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: J23Y9

Calculation Name: 3D9H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D9H

Chain ID: A

ChEMBL ID:

UniProt ID: Q96DX5

Base Structure: X-ray

Registration Date: 2023-09-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2567938.04951
FMO2-HF: Nuclear repulsion 2478104.579385
FMO2-HF: Total energy -89833.470125
FMO2-MP2: Total energy -90092.093086


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:19:PHE)


Summations of interaction energy for fragment #1(A:19: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.
-10.222-7.58525.097-6.072-21.662-0.009
Interaction energy analysis for fragmet #1(A:19:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.018
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].
3A21GLY00.014-0.0192.112-1.7450.1226.673-4.203-4.3380.011
4A22ILE0-0.0070.0113.0953.132-0.2511.0734.616-2.306-0.006
5A23ARG10.8720.9462.210-3.953-2.6593.828-1.567-3.555-0.010
6A24LEU0-0.012-0.0034.1230.3510.4900.001-0.041-0.0980.000
7A25LEU0-0.033-0.0176.4960.1410.1410.0000.0000.0000.000
8A26SER00.0730.0249.3870.0400.0400.0000.0000.0000.000
9A27ASN00.002-0.00212.6450.0180.0180.0000.0000.0000.000
10A28PRO00.0130.00315.2660.0140.0140.0000.0000.0000.000
11A29LEU0-0.032-0.01318.1190.0170.0170.0000.0000.0000.000
12A30MET0-0.086-0.03819.1880.0050.0050.0000.0000.0000.000
13A31GLY00.0400.01118.392-0.021-0.0210.0000.0000.0000.000
14A32ASP-1-0.884-0.93418.858-0.113-0.1130.0000.0000.0000.000
15A33ALA0-0.104-0.04716.340-0.018-0.0180.0000.0000.0000.000
16A34VAL00.0210.01513.1080.0050.0050.0000.0000.0000.000
17A35SER0-0.044-0.02811.243-0.041-0.0410.0000.0000.0000.000
18A36ASP-1-0.869-0.93710.609-0.190-0.1900.0000.0000.0000.000
19A37TRP00.009-0.01312.1810.0240.0240.0000.0000.0000.000
20A38SER0-0.031-0.05210.366-0.094-0.0940.0000.0000.0000.000
21A39PRO00.0510.01312.5150.0430.0430.0000.0000.0000.000
22A40MET00.0150.0129.7830.0720.0720.0000.0000.0000.000
23A41HIS0-0.0250.0017.7160.0120.0120.0000.0000.0000.000
24A42GLU-1-0.794-0.87212.696-0.072-0.0720.0000.0000.0000.000
25A43ALA0-0.018-0.01715.5570.0300.0300.0000.0000.0000.000
26A44ALA0-0.063-0.03613.1230.0240.0240.0000.0000.0000.000
27A45ILE00.0440.02015.1850.0320.0320.0000.0000.0000.000
28A46HIS0-0.061-0.00817.2930.0340.0340.0000.0000.0000.000
29A47GLY0-0.010-0.01618.9010.0030.0030.0000.0000.0000.000
30A48HIS0-0.052-0.03018.983-0.015-0.0150.0000.0000.0000.000
31A49GLN00.1160.02317.956-0.026-0.0260.0000.0000.0000.000
32A50LEU0-0.072-0.03618.794-0.020-0.0200.0000.0000.0000.000
33A51SER00.0590.01119.121-0.012-0.0120.0000.0000.0000.000
34A52LEU00.0460.03413.065-0.028-0.0280.0000.0000.0000.000
