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: GY191

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 OptHSide
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 -910044.087816
FMO2-HF: Nuclear repulsion 864942.140744
FMO2-HF: Total energy -45101.947072
FMO2-MP2: Total energy -45228.556683


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.
-4.519-1.9891.395-1.694-2.231-0.004
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 : 0.074 / 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-1-1.063-0.8494.306-1.665-1.1800.004-0.200-0.2890.000
5A106ILE00.046-0.1193.792-0.0111.686-0.016-0.921-0.7610.003
6A106ILE0-0.1100.0943.380-0.038-0.162-0.0010.248-0.1230.000
7A107THR00.062-0.0775.7210.0610.072-0.002-0.001-0.0090.000
8A107THR0-0.0320.0489.181-0.024-0.0240.0000.0000.0000.000
9A108SER00.107-0.0859.455-0.081-0.0810.0000.0000.0000.000
10A108SER00.0000.10212.8620.0190.0190.0000.0000.0000.000
11A109ASP00.106-0.03212.2200.0540.0540.0000.0000.0000.000
12A109ASP-1-0.854-0.78713.339-0.995-0.9950.0000.0000.0000.000
13A110MET00.087-0.1089.9340.2090.2090.0000.0000.0000.000
14A110MET0-0.1510.0827.984-0.123-0.1230.0000.0000.0000.000
15A111GLU00.047-0.11610.9680.0930.0930.0000.0000.0000.000
16A111GLU-1-0.842-0.7809.370-1.615-1.6150.0000.0000.0000.000
17A112GLU00.060-0.10911.5980.0990.0990.0000.0000.0000.000
18A112GLU-1-1.014-0.84115.314-0.660-0.6600.0000.0000.0000.000
19A113ASP00.078-0.09814.5280.0980.0980.0000.0000.0000.000
20A113ASP-1-0.911-0.81214.115-0.616-0.6160.0000.0000.0000.000
21A114LYS00.129-0.05912.5640.1350.1350.0000.0000.0000.000
22A114LYS10.6900.97111.1300.9470.9470.0000.0000.0000.000
23A115ASP00.073-0.14214.0160.0820.0820.0000.0000.0000.000
24A115ASP-1-0.953-0.79714.825-0.699-0.6990.0000.0000.0000.000
25A116LEU00.067-0.12016.3580.0700.0700.0000.0000.0000.000
26A116LEU0-0.0890.10818.7340.0010.0010.0000.0000.0000.000
27A117MET00.127-0.07817.3050.0620.0620.0000.0000.0000.000
28A117MET0-0.1540.08216.260-0.005-0.0050.0000.0000.0000.000
29A118LEU00.006-0.13517.2810.0610.0610.0000.0000.0000.000
30A118LEU0-0.0680.10514.7220.0000.0000.0000.0000.0000.000
31A119LYS00.192-0.04318.5060.0420.0420.0000.0000.0000.000
32A119LYS10.8261.05821.1460.2690.2690.0000.0000.0000.000
33A120LEU00.056-0.13421.5820.0330.0330.0000.0000.0000.000
34A120LEU0-0.1220.10222.3550.0030.0030.0000.0000.0000.000
35A121LEU00.072-0.08221.2510.0310.0310.0000.0000.0000.000
36A121LEU0-0.0880.07718.6250.0020.0020.0000.0000.0000.000
37A122ASP00.092-0.10122.3490.0290.0290.0000.0000.0000.000
38A122ASP-1-1.011-0.85421.715-0.217-0.2170.0000.0000.0000.000
39A123LYS00.071-0.07723.9990.0220.0220.0000.0000.0000.000
40A123LYS10.7451.01325.9060.1770.1770.0000.0000.0000.000
41A124ASN0-0.033-0.10026.1490.0140.0140.0000.0000.0000.000
42A124ASN0-0.1380.04425.9790.0090.0090.0000.0000.0000.000
43A125GLY00.079-0.09227.1990.0120.0120.0000.0000.0000.000
44A126PHE00.039-0.01023.9070.0200.0200.0000.0000.0000.000
45A126PHE0-0.1170.07523.1190.0000.0000.0000.0000.0000.000
46A127VAL00.133-0.07923.325-0.019-0.0190.0000.0000.0000.000
47A127VAL0-0.1110.08523.8630.0040.0040.0000.0000.0000.000
48A128LEU00.027-0.13419.3030.0230.0230.0000.0000.0000.000
49A128LEU0-0.0010.14017.500-0.006-0.0060.0000.0000.0000.000
