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: NN2LQ

Calculation Name: 3KV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q01494

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2326344.54544
FMO2-HF: Nuclear repulsion 2248006.177893
FMO2-HF: Total energy -78338.367546
FMO2-MP2: Total energy -78568.689667


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:14:THR)


Summations of interaction energy for fragment #1(A:14: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.
-59.643-55.69937.124-19.826-21.245-0.096
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.044
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].
3A16LEU0-0.054-0.0072.420-4.703-1.5382.401-2.354-3.2130.021
4A17GLU-1-0.877-0.9412.103-23.919-19.9809.983-5.967-7.955-0.012
5A18THR0-0.092-0.0504.065-2.029-1.4960.010-0.158-0.3860.001
6A19PHE0-0.094-0.0546.415-0.473-0.4730.0000.0000.0000.000
7A20MLY10.9230.9768.560-0.709-0.7090.0000.0000.0000.000
8A21MLY10.8310.93911.291-0.042-0.0420.0000.0000.0000.000
9A22SER00.0560.0308.5300.1180.1180.0000.0000.0000.000
10A23PHE0-0.004-0.02610.3120.0210.0210.0000.0000.0000.000
11A24VAL0-0.005-0.0059.8090.0390.0390.0000.0000.0000.000
12A25ASP-1-0.806-0.90811.260-0.383-0.3830.0000.0000.0000.000
13A26VAL0-0.038-0.01114.2720.0800.0800.0000.0000.0000.000
14A27PRO0-0.019-0.00316.995-0.029-0.0290.0000.0000.0000.000
15A28ILE0-0.008-0.01919.0760.0160.0160.0000.0000.0000.000
16A29ASP-1-0.816-0.90822.587-0.141-0.1410.0000.0000.0000.000
17A30ALA0-0.015-0.02925.7930.0100.0100.0000.0000.0000.000
18A31GLU-1-0.898-0.94727.322-0.120-0.1200.0000.0000.0000.000
19A32MLY10.8080.91929.6950.1170.1170.0000.0000.0000.000
20A33GLY0-0.0100.00230.3630.0070.0070.0000.0000.0000.000
21A34ASN0-0.059-0.04824.893-0.017-0.0170.0000.0000.0000.000
22A35ALA00.0300.03825.5790.0000.0000.0000.0000.0000.000
23A36ILE00.0040.00521.006-0.010-0.0100.0000.0000.0000.000
24A37SER0-0.031-0.03321.4170.0230.0230.0000.0000.0000.000
25A38THR0-0.023-0.04921.667-0.004-0.0040.0000.0000.0000.000
26A39ALA00.0140.01021.9030.0110.0110.0000.0000.0000.000
27A40GLU-1-0.766-0.87017.138-0.050-0.0500.0000.0000.0000.000
28A41PHE00.0250.00817.0160.0080.0080.0000.0000.0000.000
29A42LEU0-0.034-0.02317.9600.0110.0110.0000.0000.0000.000
30A43GLU-1-0.865-0.93414.9670.1390.1390.0000.0000.0000.000
31A44ALA00.0080.01713.3410.0680.0680.0000.0000.0000.000
32A45ALA0-0.003-0.00413.5430.0370.0370.0000.0000.0000.000
33A46GLU-1-0.852-0.92015.5150.2240.2240.0000.0000.0000.000
34A47SER0-0.028-0.01810.6710.1010.1010.0000.0000.0000.000
35A48LEU00.0160.02911.1660.1100.1100.0000.0000.0000.000
36A49THR0-0.062-0.05212.4180.0270.0270.0000.0000.0000.000
37A50THR0-0.007-0.01410.8590.0540.0540.0000.0000.0000.000
38A51MET00.0390.0287.2980.0930.0930.0000.0000.0000.000
39A52PHE0-0.010-0.01911.598-0.041-0.0410.0000.0000.0000.000
40A53ASP-1-0.806-0.89413.5730.3970.3970.0000.0000.0000.000
41A54VAL00.0180.0228.493-0.027-0.0270.0000.0000.0000.000
42A55LEU0-0.046-0.00411.739-0.049-0.0490.0000.0000.0000.000
43A56GLY00.051-0.00514.233-0.007-0.0070.0000.0000.0000.000
