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: VKNM1

Calculation Name: 1JOS-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 1JOS

Chain ID: A

ChEMBL ID:

UniProt ID: P45141

Base Structure: X-ray

Registration Date: 2025-07-08

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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -747227.245209
FMO2-HF: Nuclear repulsion 706736.89306
FMO2-HF: Total energy -40490.352149
FMO2-MP2: Total energy -40606.305493


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:7:ARG)


Summations of interaction energy for fragment #1(A:7:ARG)
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.
-1.2152.4540.082-1.68-2.074-0.006
Interaction energy analysis for fragmet #1(A:7:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.135 / q_NPA : 0.028
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].
4A8SER00.0260.1273.711-0.1820.3050.009-0.246-0.250-0.001
5A9ASP00.026-0.1063.112-0.6090.8690.044-0.678-0.8440.000
6A9ASP-1-0.946-0.8303.271-1.380-0.2170.030-0.633-0.561-0.005
7A10ARG00.096-0.0633.5290.3570.6030.005-0.076-0.1750.000
8A10ARG10.8181.0254.2820.6020.657-0.001-0.011-0.0430.000
9A11VAL00.051-0.0955.0200.5910.629-0.002-0.009-0.0270.000
10A11VAL0-0.0470.0905.074-0.116-0.089-0.001-0.005-0.0210.000
11A12ALA00.125-0.1046.7890.3860.3860.0000.0000.0000.000
12A12ALA0-0.0440.1268.0220.0060.0060.0000.0000.0000.000
13A13GLN00.155-0.0578.0610.1970.1970.0000.0000.0000.000
14A13GLN0-0.1080.0798.7490.0090.0090.0000.0000.0000.000
15A14GLU0-0.005-0.1409.2500.1920.1920.0000.0000.0000.000
16A14GLU-1-0.867-0.8039.000-0.653-0.6530.0000.0000.0000.000
17A15ILE00.119-0.06810.9010.1430.1430.0000.0000.0000.000
18A15ILE0-0.0670.08510.774-0.012-0.0120.0000.0000.0000.000
19A16GLN00.109-0.08812.5290.0830.0830.0000.0000.0000.000
20A16GLN0-0.1240.10813.2990.0470.0470.0000.0000.0000.000
21A17LYS00.023-0.11913.9460.0700.0700.0000.0000.0000.000
22A17LYS10.7560.96911.6450.4310.4310.0000.0000.0000.000
23A18GLU00.070-0.10615.3080.0740.0740.0000.0000.0000.000
24A18GLU-1-0.992-0.85715.318-0.416-0.4160.0000.0000.0000.000
25A19ILE00.044-0.09516.5370.0470.0470.0000.0000.0000.000
26A19ILE0-0.0680.09016.729-0.005-0.0050.0000.0000.0000.000
27A20ALA00.102-0.10118.3710.0300.0300.0000.0000.0000.000
28A20ALA0-0.0190.11619.1090.0050.0050.0000.0000.0000.000
29A21VAL00.042-0.11620.2920.0330.0330.0000.0000.0000.000
30A21VAL0-0.0910.10620.4950.0030.0030.0000.0000.0000.000
31A22ILE00.067-0.08921.3870.0350.0350.0000.0000.0000.000
32A22ILE0-0.0970.08219.3790.0010.0010.0000.0000.0000.000
33A23LEU00.051-0.11622.3920.0210.0210.0000.0000.0000.000
34A23LEU0-0.0470.12520.859-0.001-0.0010.0000.0000.0000.000
35A24GLN00.126-0.08424.1720.0170.0170.0000.0000.0000.000
36A24GLN0-0.1040.08025.2550.0010.0010.0000.0000.0000.000
37A25ARG00.032-0.14026.0830.0230.0230.0000.0000.0000.000
38A25ARG10.7511.00924.1550.2380.2380.0000.0000.0000.000
39A26GLU0-0.021-0.16526.7170.0190.0190.0000.0000.0000.000
40A26GLU-1-0.837-0.76525.832-0.221-0.2210.0000.0000.0000.000