50A129LYS00.161-0.02519.6880.0000.0000.0000.0000.0000.000
51A129LYS10.8161.02218.871-0.072-0.0720.0000.0000.0000.000
52A130LYS00.044-0.09415.7030.0140.0140.0000.0000.0000.000
53A130LYS10.7490.95113.818-0.197-0.1970.0000.0000.0000.000
54A131VAL00.085-0.09713.0850.0470.0470.0000.0000.0000.000
55A131VAL0-0.0550.14111.153-0.009-0.0090.0000.0000.0000.000
56A132GLU00.039-0.1029.983-0.014-0.0140.0000.0000.0000.000
57A132GLU-1-0.900-0.8369.9510.3250.3250.0000.0000.0000.000
58A133ILE00.116-0.0765.5000.0960.096-0.002-0.0020.0040.000
59A133ILE0-0.0520.1323.571-0.093-0.1050.0710.064-0.1220.000
60A134TYR00.107-0.1096.1950.6100.6100.0000.0000.0000.000
61A134TYR0-0.0870.0978.5450.0480.0480.0000.0000.0000.000
62A135ARG00.032-0.0875.257-0.237-0.2370.0000.0000.0000.000
63A135ARG10.8331.0227.237-0.870-0.8700.0000.0000.0000.000
64A136SER00.006-0.0873.726-0.240-0.232-0.0010.072-0.0790.000
65A136SER00.0050.0832.614-0.0020.4761.343-0.935-0.885-0.007
66A137ASN00.181-0.0484.311-0.321-0.334-0.001-0.0190.0330.000
67A137ASN0-0.0490.1018.830-0.093-0.0930.0000.0000.0000.000
68A138TYR00.103-0.0777.442-0.004-0.0040.0000.0000.0000.000
69A138TYR0-0.0990.0638.607-0.026-0.0260.0000.0000.0000.000
70A139LEU00.035-0.1089.3760.0740.0740.0000.0000.0000.000
71A139LEU0-0.1270.06210.2500.0500.0500.0000.0000.0000.000
72A140ALA00.173-0.05912.2640.0230.0230.0000.0000.0000.000
73A140ALA0-0.0300.13115.334-0.004-0.0040.0000.0000.0000.000
74A141ILE00.063-0.09115.2420.0130.0130.0000.0000.0000.000
75A141ILE0-0.1660.05414.3580.0150.0150.0000.0000.0000.000
76A142LEU00.100-0.12717.274-0.005-0.0050.0000.0000.0000.000
77A142LEU0-0.0730.11820.5380.0010.0010.0000.0000.0000.000
78A143GLU00.035-0.14020.9640.0280.0280.0000.0000.0000.000
79A143GLU-1-0.983-0.84722.421-0.022-0.0220.0000.0000.0000.000
80A144LYS00.024-0.10823.0110.0190.0190.0000.0000.0000.000
81A144LYS10.8531.08126.3110.0340.0340.0000.0000.0000.000
82A145ARG00.122-0.07225.087-0.016-0.0160.0000.0000.0000.000
83A145ARG10.8381.04721.541-0.043-0.0430.0000.0000.0000.000
84A146THR0-0.001-0.11225.9370.0100.0100.0000.0000.0000.000
85A146THR00.0060.12327.5380.0000.0000.0000.0000.0000.000
86A147ASN00.032-0.08327.495-0.004-0.0040.0000.0000.0000.000
87A147ASN0-0.0330.11429.3300.0050.0050.0000.0000.0000.000
88A148GLY00.073-0.09827.884-0.002-0.0020.0000.0000.0000.000
89A149ILE00.060-0.03024.2290.0160.0160.0000.0000.0000.000
90A149ILE0-0.0420.15422.4740.0000.0000.0000.0000.0000.000
91A150ARG00.072-0.09621.5600.0020.0020.0000.0000.0000.000
92A150ARG10.7821.00820.991-0.049-0.0490.0000.0000.0000.000
93A151ASN00.029-0.06417.4290.0100.0100.0000.0000.0000.000
94A151ASN0-0.1010.01015.500-0.008-0.0080.0000.0000.0000.000
95A152PHE00.121-0.05117.4430.0260.0260.0000.0000.0000.000
96A152PHE0-0.0200.10017.9560.0000.0000.0000.0000.0000.000
97A153GLU00.054-0.15313.880-0.024-0.0240.0000.0000.0000.000
98A153GLU-1-0.859-0.79013.305-0.089-0.0890.0000.0000.0000.000
99A154ILE00.058-0.07112.4280.0860.0860.0000.0000.0000.000
100A154ILE0-0.0570.12711.276-0.009-0.0090.0000.0000.0000.000
101A155ASN00.142-0.06410.615-0.194-0.1940.0000.0000.0000.000
102A155ASN0-0.1820.02711.8470.0270.0270.0000.0000.0000.000
103A156ASN00.174-0.0768.4260.0110.0110.0000.0000.0000.000