35A53ARG10.8940.95315.3560.1340.1340.0000.0000.0000.000
36A54ASN0-0.009-0.00117.502-0.012-0.0120.0000.0000.0000.000
37A55LEU00.0380.03514.146-0.010-0.0100.0000.0000.0000.000
38A56ILE00.0410.01311.998-0.036-0.0360.0000.0000.0000.000
39A57SER0-0.128-0.06514.213-0.010-0.0100.0000.0000.0000.000
40A58GLN0-0.033-0.03116.731-0.007-0.0070.0000.0000.0000.000
41A59GLY00.0030.01314.156-0.004-0.0040.0000.0000.0000.000
42A60TRP0-0.051-0.00910.739-0.097-0.0970.0000.0000.0000.000
43A61ALA00.011-0.0076.2440.0360.0360.0000.0000.0000.000
44A62VAL00.0660.0247.1180.0000.0000.0000.0000.0000.000
45A63ASN0-0.069-0.0252.281-0.0310.5350.636-0.229-0.9730.001
46A64ILE00.0090.0042.918-2.825-1.2560.279-0.879-0.968-0.011
47A65ILE0-0.040-0.0212.252-1.066-0.3054.450-0.939-4.2740.010
48A66THR00.0490.0394.457-0.477-0.415-0.001-0.003-0.0580.000
49A67ALA00.0540.0146.8090.0970.0970.0000.0000.0000.000
50A68ASP-1-0.881-0.9378.6380.2680.2680.0000.0000.0000.000
51A69HIS0-0.065-0.0485.338-0.334-0.3340.0000.0000.0000.000
52A70VAL00.0490.0437.0950.3320.3320.0000.0000.0000.000
53A71SER00.001-0.0085.886-0.320-0.3200.0000.0000.0000.000
54A72PRO00.0460.0057.1220.0610.0610.0000.0000.0000.000
55A73LEU00.0160.0088.8700.0240.0240.0000.0000.0000.000
56A74HIS00.0220.0378.117-0.122-0.1220.0000.0000.0000.000
57A75GLU-1-0.803-0.90611.7910.0670.0670.0000.0000.0000.000
58A76ALA0-0.027-0.01713.465-0.006-0.0060.0000.0000.0000.000
59A77CYS0-0.112-0.04913.7770.0010.0010.0000.0000.0000.000
60A78LEU00.0220.01816.0180.0020.0020.0000.0000.0000.000
61A79GLY00.0180.01417.930-0.007-0.0070.0000.0000.0000.000
62A80GLY0-0.011-0.00719.513-0.010-0.0100.0000.0000.0000.000
63A81HIS00.0260.02018.123-0.015-0.0150.0000.0000.0000.000
64A82LEU00.0360.00518.330-0.013-0.0130.0000.0000.0000.000
65A83SER0-0.032-0.03419.105-0.004-0.0040.0000.0000.0000.000
66A84CYS0-0.0160.02215.678-0.025-0.0250.0000.0000.0000.000
67A85VAL00.0570.03214.406-0.030-0.0300.0000.0000.0000.000
68A86LYS10.9700.98614.5590.0010.0010.0000.0000.0000.000
69A87ILE0-0.058-0.01614.838-0.017-0.0170.0000.0000.0000.000
70A88LEU00.0420.0189.924-0.052-0.0520.0000.0000.0000.000
71A89LEU00.0190.01310.987-0.056-0.0560.0000.0000.0000.000
72A90LYS10.9000.96612.7180.1480.1480.0000.0000.0000.000
73A91HIS0-0.110-0.06611.7820.0050.0050.0000.0000.0000.000
74A92GLY00.0480.0259.296-0.105-0.1050.0000.0000.0000.000
75A93ALA0-0.041-0.0057.029-0.159-0.1590.0000.0000.0000.000
76A94GLN0-0.029-0.0252.024-4.533-4.7718.158-2.827-5.092-0.004
77A95VAL00.0420.0126.5650.1490.1490.0000.0000.0000.000
78A96ASN0-0.015-0.0108.425-0.042-0.0420.0000.0000.0000.000
79A97GLY00.0130.0216.6200.2170.2170.0000.0000.0000.000
80A98VAL00.0080.0057.140-0.360-0.3600.0000.0000.0000.000