44A57SER0-0.094-0.03516.728-0.050-0.0500.0000.0000.0000.000
45A58ILE00.0570.01218.197-0.024-0.0240.0000.0000.0000.000
46A59ALA00.0150.02620.786-0.021-0.0210.0000.0000.0000.000
47A60PHE00.043-0.00318.306-0.028-0.0280.0000.0000.0000.000
48A61SER0-0.033-0.00820.422-0.008-0.0080.0000.0000.0000.000
49A62PRO0-0.0130.00122.052-0.006-0.0060.0000.0000.0000.000
50A63VAL0-0.0010.00520.268-0.009-0.0090.0000.0000.0000.000
51A64MLY10.8830.95317.017-0.330-0.3300.0000.0000.0000.000
52A65THR0-0.033-0.03020.1310.0010.0010.0000.0000.0000.000
53A66ASP-1-0.914-0.95823.5410.0350.0350.0000.0000.0000.000
54A67MET0-0.037-0.00417.729-0.003-0.0030.0000.0000.0000.000
55A68LEU00.0380.01618.732-0.010-0.0100.0000.0000.0000.000
56A69GLY00.0090.00921.999-0.008-0.0080.0000.0000.0000.000
57A70ASN0-0.065-0.05324.372-0.014-0.0140.0000.0000.0000.000
58A71VAL00.0420.01919.852-0.016-0.0160.0000.0000.0000.000
59A72GLU-1-0.843-0.90723.3100.0900.0900.0000.0000.0000.000
60A73MLY10.7810.89925.981-0.036-0.0360.0000.0000.0000.000
61A74ILE0-0.015-0.00424.294-0.007-0.0070.0000.0000.0000.000
62A75ARG10.8390.89520.515-0.140-0.1400.0000.0000.0000.000
63A76MLY10.9860.98926.525-0.055-0.0550.0000.0000.0000.000
64A77ARG10.8230.90830.1240.0010.0010.0000.0000.0000.000
65A78MET00.010-0.00524.969-0.006-0.0060.0000.0000.0000.000
66A79LEU0-0.026-0.02027.555-0.002-0.0020.0000.0000.0000.000
67A80ALA0-0.043-0.01330.744-0.001-0.0010.0000.0000.0000.000
68A81ALA0-0.0030.00633.210-0.002-0.0020.0000.0000.0000.000
69A82PRO00.0500.04330.930-0.007-0.0070.0000.0000.0000.000
70A83LEU00.002-0.01031.483-0.007-0.0070.0000.0000.0000.000
71A84GLU-1-0.838-0.91233.711-0.017-0.0170.0000.0000.0000.000
72A85SER0-0.020-0.02529.955-0.005-0.0050.0000.0000.0000.000
73A86GLN0-0.0050.00828.0370.0000.0000.0000.0000.0000.000
74A87ASN0-0.024-0.01126.089-0.007-0.0070.0000.0000.0000.000
75A88ILE00.0420.01723.5250.0100.0100.0000.0000.0000.000
76A89GLN00.0300.00826.5090.0120.0120.0000.0000.0000.000
77A90ASP-1-0.794-0.88429.758-0.053-0.0530.0000.0000.0000.000
78A91LEU0-0.057-0.00827.5010.0080.0080.0000.0000.0000.000
79A92VAL00.002-0.00329.9020.0070.0070.0000.0000.0000.000
80A93ARG10.7790.84432.2980.0710.0710.0000.0000.0000.000
81A94ASN0-0.032-0.03334.4140.0030.0030.0000.0000.0000.000
82A95GLU-1-0.745-0.82433.7120.0060.0060.0000.0000.0000.000
83A96LEU0-0.031-0.02735.4530.0040.0040.0000.0000.0000.000
84A97MLY10.8530.96638.4240.0200.0200.0000.0000.0000.000
85A98THR0-0.011-0.01239.4110.0040.0040.0000.0000.0000.000
86A99MLY10.9290.96141.532-0.013-0.0130.0000.0000.0000.000
87A100SER0-0.045-0.03535.7150.0040.0040.0000.0000.0000.000
88A101HIS10.9090.94735.451-0.004-0.0040.0000.0000.0000.000
89A102THR0-0.019-0.00732.438-0.002-0.0020.0000.0000.0000.000
90A103ALA00.0430.01529.7460.0030.0030.0000.0000.0000.000
91A104THR00.007-0.00629.223-0.006-0.0060.0000.0000.0000.000
92A105GLU-1-0.894-0.93230.4060.0060.0060.0000.0000.0000.000
93A106GLY0-0.005-0.00728.1620.0000.0000.0000.0000.0000.000
94A107LEU00.0320.01724.6550.0000.0000.0000.0000.0000.000
