FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: N245Q

Calculation Name: 1KAF-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAF

Chain ID: A

ChEMBL ID:

UniProt ID: P22915

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -909146.425853
FMO2-HF: Nuclear repulsion 864046.539112
FMO2-HF: Total energy -45099.886742
FMO2-MP2: Total energy -45226.506556


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:104:MET)


Summations of interaction energy for fragment #1(A:104:MET)
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.
-1.592-0.1862.045-1.333-2.118-0.008
Interaction energy analysis for fragmet #1(A:104:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.092 / 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].
4A105GLU-1-1.050-0.8524.3070.3270.6770.002-0.129-0.2230.000
5A106ILE00.049-0.1263.7920.4861.562-0.014-0.513-0.550-0.001
6A106ILE0-0.0980.1043.3010.000-0.2120.0010.340-0.1290.000
7A107THR00.091-0.0485.6870.1270.146-0.002-0.001-0.0150.000
8A107THR0-0.0400.0429.166-0.004-0.0040.0000.0000.0000.000
9A108SER00.120-0.0599.420-0.173-0.1730.0000.0000.0000.000
10A108SER00.0040.10512.6680.0540.0540.0000.0000.0000.000
11A109ASP00.211-0.05912.184-0.007-0.0070.0000.0000.0000.000
12A109ASP-1-1.046-0.86513.569-0.604-0.6040.0000.0000.0000.000
13A110MET00.030-0.0849.9020.1710.1710.0000.0000.0000.000
14A110MET0-0.1790.0497.247-0.061-0.0610.0000.0000.0000.000
15A111GLU00.056-0.11910.9460.0490.0490.0000.0000.0000.000
16A111GLU-1-0.993-0.8559.349-1.800-1.8000.0000.0000.0000.000
17A112GLU00.087-0.13811.5730.0550.0550.0000.0000.0000.000
18A112GLU-1-0.989-0.81215.161-0.621-0.6210.0000.0000.0000.000
19A113ASP00.125-0.09314.5620.0830.0830.0000.0000.0000.000
20A113ASP-1-0.944-0.82314.091-0.615-0.6150.0000.0000.0000.000
21A114LYS00.116-0.09312.5590.1410.1410.0000.0000.0000.000
22A114LYS10.8021.05511.4491.0491.0490.0000.0000.0000.000
23A115ASP00.046-0.16514.0030.0590.0590.0000.0000.0000.000
24A115ASP-1-0.993-0.81915.037-0.865-0.8650.0000.0000.0000.000
25A116LEU00.069-0.12016.3410.0650.0650.0000.0000.0000.000
26A116LEU0-0.0830.12518.7700.0020.0020.0000.0000.0000.000
27A117MET00.106-0.08517.2740.0700.0700.0000.0000.0000.000
28A117MET0-0.1490.08416.190-0.018-0.0180.0000.0000.0000.000
29A118LEU00.035-0.13317.2790.0680.0680.0000.0000.0000.000
30A118LEU0-0.0830.10014.817-0.020-0.0200.0000.0000.0000.000
31A119LYS00.181-0.05418.5010.0400.0400.0000.0000.0000.000
32A119LYS10.8381.06721.1520.3390.3390.0000.0000.0000.000
33A120LEU00.042-0.12921.5720.0360.0360.0000.0000.0000.000
34A120LEU0-0.0970.11322.3540.0030.0030.0000.0000.0000.000
35A121LEU00.074-0.08821.2640.0450.0450.0000.0000.0000.000