81A99THR00.0000.0088.2870.3010.3010.0000.0000.0000.000
82A100ALA00.0460.01010.6130.0620.0620.0000.0000.0000.000
83A101ASP-1-0.933-0.95211.7700.3340.3340.0000.0000.0000.000
84A102TRP0-0.016-0.03612.346-0.006-0.0060.0000.0000.0000.000
85A103HIS0-0.046-0.01113.621-0.050-0.0500.0000.0000.0000.000
86A104THR00.0650.03611.5990.0950.0950.0000.0000.0000.000
87A105PRO00.008-0.01210.574-0.102-0.1020.0000.0000.0000.000
88A106LEU00.0310.01413.363-0.069-0.0690.0000.0000.0000.000
89A107PHE00.0080.01316.060-0.048-0.0480.0000.0000.0000.000
90A108ASN00.042-0.01014.611-0.011-0.0110.0000.0000.0000.000
91A109ALA0-0.0120.00217.424-0.038-0.0380.0000.0000.0000.000
92A110CYS0-0.074-0.02819.221-0.027-0.0270.0000.0000.0000.000
93A111VAL0-0.023-0.01120.246-0.021-0.0210.0000.0000.0000.000
94A112SER0-0.022-0.00920.417-0.018-0.0180.0000.0000.0000.000
95A113GLY00.0150.01322.732-0.015-0.0150.0000.0000.0000.000
96A114SER00.0200.01821.829-0.012-0.0120.0000.0000.0000.000
97A115TRP00.0710.00422.7210.0160.0160.0000.0000.0000.000
98A116ASP-1-0.920-0.95023.8810.0540.0540.0000.0000.0000.000
99A117CYS0-0.047-0.02718.678-0.007-0.0070.0000.0000.0000.000
100A118VAL00.0150.00819.1470.0130.0130.0000.0000.0000.000
101A119ASN00.0550.03320.1620.0230.0230.0000.0000.0000.000
102A120LEU0-0.0260.00617.900-0.004-0.0040.0000.0000.0000.000
103A121LEU00.010-0.00713.871-0.004-0.0040.0000.0000.0000.000
104A122LEU0-0.0150.00316.5850.0170.0170.0000.0000.0000.000
105A123GLN0-0.039-0.02219.058-0.004-0.0040.0000.0000.0000.000
106A124HIS0-0.134-0.05914.457-0.045-0.0450.0000.0000.0000.000
107A125GLY00.0140.00414.6300.0090.0090.0000.0000.0000.000
108A126ALA0-0.036-0.01213.6910.0550.0550.0000.0000.0000.000
109A127SER0-0.033-0.02313.765-0.021-0.0210.0000.0000.0000.000
110A128VAL00.0170.00015.7210.0190.0190.0000.0000.0000.000
111A129GLN00.0040.01618.585-0.002-0.0020.0000.0000.0000.000
112A130PRO0-0.015-0.01213.7820.0230.0230.0000.0000.0000.000
113A131GLU-1-0.924-0.95712.4590.9570.9570.0000.0000.0000.000
114A132SER00.0370.03214.410-0.077-0.0770.0000.0000.0000.000
115A133ASP-1-0.852-0.92416.2230.3320.3320.0000.0000.0000.000
116A134LEU0-0.050-0.04117.093-0.050-0.0500.0000.0000.0000.000
117A135ALA00.0100.01616.340-0.029-0.0290.0000.0000.0000.000
118A136SER00.0080.00317.8320.0070.0070.0000.0000.0000.000
119A137PRO00.0330.00118.143-0.035-0.0350.0000.0000.0000.000
120A138ILE00.0240.01020.902-0.027-0.0270.0000.0000.0000.000
121A139HIS10.7980.87823.832-0.260-0.2600.0000.0000.0000.000
122A140GLU-1-0.734-0.84022.1720.1880.1880.0000.0000.0000.000
123A141ALA00.0180.00024.472-0.019-0.0190.0000.0000.0000.000
124A142ALA0-0.017-0.01226.144-0.017-0.0170.0000.0000.0000.000
