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: KG8Z3

Calculation Name: 1NKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NKV

Chain ID: A

ChEMBL ID:

UniProt ID: P39367

Base Structure: X-ray

Registration Date: 2023-09-23

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 245
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3052380.886109
FMO2-HF: Nuclear repulsion 2956684.649397
FMO2-HF: Total energy -95696.236711
FMO2-MP2: Total energy -95972.699797


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-4.491.341.841-2.741-4.9280.003
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.011
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].
3A6ILE00.0520.0202.192-3.3450.4811.501-2.175-3.1520.006
4A7PHE00.0080.0262.620-1.0400.1790.324-0.385-1.158-0.002
5A8THR00.021-0.0054.212-0.0720.1300.001-0.044-0.1580.000
6A9ILE0-0.064-0.0176.8440.3750.3750.0000.0000.0000.000
7A10SER00.005-0.0356.9560.1380.1380.0000.0000.0000.000
8A11GLU-1-0.758-0.8408.421-1.022-1.0220.0000.0000.0000.000
9A12SER0-0.042-0.02010.2480.0050.0050.0000.0000.0000.000
10A13GLU-1-0.924-0.96912.309-0.308-0.3080.0000.0000.0000.000
11A14HIS0-0.095-0.02912.5800.0310.0310.0000.0000.0000.000
12A15ARG10.8880.96614.8800.2710.2710.0000.0000.0000.000
13A16ILE00.001-0.00616.147-0.006-0.0060.0000.0000.0000.000
14A17HIS10.8370.91210.2210.8540.8540.0000.0000.0000.000
15A18ASN00.0380.00311.975-0.001-0.0010.0000.0000.0000.000
16A19PRO00.0270.01913.9390.0300.0300.0000.0000.0000.000
17A20PHE0-0.0420.00516.7490.0460.0460.0000.0000.0000.000
18A21THR00.0500.01618.991-0.012-0.0120.0000.0000.0000.000
19A22GLU-1-0.865-0.94021.547-0.253-0.2530.0000.0000.0000.000
20A23GLU-1-0.884-0.96123.764-0.188-0.1880.0000.0000.0000.000
21A24LYS10.8930.96322.8690.2030.2030.0000.0000.0000.000
22A25TYR00.0920.03717.741-0.005-0.0050.0000.0000.0000.000
23A26ALA0-0.0040.01423.8910.0120.0120.0000.0000.0000.000
24A27THR0-0.097-0.06227.2700.0170.0170.0000.0000.0000.000
25A28LEU0-0.0030.01522.3180.0100.0100.0000.0000.0000.000
26A29GLY00.0660.02426.4830.0110.0110.0000.0000.0000.000
27A30ARG10.9560.98027.9090.1340.1340.0000.0000.0000.000
28A31VAL0-0.121-0.04728.8580.0110.0110.0000.0000.0000.000
29A32LEU00.0340.01126.5130.0070.0070.0000.0000.0000.000
30A33ARG10.8390.93630.5450.0950.0950.0000.0000.0000.000
31A34MET00.0450.04327.7550.0020.0020.0000.0000.0000.000
32A35LYS10.9330.96333.1060.0730.0730.0000.0000.0000.000
33A36PRO00.0160.01534.357-0.004-0.0040.0000.0000.0000.000
34A37GLY00.0280.00233.7360.0060.0060.0000.0000.0000.000
35A38THR0-0.054-0.02529.6800.0040.0040.0000.0000.0000.000
36A39ARG10.9020.96329.0420.0770.0770.0000.0000.0000.000