104A156ASN0-0.0740.0736.7360.1370.1370.0000.0000.0000.000
105A157ASN00.028-0.0739.8240.0050.0050.0000.0000.0000.000
106A157ASN0-0.1020.05812.624-0.032-0.0320.0000.0000.0000.000
107A158GLY00.007-0.10812.8760.0640.0640.0000.0000.0000.000
108A159ASN00.051-0.01714.8890.0130.0130.0000.0000.0000.000
109A159ASN0-0.0930.06016.180-0.010-0.0100.0000.0000.0000.000
110A160MET00.167-0.05915.094-0.071-0.0710.0000.0000.0000.000
111A160MET0-0.1070.13117.5770.0030.0030.0000.0000.0000.000
112A161ARG00.032-0.09216.6170.0310.0310.0000.0000.0000.000
113A161ARG10.6670.95316.3340.0860.0860.0000.0000.0000.000
114A162ILE00.150-0.08117.996-0.025-0.0250.0000.0000.0000.000
115A162ILE0-0.0680.11721.1170.0020.0020.0000.0000.0000.000
116A163PHE00.077-0.11819.3370.0130.0130.0000.0000.0000.000
117A163PHE0-0.1500.08918.3900.0170.0170.0000.0000.0000.000
118A164GLY00.025-0.09020.506-0.003-0.0030.0000.0000.0000.000
119A165TYR00.0630.00923.9310.0130.0130.0000.0000.0000.000
120A165TYR0-0.1300.05325.5690.0010.0010.0000.0000.0000.000
121A166LYS0-0.004-0.08026.756-0.005-0.0050.0000.0000.0000.000
122A166LYS10.8251.03330.261-0.035-0.0350.0000.0000.0000.000
123A167MET00.193-0.07929.2140.0030.0030.0000.0000.0000.000
124A167MET0-0.0870.10726.4780.0000.0000.0000.0000.0000.000
125A168MET00.051-0.13230.2920.0050.0050.0000.0000.0000.000
126A168MET0-0.0830.12033.6790.0000.0000.0000.0000.0000.000
127A169GLU00.170-0.06732.785-0.007-0.0070.0000.0000.0000.000
128A169GLU-1-0.963-0.82434.315-0.033-0.0330.0000.0000.0000.000
129A170HIS00.120-0.07734.290-0.005-0.0050.0000.0000.0000.000
130A170HIS0-0.0410.10637.0720.0030.0030.0000.0000.0000.000
131A171HIS00.041-0.08832.034-0.005-0.0050.0000.0000.0000.000
132A171HIS0-0.1200.05131.055-0.002-0.0020.0000.0000.0000.000
133A172ILE00.142-0.06529.764-0.011-0.0110.0000.0000.0000.000
134A172ILE0-0.0850.07729.0800.0010.0010.0000.0000.0000.000
135A173GLN00.076-0.11830.694-0.009-0.0090.0000.0000.0000.000
136A173GLN0-0.1070.07034.959-0.001-0.0010.0000.0000.0000.000
137A174LYS00.089-0.08232.570-0.003-0.0030.0000.0000.0000.000
138A174LYS10.8060.99931.8220.0740.0740.0000.0000.0000.000
139A175PHE00.048-0.05627.947-0.008-0.0080.0000.0000.0000.000
140A175PHE0-0.1130.05025.9450.0010.0010.0000.0000.0000.000
141A176THR00.052-0.08128.625-0.014-0.0140.0000.0000.0000.000
142A176THR0-0.0520.05729.1550.0050.0050.0000.0000.0000.000
143A177ASP00.001-0.11830.190-0.004-0.0040.0000.0000.0000.000
144A177ASP-1-0.986-0.84733.176-0.085-0.0850.0000.0000.0000.000
145A178ILE0-0.005-0.10829.5960.0010.0010.0000.0000.0000.000
146A178ILE0-0.0920.10426.975-0.002-0.0020.0000.0000.0000.000
147A179GLY00.012-0.11028.220-0.015-0.0150.0000.0000.0000.000
148A180MET0-0.005-0.03325.223-0.010-0.0100.0000.0000.0000.000
149A180MET0-0.0790.11122.2260.0040.0040.0000.0000.0000.000
150A181SER00.079-0.07024.5910.0150.0150.0000.0000.0000.000
151A181SER0-0.0510.07423.9410.0020.0020.0000.0000.0000.000
152A182CYS00.066-0.10824.922-0.008-0.0080.0000.0000.0000.000
153A182CYS0-0.1070.09827.4890.0040.0040.0000.0000.0000.000
154A183LYS00.119-0.08225.0530.0040.0040.0000.0000.0000.000
155A183LYS10.8201.05823.198-0.023-0.0230.0000.0000.0000.000
156A184ILE00.100-0.10025.5830.0010.0010.0000.0000.0000.000
157A184ILE0-0.0330.14028.7810.0010.0010.0000.0000.0000.000
