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: 8NL3Y

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 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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -911084.474099
FMO2-HF: Nuclear repulsion 865982.361126
FMO2-HF: Total energy -45102.112972
FMO2-MP2: Total energy -45228.73406


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.
-4.648-2.350.444-1.015-1.726-0.001
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 : 0.083 / q_NPA : 0.000
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-1-1.061-0.8574.381-1.537-1.1010.002-0.167-0.2700.000
5A106ILE00.017-0.1163.869-0.2061.195-0.009-0.774-0.6170.003
6A106ILE0-0.0720.0953.823-0.130-0.074-0.0010.017-0.0710.000
7A107THR00.030-0.0826.2790.0300.0300.0000.0000.0000.000
8A107THR0-0.0270.0429.448-0.032-0.0320.0000.0000.0000.000
9A108SER00.090-0.07910.054-0.057-0.0570.0000.0000.0000.000
10A108SER0-0.0200.09413.9250.0030.0030.0000.0000.0000.000
11A109ASP00.144-0.02912.9900.0290.0290.0000.0000.0000.000
12A109ASP-1-0.840-0.77513.705-0.976-0.9760.0000.0000.0000.000
13A110MET00.081-0.10510.2930.2040.2040.0000.0000.0000.000
14A110MET0-0.1390.0768.298-0.112-0.1120.0000.0000.0000.000
15A111GLU00.048-0.09211.4950.0320.0320.0000.0000.0000.000
16A111GLU-1-0.864-0.7849.190-1.717-1.7170.0000.0000.0000.000
17A112GLU00.082-0.11412.0290.0920.0920.0000.0000.0000.000
18A112GLU-1-1.002-0.85115.839-0.674-0.6740.0000.0000.0000.000
19A113ASP00.099-0.10614.9810.0890.0890.0000.0000.0000.000
20A113ASP-1-0.892-0.79614.447-0.587-0.5870.0000.0000.0000.000
21A114LYS00.087-0.06412.6550.1290.1290.0000.0000.0000.000
22A114LYS10.6810.96111.3360.9900.9900.0000.0000.0000.000
23A115ASP00.093-0.12014.1150.0790.0790.0000.0000.0000.000
24A115ASP-1-0.936-0.80814.981-0.735-0.7350.0000.0000.0000.000
25A116LEU00.068-0.11816.4870.0720.0720.0000.0000.0000.000
26A116LEU0-0.0980.11418.7130.0030.0030.0000.0000.0000.000
27A117MET00.120-0.08217.2860.0620.0620.0000.0000.0000.000
28A117MET0-0.1580.08116.283-0.008-0.0080.0000.0000.0000.000
29A118LEU00.022-0.12017.3070.0610.0610.0000.0000.0000.000
30A118LEU0-0.0870.09614.9130.0010.0010.0000.0000.0000.000
31A119LYS00.191-0.05318.5430.0450.0450.0000.0000.0000.000
32A119LYS10.8331.05921.2230.2830.2830.0000.0000.0000.000
33A120LEU00.062-0.11521.4540.0330.0330.0000.0000.0000.000
34A120LEU0-0.1140.09722.2080.0010.0010.0000.0000.0000.000
35A121LEU00.104-0.07421.2550.0320.0320.0000.0000.0000.000
36A121LEU0-0.1100.07518.6410.0030.0030.0000.0000.0000.000
37A122ASP00.074-0.11322.3420.0300.0300.0000.0000.0000.000
38A122ASP-1-0.996-0.85621.453-0.235-0.2350.0000.0000.0000.000
39A123LYS00.045-0.10124.0910.0220.0220.0000.0000.0000.000
40A123LYS10.7180.99825.8830.1840.1840.0000.0000.0000.000
41A124ASN0-0.014-0.09826.1620.0130.0130.0000.0000.0000.000
42A124ASN0-0.1130.05826.1050.0100.0100.0000.0000.0000.000
43A125GLY00.052-0.09627.0210.0130.0130.0000.0000.0000.000
44A126PHE00.035-0.01123.7260.0210.0210.0000.0000.0000.000
45A126PHE0-0.1140.08022.8480.0000.0000.0000.0000.0000.000
46A127VAL00.144-0.07422.700-0.023-0.0230.0000.0000.0000.000
47A127VAL0-0.1210.07123.6390.0060.0060.0000.0000.0000.000
48A128LEU00.065-0.12318.9800.0330.0330.0000.0000.0000.000
