Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YZ7G2

Calculation Name: 3HKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q84T68

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptAll
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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2313732.471471
FMO2-HF: Nuclear repulsion 2233386.116364
FMO2-HF: Total energy -80346.355107
FMO2-MP2: Total energy -80576.079242


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:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-238.55-239.99969.162-28.504-39.21-0.294
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.780 / q_NPA : 0.851
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].
3A7ASP-1-0.862-0.9222.733-62.895-59.1681.265-2.091-2.900-0.007
4A8GLY00.0020.0033.5314.5675.1820.004-0.220-0.3990.000
5A9ARG10.7670.8982.51070.47574.1402.504-1.636-4.5330.005
6A10ASN00.0350.0131.953-11.380-12.4079.573-3.906-4.640-0.047
7A11PRO00.0620.0092.035-25.010-24.1947.372-2.905-5.283-0.035
8A12ASN00.0240.0173.012-3.510-3.9010.1190.898-0.627-0.003
9A13GLN0-0.0200.0032.8697.3248.0440.034-0.213-0.5410.000
10A14LEU00.0360.0152.654-14.468-13.4050.664-0.610-1.116-0.007
11A15ARG10.7410.8535.05141.68741.802-0.001-0.002-0.1120.000
12A16PRO00.004-0.0156.5852.8322.8320.0000.0000.0000.000
13A17PHE0-0.0020.0109.3700.0370.0370.0000.0000.0000.000
14A18SER0-0.054-0.02412.1331.6481.6480.0000.0000.0000.000
15A19CYS0-0.002-0.01015.933-0.182-0.1820.0000.0000.0000.000
16A20THR0-0.0300.00918.9210.5800.5800.0000.0000.0000.000
17A21ARG10.8590.90922.53712.50512.5050.0000.0000.0000.000
18A22ASN00.0180.00525.2310.1980.1980.0000.0000.0000.000
19A23PRO0-0.037-0.01524.0040.3270.3270.0000.0000.0000.000
20A24LEU0-0.027-0.01627.2110.0970.0970.0000.0000.0000.000
21A25ASP-1-0.848-0.92030.056-9.403-9.4030.0000.0000.0000.000
22A26ARG10.8780.93933.1678.5478.5470.0000.0000.0000.000
23A27ALA0-0.034-0.02030.0470.1480.1480.0000.0000.0000.000
24A28HIS00.0250.01531.698-0.239-0.2390.0000.0000.0000.000
25A29GLY00.0540.03228.437-0.002-0.0020.0000.0000.0000.000
26A30SER0-0.006-0.01125.394-0.078-0.0780.0000.0000.0000.000
27A31ALA00.0110.00420.5640.0560.0560.0000.0000.0000.000
28A32ARG10.9380.98919.57213.67913.6790.0000.0000.0000.000
29A33TRP00.045-0.00212.6651.0941.0940.0000.0000.0000.000
30A34ALA0-0.011-0.01414.0290.1550.1550.0000.0000.0000.000
31A35GLN00.0590.0217.8163.0673.0670.0000.0000.0000.000
32A36GLY00.0390.0249.349-2.267-2.2670.0000.0000.0000.000
33A37ASP-1-0.890-0.95410.720-22.005-22.0050.0000.0000.0000.000
34A38THR0-0.068-0.0369.6492.2552.2550.0000.0000.0000.000
35A39ILE00.0070.01712.0360.0410.0410.0000.0000.0000.000
36A40VAL00.0280.00215.0140.7900.7900.0000.0000.0000.000
37A41LEU0-0.040-0.02417.6510.1360.1360.0000.0000.0000.000
38A42ALA00.0360.03120.6860.1930.1930.0000.0000.0000.000
39A43ALA0-0.020-0.02322.4630.1850.1850.0000.0000.0000.000
40A44VAL00.0170.01025.826-0.001-0.0010.0000.0000.0000.000
41A45TYR0-0.043-0.02128.5290.2140.2140.0000.0000.0000.000
42A46GLY00.0790.04031.7570.2930.2930.0000.0000.0000.000
43A47PRO0-0.0030.01833.471-0.123-0.1230.0000.0000.0000.000
44A48LYS10.9690.99335.7278.3328.3320.0000.0000.0000.000
45A49PRO0-0.002-0.00637.940-0.013-0.0130.0000.0000.0000.000
