FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2NKQR

Calculation Name: 4H05-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H05

Chain ID: A

ChEMBL ID:

UniProt ID: Q9F9M5

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 270
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3512133.604453
FMO2-HF: Nuclear repulsion 3408515.955652
FMO2-HF: Total energy -103617.648801
FMO2-MP2: Total energy -103922.082728


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:-2:HIS)


Summations of interaction energy for fragment #1(A:-2:HIS)
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.
-20.188-25.17635.977-14.155-16.834-0.018
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.004
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].
3A0HIS00.0970.0542.685-12.282-7.0713.146-2.776-5.5820.021
4A1MET0-0.0190.0092.275-5.081-2.5651.507-1.267-2.7550.007
5A2ASP-1-0.861-0.9274.007-3.989-3.4680.003-0.142-0.3820.000
6A3ASP-1-0.972-0.9865.8300.3230.3230.0000.0000.0000.000
7A4ALA0-0.0160.0107.491-0.139-0.1390.0000.0000.0000.000
8A5LEU00.0480.0256.7840.0950.0950.0000.0000.0000.000
9A6ARG10.9320.9669.7680.2110.2110.0000.0000.0000.000
10A7ALA0-0.058-0.04211.5820.0540.0540.0000.0000.0000.000
11A8LEU00.007-0.00111.3760.0450.0450.0000.0000.0000.000
12A9ARG10.9300.96712.7790.3730.3730.0000.0000.0000.000
13A10GLY0-0.055-0.02815.7140.0380.0380.0000.0000.0000.000
14A11ARG10.8540.93113.9940.5420.5420.0000.0000.0000.000
15A12TYR0-0.114-0.09217.6670.0300.0300.0000.0000.0000.000
16A13PRO00.0200.02320.5380.0110.0110.0000.0000.0000.000
17A14GLY0-0.025-0.03222.0810.0040.0040.0000.0000.0000.000
18A15CYS0-0.074-0.00520.8680.0150.0150.0000.0000.0000.000
19A16GLU-1-0.869-0.94220.175-0.126-0.1260.0000.0000.0000.000
20A17TRP0-0.042-0.01612.788-0.014-0.0140.0000.0000.0000.000
21A18VAL0-0.010-0.01117.9010.0250.0250.0000.0000.0000.000
22A19VAL00.0110.00113.627-0.038-0.0380.0000.0000.0000.000
23A20VAL0-0.079-0.03416.3170.0350.0350.0000.0000.0000.000
24A21GLU-1-0.866-0.92915.391-0.202-0.2020.0000.0000.0000.000
25A22ASP-1-0.920-0.9569.866-0.171-0.1710.0000.0000.0000.000
26A23GLY00.0430.0159.9610.0020.0020.0000.0000.0000.000
27A24ALA0-0.050-0.0235.267-0.286-0.2860.0000.0000.0000.000
28A25SER0-0.003-0.0081.6914.058-11.27227.620-8.113-4.177-0.037
29A26GLY00.0680.0584.189-0.437-0.0650.001-0.255-0.118-0.001
30A27ALA0-0.0410.0005.718-0.204-0.2040.0000.0000.0000.000
31A28GLY00.1000.0597.7090.0310.0310.0000.0000.0000.000
32A29VAL00.0350.03611.361-0.113-0.1130.0000.0000.0000.000
33A30TYR0-0.084-0.1259.7080.1120.1120.0000.0000.0000.000
34A31ARG10.9300.95716.3520.1800.1800.0000.0000.0000.000
35A32LEU0-0.042-0.02216.5640.0220.0220.0000.0000.0000.000