41A27VAL00.043-0.08527.7790.0090.0090.0000.0000.0000.000
42A27VAL0-0.0560.12526.400-0.001-0.0010.0000.0000.0000.000
43A28LYS00.067-0.09529.1720.0030.0030.0000.0000.0000.000
44A28LYS10.7791.02330.4830.1560.1560.0000.0000.0000.000
45A29ASP00.108-0.11832.7830.0040.0040.0000.0000.0000.000
46A29ASP-1-0.878-0.78332.784-0.122-0.1220.0000.0000.0000.000
47A30PRO0-0.049-0.13034.2850.0000.0000.0000.0000.0000.000
48A31ARG00.040-0.02136.6510.0050.0050.0000.0000.0000.000
49A31ARG10.8451.03736.5070.0880.0880.0000.0000.0000.000
50A32ILE00.037-0.09432.2980.0070.0070.0000.0000.0000.000
51A32ILE0-0.0880.13129.910-0.001-0.0010.0000.0000.0000.000
52A33GLY00.012-0.11732.2710.0010.0010.0000.0000.0000.000
53A34MET00.1200.00329.613-0.009-0.0090.0000.0000.0000.000
54A34MET0-0.1040.12126.6330.0020.0020.0000.0000.0000.000
55A35VAL00.109-0.10326.2630.0120.0120.0000.0000.0000.000
56A35VAL0-0.1040.10324.194-0.003-0.0030.0000.0000.0000.000
57A36THR0-0.008-0.12323.972-0.015-0.0150.0000.0000.0000.000
58A36THR0-0.0220.09223.0430.0050.0050.0000.0000.0000.000
59A37VAL00.051-0.08319.4540.0090.0090.0000.0000.0000.000
60A37VAL0-0.1170.09218.323-0.006-0.0060.0000.0000.0000.000
61A38SER0-0.004-0.11819.6900.0010.0010.0000.0000.0000.000
62A38SER0-0.0490.04120.286-0.006-0.0060.0000.0000.0000.000
63A39ASP00.080-0.10915.6740.0230.0230.0000.0000.0000.000
64A39ASP-1-0.883-0.80113.825-0.322-0.3220.0000.0000.0000.000
65A40VAL0-0.007-0.13213.1840.0240.0240.0000.0000.0000.000
66A40VAL0-0.1120.08311.413-0.027-0.0270.0000.0000.0000.000
67A41GLU00.127-0.11310.230-0.047-0.0470.0000.0000.0000.000
68A41GLU-1-0.850-0.75611.098-0.327-0.3270.0000.0000.0000.000
69A42VAL00.052-0.1018.1710.1520.1520.0000.0000.0000.000
70A42VAL0-0.1400.1046.876-0.083-0.0830.0000.0000.0000.000
71A43SER00.087-0.0707.411-0.083-0.0830.0000.0000.0000.000
72A43SER0-0.0780.0379.3390.0040.0040.0000.0000.0000.000
73A44SER00.095-0.0564.569-0.703-0.708-0.002-0.0030.0090.000
74A44SER0-0.0440.0805.5540.1780.1780.0000.0000.0000.000
75A45ASP0-0.018-0.1354.608-0.636-0.632-0.002-0.0060.0030.000
76A45ASP-1-0.843-0.7818.797-0.825-0.8250.0000.0000.0000.000
77A46LEU0-0.005-0.1146.3200.1570.1570.0000.0000.0000.000
78A46LEU0-0.1140.0773.575-0.341-0.1650.002-0.013-0.1650.000
79A47SER00.093-0.0777.2990.0480.0480.0000.0000.0000.000
80A47SER0-0.0250.08211.1510.0610.0610.0000.0000.0000.000
81A48TYR00.022-0.10710.4250.1000.1000.0000.0000.0000.000
82A48TYR0-0.1050.08011.8290.0370.0370.0000.0000.0000.000
83A49ALA00.156-0.08010.758-0.150-0.1500.0000.0000.0000.000
84A49ALA0-0.0780.10811.893-0.014-0.0140.0000.0000.0000.000
85A50LYS0-0.006-0.11312.7380.0750.0750.0000.0000.0000.000
86A50LYS10.7140.95813.8060.3500.3500.0000.0000.0000.000
87A51ILE00.068-0.09314.704-0.048-0.0480.0000.0000.0000.000
88A51ILE0-0.0870.08515.026-0.010-0.0100.0000.0000.0000.000
89A52PHE00.160-0.06617.2180.0260.0260.0000.0000.0000.000
90A52PHE0-0.0970.10115.0630.0080.0080.0000.0000.0000.000
91A53VAL00.022-0.11319.144-0.011-0.0110.0000.0000.0000.000