95A108LEU0-0.017-0.01025.894-0.008-0.0080.0000.0000.0000.000
96A109TRP0-0.029-0.02826.816-0.010-0.0100.0000.0000.0000.000
97A110LEU00.0270.02219.976-0.002-0.0020.0000.0000.0000.000
98A111VAL00.0210.00821.733-0.008-0.0080.0000.0000.0000.000
99A112ARG10.9430.98522.2760.0190.0190.0000.0000.0000.000
100A113GLY00.0150.00921.578-0.007-0.0070.0000.0000.0000.000
101A114LEU0-0.0090.00316.5340.0010.0010.0000.0000.0000.000
102A115GLU-1-0.835-0.92717.884-0.147-0.1470.0000.0000.0000.000
103A116PHE0-0.056-0.02919.686-0.018-0.0180.0000.0000.0000.000
104A117THR00.0220.00314.3230.0020.0020.0000.0000.0000.000
105A118CYS00.0400.02615.087-0.045-0.0450.0000.0000.0000.000
106A119ILE00.0000.01016.139-0.052-0.0520.0000.0000.0000.000
107A120ALA0-0.025-0.00717.511-0.017-0.0170.0000.0000.0000.000
108A121LEU00.0350.01211.281-0.001-0.0010.0000.0000.0000.000
109A122SER00.022-0.00414.488-0.083-0.0830.0000.0000.0000.000
110A123MLY10.8180.92015.7870.1480.1480.0000.0000.0000.000
111A124ASN0-0.0170.01114.927-0.019-0.0190.0000.0000.0000.000
112A125ILE00.0600.03411.1920.0210.0210.0000.0000.0000.000
113A126GLY0-0.0070.01214.487-0.045-0.0450.0000.0000.0000.000
114A127SER0-0.097-0.05917.7820.0540.0540.0000.0000.0000.000
115A128THR00.0290.00018.053-0.025-0.0250.0000.0000.0000.000
116A129GLU-1-0.785-0.85320.033-0.110-0.1100.0000.0000.0000.000
117A130GLU-1-0.712-0.85218.254-0.050-0.0500.0000.0000.0000.000
118A131LEU00.0170.00813.629-0.008-0.0080.0000.0000.0000.000
119A132ALA00.0350.02017.999-0.003-0.0030.0000.0000.0000.000
120A133ASP-1-0.868-0.92921.238-0.034-0.0340.0000.0000.0000.000
121A134SER0-0.030-0.02618.595-0.011-0.0110.0000.0000.0000.000
122A135PHE00.0170.00015.513-0.010-0.0100.0000.0000.0000.000
123A136ARG10.8580.88520.7420.0020.0020.0000.0000.0000.000
124A137GLY0-0.063-0.04423.8010.0020.0020.0000.0000.0000.000
125A138SER00.006-0.00820.541-0.001-0.0010.0000.0000.0000.000
126A139TYR00.027-0.00923.1700.0040.0040.0000.0000.0000.000
127A140ARG10.8790.93025.3290.0710.0710.0000.0000.0000.000
128A141VAL0-0.0070.00125.5280.0050.0050.0000.0000.0000.000
129A142THR00.0120.02023.0010.0030.0030.0000.0000.0000.000
130A143LEU0-0.011-0.01023.6970.0080.0080.0000.0000.0000.000
131A144MLY10.9450.99027.6420.0270.0270.0000.0000.0000.000
132A145PRO0-0.026-0.03030.0060.0060.0060.0000.0000.0000.000
133A146HIS0-0.011-0.00129.6850.0080.0080.0000.0000.0000.000
134A147HIS00.0570.06226.7300.0020.0020.0000.0000.0000.000
135A148SER00.0520.01232.313-0.003-0.0030.0000.0000.0000.000
136A149PHE00.025-0.02134.3290.0010.0010.0000.0000.0000.000
137A150LEU00.0270.02235.5550.0010.0010.0000.0000.0000.000
138A151VAL00.0210.01129.6250.0060.0060.0000.0000.0000.000
139A152MLY10.8580.96230.0250.0100.0100.0000.0000.0000.000
140A153PRO0-0.004-0.00729.975-0.001-0.0010.0000.0000.0000.000
141A154ILE00.0240.02927.0640.0040.0040.0000.0000.0000.000
142A155PHE00.0690.02623.4970.0090.0090.0000.0000.0000.000
143A156SER0-0.016-0.01025.242-0.004-0.0040.0000.0000.0000.000
144A157ALA0-0.033-0.00126.768-0.002-0.0020.0000.0000.0000.000
145A158ALA00.0180.01022.4630.0050.0050.0000.0000.0000.000