46A50GLY0-0.013-0.00241.1900.0630.0630.0000.0000.0000.000
47A51THR00.0230.00938.606-0.274-0.2740.0000.0000.0000.000
48A52ARG10.8430.91534.5718.9588.9580.0000.0000.0000.000
49A53LYS10.9600.96139.7986.7036.7030.0000.0000.0000.000
50A54GLY0-0.0010.00540.7840.1710.1710.0000.0000.0000.000
51A55GLU-1-0.892-0.93635.117-8.900-8.9000.0000.0000.0000.000
52A56ASN0-0.014-0.01238.5950.1460.1460.0000.0000.0000.000
53A57PRO00.013-0.00339.880-0.105-0.1050.0000.0000.0000.000
54A58GLU-1-0.903-0.94241.524-7.064-7.0640.0000.0000.0000.000
55A59LYS10.8320.91636.1948.0458.0450.0000.0000.0000.000
56A60ALA0-0.0090.01134.3700.0690.0690.0000.0000.0000.000
57A61SER00.0150.00634.087-0.148-0.1480.0000.0000.0000.000
58A62ILE0-0.014-0.01727.711-0.032-0.0320.0000.0000.0000.000
59A63GLU-1-0.802-0.88729.763-9.216-9.2160.0000.0000.0000.000
60A64VAL0-0.004-0.01823.470-0.236-0.2360.0000.0000.0000.000
61A65VAL0-0.0100.00926.5140.2580.2580.0000.0000.0000.000
62A66TRP00.029-0.00517.102-0.291-0.2910.0000.0000.0000.000
63A67LYS10.8870.93123.33411.84111.8410.0000.0000.0000.000
64A68PRO00.0500.01621.356-0.577-0.5770.0000.0000.0000.000
65A69MET0-0.0110.00917.4810.1940.1940.0000.0000.0000.000
66A70THR00.0010.00022.1620.5160.5160.0000.0000.0000.000
67A71GLY00.0130.01924.738-0.240-0.2400.0000.0000.0000.000
68A72GLN0-0.016-0.01927.3390.2080.2080.0000.0000.0000.000
69A73ILE0-0.012-0.00224.162-0.201-0.2010.0000.0000.0000.000
70A74GLY00.0770.04624.0930.4980.4980.0000.0000.0000.000
71A75LYS10.8280.87821.64213.70113.7010.0000.0000.0000.000
72A76GLN00.0270.05015.997-0.606-0.6060.0000.0000.0000.000
73A77GLU-1-0.786-0.89519.895-14.097-14.0970.0000.0000.0000.000
74A78LYS10.9080.94720.97111.69011.6900.0000.0000.0000.000
75A79GLU-1-0.810-0.89219.881-14.227-14.2270.0000.0000.0000.000
76A80TYR0-0.009-0.01814.387-0.571-0.5710.0000.0000.0000.000
77A81GLU-1-0.866-0.93419.363-11.809-11.8090.0000.0000.0000.000
78A82MET0-0.0160.00422.6070.1460.1460.0000.0000.0000.000
79A83THR0-0.022-0.03717.8000.1780.1780.0000.0000.0000.000
80A84LEU00.0280.00118.7220.0400.0400.0000.0000.0000.000
81A85LYN00.0080.01620.7590.1530.1530.0000.0000.0000.000
82A86ARG10.9560.98920.89913.72113.7210.0000.0000.0000.000
83A87THR0-0.0010.00418.8020.1370.1370.0000.0000.0000.000
84A88LEU00.002-0.01221.0730.1620.1620.0000.0000.0000.000
85A89GLN0-0.013-0.01324.0210.2350.2350.0000.0000.0000.000
86A90SER0-0.0190.00624.0900.4270.4270.0000.0000.0000.000
87A91ILE00.0270.00721.8780.2400.2400.0000.0000.0000.000
88A92CYS0-0.0170.01225.3490.2950.2950.0000.0000.0000.000
89A93LEU0-0.025-0.01028.4550.1410.1410.0000.0000.0000.000
90A94LEU00.017-0.00731.2590.3090.3090.0000.0000.0000.000
91A95THR00.014-0.00333.7830.2490.2490.0000.0000.0000.000
92A96VAL0-0.037-0.00635.2330.2130.2130.0000.0000.0000.000
93A97HIS00.0120.00535.0330.2990.2990.0000.0000.0000.000
94A98PRO00.0370.00938.161-0.119-0.1190.0000.0000.0000.000
95A99ASN0-0.0110.00940.400-0.019-0.0190.0000.0000.0000.000
96A100THR00.0190.03135.9250.0510.0510.0000.0000.0000.000
97A101THR0-0.036-0.03634.527-0.131-0.1310.0000.0000.0000.000
98A102THR0-0.038-0.03329.7010.0790.0790.0000.0000.0000.000
99A103SER0-0.049-0.03730.507-0.195-0.1950.0000.0000.0000.000
100A104VAL0-0.012-0.01024.261-0.020-0.0200.0000.0000.0000.000