49A128LEU0-0.0010.14217.262-0.007-0.0070.0000.0000.0000.000
50A129LYS00.071-0.07419.441-0.001-0.0010.0000.0000.0000.000
51A129LYS10.7640.98318.867-0.020-0.0200.0000.0000.0000.000
52A130LYS00.033-0.09015.4380.0190.0190.0000.0000.0000.000
53A130LYS10.7400.96513.560-0.194-0.1940.0000.0000.0000.000
54A131VAL00.071-0.12513.0550.0490.0490.0000.0000.0000.000
55A131VAL0-0.0420.14111.443-0.006-0.0060.0000.0000.0000.000
56A132GLU00.050-0.0869.554-0.051-0.0510.0000.0000.0000.000
57A132GLU-1-0.893-0.8259.4380.2950.2950.0000.0000.0000.000
58A133ILE00.125-0.0955.1150.2460.257-0.002-0.004-0.0050.000
59A133ILE0-0.0530.1383.3530.252-0.2330.1770.473-0.1660.000
60A134TYR00.110-0.0985.5770.6320.687-0.002-0.003-0.0510.000
61A134TYR0-0.0810.0968.0440.0710.0710.0000.0000.0000.000
62A135ARG00.004-0.0905.094-0.252-0.2520.0000.0000.0000.000
63A135ARG10.8371.0147.091-0.931-0.9310.0000.0000.0000.000
64A136SER00.045-0.0673.721-0.227-0.1520.0000.005-0.0790.000
65A136SER0-0.0050.0843.014-0.3360.4230.279-0.543-0.496-0.004
66A137ASN00.156-0.0644.278-0.284-0.2940.000-0.0190.0290.000
67A137ASN0-0.0580.0958.638-0.071-0.0710.0000.0000.0000.000
68A138TYR00.131-0.0747.111-0.095-0.0950.0000.0000.0000.000
69A138TYR0-0.1070.0718.785-0.006-0.0060.0000.0000.0000.000
70A139LEU00.039-0.1059.2330.1090.1090.0000.0000.0000.000
71A139LEU0-0.1050.07310.0190.0560.0560.0000.0000.0000.000
72A140ALA00.166-0.07111.9620.0170.0170.0000.0000.0000.000
73A140ALA0-0.0400.12815.093-0.004-0.0040.0000.0000.0000.000
74A141ILE00.073-0.09015.0410.0170.0170.0000.0000.0000.000
75A141ILE0-0.1350.06213.8220.0170.0170.0000.0000.0000.000
76A142LEU00.087-0.11917.008-0.009-0.0090.0000.0000.0000.000
77A142LEU0-0.0730.12420.4400.0020.0020.0000.0000.0000.000
78A143GLU00.076-0.11520.7700.0300.0300.0000.0000.0000.000
79A143GLU-1-0.892-0.78822.312-0.015-0.0150.0000.0000.0000.000
80A144LYS00.068-0.08422.8780.0190.0190.0000.0000.0000.000
81A144LYS10.7931.04326.1390.0370.0370.0000.0000.0000.000
82A145ARG00.090-0.09624.852-0.017-0.0170.0000.0000.0000.000
83A145ARG10.8201.04320.870-0.037-0.0370.0000.0000.0000.000
84A146THR00.000-0.10025.6460.0110.0110.0000.0000.0000.000
85A146THR00.0080.10927.1950.0000.0000.0000.0000.0000.000
86A147ASN00.010-0.09027.389-0.004-0.0040.0000.0000.0000.000
87A147ASN0-0.0320.10929.2800.0060.0060.0000.0000.0000.000
88A148GLY00.087-0.09127.922-0.001-0.0010.0000.0000.0000.000
89A149ILE00.065-0.02824.0770.0180.0180.0000.0000.0000.000
90A149ILE0-0.0440.14922.3570.0000.0000.0000.0000.0000.000
91A150ARG00.051-0.11221.4710.0040.0040.0000.0000.0000.000
92A150ARG10.7841.01220.844-0.051-0.0510.0000.0000.0000.000
93A151ASN00.025-0.05917.2580.0150.0150.0000.0000.0000.000
94A151ASN0-0.1130.00815.526-0.010-0.0100.0000.0000.0000.000
95A152PHE00.140-0.05917.2740.0290.0290.0000.0000.0000.000
96A152PHE0-0.0150.10017.8540.0000.0000.0000.0000.0000.000
97A153GLU00.027-0.12913.788-0.021-0.0210.0000.0000.0000.000
98A153GLU-1-0.855-0.79213.383-0.110-0.1100.0000.0000.0000.000
99A154ILE00.057-0.09112.4290.0930.0930.0000.0000.0000.000
100A154ILE0-0.0520.12611.496-0.009-0.0090.0000.0000.0000.000
101A155ASN00.138-0.06510.706-0.205-0.2050.0000.0000.0000.000
102A155ASN0-0.1670.01911.8350.0360.0360.0000.0000.0000.000
103A156ASN00.155-0.0558.9230.0190.0190.0000.0000.0000.000