36A33ARG10.8970.94920.4970.1390.1390.0000.0000.0000.000
37A34GLY00.0540.01523.9550.0080.0080.0000.0000.0000.000
38A35GLY0-0.042-0.02426.274-0.007-0.0070.0000.0000.0000.000
39A36GLY0-0.0100.01629.8700.0010.0010.0000.0000.0000.000
40A37ARG10.9300.95223.9860.2110.2110.0000.0000.0000.000
41A38GLU-1-0.864-0.93924.681-0.171-0.1710.0000.0000.0000.000
42A39LEU0-0.024-0.00720.8250.0020.0020.0000.0000.0000.000
43A40PHE00.0140.01619.4020.0270.0270.0000.0000.0000.000
44A41VAL0-0.012-0.02013.597-0.021-0.0210.0000.0000.0000.000
45A42LYS10.8160.91813.4290.6110.6110.0000.0000.0000.000
46A43VAL0-0.028-0.0377.266-0.064-0.0640.0000.0000.0000.000
47A44ALA00.0450.0278.2860.1280.1280.0000.0000.0000.000
48A45ALA00.012-0.0124.754-0.889-0.832-0.001-0.005-0.0510.000
49A46LEU0-0.020-0.0145.6540.4090.4090.0000.0000.0000.000
50A47GLY00.0660.0406.7910.0240.0240.0000.0000.0000.000
51A48ALA00.0000.0008.9860.2340.2340.0000.0000.0000.000
52A49GLY0-0.021-0.0138.8270.1790.1790.0000.0000.0000.000
53A50VAL00.0230.0049.8370.1530.1530.0000.0000.0000.000
54A51GLY0-0.0050.00312.3790.1620.1620.0000.0000.0000.000
55A52LEU00.0270.01410.7590.1080.1080.0000.0000.0000.000
56A53LEU0-0.045-0.01211.4910.1090.1090.0000.0000.0000.000
57A54GLY00.0120.01215.2550.1090.1090.0000.0000.0000.000
58A55GLU-1-0.811-0.91017.172-0.494-0.4940.0000.0000.0000.000
59A56ALA0-0.0030.00618.0950.0690.0690.0000.0000.0000.000
60A57GLU-1-0.965-0.98019.857-0.454-0.4540.0000.0000.0000.000
61A58ARG10.8870.94220.9100.5030.5030.0000.0000.0000.000
62A59LEU00.025-0.00120.4790.0390.0390.0000.0000.0000.000
63A60VAL0-0.060-0.02323.7610.0360.0360.0000.0000.0000.000
64A61TRP00.0420.01026.0990.0220.0220.0000.0000.0000.000
65A62LEU00.0350.00325.8340.0200.0200.0000.0000.0000.000
66A63ALA0-0.0330.00528.4160.0200.0200.0000.0000.0000.000
67A64GLU-1-1.020-1.00530.190-0.180-0.1800.0000.0000.0000.000
68A65VAL0-0.059-0.03631.5840.0150.0150.0000.0000.0000.000
69A66GLY0-0.0140.00433.3350.0110.0110.0000.0000.0000.000
70A67ILE0-0.044-0.01430.0050.0110.0110.0000.0000.0000.000
71A68PRO0-0.0280.00031.084-0.009-0.0090.0000.0000.0000.000
72A69VAL00.0160.00925.487-0.006-0.0060.0000.0000.0000.000
73A70PRO00.0090.02123.6150.0140.0140.0000.0000.0000.000
74A71ARG10.9690.97925.1620.2150.2150.0000.0000.0000.000
75A72VAL00.0260.00520.456-0.008-0.0080.0000.0000.0000.000
76A73VAL0-0.088-0.03820.8490.0280.0280.0000.0000.0000.000
77A74GLU-1-0.804-0.87216.751-0.502-0.5020.0000.0000.0000.000
78A75GLY00.0530.02015.418-0.002-0.0020.0000.0000.0000.000
79A76GLY0-0.052-0.01513.1390.0870.0870.0000.0000.0000.000
80A77GLY00.0090.0259.134-0.137-0.1370.0000.0000.0000.000