37A40ILE0-0.001-0.02523.3110.0030.0030.0000.0000.0000.000
38A41LEU0-0.015-0.00721.1860.0050.0050.0000.0000.0000.000
39A42ASP-1-0.877-0.94418.080-0.310-0.3100.0000.0000.0000.000
40A43LEU0-0.021-0.02215.709-0.003-0.0030.0000.0000.0000.000
41A44GLY00.0310.00412.571-0.032-0.0320.0000.0000.0000.000
42A45SER00.0130.00613.244-0.032-0.0320.0000.0000.0000.000
43A46GLY00.0480.03112.5610.0130.0130.0000.0000.0000.000
44A47SER0-0.070-0.04713.5420.0060.0060.0000.0000.0000.000
45A48GLY0-0.005-0.02016.3360.0500.0500.0000.0000.0000.000
46A49GLU-1-0.762-0.87018.621-0.236-0.2360.0000.0000.0000.000
47A50MET00.0040.02719.7380.0290.0290.0000.0000.0000.000
48A51LEU00.005-0.00221.1470.0250.0250.0000.0000.0000.000
49A52CYS0-0.042-0.01122.1640.0240.0240.0000.0000.0000.000
50A53THR00.010-0.00323.9330.0240.0240.0000.0000.0000.000
51A54TRP00.0580.01623.7880.0180.0180.0000.0000.0000.000
52A55ALA00.0050.01127.2010.0150.0150.0000.0000.0000.000
53A56ARG10.8340.89228.2880.1710.1710.0000.0000.0000.000
54A57ASP-1-0.849-0.89229.900-0.139-0.1390.0000.0000.0000.000
55A58HIS0-0.071-0.04929.6270.0030.0030.0000.0000.0000.000
56A59GLY0-0.014-0.00332.4640.0070.0070.0000.0000.0000.000
57A60ILE0-0.047-0.00726.5310.0070.0070.0000.0000.0000.000
58A61THR00.022-0.00629.0850.0010.0010.0000.0000.0000.000
59A62GLY00.0330.01625.4130.0000.0000.0000.0000.0000.000
60A63THR0-0.063-0.02922.617-0.001-0.0010.0000.0000.0000.000
61A64GLY00.0460.01819.104-0.002-0.0020.0000.0000.0000.000
62A65ILE0-0.029-0.00215.4370.0010.0010.0000.0000.0000.000
63A66ASP-1-0.796-0.90610.856-0.818-0.8180.0000.0000.0000.000
64A67MET00.0880.0508.8890.0390.0390.0000.0000.0000.000
65A68SER0-0.0380.0048.8320.0740.0740.0000.0000.0000.000
66A69SER00.0220.00710.2850.0650.0650.0000.0000.0000.000
67A70LEU00.0360.01112.0430.0600.0600.0000.0000.0000.000
68A71PHE00.0140.0028.9970.0540.0540.0000.0000.0000.000
69A72THR00.0540.03213.9230.0830.0830.0000.0000.0000.000
70A73ALA0-0.041-0.02716.0810.0520.0520.0000.0000.0000.000
71A74GLN0-0.047-0.06314.899-0.006-0.0060.0000.0000.0000.000
72A75ALA00.0420.04417.8490.0240.0240.0000.0000.0000.000
73A76LYS10.8960.95119.5380.2080.2080.0000.0000.0000.000
74A77ARG10.9220.98018.8440.2920.2920.0000.0000.0000.000
75A78ARG10.8530.93821.5340.2520.2520.0000.0000.0000.000
76A79ALA00.037-0.00823.3970.0150.0150.0000.0000.0000.000
77A80GLU-1-0.955-0.97525.535-0.115-0.1150.0000.0000.0000.000
78A81GLU-1-0.924-0.94925.184-0.192-0.1920.0000.0000.0000.000
79A82LEU0-0.101-0.05826.1280.0090.0090.0000.0000.0000.000
80A83GLY0-0.0040.01029.4010.0080.0080.0000.0000.0000.000
81A84VAL0-0.031-0.02127.9750.0090.0090.0000.0000.0000.000
82A85SER0-0.040-0.03427.383-0.001-0.0010.0000.0000.0000.000