36A121LEU0-0.0920.07618.595-0.002-0.0020.0000.0000.0000.000
37A122ASP00.122-0.10022.3280.0340.0340.0000.0000.0000.000
38A122ASP-1-1.019-0.85421.781-0.392-0.3920.0000.0000.0000.000
39A123LYS00.063-0.10223.9970.0260.0260.0000.0000.0000.000
40A123LYS10.8341.05926.1780.2260.2260.0000.0000.0000.000
41A124ASN0-0.074-0.12026.1440.0190.0190.0000.0000.0000.000
42A124ASN0-0.1230.05726.1610.0160.0160.0000.0000.0000.000
43A125GLY00.069-0.08527.2030.0150.0150.0000.0000.0000.000
44A126PHE00.037-0.01723.8960.0220.0220.0000.0000.0000.000
45A126PHE0-0.1250.08023.150-0.002-0.0020.0000.0000.0000.000
46A127VAL00.131-0.08023.331-0.029-0.0290.0000.0000.0000.000
47A127VAL0-0.1040.08523.8180.0060.0060.0000.0000.0000.000
48A128LEU00.029-0.14319.3050.0310.0310.0000.0000.0000.000
49A128LEU0-0.0200.14617.401-0.012-0.0120.0000.0000.0000.000
50A129LYS00.209-0.00919.7160.0010.0010.0000.0000.0000.000
51A129LYS10.7981.01618.5410.2250.2250.0000.0000.0000.000
52A130LYS00.026-0.10515.7500.0170.0170.0000.0000.0000.000
53A130LYS10.8031.01414.1660.3400.3400.0000.0000.0000.000
54A131VAL00.082-0.11612.9650.0900.0900.0000.0000.0000.000
55A131VAL0-0.0360.13710.949-0.010-0.0100.0000.0000.0000.000
56A132GLU0-0.023-0.13010.009-0.069-0.0690.0000.0000.0000.000
57A132GLU-1-0.913-0.8539.860-0.309-0.3090.0000.0000.0000.000
58A133ILE00.116-0.0665.4590.3620.369-0.002-0.002-0.0020.000
59A133ILE0-0.0500.1273.500-0.115-0.1150.0850.053-0.1380.000
60A134TYR00.101-0.1136.2260.0210.0210.0000.0000.0000.000
61A134TYR0-0.0750.1018.5820.1630.1630.0000.0000.0000.000
62A135ARG00.018-0.0995.298-0.051-0.0510.0000.0000.0000.000
63A135ARG10.8471.0437.243-0.615-0.6150.0000.0000.0000.000
64A136SER00.039-0.0803.723-0.103-0.061-0.0010.049-0.0910.000
65A136SER0-0.0030.1032.5190.0060.1221.977-1.101-0.992-0.007
66A137ASN00.156-0.0784.292-0.089-0.081-0.001-0.0290.0220.000
67A137ASN0-0.0290.0998.851-0.035-0.0350.0000.0000.0000.000
68A138TYR00.082-0.0797.456-0.244-0.2440.0000.0000.0000.000
69A138TYR0-0.0150.1308.450-0.061-0.0610.0000.0000.0000.000
70A139LEU00.033-0.1149.3820.1640.1640.0000.0000.0000.000
71A139LEU0-0.1170.08510.3860.0400.0400.0000.0000.0000.000
72A140ALA00.146-0.07812.279-0.056-0.0560.0000.0000.0000.000
73A140ALA0-0.0260.13915.4350.0050.0050.0000.0000.0000.000
74A141ILE00.072-0.08915.2540.0570.0570.0000.0000.0000.000
75A141ILE0-0.1700.04714.2570.0160.0160.0000.0000.0000.000
76A142LEU00.085-0.12517.293-0.019-0.0190.0000.0000.0000.000
77A142LEU0-0.0810.12120.5880.0040.0040.0000.0000.0000.000
78A143GLU00.059-0.14720.9810.0190.0190.0000.0000.0000.000
79A143GLU-1-1.012-0.83522.383-0.213-0.2130.0000.0000.0000.000
