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: 8581Y

Calculation Name: 5F9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F9Q

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972304.131697
FMO2-HF: Nuclear repulsion 1897811.663325
FMO2-HF: Total energy -74492.468373
FMO2-MP2: Total energy -74707.722359


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:16:ASN)


Summations of interaction energy for fragment #1(A:16:ASN)
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.
-22.317-12.1313.562-4.968-8.781-0.008
Interaction energy analysis for fragmet #1(A:16:ASN)
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 : -0.012
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].
3A18ILE0-0.014-0.0063.749-0.8901.054-0.037-0.884-1.0230.003
4A19GLU-1-0.915-0.9566.5640.0730.0730.0000.0000.0000.000
5A20LEU0-0.028-0.00710.041-0.011-0.0110.0000.0000.0000.000
6A21PHE0-0.009-0.00812.3820.0570.0570.0000.0000.0000.000
7A22TYR00.0150.00016.427-0.046-0.0460.0000.0000.0000.000
8A23MET0-0.052-0.02317.6220.0400.0400.0000.0000.0000.000
9A24PRO00.0360.02322.116-0.005-0.0050.0000.0000.0000.000
10A25SER00.0500.02725.1620.0170.0170.0000.0000.0000.000
11A26ASP-1-0.842-0.93427.0570.0230.0230.0000.0000.0000.000
12A27GLU-1-0.903-0.93429.553-0.053-0.0530.0000.0000.0000.000
13A28GLU-1-0.801-0.88625.716-0.111-0.1110.0000.0000.0000.000
14A29LEU00.005-0.00628.956-0.007-0.0070.0000.0000.0000.000
15A30THR0-0.119-0.07331.146-0.004-0.0040.0000.0000.0000.000
16A31ALA0-0.0140.00631.959-0.001-0.0010.0000.0000.0000.000
17A32ASN0-0.018-0.01729.751-0.002-0.0020.0000.0000.0000.000
18A33PRO00.0480.02432.1790.0030.0030.0000.0000.0000.000
19A34ASN0-0.085-0.07433.649-0.007-0.0070.0000.0000.0000.000
20A35ALA00.0550.05331.3530.0010.0010.0000.0000.0000.000
21A36LEU0-0.0270.00729.020-0.008-0.0080.0000.0000.0000.000
22A37GLN0-0.051-0.01425.6010.0020.0020.0000.0000.0000.000
23A38GLU-1-0.882-0.93824.2390.0290.0290.0000.0000.0000.000
24A39ALA00.001-0.03619.991-0.023-0.0230.0000.0000.0000.000
25A40SER0-0.086-0.03722.034-0.003-0.0030.0000.0000.0000.000
26A41PHE0-0.0150.00016.579-0.035-0.0350.0000.0000.0000.000
27A42THR00.0710.01720.5130.0090.0090.0000.0000.0000.000
28A43GLU-1-0.827-0.92720.726-0.280-0.2800.0000.0000.0000.000
29A44GLU-1-0.949-0.94920.842-0.363-0.3630.0000.0000.0000.000
30A45ASP-1-0.714-0.81018.555-0.382-0.3820.0000.0000.0000.000
31A46ILE0-0.052-0.02616.194-0.092-0.0920.0000.0000.0000.000
32A47ASN0-0.078-0.05716.065-0.139-0.1390.0000.0000.0000.000
33A48GLY00.0290.01817.551-0.065-0.0650.0000.0000.0000.000
34A49LEU00.006-0.01112.856-0.099-0.0990.0000.0000.0000.000
35A50LYS10.8240.90411.7791.2451.2450.0000.0000.0000.000
36A51GLY0-0.028-0.00813.360-0.141-0.1410.0000.0000.0000.000
37A52VAL0-0.040-0.00311.8990.0680.0680.0000.0000.0000.000
38A53ASP-1-0.872-0.92911.885-1.699-1.6990.0000.0000.0000.000
39A54GLY00.0310.0188.629-0.019-0.0190.0000.0000.0000.000
40A55VAL0-0.071-0.0316.842-1.374-1.3740.0000.0000.0000.000
41A56LYS10.9140.9645.8063.2263.2260.0000.0000.0000.000