104A156ASN0-0.0940.0666.9080.1610.1610.0000.0000.0000.000
105A157ASN00.043-0.07810.2870.0140.0140.0000.0000.0000.000
106A157ASN0-0.0990.06513.140-0.036-0.0360.0000.0000.0000.000
107A158GLY00.045-0.09313.4340.0670.0670.0000.0000.0000.000
108A159ASN00.0810.01215.0430.0190.0190.0000.0000.0000.000
109A159ASN0-0.1210.04715.952-0.007-0.0070.0000.0000.0000.000
110A160MET00.183-0.07915.215-0.079-0.0790.0000.0000.0000.000
111A160MET0-0.0960.13617.8830.0050.0050.0000.0000.0000.000
112A161ARG00.010-0.07716.9480.0370.0370.0000.0000.0000.000
113A161ARG10.6750.94916.1080.0920.0920.0000.0000.0000.000
114A162ILE00.124-0.10918.232-0.030-0.0300.0000.0000.0000.000
115A162ILE0-0.0600.12520.9950.0030.0030.0000.0000.0000.000
116A163PHE00.101-0.07519.1140.0160.0160.0000.0000.0000.000
117A163PHE0-0.1550.06518.2430.0170.0170.0000.0000.0000.000
118A164GLY00.035-0.09520.298-0.008-0.0080.0000.0000.0000.000
119A165TYR00.0700.00023.7420.0150.0150.0000.0000.0000.000
120A165TYR0-0.1290.05525.4370.0010.0010.0000.0000.0000.000
121A166LYS0-0.016-0.08026.682-0.006-0.0060.0000.0000.0000.000
122A166LYS10.8351.03830.143-0.039-0.0390.0000.0000.0000.000
123A167MET00.187-0.07628.9260.0020.0020.0000.0000.0000.000
124A167MET0-0.0890.10726.1530.0010.0010.0000.0000.0000.000
125A168MET00.053-0.12830.0530.0050.0050.0000.0000.0000.000
126A168MET0-0.0880.11833.6700.0000.0000.0000.0000.0000.000
127A169GLU00.149-0.06232.671-0.007-0.0070.0000.0000.0000.000
128A169GLU-1-0.959-0.82433.916-0.034-0.0340.0000.0000.0000.000
129A170HIS00.116-0.07634.146-0.005-0.0050.0000.0000.0000.000
130A170HIS0-0.0490.10136.4410.0040.0040.0000.0000.0000.000
131A171HIS00.042-0.10032.009-0.005-0.0050.0000.0000.0000.000
132A171HIS0-0.1250.05430.998-0.002-0.0020.0000.0000.0000.000
133A172ILE00.147-0.06229.624-0.012-0.0120.0000.0000.0000.000
134A172ILE0-0.0950.07328.9390.0010.0010.0000.0000.0000.000
135A173GLN00.108-0.09530.568-0.009-0.0090.0000.0000.0000.000
136A173GLN0-0.1220.06434.886-0.001-0.0010.0000.0000.0000.000
137A174LYS00.093-0.08332.375-0.003-0.0030.0000.0000.0000.000
138A174LYS10.7900.98031.5270.0760.0760.0000.0000.0000.000
139A175PHE00.066-0.05427.796-0.008-0.0080.0000.0000.0000.000
140A175PHE0-0.1140.05125.7300.0010.0010.0000.0000.0000.000
141A176THR00.019-0.07428.555-0.014-0.0140.0000.0000.0000.000
142A176THR0-0.0870.02929.4220.0050.0050.0000.0000.0000.000
143A177ASP00.072-0.08630.326-0.004-0.0040.0000.0000.0000.000
144A177ASP-1-1.018-0.86033.186-0.087-0.0870.0000.0000.0000.000
145A178ILE00.008-0.10729.5490.0010.0010.0000.0000.0000.000
146A178ILE0-0.1030.09427.041-0.002-0.0020.0000.0000.0000.000
147A179GLY00.031-0.10228.368-0.016-0.0160.0000.0000.0000.000
148A180MET0-0.009-0.03925.220-0.010-0.0100.0000.0000.0000.000
149A180MET0-0.0900.10921.9440.0040.0040.0000.0000.0000.000
150A181SER00.107-0.06624.8480.0160.0160.0000.0000.0000.000
151A181SER0-0.0630.07223.9740.0030.0030.0000.0000.0000.000
152A182CYS00.064-0.09924.988-0.009-0.0090.0000.0000.0000.000
153A182CYS0-0.0950.10627.7330.0040.0040.0000.0000.0000.000
154A183LYS00.096-0.09624.9420.0040.0040.0000.0000.0000.000
155A183LYS10.8371.06222.989-0.024-0.0240.0000.0000.0000.000
156A184ILE00.085-0.09325.5640.0000.0000.0000.0000.0000.000