158A185ALA00.069-0.12125.9610.0000.0000.0000.0000.0000.000
159A185ALA0-0.0940.10125.0860.0030.0030.0000.0000.0000.000
160A186LYS0-0.015-0.14727.238-0.006-0.0060.0000.0000.0000.000
161A186LYS10.9331.11529.548-0.034-0.0340.0000.0000.0000.000
162A187ASN00.103-0.07227.830-0.004-0.0040.0000.0000.0000.000
163A187ASN0-0.0490.08324.507-0.010-0.0100.0000.0000.0000.000
164A188GLY0-0.025-0.12628.9970.0020.0020.0000.0000.0000.000
165A189ASN00.1010.02724.449-0.011-0.0110.0000.0000.0000.000
166A189ASN0-0.1060.04622.566-0.001-0.0010.0000.0000.0000.000
167A190VAL00.073-0.11424.8770.0070.0070.0000.0000.0000.000
168A190VAL0-0.0610.12925.7050.0000.0000.0000.0000.0000.000
169A191TYR00.105-0.05421.711-0.002-0.0020.0000.0000.0000.000
170A191TYR0-0.1470.05619.2000.0130.0130.0000.0000.0000.000
171A192LEU00.140-0.09122.1180.0090.0090.0000.0000.0000.000
172A192LEU0-0.0610.10223.1180.0000.0000.0000.0000.0000.000
173A193ASP00.105-0.06820.385-0.015-0.0150.0000.0000.0000.000
174A193ASP-1-0.866-0.80018.459-0.133-0.1330.0000.0000.0000.000
175A194ILE00.086-0.09320.3010.0230.0230.0000.0000.0000.000
176A194ILE0-0.0110.15521.211-0.001-0.0010.0000.0000.0000.000
177A195LYS00.070-0.09419.517-0.028-0.0280.0000.0000.0000.000
178A195LYS10.8331.05517.8400.2840.2840.0000.0000.0000.000
179A196ARG00.089-0.10817.1420.0450.0450.0000.0000.0000.000
180A196ARG10.6980.95712.5050.7660.7660.0000.0000.0000.000
181A197SER0-0.016-0.06918.618-0.015-0.0150.0000.0000.0000.000
182A197SER0-0.0120.05022.1080.0090.0090.0000.0000.0000.000
183A198ALA00.184-0.06320.9830.0000.0000.0000.0000.0000.000
184A198ALA0-0.0820.11022.1320.0010.0010.0000.0000.0000.000
185A199GLU00.004-0.14222.3380.0090.0090.0000.0000.0000.000
186A199GLU-1-0.866-0.78924.586-0.281-0.2810.0000.0000.0000.000
187A200ASN00.104-0.08523.2800.0220.0220.0000.0000.0000.000
188A200ASN0-0.1380.06622.3810.0180.0180.0000.0000.0000.000
189A201ILE00.136-0.07420.5540.0310.0310.0000.0000.0000.000
190A201ILE0-0.1030.09417.637-0.002-0.0020.0000.0000.0000.000
191A202GLU00.102-0.11221.7090.0120.0120.0000.0000.0000.000
192A202GLU-1-0.916-0.82625.031-0.217-0.2170.0000.0000.0000.000
193A203ALA00.059-0.10824.8860.0170.0170.0000.0000.0000.000
194A203ALA0-0.0540.12126.5520.0010.0010.0000.0000.0000.000
195A204VAL00.074-0.10723.6120.0230.0230.0000.0000.0000.000
196A204VAL0-0.0960.09122.1730.0000.0000.0000.0000.0000.000
197A205ILE00.055-0.11823.9730.0230.0230.0000.0000.0000.000
198A205ILE0-0.0530.11420.745-0.001-0.0010.0000.0000.0000.000
199A206THR00.080-0.05924.7870.0160.0160.0000.0000.0000.000
200A206THR0-0.0550.06027.8060.0020.0020.0000.0000.0000.000
201A207VAL00.098-0.09828.1420.0120.0120.0000.0000.0000.000
202A207VAL0-0.0890.11728.1430.0010.0010.0000.0000.0000.000
203A208ALA00.085-0.11026.0540.0160.0160.0000.0000.0000.000
204A208ALA0-0.0740.08825.545-0.002-0.0020.0000.0000.0000.000
205A209SER0-0.029-0.14327.5660.0140.0140.0000.0000.0000.000
206A209SER0-0.0350.06827.444-0.003-0.0030.0000.0000.0000.000
207A210GLU00.010-0.08829.3790.0070.0070.0000.0000.0000.000
208A210GLU-1-0.916-0.78931.875-0.090-0.0900.0000.0000.0000.000
209A211LEU0-0.177-0.17031.3180.0160.0160.0000.0000.0000.000
210A211LEU0-0.0010.01029.0080.0020.0020.0000.0000.0000.000