42A57GLN0-0.098-0.0727.8030.7080.7080.0000.0000.0000.000
43A58VAL00.0500.0458.804-0.239-0.2390.0000.0000.0000.000
44A59VAL0-0.049-0.0258.8990.2050.2050.0000.0000.0000.000
45A60ALA00.0340.02411.8160.0630.0630.0000.0000.0000.000
46A61SER00.008-0.02115.2890.0460.0460.0000.0000.0000.000
47A62ALA00.0100.02317.900-0.004-0.0040.0000.0000.0000.000
48A63VAL00.0040.01418.5660.0060.0060.0000.0000.0000.000
49A64LYS10.9190.95421.732-0.007-0.0070.0000.0000.0000.000
50A65SER00.0280.02325.3320.0080.0080.0000.0000.0000.000
51A66MET0-0.038-0.01027.505-0.018-0.0180.0000.0000.0000.000
52A67THR00.0270.01030.6140.0080.0080.0000.0000.0000.000
53A68ALA0-0.057-0.02831.236-0.010-0.0100.0000.0000.0000.000
54A69ARG10.8580.89033.322-0.040-0.0400.0000.0000.0000.000
55A70TYR0-0.013-0.01336.393-0.011-0.0110.0000.0000.0000.000
56A71HIS0-0.012-0.01038.1930.0040.0040.0000.0000.0000.000
57A72GLU-1-0.959-0.98741.9590.0400.0400.0000.0000.0000.000
58A73GLU-1-0.941-0.94037.9530.0760.0760.0000.0000.0000.000
59A74ASP-1-0.794-0.87936.8390.0510.0510.0000.0000.0000.000
60A75THR0-0.061-0.04331.5130.0130.0130.0000.0000.0000.000
61A76ASP-1-0.872-0.90530.8480.0890.0890.0000.0000.0000.000
62A77ILE0-0.070-0.05727.4130.0150.0150.0000.0000.0000.000
63A78THR0-0.001-0.00621.695-0.004-0.0040.0000.0000.0000.000
64A79LEU0-0.032-0.01324.5870.0020.0020.0000.0000.0000.000
65A80ASN00.016-0.00919.557-0.007-0.0070.0000.0000.0000.000
66A81GLY00.0180.00221.675-0.011-0.0110.0000.0000.0000.000
67A82ILE0-0.023-0.01417.269-0.004-0.0040.0000.0000.0000.000
68A83ASN00.0590.01414.2680.0580.0580.0000.0000.0000.000
69A84SER00.0190.00316.8700.0230.0230.0000.0000.0000.000
70A85GLY00.0290.01412.880-0.012-0.0120.0000.0000.0000.000
71A86TYR00.0460.01211.6580.0620.0620.0000.0000.0000.000
72A87MET0-0.032-0.02912.6190.1620.1620.0000.0000.0000.000
73A88ASP-1-0.886-0.90110.664-1.044-1.0440.0000.0000.0000.000
74A89VAL0-0.018-0.0086.5440.1070.1070.0000.0000.0000.000
75A90LYS10.9020.9658.9700.0550.0550.0000.0000.0000.000
76A91LYS10.8990.9649.471-0.726-0.7260.0000.0000.0000.000
77A92LEU0-0.009-0.02212.9190.0240.0240.0000.0000.0000.000
78A93ASP-1-0.877-0.94116.2100.1700.1700.0000.0000.0000.000
79A94VAL0-0.033-0.01619.0460.0150.0150.0000.0000.0000.000
80A95GLN0-0.072-0.03922.5320.0160.0160.0000.0000.0000.000
81A96ASP-1-0.877-0.92625.3880.0780.0780.0000.0000.0000.000
82A97GLY0-0.002-0.00927.7100.0010.0010.0000.0000.0000.000
83A98ARG10.9100.95225.4990.0560.0560.0000.0000.0000.000
84A99THR00.0550.01919.4920.0170.0170.0000.0000.0000.000
85A100PHE0-0.027-0.01620.804-0.014-0.0140.0000.0000.0000.000
86A101THR0-0.026-0.02821.390-0.028-0.0280.0000.0000.0000.000
87A102ASP-1-0.800-0.92119.604-0.422-0.4220.0000.0000.0000.000
88A103ASN0-0.002-0.01022.217-0.003-0.0030.0000.0000.0000.000
89A104ASP-1-0.857-0.89724.545-0.122-0.1220.0000.0000.0000.000
90A105PHE00.0330.01219.2790.0100.0100.0000.0000.0000.000
91A106LEU0-0.0160.01023.5340.0060.0060.0000.0000.0000.000
92A107SER0-0.042-0.04125.7540.0160.0160.0000.0000.0000.000