80A144LYS0-0.012-0.13423.0310.0240.0240.0000.0000.0000.000
81A144LYS10.8931.09426.4460.1680.1680.0000.0000.0000.000
82A145ARG00.125-0.06625.103-0.014-0.0140.0000.0000.0000.000
83A145ARG10.8471.04621.7670.1250.1250.0000.0000.0000.000
84A146THR00.018-0.11325.9560.0150.0150.0000.0000.0000.000
85A146THR00.0340.12827.5040.0020.0020.0000.0000.0000.000
86A147ASN00.008-0.09927.510-0.006-0.0060.0000.0000.0000.000
87A147ASN0-0.0480.12229.1120.0090.0090.0000.0000.0000.000
88A148GLY00.069-0.08827.9040.0020.0020.0000.0000.0000.000
89A149ILE00.062-0.03624.2450.0140.0140.0000.0000.0000.000
90A149ILE0-0.0320.15822.4500.0010.0010.0000.0000.0000.000
91A150ARG00.068-0.10521.578-0.001-0.0010.0000.0000.0000.000
92A150ARG10.7911.02120.9310.0820.0820.0000.0000.0000.000
93A151ASN00.028-0.07917.440-0.004-0.0040.0000.0000.0000.000
94A151ASN0-0.0650.06116.4320.0060.0060.0000.0000.0000.000
95A152PHE00.133-0.05517.4350.0500.0500.0000.0000.0000.000
96A152PHE0-0.0220.09917.9020.0010.0010.0000.0000.0000.000
97A153GLU00.034-0.15013.900-0.070-0.0700.0000.0000.0000.000
98A153GLU-1-0.937-0.82613.308-0.244-0.2440.0000.0000.0000.000
99A154ILE00.078-0.10112.4240.1320.1320.0000.0000.0000.000
100A154ILE0-0.0250.14011.348-0.014-0.0140.0000.0000.0000.000
101A155ASN00.150-0.06810.613-0.246-0.2460.0000.0000.0000.000
102A155ASN0-0.1720.05311.746-0.025-0.0250.0000.0000.0000.000
103A156ASN00.140-0.0748.402-0.009-0.0090.0000.0000.0000.000
104A156ASN0-0.0500.0937.0980.1670.1670.0000.0000.0000.000
105A157ASN00.031-0.0869.8050.0660.0660.0000.0000.0000.000
106A157ASN0-0.1000.06212.728-0.054-0.0540.0000.0000.0000.000
107A158GLY00.019-0.09412.8610.0600.0600.0000.0000.0000.000
108A159ASN00.0450.00814.880-0.001-0.0010.0000.0000.0000.000
109A159ASN0-0.0550.08716.3580.0110.0110.0000.0000.0000.000
110A160MET00.193-0.07715.090-0.079-0.0790.0000.0000.0000.000
111A160MET0-0.0860.13417.4340.0050.0050.0000.0000.0000.000
112A161ARG00.014-0.10016.6200.0470.0470.0000.0000.0000.000
113A161ARG10.6720.94816.4700.1150.1150.0000.0000.0000.000
114A162ILE00.096-0.09018.004-0.051-0.0510.0000.0000.0000.000
115A162ILE0-0.0430.11721.3480.0030.0030.0000.0000.0000.000
116A163PHE00.077-0.11119.3490.0340.0340.0000.0000.0000.000
117A163PHE0-0.1480.08918.5350.0130.0130.0000.0000.0000.000
118A164GLY00.020-0.09120.523-0.018-0.0180.0000.0000.0000.000
119A165TYR00.0740.00623.9500.0170.0170.0000.0000.0000.000
120A165TYR0-0.1440.05325.6300.0040.0040.0000.0000.0000.000
121A166LYS00.002-0.10026.779-0.007-0.0070.0000.0000.0000.000
122A166LYS10.8401.05130.4510.0220.0220.0000.0000.0000.000
123A167MET00.160-0.08129.2370.0010.0010.0000.0000.0000.000