125A143ARG10.8820.93624.996-0.208-0.2080.0000.0000.0000.000
126A144ARG10.8310.91124.352-0.168-0.1680.0000.0000.0000.000
127A145GLY00.0040.01229.377-0.010-0.0100.0000.0000.0000.000
128A146HIS0-0.081-0.03825.495-0.018-0.0180.0000.0000.0000.000
129A147VAL00.0460.00428.7270.0090.0090.0000.0000.0000.000
130A148GLU-1-0.847-0.90429.0610.0870.0870.0000.0000.0000.000
131A149CYS0-0.0130.01824.4870.0020.0020.0000.0000.0000.000
132A150VAL0-0.011-0.00925.7350.0130.0130.0000.0000.0000.000
133A151ASN0-0.011-0.02127.6720.0080.0080.0000.0000.0000.000
134A152SER0-0.024-0.02124.5590.0000.0000.0000.0000.0000.000
135A153LEU0-0.009-0.01821.1150.0090.0090.0000.0000.0000.000
136A154ILE0-0.0060.00824.3170.0100.0100.0000.0000.0000.000
137A155ALA0-0.019-0.00327.0780.0000.0000.0000.0000.0000.000
138A156TYR0-0.051-0.02921.781-0.007-0.0070.0000.0000.0000.000
139A157GLY00.0180.01122.9340.0190.0190.0000.0000.0000.000
140A158GLY0-0.038-0.01223.9030.0140.0140.0000.0000.0000.000
141A159ASN0-0.004-0.00624.745-0.027-0.0270.0000.0000.0000.000
142A160ILE00.0330.00627.2410.0110.0110.0000.0000.0000.000
143A161ASP-1-0.831-0.91029.7600.1400.1400.0000.0000.0000.000
144A162HIS0-0.113-0.07122.480-0.021-0.0210.0000.0000.0000.000
145A163LYS10.8910.92527.490-0.160-0.1600.0000.0000.0000.000
146A164ILE0-0.0060.02422.5700.0070.0070.0000.0000.0000.000
147A165SER00.023-0.00926.051-0.024-0.0240.0000.0000.0000.000
148A166HIS0-0.032-0.01926.6440.0050.0050.0000.0000.0000.000
149A167LEU00.0010.00724.551-0.004-0.0040.0000.0000.0000.000
150A168GLY00.0390.00728.464-0.016-0.0160.0000.0000.0000.000
151A169THR00.0000.02028.5650.0170.0170.0000.0000.0000.000
152A170PRO00.002-0.01027.404-0.004-0.0040.0000.0000.0000.000
153A171LEU00.0500.03629.721-0.007-0.0070.0000.0000.0000.000
154A172TYR0-0.048-0.02732.504-0.006-0.0060.0000.0000.0000.000
155A173LEU0-0.0010.00527.185-0.003-0.0030.0000.0000.0000.000
156A174ALA00.0190.01931.641-0.006-0.0060.0000.0000.0000.000
157A175CYS0-0.065-0.03433.388-0.010-0.0100.0000.0000.0000.000
158A176GLU-1-0.885-0.94831.9830.1390.1390.0000.0000.0000.000
159A177ASN0-0.092-0.05731.566-0.002-0.0020.0000.0000.0000.000
160A178GLN0-0.036-0.01934.620-0.007-0.0070.0000.0000.0000.000
161A179GLN00.0280.02932.541-0.012-0.0120.0000.0000.0000.000
162A180ARG10.8480.88736.283-0.061-0.0610.0000.0000.0000.000
163A181ALA0-0.007-0.00737.2770.0000.0000.0000.0000.0000.000
164A182CYS00.0240.01232.6040.0030.0030.0000.0000.0000.000
165A183VAL00.0080.01335.2640.0040.0040.0000.0000.0000.000
166A184LYS10.8260.90137.072-0.066-0.0660.0000.0000.0000.000
167A185LYS10.9040.95833.927-0.089-0.0890.0000.0000.0000.000
168A186LEU0-0.016-0.00931.1830.0020.0020.0000.0000.0000.000