81A78ASP-1-0.910-0.9706.653-2.610-2.6100.0000.0000.0000.000
82A79GLU-1-0.784-0.9137.471-2.607-2.6070.0000.0000.0000.000
83A80ARG10.7920.9011.8273.8034.3613.080-1.214-2.425-0.006
84A81VAL0-0.024-0.0082.719-1.895-0.8020.622-0.382-1.333-0.002
85A82ALA00.0400.0295.2560.6890.703-0.001-0.001-0.0110.000
86A83TRP0-0.062-0.0539.034-0.007-0.0070.0000.0000.0000.000
87A84LEU00.0330.02211.5810.0550.0550.0000.0000.0000.000
88A85VAL0-0.027-0.01215.2280.0240.0240.0000.0000.0000.000
89A86THR00.0370.01117.9080.0090.0090.0000.0000.0000.000
90A87GLU-1-0.940-0.97321.331-0.222-0.2220.0000.0000.0000.000
91A88ALA0-0.025-0.00823.764-0.011-0.0110.0000.0000.0000.000
92A89VAL0-0.0050.02524.6760.0090.0090.0000.0000.0000.000
93A90PRO0-0.033-0.01427.1370.0070.0070.0000.0000.0000.000
94A91GLY00.0270.00830.017-0.002-0.0020.0000.0000.0000.000
95A92ARG10.8450.93229.9080.0920.0920.0000.0000.0000.000
96A93PRO00.0930.04026.4130.0020.0020.0000.0000.0000.000
97A94ALA0-0.0070.00428.9960.0150.0150.0000.0000.0000.000
98A95SER00.010-0.02525.8320.0160.0160.0000.0000.0000.000
99A96ALA0-0.035-0.00229.1260.0100.0100.0000.0000.0000.000
100A97ARG10.9330.98330.7970.0510.0510.0000.0000.0000.000
101A98TRP0-0.022-0.03532.5210.0070.0070.0000.0000.0000.000
102A99PRO0-0.039-0.02036.5630.0060.0060.0000.0000.0000.000
103A100ARG11.0341.00440.2150.0390.0390.0000.0000.0000.000
104A101GLU-1-0.948-0.98442.108-0.055-0.0550.0000.0000.0000.000
105A102GLN0-0.008-0.01939.8630.0000.0000.0000.0000.0000.000
106A103ARG10.8680.96238.1390.0540.0540.0000.0000.0000.000
107A104LEU00.0520.01239.177-0.004-0.0040.0000.0000.0000.000
108A105ASP-1-0.871-0.94241.019-0.079-0.0790.0000.0000.0000.000
109A106VAL0-0.0040.00734.480-0.006-0.0060.0000.0000.0000.000
110A107ALA0-0.0020.01036.577-0.008-0.0080.0000.0000.0000.000
111A108VAL0-0.005-0.01137.909-0.004-0.0040.0000.0000.0000.000
112A109ALA00.0250.01236.717-0.004-0.0040.0000.0000.0000.000
113A110LEU0-0.007-0.00931.621-0.008-0.0080.0000.0000.0000.000
114A111ALA00.004-0.00235.030-0.008-0.0080.0000.0000.0000.000
115A112GLY0-0.005-0.01137.500-0.002-0.0020.0000.0000.0000.000
116A113LEU0-0.0080.00730.637-0.003-0.0030.0000.0000.0000.000
117A114ALA00.0240.00533.667-0.008-0.0080.0000.0000.0000.000
118A115ARG10.8530.93234.6570.1020.1020.0000.0000.0000.000
119A116SER0-0.046-0.02035.6790.0030.0030.0000.0000.0000.000
120A117LEU00.006-0.00429.592-0.005-0.0050.0000.0000.0000.000
121A118HIS0-0.079-0.04432.2740.0100.0100.0000.0000.0000.000
122A119ALA0-0.0200.01635.9590.0060.0060.0000.0000.0000.000
123A120LEU0-0.033-0.00932.7290.0020.0020.0000.0000.0000.000
124A121ASP-1-0.850-0.92036.657-0.149-0.1490.0000.0000.0000.000
125A122TRP00.054-0.00233.830-0.015-0.0150.0000.0000.0000.000