93A108GLY00.0210.01826.8720.0140.0140.0000.0000.0000.000
94A109LYS10.8370.91827.8600.1550.1550.0000.0000.0000.000
95A110ARG10.8850.93428.8300.0480.0480.0000.0000.0000.000
96A111ALA0-0.0040.00327.7310.0090.0090.0000.0000.0000.000
97A112GLY00.043-0.00226.403-0.006-0.0060.0000.0000.0000.000
98A113ILE0-0.046-0.00421.9910.0020.0020.0000.0000.0000.000
99A114ILE00.0140.00624.2360.0150.0150.0000.0000.0000.000
100A115SER00.032-0.00623.317-0.002-0.0020.0000.0000.0000.000
101A116LYS10.8750.91124.699-0.222-0.2220.0000.0000.0000.000
102A117LYS10.9560.99426.298-0.238-0.2380.0000.0000.0000.000
103A118MET0-0.0110.01026.787-0.018-0.0180.0000.0000.0000.000
104A119ALA00.0190.01528.991-0.016-0.0160.0000.0000.0000.000
105A120GLU-1-0.846-0.91430.1060.1630.1630.0000.0000.0000.000
106A121LYS10.8800.93731.747-0.145-0.1450.0000.0000.0000.000
107A122LEU00.0210.02032.461-0.007-0.0070.0000.0000.0000.000
108A123PHE00.013-0.00533.074-0.010-0.0100.0000.0000.0000.000
109A124GLY0-0.0050.01035.712-0.006-0.0060.0000.0000.0000.000
110A125LYS10.9390.95735.186-0.065-0.0650.0000.0000.0000.000
111A126THR0-0.068-0.03437.180-0.004-0.0040.0000.0000.0000.000
112A127SER00.0410.02234.9620.0040.0040.0000.0000.0000.000
113A128PRO00.0700.04031.441-0.008-0.0080.0000.0000.0000.000
114A129LEU0-0.0150.00629.800-0.009-0.0090.0000.0000.0000.000
115A130GLY00.0090.00633.370-0.002-0.0020.0000.0000.0000.000
116A131LYS10.7890.90235.208-0.030-0.0300.0000.0000.0000.000
117A132ILE0-0.018-0.01034.810-0.001-0.0010.0000.0000.0000.000
118A133VAL00.0150.01132.2050.0060.0060.0000.0000.0000.000
119A134TRP0-0.003-0.01834.464-0.012-0.0120.0000.0000.0000.000
120A135ALA00.0180.01430.6380.0100.0100.0000.0000.0000.000
121A136GLY00.0530.02032.769-0.010-0.0100.0000.0000.0000.000
122A137GLY0-0.009-0.00334.171-0.006-0.0060.0000.0000.0000.000
123A138GLN00.0340.01733.378-0.013-0.0130.0000.0000.0000.000
124A139PRO0-0.0450.00634.4790.0070.0070.0000.0000.0000.000
125A140VAL00.007-0.01929.358-0.011-0.0110.0000.0000.0000.000
126A141GLU-1-0.901-0.94032.384-0.026-0.0260.0000.0000.0000.000
127A142VAL0-0.008-0.00329.247-0.003-0.0030.0000.0000.0000.000
128A143ILE0-0.036-0.02325.588-0.005-0.0050.0000.0000.0000.000
129A144GLY00.0300.01025.927-0.008-0.0080.0000.0000.0000.000
130A145VAL0-0.031-0.00926.4890.0050.0050.0000.0000.0000.000
131A146LEU0-0.004-0.01520.003-0.004-0.0040.0000.0000.0000.000
132A147LYS10.8820.95118.860-0.375-0.3750.0000.0000.0000.000
133A148GLU-1-0.895-0.93421.0850.3170.3170.0000.0000.0000.000
134A156GLY00.0230.00022.1540.0070.0070.0000.0000.0000.000
135A157LEU00.0040.00021.051-0.015-0.0150.0000.0000.0000.000
136A158SER00.0110.03124.103-0.001-0.0010.0000.0000.0000.000
137A159GLU-1-0.794-0.87319.5780.2780.2780.0000.0000.0000.000
138A160MET0-0.017-0.00424.312-0.001-0.0010.0000.0000.0000.000
139A161TYR0-0.056-0.04617.587-0.007-0.0070.0000.0000.0000.000
140A162VAL00.030-0.00122.748-0.009-0.0090.0000.0000.0000.000
141A163PRO00.0010.01422.553-0.009-0.0090.0000.0000.0000.000
142A164PHE00.0190.01121.3160.0150.0150.0000.0000.0000.000