83A86GLU-1-0.961-0.96728.308-0.087-0.0870.0000.0000.0000.000
84A87ARG10.8380.93029.9760.1150.1150.0000.0000.0000.000
85A88VAL0-0.025-0.00824.358-0.002-0.0020.0000.0000.0000.000
86A89HIS00.0080.00323.926-0.004-0.0040.0000.0000.0000.000
87A90PHE00.0150.02619.059-0.009-0.0090.0000.0000.0000.000
88A91ILE0-0.061-0.03118.5100.0180.0180.0000.0000.0000.000
89A92HIS0-0.023-0.01511.995-0.004-0.0040.0000.0000.0000.000
90A93ASN0-0.053-0.02214.8050.0620.0620.0000.0000.0000.000
91A94ASP-1-0.744-0.92112.265-0.031-0.0310.0000.0000.0000.000
92A95ALA0-0.051-0.03713.2420.0030.0030.0000.0000.0000.000
93A96ALA00.0150.00612.543-0.001-0.0010.0000.0000.0000.000
94A97GLY00.0230.01314.3200.0170.0170.0000.0000.0000.000
95A98TYR0-0.068-0.01917.9380.0040.0040.0000.0000.0000.000
96A99VAL00.0590.01919.552-0.005-0.0050.0000.0000.0000.000
97A100ALA0-0.037-0.00923.1100.0030.0030.0000.0000.0000.000
98A101ASN0-0.005-0.00425.3670.0120.0120.0000.0000.0000.000
99A102GLU-1-1.016-1.00428.615-0.058-0.0580.0000.0000.0000.000
100A103LYS10.9660.97528.6610.0390.0390.0000.0000.0000.000
101A104CYS0-0.066-0.04326.587-0.002-0.0020.0000.0000.0000.000
102A105ASP-1-0.858-0.93828.705-0.080-0.0800.0000.0000.0000.000
103A106VAL00.0090.00324.8170.0020.0020.0000.0000.0000.000
104A107ALA00.0080.01822.922-0.008-0.0080.0000.0000.0000.000
105A108ALA0-0.001-0.02220.3190.0040.0040.0000.0000.0000.000
106A109CYS00.0260.05514.440-0.008-0.0080.0000.0000.0000.000
107A110VAL0-0.005-0.00816.0870.0030.0030.0000.0000.0000.000
108A111GLY00.0160.01512.591-0.049-0.0490.0000.0000.0000.000
109A112ALA0-0.030-0.0029.770-0.059-0.0590.0000.0000.0000.000
110A113THR00.047-0.05110.7970.0850.0850.0000.0000.0000.000
111A114TRP0-0.061-0.0223.386-0.625-0.1720.016-0.121-0.347-0.001
112A115ILE0-0.061-0.0129.5830.1010.1010.0000.0000.0000.000
113A116ALA00.0170.00610.7340.0880.0880.0000.0000.0000.000
114A117GLY0-0.019-0.00712.4620.0580.0580.0000.0000.0000.000
115A118GLY0-0.012-0.00912.552-0.004-0.0040.0000.0000.0000.000
116A119PHE00.0680.06614.196-0.045-0.0450.0000.0000.0000.000
117A120ALA00.0180.01416.9370.0070.0070.0000.0000.0000.000
118A121GLY00.0280.02317.4290.0120.0120.0000.0000.0000.000
119A122ALA0-0.015-0.02215.9960.0030.0030.0000.0000.0000.000
120A123GLU-1-0.917-0.96617.744-0.060-0.0600.0000.0000.0000.000
121A124GLU-1-0.880-0.94021.0760.0040.0040.0000.0000.0000.000
122A125LEU0-0.028-0.00516.5700.0010.0010.0000.0000.0000.000
123A126LEU00.0180.01618.4380.0020.0020.0000.0000.0000.000
124A127ALA00.0420.03021.9790.0050.0050.0000.0000.0000.000
125A128GLN0-0.094-0.04623.1360.0130.0130.0000.0000.0000.000
126A129SER0-0.114-0.06124.0430.0010.0010.0000.0000.0000.000
