0.003-0.0030.0000.0000.0000.000
161A165VAL00.0170.01543.063-0.002-0.0020.0000.0000.0000.000
162A166ALA0-0.044-0.02544.579-0.002-0.0020.0000.0000.0000.000
163A167MET0-0.0160.01141.895-0.002-0.0020.0000.0000.0000.000
164A168PHE00.0420.01336.444-0.002-0.0020.0000.0000.0000.000
165A169ALA00.0060.00641.190-0.002-0.0020.0000.0000.0000.000
166A170TYR0-0.073-0.04443.6300.0000.0000.0000.0000.0000.000
167A171VAL00.0230.00538.289-0.002-0.0020.0000.0000.0000.000
168A172ASP-1-0.897-0.93137.844-0.048-0.0480.0000.0000.0000.000
169A173GLY0-0.009-0.01939.782-0.001-0.0010.0000.0000.0000.000
170A174LEU0-0.046-0.02441.9530.0000.0000.0000.0000.0000.000
171A175ILE00.0220.01235.534-0.002-0.0020.0000.0000.0000.000
172A176ARG10.9260.97438.5250.0360.0360.0000.0000.0000.000
173A177ARG10.9210.94739.9920.0460.0460.0000.0000.0000.000
174A178TRP0-0.0030.00335.404-0.002-0.0020.0000.0000.0000.000
175A179LEU0-0.017-0.01334.596-0.003-0.0030.0000.0000.0000.000
176A180LEU0-0.062-0.00938.5400.0010.0010.0000.0000.0000.000
177A181LEU0-0.070-0.04941.4300.0020.0020.0000.0000.0000.000
178A182PRO00.0990.06439.6720.0010.0010.0000.0000.0000.000
179A183ASP-1-0.932-0.96341.968-0.068-0.0680.0000.0000.0000.000
180A184SER0-0.128-0.07244.9500.0040.0040.0000.0000.0000.000
181A185VAL0-0.042-0.03143.4130.0020.0020.0000.0000.0000.000
182A186ASP-1-0.806-0.87843.271-0.080-0.0800.0000.0000.0000.000
183A187LEU0-0.018-0.02438.2990.0000.0000.0000.0000.0000.000
184A188LEU00.017-0.00237.130-0.001-0.0010.0000.0000.0000.000
185A189GLY00.0140.00640.172-0.001-0.0010.0000.0000.0000.000
186A190ASP-1-0.806-0.89243.442-0.059-0.0590.0000.0000.0000.000
187A191VAL0-0.0130.01238.8890.0040.0040.0000.0000.0000.000
188A192GLU-1-0.830-0.90542.169-0.078-0.0780.0000.0000.0000.000
189A193LYS10.8540.91444.4390.0620.0620.0000.0000.0000.000
190A194TRP0-0.0430.01143.2160.0060.0060.0000.0000.0000.000
191A195VAL00.0220.00540.5090.0030.0030.0000.0000.0000.000
192A196ASP-1-0.793-0.88743.558-0.059-0.0590.0000.0000.0000.000
193A197THR0-0.068-0.04246.9990.0040.0040.0000.0000.0000.000
194A198GLY0-0.010-0.00345.8640.0030.0030.0000.0000.0000.000
195A199LEU00.025-0.00143.1650.0030.0030.0000.0000.0000.000
196A200ASP-1-0.839-0.90246.997-0.043-0.0430.0000.0000.0000.000
197A201MET0-0.067-0.02047.8090.0040.0040.0000.0000.0000.000
198A202LEU0-0.009-0.02245.0550.0030.0030.0000.0000.0000.000
199A203ARG10.8660.89849.7190.0460.0460.0000.0000.0000.000
200A204LEU0-0.024-0.01151.9690.0020.0020.0000.0000.0000.000
201A205SER0-0.0040.01453.5780.0020.0020.0000.0000.0000.000
202A206PRO00.002-0.01855.4370.0000.0000.0000.0000.0000.000
203A207ALA00.0200.02055.9750.0010.0010.0000.0000.0000.000
204A208LEU0-0.0130.00550.1530.0010.0010.0000.0000.0000.000
205A209ARG10.8760.94853.1940.0280.0280.0000.0000.0000.000
206A210LYS10.8460.94553.0620.0230.0230.0000.0000.0000.000