101A105ILE0-0.045-0.02426.1710.0630.0630.0000.0000.0000.000
102A106LEU00.0050.00918.713-0.267-0.2670.0000.0000.0000.000
103A107GLN0-0.054-0.03421.8590.9210.9210.0000.0000.0000.000
104A108VAL00.0380.02116.776-0.502-0.5020.0000.0000.0000.000
105A109VAL0-0.075-0.03818.1740.9640.9640.0000.0000.0000.000
106A110GLY00.0310.02016.2890.5130.5130.0000.0000.0000.000
107A111ASN0-0.020-0.02312.767-1.663-1.6630.0000.0000.0000.000
108A112ASP-1-0.750-0.8728.115-33.800-33.8000.0000.0000.0000.000
109A113GLY00.1040.0718.034-3.643-3.6430.0000.0000.0000.000
110A114SER00.000-0.0166.0160.0160.0160.0000.0000.0000.000
111A115LEU0-0.041-0.0138.5761.8311.8310.0000.0000.0000.000
112A116LEU0-0.0090.00912.2311.1321.1320.0000.0000.0000.000
113A117PRO00.0380.0049.5851.1871.1870.0000.0000.0000.000
114A118CYS0-0.0200.01210.9401.4971.4970.0000.0000.0000.000
115A119ALA00.0190.00212.5261.3691.3690.0000.0000.0000.000
116A120ILE00.0160.00515.0401.2621.2620.0000.0000.0000.000
117A121ASN0-0.011-0.00511.6922.1162.1160.0000.0000.0000.000
118A122ALA00.0280.01015.8020.9770.9770.0000.0000.0000.000
119A123CYS0-0.037-0.01917.9771.1581.1580.0000.0000.0000.000
120A124CYS0-0.0100.01919.1010.8560.8560.0000.0000.0000.000
121A125ALA00.0290.01719.3220.6360.6360.0000.0000.0000.000
122A126ALA0-0.031-0.00621.2340.6410.6410.0000.0000.0000.000
123A127LEU0-0.010-0.01723.3620.5960.5960.0000.0000.0000.000
124A128VAL00.0230.01423.7480.4760.4760.0000.0000.0000.000
125A129PHE00.002-0.00525.9320.3560.3560.0000.0000.0000.000
126A130ALA0-0.028-0.00627.7670.3780.3780.0000.0000.0000.000
127A131GLY0-0.0060.00529.8900.3530.3530.0000.0000.0000.000
128A132ILE0-0.060-0.02528.6180.3260.3260.0000.0000.0000.000
129A133PRO00.0030.00229.463-0.274-0.2740.0000.0000.0000.000
130A134LEU00.0000.00624.238-0.111-0.1110.0000.0000.0000.000
131A135LYS10.8110.89627.32110.98710.9870.0000.0000.0000.000
132A136HIS0-0.050-0.02422.6450.3810.3810.0000.0000.0000.000
133A137LEU00.0330.00619.351-0.002-0.0020.0000.0000.0000.000
134A138ALA00.014-0.00118.4860.1410.1410.0000.0000.0000.000
135A139VAL0-0.007-0.00213.254-0.128-0.1280.0000.0000.0000.000
136A140ALA0-0.024-0.01112.9050.1090.1090.0000.0000.0000.000
137A141ILE0-0.002-0.0066.977-1.297-1.2970.0000.0000.0000.000
138A142GLY00.0400.0327.4122.5452.5450.0000.0000.0000.000
139A143CYS0-0.067-0.0255.751-6.744-6.7440.0000.0000.0000.000
140A144GLY00.0580.0155.9913.9133.9130.0000.0000.0000.000
141A145VAL0-0.025-0.0127.362-1.500-1.5000.0000.0000.0000.000
142A146LEU0-0.024-0.0084.477-0.487-0.367-0.001-0.008-0.1110.000
143A147GLU-1-0.946-0.9868.520-24.006-24.0060.0000.0000.0000.000
144A148ASP-1-0.946-0.96411.429-16.118-16.1180.0000.0000.0000.000
145A149GLY00.0310.02811.9220.8280.8280.0000.0000.0000.000
146A150GLU-1-0.936-0.9837.872-25.437-25.4370.0000.0000.0000.000
147A151VAL0-0.013-0.0067.635-3.770-3.7700.0000.0000.0000.000
148A152ILE0-0.022-0.0162.389-5.003-3.4922.453-0.767-3.1970.002
149A153LEU0-0.022-0.0112.9076.0147.2480.110-0.462-0.8820.002
150A154ASP-1-0.821-0.9021.948-77.859-81.28712.400-4.215-4.758-0.066
151A155THR0-0.005-0.0122.721-11.325-9.6180.561-0.978-1.291-0.009
152A156ASN0-0.008-0.0223.2657.6237.9880.003-0.071-0.2970.000
153A157LYS10.8660.9405.17123.59723.634-0.0010.000-0.0360.000
154A158ALA0-0.0160.0036.9632.8192.8190.0000.0000.0000.000