169A187LEU00.0020.01035.2220.0020.0020.0000.0000.0000.000
170A188GLU-1-0.837-0.91538.6280.0680.0680.0000.0000.0000.000
171A189SER0-0.116-0.07334.401-0.003-0.0030.0000.0000.0000.000
172A190GLY0-0.013-0.00335.5970.0040.0040.0000.0000.0000.000
173A191ALA0-0.046-0.01234.4410.0040.0040.0000.0000.0000.000
174A192ASP-1-0.801-0.91735.3120.1080.1080.0000.0000.0000.000
175A193VAL0-0.022-0.00936.9170.0050.0050.0000.0000.0000.000
176A194ASN0-0.008-0.00539.376-0.003-0.0030.0000.0000.0000.000
177A195GLN0-0.039-0.00134.2980.0090.0090.0000.0000.0000.000
178A196GLY00.011-0.00435.0580.0020.0020.0000.0000.0000.000
179A197LYS10.8990.96330.982-0.144-0.1440.0000.0000.0000.000
180A198GLY0-0.025-0.00933.179-0.007-0.0070.0000.0000.0000.000
181A199GLN0-0.020-0.02134.9160.0020.0020.0000.0000.0000.000
182A200ASP-1-0.755-0.81937.1920.1010.1010.0000.0000.0000.000
183A201SER00.041-0.01237.4660.0060.0060.0000.0000.0000.000
184A202PRO00.0450.00436.652-0.001-0.0010.0000.0000.0000.000
185A203LEU00.0380.02338.888-0.003-0.0030.0000.0000.0000.000
186A204HIS00.0100.02341.3520.0000.0000.0000.0000.0000.000
187A205ALA0-0.0060.00338.315-0.003-0.0030.0000.0000.0000.000
188A206VAL0-0.013-0.01140.096-0.002-0.0020.0000.0000.0000.000
189A207VAL0-0.0140.00042.087-0.004-0.0040.0000.0000.0000.000
190A208ARG10.8330.91439.893-0.100-0.1000.0000.0000.0000.000
191A209THR0-0.053-0.02840.310-0.003-0.0030.0000.0000.0000.000
192A210ALA0-0.018-0.01143.723-0.003-0.0030.0000.0000.0000.000
193A211SER00.0250.02142.999-0.003-0.0030.0000.0000.0000.000
194A212GLU-1-0.864-0.95445.1850.0550.0550.0000.0000.0000.000
195A213GLU-1-0.802-0.86444.8890.0580.0580.0000.0000.0000.000
196A214LEU0-0.008-0.01039.7160.0010.0010.0000.0000.0000.000
197A215ALA00.0290.01343.3890.0020.0020.0000.0000.0000.000
198A216CYS0-0.013-0.01845.7020.0000.0000.0000.0000.0000.000
199A217LEU0-0.0170.00541.2520.0000.0000.0000.0000.0000.000
200A218LEU00.011-0.01039.5090.0020.0020.0000.0000.0000.000
201A219MET0-0.044-0.02643.5510.0000.0000.0000.0000.0000.000
202A220ASP-1-0.929-0.95046.8910.0580.0580.0000.0000.0000.000
203A221PHE0-0.080-0.04142.363-0.001-0.0010.0000.0000.0000.000
204A222GLY0-0.008-0.00443.9120.0040.0040.0000.0000.0000.000
205A223ALA0-0.044-0.02343.6790.0020.0020.0000.0000.0000.000
206A224ASP-1-0.850-0.93044.4230.0750.0750.0000.0000.0000.000
207A225THR0-0.032-0.02546.1030.0010.0010.0000.0000.0000.000
208A226GLN0-0.046-0.03448.710-0.001-0.0010.0000.0000.0000.000
209A227ALA00.0270.03643.8170.0010.0010.0000.0000.0000.000
210A228LYS10.8710.91945.548-0.075-0.0750.0000.0000.0000.000
211A229ASN0-0.010-0.02341.8060.0020.0020.0000.0000.0000.000
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