127A130LEU0-0.0130.02326.131-0.007-0.0070.0000.0000.0000.000
128A131LYS10.8320.91227.8770.0800.0800.0000.0000.0000.000
129A132PRO00.0250.01231.295-0.002-0.0020.0000.0000.0000.000
130A133GLY00.0100.00232.9200.0000.0000.0000.0000.0000.000
131A134GLY0-0.0050.00730.212-0.002-0.0020.0000.0000.0000.000
132A135ILE00.014-0.00326.7070.0000.0000.0000.0000.0000.000
133A136MET0-0.0100.00322.724-0.006-0.0060.0000.0000.0000.000
134A137LEU0-0.020-0.01021.267-0.001-0.0010.0000.0000.0000.000
135A138ILE00.0500.01917.985-0.011-0.0110.0000.0000.0000.000
136A139GLY0-0.033-0.01216.7880.0100.0100.0000.0000.0000.000
137A140GLU-1-0.819-0.92414.783-0.307-0.3070.0000.0000.0000.000
138A141PRO0-0.081-0.04512.8800.0180.0180.0000.0000.0000.000
139A142TYR00.0010.01316.0900.0320.0320.0000.0000.0000.000
140A143TRP0-0.015-0.04415.630-0.021-0.0210.0000.0000.0000.000
141A144ARG10.8090.91620.2710.1630.1630.0000.0000.0000.000
142A145GLN0-0.051-0.03521.8390.0130.0130.0000.0000.0000.000
143A146LEU0-0.0180.00022.021-0.004-0.0040.0000.0000.0000.000
144A147PRO00.0020.01419.4070.0090.0090.0000.0000.0000.000
145A148ALA00.017-0.00222.4980.0060.0060.0000.0000.0000.000
146A149THR00.008-0.00823.1300.0060.0060.0000.0000.0000.000
147A150GLU-1-0.705-0.84519.302-0.034-0.0340.0000.0000.0000.000
148A151GLU-1-0.902-0.93518.3090.0080.0080.0000.0000.0000.000
149A152ILE0-0.027-0.01518.151-0.011-0.0110.0000.0000.0000.000
150A153ALA00.0240.00617.080-0.019-0.0190.0000.0000.0000.000
151A154GLN00.0120.00814.448-0.023-0.0230.0000.0000.0000.000
152A155ALA0-0.106-0.03513.855-0.004-0.0040.0000.0000.0000.000
153A156CYS0-0.120-0.06014.310-0.017-0.0170.0000.0000.0000.000
154A157GLY0-0.041-0.02310.248-0.054-0.0540.0000.0000.0000.000
155A158VAL0-0.0190.0169.249-0.084-0.0840.0000.0000.0000.000
156A159SER0-0.035-0.01811.2300.0630.0630.0000.0000.0000.000
157A160SER0-0.041-0.03913.2980.0220.0220.0000.0000.0000.000
158A161THR0-0.055-0.05116.349-0.030-0.0300.0000.0000.0000.000
159A162SER0-0.048-0.02018.567-0.010-0.0100.0000.0000.0000.000
160A163ASP-1-0.815-0.90412.974-0.085-0.0850.0000.0000.0000.000
161A164PHE00.0190.00611.685-0.030-0.0300.0000.0000.0000.000
162A165LEU00.0690.04117.4590.0230.0230.0000.0000.0000.000
163A166THR00.0090.02820.772-0.016-0.0160.0000.0000.0000.000
164A167LEU00.0570.02323.5030.0000.0000.0000.0000.0000.000
165A168PRO00.014-0.02424.9130.0010.0010.0000.0000.0000.000
166A169GLY00.018-0.00725.3600.0070.0070.0000.0000.0000.000
167A170LEU0-0.0140.00320.0270.0050.0050.0000.0000.0000.000
168A171VAL0-0.023-0.01523.4600.0020.0020.0000.0000.0000.000
169A172GLY0-0.001-0.00526.3570.0050.0050.0000.0000.0000.000
170A173ALA00.0360.03223.5910.0070.0070.0000.0000.0000.000