146A159MET0-0.0260.00321.3330.0000.0000.0000.0000.0000.000
147A160SER0-0.058-0.04221.994-0.011-0.0110.0000.0000.0000.000
148A161ALA0-0.0190.00822.5040.0000.0000.0000.0000.0000.000
149A162CYS0-0.087-0.02617.9750.0200.0200.0000.0000.0000.000
150A163PRO0-0.0130.01114.746-0.004-0.0040.0000.0000.0000.000
151A164TYR00.0060.00517.302-0.035-0.0350.0000.0000.0000.000
152A165ARG10.8190.87314.2220.2810.2810.0000.0000.0000.000
153A166MLY10.8190.92612.2480.1770.1770.0000.0000.0000.000
154A167ASP-1-0.821-0.92012.2160.2000.2000.0000.0000.0000.000
155A168PHE0-0.049-0.03410.2500.0980.0980.0000.0000.0000.000
156A169TYR0-0.010-0.0498.0120.0590.0590.0000.0000.0000.000
157A170ALA00.0470.0346.894-0.040-0.0400.0000.0000.0000.000
158A171MLY10.8280.9177.112-0.200-0.2000.0000.0000.0000.000
159A172LEU0-0.047-0.0233.7650.1060.3790.002-0.079-0.1960.000
160A173GLY00.0560.0212.476-1.5270.0002.894-1.920-2.501-0.023
161A174ASP-1-0.929-0.9553.8771.0931.1600.004-0.039-0.0320.000
162A175ASP-1-0.884-0.9374.668-1.589-1.597-0.001-0.0090.0180.000
163A176GLU-1-0.851-0.9525.507-1.000-1.0000.0000.0000.0000.000
164A177GLN0-0.086-0.0457.883-0.018-0.0180.0000.0000.0000.000
165A178MLY10.9370.9802.4854.7675.6330.667-0.317-1.2160.002
166A179VAL00.0050.0022.962-1.653-1.0280.085-0.149-0.5610.000
167A180GLN0-0.012-0.0084.4730.2810.276-0.001-0.0080.0130.000
168A181GLU-1-0.911-0.9457.315-1.278-1.2780.0000.0000.0000.000
169A182GLU-1-0.745-0.8521.637-29.428-36.46621.080-8.826-5.216-0.085
170A183LEU00.002-0.0016.0810.8150.8150.0000.0000.0000.000
171A184ARG10.8150.8937.4211.3651.3650.0000.0000.0000.000
172A185GLU-1-0.928-0.9588.103-1.724-1.7240.0000.0000.0000.000
173A186TYR00.009-0.0027.4280.3770.3770.0000.0000.0000.000
174A187LEU0-0.025-0.0279.5370.2600.2600.0000.0000.0000.000
175A188VAL00.0090.01312.4260.1370.1370.0000.0000.0000.000
176A189ALA0-0.0140.00512.8020.0950.0950.0000.0000.0000.000
177A190LEU0-0.026-0.01213.4270.0900.0900.0000.0000.0000.000
178A191ASP-1-0.852-0.93115.220-0.229-0.2290.0000.0000.0000.000
179A192MLY10.9590.99317.8530.3640.3640.0000.0000.0000.000
180A193ILE00.001-0.00716.3860.0440.0440.0000.0000.0000.000
181A194VAL00.0200.00718.7330.0370.0370.0000.0000.0000.000
182A195ASN0-0.013-0.02421.0500.0500.0500.0000.0000.0000.000
183A196ILE0-0.107-0.04021.8420.0160.0160.0000.0000.0000.000
184A197LEU00.0190.01221.8940.0180.0180.0000.0000.0000.000
185A198MLY10.8210.92924.4230.1380.1380.0000.0000.0000.000
186A199ARG10.9510.97325.1380.1790.1790.0000.0000.0000.000
187A200PHE0-0.0110.00728.4780.0080.0080.0000.0000.0000.000
188A201LEU0-0.0020.00827.1070.0100.0100.0000.0000.0000.000
189A202GLU-1-0.909-0.96729.388-0.097-0.0970.0000.0000.0000.000
190A203SER0-0.046-0.03232.8300.0060.0060.0000.0000.0000.000
191A204MLY10.9380.94135.0650.0590.0590.0000.0000.0000.000
192A205GLU-1-0.808-0.87034.247-0.062-0.0620.0000.0000.0000.000
193A206ALA00.0280.03032.4150.0040.0040.0000.0000.0000.000
194A207MLY10.8220.92234.4530.0550.0550.0000.0000.0000.000
195A208TRP00.0330.01533.6690.0020.0020.0000.0000.0000.000