143A165ASN00.024-0.00923.2980.0200.0200.0000.0000.0000.000
144A166MET0-0.0350.01326.1320.0100.0100.0000.0000.0000.000
145A167LEU0-0.029-0.02224.3800.0150.0150.0000.0000.0000.000
146A168LYS10.8690.93426.6090.2080.2080.0000.0000.0000.000
147A169THR0-0.028-0.01029.6600.0100.0100.0000.0000.0000.000
148A170SER0-0.066-0.02631.4810.0100.0100.0000.0000.0000.000
149A171PHE0-0.055-0.05029.5750.0100.0100.0000.0000.0000.000
150A172GLY00.0400.04531.9290.0050.0050.0000.0000.0000.000
151A173THR0-0.100-0.05625.7810.0060.0060.0000.0000.0000.000
152A174ASN00.017-0.02627.239-0.018-0.0180.0000.0000.0000.000
153A175ASP-1-0.791-0.83523.494-0.171-0.1710.0000.0000.0000.000
154A176TYR0-0.074-0.06118.7170.0150.0150.0000.0000.0000.000
155A177SER00.025-0.00919.291-0.009-0.0090.0000.0000.0000.000
156A178ASN0-0.037-0.01114.9420.0070.0070.0000.0000.0000.000
157A179VAL00.0620.02312.899-0.035-0.0350.0000.0000.0000.000
158A180SER0-0.019-0.0078.4010.1520.1520.0000.0000.0000.000
159A181VAL00.0210.0257.4290.0060.0060.0000.0000.0000.000
160A182GLN00.0110.0023.295-1.013-0.5920.024-0.111-0.3340.000
161A183THR00.013-0.0082.700-4.113-1.5100.513-1.282-1.834-0.013
162A184GLU-1-0.901-0.9493.187-8.739-7.3020.104-0.761-0.780-0.006
163A185SER0-0.055-0.0402.746-3.662-2.4750.689-0.817-1.059-0.002
164A186ALA00.0270.0112.647-1.3580.7581.422-0.884-2.6540.011
165A187ASP-1-0.939-0.9713.715-0.270-0.1010.0820.008-0.2590.002
166A188GLN00.0270.0255.808-1.078-1.0780.0000.0000.0000.000
167A189ILE0-0.0310.0072.481-0.2380.0710.765-0.237-0.838-0.003
168A190LYS10.9550.9736.188-0.751-0.7510.0000.0000.0000.000
169A191SER00.0400.0199.6720.0570.0570.0000.0000.0000.000
170A192THR00.0350.0057.771-0.017-0.0170.0000.0000.0000.000
171A193GLY0-0.004-0.0059.0990.0830.0830.0000.0000.0000.000
172A194LYS10.9330.96310.1680.3910.3910.0000.0000.0000.000
173A195GLU-1-0.913-0.96213.227-0.821-0.8210.0000.0000.0000.000
174A196ALA00.0280.00811.8000.0660.0660.0000.0000.0000.000
175A197ALA00.0130.00113.8090.0880.0880.0000.0000.0000.000
176A198ARG10.7550.85015.7910.3570.3570.0000.0000.0000.000
177A199LEU00.0330.02916.5610.0370.0370.0000.0000.0000.000
178A200LEU0-0.014-0.00115.8430.0410.0410.0000.0000.0000.000
179A201ASN00.000-0.00819.3810.0670.0670.0000.0000.0000.000
180A202ASP-1-0.785-0.86021.751-0.285-0.2850.0000.0000.0000.000
181A203ASN0-0.080-0.04420.6180.0160.0160.0000.0000.0000.000
182A204HIS10.7770.86422.3300.2470.2470.0000.0000.0000.000
183A205GLY0-0.0360.00625.5300.0220.0220.0000.0000.0000.000
184A206THR0-0.067-0.04123.4230.0160.0160.0000.0000.0000.000
185A207LYS10.7390.84924.9320.0440.0440.0000.0000.0000.000
186A208GLU-1-0.954-0.99921.712-0.109-0.1090.0000.0000.0000.000
187A209ALA00.0220.02821.5070.0210.0210.0000.0000.0000.000
188A210TYR0-0.042-0.02817.6530.0200.0200.0000.0000.0000.000
189A211GLN0-0.038-0.02116.0750.0120.0120.0000.0000.0000.000
190A212VAL00.0070.01310.333-0.007-0.0070.0000.0000.0000.000
191A213MET00.0180.0099.8830.0500.0500.0000.0000.0000.000
192A214ASN0-0.052-0.02611.9140.0990.0990.0000.0000.0000.000