171A174PHE00.011-0.01920.6230.0040.0040.0000.0000.0000.000
172A175ASP-1-0.868-0.91625.734-0.049-0.0490.0000.0000.0000.000
173A176ASP-1-0.935-0.95227.602-0.040-0.0400.0000.0000.0000.000
174A177LEU0-0.070-0.03523.3450.0060.0060.0000.0000.0000.000
175A178GLY0-0.075-0.03827.9870.0010.0010.0000.0000.0000.000
176A179TYR0-0.045-0.03026.429-0.004-0.0040.0000.0000.0000.000
177A180ASP-1-0.857-0.91029.613-0.060-0.0600.0000.0000.0000.000
178A181VAL0-0.010-0.01427.512-0.005-0.0050.0000.0000.0000.000
179A182VAL0-0.043-0.02229.2870.0030.0030.0000.0000.0000.000
180A183GLU-1-0.870-0.94228.538-0.116-0.1160.0000.0000.0000.000
181A184MET0-0.035-0.01725.373-0.007-0.0070.0000.0000.0000.000
182A185VAL0-0.0240.00324.2200.0040.0040.0000.0000.0000.000
183A186LEU00.007-0.00422.870-0.021-0.0210.0000.0000.0000.000
184A187ALA0-0.044-0.04420.0680.0060.0060.0000.0000.0000.000
185A188ASP-1-0.857-0.94521.995-0.182-0.1820.0000.0000.0000.000
186A189GLN0-0.020-0.02021.274-0.012-0.0120.0000.0000.0000.000
187A190GLU-1-0.880-0.91421.051-0.206-0.2060.0000.0000.0000.000
188A191GLY00.006-0.01520.580-0.013-0.0130.0000.0000.0000.000
189A192TRP0-0.010-0.00713.151-0.046-0.0460.0000.0000.0000.000
190A193ASP-1-0.814-0.86616.852-0.244-0.2440.0000.0000.0000.000
191A194ARG10.8540.92817.8590.2200.2200.0000.0000.0000.000
192A195TYR0-0.074-0.0739.170-0.007-0.0070.0000.0000.0000.000
193A196GLU-1-0.820-0.94312.006-0.593-0.5930.0000.0000.0000.000
194A197ALA0-0.038-0.02814.0860.0000.0000.0000.0000.0000.000
195A198ALA0-0.0150.00914.8690.0120.0120.0000.0000.0000.000
196A199LYS10.9270.9768.2720.8260.8260.0000.0000.0000.000
197A200TRP0-0.0170.00112.4600.0450.0450.0000.0000.0000.000
198A201LEU0-0.038-0.01414.8340.0410.0410.0000.0000.0000.000
199A202THR00.0200.00812.8070.0560.0560.0000.0000.0000.000
200A203MET00.0130.0219.4490.0060.0060.0000.0000.0000.000
201A204ARG10.9290.97612.6130.1670.1670.0000.0000.0000.000
202A205ARG10.8970.93516.0840.2170.2170.0000.0000.0000.000
203A206TRP00.0670.03511.5720.0100.0100.0000.0000.0000.000
204A207LEU0-0.009-0.01312.8700.0270.0270.0000.0000.0000.000
205A208GLU-1-1.021-1.00715.536-0.073-0.0730.0000.0000.0000.000
206A209ALA0-0.046-0.01217.6440.0130.0130.0000.0000.0000.000
207A210ASN0-0.043-0.02714.954-0.021-0.0210.0000.0000.0000.000
208A211PRO0-0.035-0.01115.7510.0040.0040.0000.0000.0000.000
209A212ASP-1-0.904-0.95517.6050.0100.0100.0000.0000.0000.000
210A213ASP-1-0.874-0.93112.078-0.087-0.0870.0000.0000.0000.000
211A214ASP-1-0.848-0.93111.8370.1780.1780.0000.0000.0000.000
212A215PHE0-0.105-0.0504.260-0.153-0.023-0.001-0.016-0.1130.000
213A216ALA00.0180.0059.483-0.045-0.0450.0000.0000.0000.000
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