157A184ILE0-0.0360.13828.4590.0010.0010.0000.0000.0000.000
158A185ALA00.108-0.11525.6980.0010.0010.0000.0000.0000.000
159A185ALA0-0.0860.11024.8150.0030.0030.0000.0000.0000.000
160A186LYS0-0.064-0.15726.962-0.007-0.0070.0000.0000.0000.000
161A186LYS10.9221.10729.815-0.035-0.0350.0000.0000.0000.000
162A187ASN00.135-0.05727.985-0.003-0.0030.0000.0000.0000.000
163A187ASN0-0.0440.08124.668-0.010-0.0100.0000.0000.0000.000
164A188GLY0-0.015-0.12128.951-0.001-0.0010.0000.0000.0000.000
165A189ASN00.0870.02424.332-0.009-0.0090.0000.0000.0000.000
166A189ASN0-0.1070.04222.3320.0000.0000.0000.0000.0000.000
167A190VAL00.067-0.12124.7800.0080.0080.0000.0000.0000.000
168A190VAL0-0.0560.12825.6660.0000.0000.0000.0000.0000.000
169A191TYR00.095-0.06321.677-0.001-0.0010.0000.0000.0000.000
170A191TYR0-0.1280.06119.0650.0150.0150.0000.0000.0000.000
171A192LEU00.118-0.08722.0290.0110.0110.0000.0000.0000.000
172A192LEU0-0.0390.10823.0610.0000.0000.0000.0000.0000.000
173A193ASP00.112-0.07120.435-0.017-0.0170.0000.0000.0000.000
174A193ASP-1-0.883-0.80018.610-0.129-0.1290.0000.0000.0000.000
175A194ILE00.079-0.09720.5220.0240.0240.0000.0000.0000.000
176A194ILE0-0.0230.15221.306-0.002-0.0020.0000.0000.0000.000
177A195LYS00.067-0.10219.579-0.028-0.0280.0000.0000.0000.000
178A195LYS10.7941.03117.6720.2750.2750.0000.0000.0000.000
179A196ARG00.073-0.11317.4060.0450.0450.0000.0000.0000.000
180A196ARG10.6610.95813.2470.7410.7410.0000.0000.0000.000
181A197SER0-0.008-0.08118.839-0.015-0.0150.0000.0000.0000.000
182A197SER0-0.0140.04822.4610.0080.0080.0000.0000.0000.000
183A198ALA00.185-0.06821.2200.0000.0000.0000.0000.0000.000
184A198ALA0-0.0810.10422.0260.0000.0000.0000.0000.0000.000
185A199GLU0-0.006-0.13522.4060.0080.0080.0000.0000.0000.000
186A199GLU-1-0.846-0.78424.706-0.280-0.2800.0000.0000.0000.000
187A200ASN00.133-0.07023.4420.0210.0210.0000.0000.0000.000
188A200ASN0-0.1490.06222.6000.0170.0170.0000.0000.0000.000
189A201ILE00.129-0.07120.8080.0310.0310.0000.0000.0000.000
190A201ILE0-0.1050.09117.867-0.002-0.0020.0000.0000.0000.000
191A202GLU00.133-0.09521.9820.0120.0120.0000.0000.0000.000
192A202GLU-1-0.884-0.79925.256-0.209-0.2090.0000.0000.0000.000
193A203ALA00.069-0.10125.1840.0170.0170.0000.0000.0000.000
194A203ALA0-0.0620.11426.6710.0010.0010.0000.0000.0000.000
195A204VAL00.081-0.10723.7900.0230.0230.0000.0000.0000.000
196A204VAL0-0.0950.09022.3320.0000.0000.0000.0000.0000.000
197A205ILE00.051-0.11323.8250.0230.0230.0000.0000.0000.000
198A205ILE0-0.0660.10920.608-0.001-0.0010.0000.0000.0000.000
199A206THR00.088-0.06624.6850.0150.0150.0000.0000.0000.000
200A206THR0-0.0630.05827.9710.0030.0030.0000.0000.0000.000
201A207VAL00.072-0.10128.2780.0120.0120.0000.0000.0000.000
202A207VAL0-0.0800.12228.1610.0010.0010.0000.0000.0000.000
203A208ALA00.102-0.11925.9310.0180.0180.0000.0000.0000.000
204A208ALA0-0.0690.09425.411-0.002-0.0020.0000.0000.0000.000
205A209SER0-0.031-0.10827.4420.0130.0130.0000.0000.0000.000
206A209SER0-0.0600.06227.580-0.002-0.0020.0000.0000.0000.000
207A210GLU00.053-0.10729.5480.0090.0090.0000.0000.0000.000
208A210GLU-1-0.908-0.78932.120-0.091-0.0910.0000.0000.0000.000
209A211LEU0-0.182-0.18130.7680.0200.0200.0000.0000.0000.000
210A211LEU00.0040.03628.4860.0020.0020.0000.0000.0000.000