124A167MET0-0.0810.10826.543-0.001-0.0010.0000.0000.0000.000
125A168MET00.070-0.12730.3100.0090.0090.0000.0000.0000.000
126A168MET0-0.0970.12133.8840.0010.0010.0000.0000.0000.000
127A169GLU00.176-0.08632.798-0.009-0.0090.0000.0000.0000.000
128A169GLU-1-1.008-0.84334.765-0.051-0.0510.0000.0000.0000.000
129A170HIS00.132-0.06134.301-0.003-0.0030.0000.0000.0000.000
130A170HIS0-0.0580.09337.0050.0040.0040.0000.0000.0000.000
131A171HIS00.045-0.09832.013-0.003-0.0030.0000.0000.0000.000
132A171HIS0-0.1130.06131.0250.0000.0000.0000.0000.0000.000
133A172ILE00.124-0.06929.766-0.013-0.0130.0000.0000.0000.000
134A172ILE0-0.0660.07629.1320.0010.0010.0000.0000.0000.000
135A173GLN00.053-0.10630.701-0.007-0.0070.0000.0000.0000.000
136A173GLN0-0.0500.10034.973-0.001-0.0010.0000.0000.0000.000
137A174LYS00.116-0.05732.5870.0020.0020.0000.0000.0000.000
138A174LYS10.8941.07131.9410.1030.1030.0000.0000.0000.000
139A175PHE00.076-0.06827.945-0.006-0.0060.0000.0000.0000.000
140A175PHE0-0.1230.04826.1010.0000.0000.0000.0000.0000.000
141A176THR00.058-0.07328.625-0.011-0.0110.0000.0000.0000.000
142A176THR0-0.0530.04629.1320.0040.0040.0000.0000.0000.000
143A177ASP0-0.009-0.12630.1930.0030.0030.0000.0000.0000.000
144A177ASP-1-1.000-0.85033.068-0.096-0.0960.0000.0000.0000.000
145A178ILE00.003-0.11329.4860.0050.0050.0000.0000.0000.000
146A178ILE0-0.0770.10626.831-0.003-0.0030.0000.0000.0000.000
147A179GLY0-0.001-0.09928.214-0.012-0.0120.0000.0000.0000.000
148A180MET0-0.010-0.03425.204-0.002-0.0020.0000.0000.0000.000
149A180MET0-0.0800.11922.3150.0000.0000.0000.0000.0000.000
150A181SER00.074-0.07724.5700.0130.0130.0000.0000.0000.000
151A181SER0-0.0450.07723.9390.0080.0080.0000.0000.0000.000
152A182CYS00.099-0.10924.904-0.014-0.0140.0000.0000.0000.000
153A182CYS0-0.1110.09527.4510.0020.0020.0000.0000.0000.000
154A183LYS00.112-0.08925.0510.0100.0100.0000.0000.0000.000
155A183LYS10.8261.06323.188-0.042-0.0420.0000.0000.0000.000
156A184ILE00.104-0.10425.570-0.007-0.0070.0000.0000.0000.000
157A184ILE0-0.0300.14428.8470.0010.0010.0000.0000.0000.000
158A185ALA00.054-0.12625.9980.0100.0100.0000.0000.0000.000
159A185ALA0-0.1010.09925.0980.0020.0020.0000.0000.0000.000
160A186LYS0-0.005-0.15527.228-0.009-0.0090.0000.0000.0000.000
161A186LYS10.9501.12429.354-0.025-0.0250.0000.0000.0000.000
162A187ASN00.080-0.07327.830-0.003-0.0030.0000.0000.0000.000
163A187ASN0-0.0390.09424.649-0.010-0.0100.0000.0000.0000.000
164A188GLY0-0.016-0.11528.988-0.004-0.0040.0000.0000.0000.000
165A189ASN00.1340.04624.441-0.013-0.0130.0000.0000.0000.000
166A189ASN0-0.1100.04823.125-0.011-0.0110.0000.0000.0000.000