155A159GLU-1-0.707-0.8301.692-126.231-138.52932.103-11.318-8.487-0.129
156A160GLU-1-0.809-0.8846.000-29.675-29.6750.0000.0000.0000.000
157A161GLN0-0.098-0.0358.5243.8083.8080.0000.0000.0000.000
158A162GLN0-0.049-0.0256.4450.6870.6870.0000.0000.0000.000
159A163LEU00.0000.0135.9891.2521.2520.0000.0000.0000.000
160A164LYS10.9330.96610.03020.08920.0890.0000.0000.0000.000
161A165SER0-0.001-0.01411.5241.9351.9350.0000.0000.0000.000
162A166PHE0-0.004-0.0039.219-2.922-2.9220.0000.0000.0000.000
163A167ALA00.0340.00810.1842.9262.9260.0000.0000.0000.000
164A168HIS0-0.0020.0149.932-2.901-2.9010.0000.0000.0000.000
165A169LEU00.0180.00511.5242.4252.4250.0000.0000.0000.000
166A170VAL0-0.026-0.01712.911-0.844-0.8440.0000.0000.0000.000
167A171PHE00.0720.03311.9581.3121.3120.0000.0000.0000.000
168A172PRO00.0110.01617.1640.0000.0000.0000.0000.0000.000
169A173ASN00.0440.03117.4670.9980.9980.0000.0000.0000.000
170A194LEU00.0110.00616.639-0.169-0.1690.0000.0000.0000.000
171A195ILE0-0.114-0.04919.3440.7700.7700.0000.0000.0000.000
172A196THR0-0.002-0.02218.5910.8390.8390.0000.0000.0000.000
173A197SER0-0.0050.00815.990-0.825-0.8250.0000.0000.0000.000
174A198ILE0-0.023-0.00915.5681.0401.0400.0000.0000.0000.000
175A199THR00.0340.02314.747-1.260-1.2600.0000.0000.0000.000
176A200HIS0-0.054-0.02613.7671.4581.4580.0000.0000.0000.000
177A201GLY00.0400.02514.339-1.212-1.2120.0000.0000.0000.000
178A202VAL0-0.033-0.01316.3830.7960.7960.0000.0000.0000.000
179A203MET0-0.018-0.00212.685-1.643-1.6430.0000.0000.0000.000
180A204SER0-0.021-0.01217.3811.0621.0620.0000.0000.0000.000
181A205GLU-1-0.934-0.97518.402-13.749-13.7490.0000.0000.0000.000
182A206GLU-1-0.863-0.94718.319-15.168-15.1680.0000.0000.0000.000
183A207ASP-1-0.788-0.86714.414-20.452-20.4520.0000.0000.0000.000
184A208TYR0-0.014-0.02614.156-1.496-1.4960.0000.0000.0000.000
185A209PHE0-0.010-0.00415.417-0.551-0.5510.0000.0000.0000.000
186A210SER00.007-0.01012.270-0.989-0.9890.0000.0000.0000.000
187A211CYS0-0.075-0.03810.774-2.346-2.3460.0000.0000.0000.000
188A212ILE0-0.030-0.02811.437-1.071-1.0710.0000.0000.0000.000
189A213GLU-1-0.877-0.92612.636-23.233-23.2330.0000.0000.0000.000
190A214ARG10.8990.9547.03131.58831.5880.0000.0000.0000.000
191A215GLY00.014-0.0059.271-1.491-1.4910.0000.0000.0000.000
192A216LEU0-0.020-0.00510.2460.3480.3480.0000.0000.0000.000
193A217ALA00.0080.01511.7560.6340.6340.0000.0000.0000.000
194A218ALA0-0.027-0.0108.1260.1420.1420.0000.0000.0000.000
195A219SER0-0.069-0.05110.0650.7920.7920.0000.0000.0000.000
196A220SER00.008-0.01012.4630.2990.2990.0000.0000.0000.000
197A221ARG10.9640.9799.67924.89124.8910.0000.0000.0000.000
198A222ILE00.0100.0159.7770.3970.3970.0000.0000.0000.000
199A223SER00.015-0.01813.6940.9850.9850.0000.0000.0000.000
200A224ASP-1-0.841-0.89516.648-15.609-15.6090.0000.0000.0000.000
201A225PHE00.0020.00515.6920.8430.8430.0000.0000.0000.000
202A226MET0-0.049-0.03216.0530.9240.9240.0000.0000.0000.000
203A227ARG10.8960.93419.40214.35914.3590.0000.0000.0000.000
204A228THR0-0.0200.00221.2360.8990.8990.0000.0000.0000.000
205A229THR0-0.018-0.01019.3430.2340.2340.0000.0000.0000.000
206A230LEU0-0.051-0.00518.5680.2800.2800.0000.0000.0000.000
207A231GLN0-0.046-0.01222.5070.6860.6860.0000.0000.0000.000