126A123GLU-1-0.955-0.96933.782-0.159-0.1590.0000.0000.0000.000
127A124ARG10.8050.89334.8970.1530.1530.0000.0000.0000.000
128A125CYS0-0.0710.00529.546-0.016-0.0160.0000.0000.0000.000
129A126PRO0-0.020-0.01226.9950.0020.0020.0000.0000.0000.000
130A127PHE0-0.023-0.01423.508-0.016-0.0160.0000.0000.0000.000
131A128ASP-1-0.841-0.92525.682-0.235-0.2350.0000.0000.0000.000
132A129ARG10.9130.96822.6220.2660.2660.0000.0000.0000.000
133A130SER00.0240.00926.2400.0160.0160.0000.0000.0000.000
134A131LEU0-0.016-0.01627.772-0.016-0.0160.0000.0000.0000.000
135A132ALA0-0.080-0.03828.7580.0010.0010.0000.0000.0000.000
136A133VAL0-0.009-0.00223.007-0.009-0.0090.0000.0000.0000.000
137A134THR0-0.018-0.02623.911-0.011-0.0110.0000.0000.0000.000
138A135VAL00.0400.02324.7300.0020.0020.0000.0000.0000.000
139A136PRO0-0.042-0.02524.1440.0020.0020.0000.0000.0000.000
140A137GLN0-0.015-0.02019.6030.0170.0170.0000.0000.0000.000
141A138ALA00.0500.05820.948-0.009-0.0090.0000.0000.0000.000
142A139ALA00.010-0.01322.8970.0160.0160.0000.0000.0000.000
143A140ARG10.9140.94818.6530.3600.3600.0000.0000.0000.000
144A141ALA00.0860.06718.2280.0030.0030.0000.0000.0000.000
145A142VAL00.007-0.00819.2740.0350.0350.0000.0000.0000.000
146A143ALA0-0.075-0.03021.1980.0310.0310.0000.0000.0000.000
147A144GLU-1-0.970-0.99614.849-0.373-0.3730.0000.0000.0000.000
148A145GLY0-0.092-0.03816.8530.0390.0390.0000.0000.0000.000
149A146SER0-0.058-0.03414.7590.0150.0150.0000.0000.0000.000
150A147VAL0-0.045-0.01816.536-0.024-0.0240.0000.0000.0000.000
151A148ASP-1-0.849-0.93218.9220.0510.0510.0000.0000.0000.000
152A149LEU0-0.051-0.03220.333-0.005-0.0050.0000.0000.0000.000
153A150GLU-1-1.037-1.02822.3080.1510.1510.0000.0000.0000.000
154A151ASP-1-1.003-0.97122.763-0.008-0.0080.0000.0000.0000.000
155A152LEU0-0.0270.01224.530-0.020-0.0200.0000.0000.0000.000
156A153ASP-1-0.835-0.90926.811-0.067-0.0670.0000.0000.0000.000
157A154GLU-1-0.889-0.95030.055-0.004-0.0040.0000.0000.0000.000
158A155GLU-1-1.030-1.01933.138-0.050-0.0500.0000.0000.0000.000
159A156ARG10.8140.89629.9770.0670.0670.0000.0000.0000.000
160A157LYS10.8900.94128.3150.0110.0110.0000.0000.0000.000
161A158GLY0-0.022-0.02029.1690.0020.0020.0000.0000.0000.000
162A159TRP0-0.054-0.03029.601-0.001-0.0010.0000.0000.0000.000
163A160SER00.0280.03427.4800.0000.0000.0000.0000.0000.000
164A161GLY00.1580.05424.788-0.011-0.0110.0000.0000.0000.000
165A162GLU-1-0.923-0.97225.681-0.039-0.0390.0000.0000.0000.000
166A163ARG10.7870.89728.3150.0330.0330.0000.0000.0000.000
167A164LEU00.0660.02925.556-0.002-0.0020.0000.0000.0000.000
168A165LEU00.0150.01026.281-0.009-0.0090.0000.0000.0000.000