92A53VAL0-0.0590.08620.996-0.003-0.0030.0000.0000.0000.000
93A54THR00.096-0.04922.3340.0100.0100.0000.0000.0000.000
94A54THR00.0120.09223.998-0.003-0.0030.0000.0000.0000.000
95A55PHE00.020-0.12025.669-0.014-0.0140.0000.0000.0000.000
96A55PHE0-0.0410.09026.429-0.003-0.0030.0000.0000.0000.000
97A56LEU00.159-0.02528.9830.0070.0070.0000.0000.0000.000
98A56LEU0-0.1490.05331.1850.0000.0000.0000.0000.0000.000
99A57PHE00.061-0.09531.5590.0080.0080.0000.0000.0000.000
100A57PHE0-0.1680.05435.0210.0020.0020.0000.0000.0000.000
101A58ASP00.069-0.12732.023-0.006-0.0060.0000.0000.0000.000
102A58ASP-1-0.944-0.81131.173-0.090-0.0900.0000.0000.0000.000
103A59HIS00.112-0.08233.3430.0010.0010.0000.0000.0000.000
104A59HIS0-0.0960.07337.604-0.001-0.0010.0000.0000.0000.000
105A60ASP00.116-0.07436.5970.0050.0050.0000.0000.0000.000
106A60ASP-1-0.969-0.84537.624-0.083-0.0830.0000.0000.0000.000
107A61GLU00.122-0.13234.826-0.008-0.0080.0000.0000.0000.000
108A61GLU-1-0.992-0.82834.254-0.082-0.0820.0000.0000.0000.000
109A62MET00.141-0.08234.757-0.007-0.0070.0000.0000.0000.000
110A62MET0-0.1140.09038.0230.0020.0020.0000.0000.0000.000
111A63ALA00.036-0.11435.807-0.006-0.0060.0000.0000.0000.000
112A63ALA0-0.0830.09336.0010.0010.0010.0000.0000.0000.000
113A64ILE00.113-0.09431.871-0.009-0.0090.0000.0000.0000.000
114A64ILE0-0.0750.11629.844-0.001-0.0010.0000.0000.0000.000
115A65GLU00.112-0.08930.914-0.015-0.0150.0000.0000.0000.000
116A65GLU-1-0.932-0.79331.128-0.134-0.1340.0000.0000.0000.000
117A66GLN00.085-0.10731.476-0.012-0.0120.0000.0000.0000.000
118A66GLN0-0.1300.08134.7710.0050.0050.0000.0000.0000.000
119A67GLY00.011-0.10030.853-0.008-0.0080.0000.0000.0000.000
120A68MET00.078-0.03327.327-0.016-0.0160.0000.0000.0000.000
121A68MET0-0.0820.13123.961-0.002-0.0020.0000.0000.0000.000
122A69LYS00.121-0.09927.395-0.020-0.0200.0000.0000.0000.000
123A69LYS10.7341.01330.3420.1480.1480.0000.0000.0000.000
124A70GLY0-0.082-0.12629.414-0.007-0.0070.0000.0000.0000.000
125A71LEU00.039-0.02025.637-0.006-0.0060.0000.0000.0000.000
126A71LEU0-0.0400.12024.258-0.003-0.0030.0000.0000.0000.000
127A72GLU00.083-0.11524.684-0.028-0.0280.0000.0000.0000.000
128A72GLU-1-0.947-0.80625.184-0.192-0.1920.0000.0000.0000.000
129A73LYS00.081-0.09925.744-0.015-0.0150.0000.0000.0000.000
130A73LYS10.8441.04929.9430.1600.1600.0000.0000.0000.000
131A74ALA00.035-0.12126.815-0.001-0.0010.0000.0000.0000.000
132A74ALA0-0.0510.12226.4990.0020.0020.0000.0000.0000.000
133A75SER00.001-0.11522.781-0.013-0.0130.0000.0000.0000.000
134A75SER0-0.0330.09921.828-0.011-0.0110.0000.0000.0000.000
135A76PRO00.003-0.11022.106-0.032-0.0320.0000.0000.0000.000
136A77TYR00.0990.02522.862-0.030-0.0300.0000.0000.0000.000
137A77TYR0-0.1060.06126.2200.0000.0000.0000.0000.0000.000
138A78ILE00.114-0.07422.032-0.006-0.0060.0000.0000.0000.000
139A78ILE0-0.0540.11919.885-0.002-0.0020.0000.0000.0000.000
140A79ARG00.120-0.09518.556-0.032-0.0320.0000.0000.0000.000
141A79ARG10.7020.96716.5780.5430.5430.0000.0000.0000.000
142A80SER0-0.014-0.09818.807-0.059-0.0590.0000.0000.0000.000