167A190VAL00.060-0.13924.8540.0180.0180.0000.0000.0000.000
168A190VAL0-0.0610.13825.6290.0000.0000.0000.0000.0000.000
169A191TYR00.074-0.06521.701-0.017-0.0170.0000.0000.0000.000
170A191TYR0-0.1620.03719.1160.0150.0150.0000.0000.0000.000
171A192LEU00.142-0.08522.0980.0230.0230.0000.0000.0000.000
172A192LEU0-0.0840.11623.085-0.001-0.0010.0000.0000.0000.000
173A193ASP00.123-0.07820.388-0.030-0.0300.0000.0000.0000.000
174A193ASP-1-0.896-0.80618.803-0.122-0.1220.0000.0000.0000.000
175A194ILE00.076-0.10420.2870.0290.0290.0000.0000.0000.000
176A194ILE0-0.0160.15921.089-0.002-0.0020.0000.0000.0000.000
177A195LYS00.061-0.11219.493-0.031-0.0310.0000.0000.0000.000
178A195LYS10.8451.05018.7280.1560.1560.0000.0000.0000.000
179A196ARG00.073-0.10017.1220.0300.0300.0000.0000.0000.000
180A196ARG10.7611.01612.3080.6840.6840.0000.0000.0000.000
181A197SER00.022-0.05518.6040.0030.0030.0000.0000.0000.000
182A197SER00.0190.08022.0850.0050.0050.0000.0000.0000.000
183A198ALA00.187-0.07520.964-0.013-0.0130.0000.0000.0000.000
184A198ALA0-0.0650.12622.1990.0010.0010.0000.0000.0000.000
185A199GLU00.025-0.15322.319-0.004-0.0040.0000.0000.0000.000
186A199GLU-1-0.925-0.81724.803-0.255-0.2550.0000.0000.0000.000
187A200ASN00.099-0.09123.2920.0150.0150.0000.0000.0000.000
188A200ASN0-0.1440.06622.4170.0160.0160.0000.0000.0000.000
189A201ILE00.113-0.09020.6100.0260.0260.0000.0000.0000.000
190A201ILE0-0.0960.09717.706-0.004-0.0040.0000.0000.0000.000
191A202GLU00.111-0.13421.698-0.002-0.0020.0000.0000.0000.000
192A202GLU-1-0.988-0.83025.089-0.270-0.2700.0000.0000.0000.000
193A203ALA00.058-0.10924.8750.0090.0090.0000.0000.0000.000
194A203ALA0-0.0550.12426.5400.0030.0030.0000.0000.0000.000
195A204VAL00.053-0.11923.5500.0230.0230.0000.0000.0000.000
196A204VAL0-0.0680.09322.230-0.001-0.0010.0000.0000.0000.000
197A205ILE00.050-0.11824.0390.0210.0210.0000.0000.0000.000
198A205ILE0-0.0550.12420.892-0.001-0.0010.0000.0000.0000.000
199A206THR00.036-0.08124.7850.0080.0080.0000.0000.0000.000
200A206THR0-0.0400.06927.9590.0020.0020.0000.0000.0000.000
201A207VAL00.113-0.08228.1560.0090.0090.0000.0000.0000.000
202A207VAL0-0.0810.10528.0800.0010.0010.0000.0000.0000.000
203A208ALA00.082-0.11426.0740.0180.0180.0000.0000.0000.000
204A208ALA0-0.0740.08925.539-0.004-0.0040.0000.0000.0000.000
205A209SER0-0.055-0.13927.5700.0100.0100.0000.0000.0000.000
206A209SER0-0.0290.08627.362-0.006-0.0060.0000.0000.0000.000
207A210GLU00.026-0.10929.3820.0040.0040.0000.0000.0000.000
208A210GLU-1-1.011-0.83531.565-0.134-0.1340.0000.0000.0000.000
209A211LEU0-0.190-0.17231.3340.0190.0190.0000.0000.0000.000
210A211LEU0-0.0040.00228.8800.0020.0020.0000.0000.0000.000