169A166ALA0-0.0010.00528.758-0.003-0.0030.0000.0000.0000.000
170A167GLU-1-0.839-0.89531.965-0.058-0.0580.0000.0000.0000.000
171A168LEU00.0040.01727.885-0.003-0.0030.0000.0000.0000.000
172A169GLU-1-0.941-0.97830.816-0.112-0.1120.0000.0000.0000.000
173A170ARG10.7450.86233.1120.0620.0620.0000.0000.0000.000
174A171THR0-0.077-0.06834.5940.0010.0010.0000.0000.0000.000
175A172ARG10.9230.99231.4480.1460.1460.0000.0000.0000.000
176A173PRO00.010-0.00334.3410.0070.0070.0000.0000.0000.000
177A174ALA0-0.045-0.02437.269-0.004-0.0040.0000.0000.0000.000
178A175ASP-1-0.932-0.95539.224-0.110-0.1100.0000.0000.0000.000
179A176GLU-1-0.814-0.90732.285-0.185-0.1850.0000.0000.0000.000
180A177ASP-1-0.881-0.93536.690-0.122-0.1220.0000.0000.0000.000
181A178LEU0-0.079-0.03533.249-0.007-0.0070.0000.0000.0000.000
182A179ALA00.0220.01534.1860.0090.0090.0000.0000.0000.000
183A180VAL00.003-0.01229.969-0.013-0.0130.0000.0000.0000.000
184A181CYS0-0.047-0.00429.1540.0140.0140.0000.0000.0000.000
185A182HIS0-0.003-0.00723.579-0.011-0.0110.0000.0000.0000.000
186A183GLY0-0.030-0.02624.787-0.028-0.0280.0000.0000.0000.000
187A184ASP-1-0.857-0.94521.440-0.278-0.2780.0000.0000.0000.000
188A185LEU0-0.0090.01924.3110.0000.0000.0000.0000.0000.000
189A186CYS00.0540.02624.1980.0220.0220.0000.0000.0000.000
190A187PRO0-0.007-0.03727.178-0.010-0.0100.0000.0000.0000.000
191A188ASP-1-0.766-0.86623.449-0.162-0.1620.0000.0000.0000.000
192A189ASN0-0.0160.01322.034-0.016-0.0160.0000.0000.0000.000
193A190VAL0-0.010-0.00824.848-0.009-0.0090.0000.0000.0000.000
194A191LEU0-0.031-0.00525.2580.0140.0140.0000.0000.0000.000
195A192LEU00.009-0.00829.4470.0000.0000.0000.0000.0000.000
196A193ASP-1-0.820-0.88333.051-0.103-0.1030.0000.0000.0000.000
197A194PRO0-0.056-0.05034.2700.0060.0060.0000.0000.0000.000
198A195ARG10.8770.95136.8230.0900.0900.0000.0000.0000.000
199A196THR0-0.028-0.04539.5160.0040.0040.0000.0000.0000.000
200A197CYS00.0070.02237.2480.0040.0040.0000.0000.0000.000
201A198GLU-1-0.937-0.95836.746-0.124-0.1240.0000.0000.0000.000
202A199VAL00.0140.00631.775-0.001-0.0010.0000.0000.0000.000
203A200THR0-0.056-0.04531.0580.0010.0010.0000.0000.0000.000
204A201GLY0-0.014-0.03328.363-0.006-0.0060.0000.0000.0000.000
205A202LEU0-0.037-0.00526.3840.0070.0070.0000.0000.0000.000
206A203ILE0-0.026-0.03121.251-0.015-0.0150.0000.0000.0000.000
207A204ASP-1-0.782-0.87718.679-0.416-0.4160.0000.0000.0000.000
208A205VAL0-0.025-0.00920.3370.0110.0110.0000.0000.0000.000
209A206GLY00.0190.00518.491-0.005-0.0050.0000.0000.0000.000
210A207ARG10.8130.89319.0730.3120.3120.0000.0000.0000.000
211A208VAL00.0080.01821.9720.0290.0290.0000.0000.0000.000
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