143A80SER0-0.0870.04422.8390.0170.0170.0000.0000.0000.000
144A81LEU00.032-0.12220.883-0.010-0.0100.0000.0000.0000.000
145A81LEU0-0.0580.11521.7770.0020.0020.0000.0000.0000.000
146A82LEU00.070-0.11016.8580.0190.0190.0000.0000.0000.000
147A82LEU0-0.0600.12415.304-0.016-0.0160.0000.0000.0000.000
148A83GLY00.005-0.10516.188-0.050-0.0500.0000.0000.0000.000
149A84LYS00.1010.03017.242-0.026-0.0260.0000.0000.0000.000
150A84LYS10.8241.04321.1940.2880.2880.0000.0000.0000.000
151A85ALA0-0.019-0.15618.4010.0200.0200.0000.0000.0000.000
152A85ALA0-0.0490.12817.8360.0020.0020.0000.0000.0000.000
153A86MET00.065-0.13513.7470.0540.0540.0000.0000.0000.000
154A86MET0-0.1060.11210.464-0.017-0.0170.0000.0000.0000.000
155A87ARG00.014-0.06813.671-0.073-0.0730.0000.0000.0000.000
156A87ARG10.8451.04115.4180.3850.3850.0000.0000.0000.000
157A88LEU00.095-0.13212.193-0.012-0.0120.0000.0000.0000.000
158A88LEU0-0.0250.1259.510-0.028-0.0280.0000.0000.0000.000
159A89ARG00.108-0.02912.3570.1000.1000.0000.0000.0000.000
160A89ARG10.8341.04212.7590.6560.6560.0000.0000.0000.000
161A90ILE00.045-0.12312.2300.1250.1250.0000.0000.0000.000
162A90ILE0-0.1020.09210.7310.0130.0130.0000.0000.0000.000
163A91VAL00.131-0.11511.834-0.224-0.2240.0000.0000.0000.000
164A91VAL0-0.0880.11914.8030.0050.0050.0000.0000.0000.000
165A92PRO0-0.025-0.07810.5100.1050.1050.0000.0000.0000.000
166A93GLU00.1210.02113.2130.0660.0660.0000.0000.0000.000
167A93GLU-1-0.887-0.81015.716-0.456-0.4560.0000.0000.0000.000
168A94ILE0-0.030-0.11514.866-0.081-0.0810.0000.0000.0000.000
169A94ILE0-0.0690.09615.421-0.001-0.0010.0000.0000.0000.000
170A95ARG00.133-0.04917.1120.0430.0430.0000.0000.0000.000
171A95ARG10.8441.04816.8280.3080.3080.0000.0000.0000.000
172A96PHE00.084-0.11818.472-0.039-0.0390.0000.0000.0000.000
173A96PHE0-0.0640.10520.964-0.004-0.0040.0000.0000.0000.000
174A97ILE00.077-0.10620.6030.0200.0200.0000.0000.0000.000
175A97ILE0-0.1140.08018.410-0.003-0.0030.0000.0000.0000.000
176A98TYR00.154-0.07221.765-0.015-0.0150.0000.0000.0000.000
177A98TYR0-0.0820.10225.872-0.002-0.0020.0000.0000.0000.000
178A99ASP00.081-0.12222.3130.0100.0100.0000.0000.0000.000
179A99ASP-1-0.890-0.72421.210-0.148-0.1480.0000.0000.0000.000
180A100GLN00.047-0.08723.1960.0030.0030.0000.0000.0000.000
181A100GLN0-0.1270.06026.6380.0040.0040.0000.0000.0000.000
182A101SER00.033-0.10423.6250.0150.0150.0000.0000.0000.000
183A101SER0-0.0540.03922.2930.0050.0050.0000.0000.0000.000
184A102LEU00.088-0.08224.952-0.006-0.0060.0000.0000.0000.000
185A102LEU0-0.1220.09127.8260.0020.0020.0000.0000.0000.000
186A103VAL00.044-0.12526.5370.0020.0020.0000.0000.0000.000
187A103VAL0-0.0640.11226.222-0.002-0.0020.0000.0000.0000.000
188A104GLU00.098-0.06728.5640.0000.0000.0000.0000.0000.000
189A104GLU-1-1.051-0.88330.370-0.025-0.0250.0000.0000.0000.000
190A105GLY00.019-0.09630.414-0.004-0.0040.0000.0000.0000.000
191A106MET0-0.084-0.04931.5060.0040.0040.0000.0000.0000.000
192A106MET00.0250.01635.207-0.001-0.0010.0000.0000.0000.000