FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VVRN1

Calculation Name: 4J2C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J2C

Chain ID: A

ChEMBL ID:

UniProt ID: O43752

Base Structure: X-ray

Registration Date: 2025-07-11

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
Remarks
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 -805382.148564
FMO2-HF: Nuclear repulsion 761469.499404
FMO2-HF: Total energy -43912.64916
FMO2-MP2: Total energy -44040.154322


3D Structure Molmil
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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.2590.7610-0.466-0.5530.001
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.025
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].
3A2ALA0-0.0690.0974.6550.4710.635-0.001-0.067-0.0960.000
4A3MET00.067-0.1103.840-0.8170.0390.001-0.399-0.4570.001
5A3MET0-0.1000.0895.7910.0410.0410.0000.0000.0000.000
6A4GLU00.069-0.1176.5170.1860.1860.0000.0000.0000.000
7A4GLU-1-0.977-0.83510.126-0.090-0.0900.0000.0000.0000.000
8A5ASP00.092-0.11610.088-0.130-0.1300.0000.0000.0000.000
9A5ASP-1-0.877-0.76413.045-0.309-0.3090.0000.0000.0000.000
10A6PRO00.000-0.10012.6910.0780.0780.0000.0000.0000.000
11A7PHE00.1570.01815.3000.0400.0400.0000.0000.0000.000
12A7PHE0-0.0940.09517.7340.0070.0070.0000.0000.0000.000
13A8PHE00.080-0.08818.0290.0180.0180.0000.0000.0000.000
14A8PHE0-0.0850.08615.1760.0080.0080.0000.0000.0000.000
15A9VAL00.031-0.11618.3720.0270.0270.0000.0000.0000.000
16A9VAL0-0.0620.10916.7140.0000.0000.0000.0000.0000.000
17A10VAL00.108-0.08419.4810.0230.0230.0000.0000.0000.000
18A10VAL0-0.0440.12218.831-0.003-0.0030.0000.0000.0000.000
19A11LYS00.097-0.08021.3710.0120.0120.0000.0000.0000.000
20A11LYS10.8251.06022.6910.0800.0800.0000.0000.0000.000
21A12GLY0-0.008-0.11522.9730.0120.0120.0000.0000.0000.000
22A13GLU00.064-0.01323.7190.0150.0150.0000.0000.0000.000
23A13GLU-1-0.881-0.77522.896-0.076-0.0760.0000.0000.0000.000
24A14VAL00.140-0.07925.3910.0090.0090.0000.0000.0000.000
25A14VAL0-0.0820.12325.4910.0000.0000.0000.0000.0000.000
26A15GLN00.103-0.07427.4290.0050.0050.0000.0000.0000.000
27A15GLN0-0.0990.05927.853-0.002-0.0020.0000.0000.0000.000
28A16LYS00.082-0.08128.4260.0070.0070.0000.0000.0000.000
29A16LYS10.7030.97726.5070.0640.0640.0000.0000.0000.000
30A17ALA00.117-0.09629.5480.0090.0090.0000.0000.0000.000
31A17ALA0-0.0360.12129.780-0.002-0.0020.0000.0000.0000.000
32A18VAL00.064-0.11931.3640.0040.0040.0000.0000.0000.000
33A18VAL0-0.1000.10331.5820.0000.0000.0000.0000.0000.000
34A19ASN00.159-0.05633.1780.0030.0030.0000.0000.0000.000
35A19ASN0-0.1490.04533.081-0.001-0.0010.0000.0000.0000.000
36A20THR0-0.020-0.09634.1860.0050.0050.0000.0000.0000.000
37A20THR0-0.0650.06133.3510.0010.0010.0000.0000.0000.000
38A21ALA00.102-0.08435.4560.0040.0040.0000.0000.0000.000
39A21ALA0-0.0690.09835.756-0.001-0.0010.0000.0000.0000.000
40A22GLN00.103-0.10037.3190.0020.0020.0000.0000.0000.000
41A22GLN0-0.0960.09337.5450.0010.0010.0000.0000.0000.000
42A23GLY0-0.009-0.10438.9450.0020.0020.0000.0000.0000.000
43A24LEU00.069-0.00639.9680.0030.0030.0000.0000.0000.000
44A24LEU0-0.1020.10438.7410.0000.0000.0000.0000.0000.000
45A25PHE00.178-0.07941.3970.0020.0020.0000.0000.0000.000
46A25PHE0-0.0900.09641.731-0.001-0.0010.0000.0000.0000.000
47A26GLN00.095-0.08343.2530.0010.0010.0000.0000.0000.000
48A26GLN0-0.1540.06044.2490.0000.0000.0000.0000.0000.000
49A27ARG00.087-0.09944.8320.0010.0010.0000.0000.0000.000
50A27ARG10.7140.97444.9910.0210.0210.0000.0000.0000.000
51A28TRP00.091-0.08245.5860.0020.0020.0000.0000.0000.000
52A28TRP0-0.0790.07545.235-0.001-0.0010.0000.0000.0000.000
53A29THR00.031-0.08447.1620.0010.0010.0000.0000.0000.000
54A29THR0-0.0570.05146.9540.0000.0000.0000.0000.0000.000
55A30GLU00.031-0.14049.2000.0010.0010.0000.0000.0000.000
56A30GLU-1-0.876-0.78548.592-0.020-0.0200.0000.0000.0000.000
57A31LEU00.056-0.08550.2690.0020.0020.0000.0000.0000.000
58A31LEU0-0.1510.08148.3590.0000.0000.0000.0000.0000.000
59A32LEU00.054-0.10951.2820.0010.0010.0000.0000.0000.000
60A32LEU0-0.1080.10449.8610.0000.0000.0000.0000.0000.000
61A33GLN00.075-0.08153.0150.0000.0000.0000.0000.0000.000
62A33GLN0-0.1090.07453.7460.0000.0000.0000.0000.0000.000
63A34ASP00.001-0.13355.2730.0010.0010.0000.0000.0000.000
64A34ASP-1-0.850-0.76456.067-0.016-0.0160.0000.0000.0000.000
65A35PRO00.027-0.11356.6740.0000.0000.0000.0000.0000.000
66A36SER0-0.0120.00958.4050.0000.0000.0000.0000.0000.000
67A36SER0-0.0640.02360.1040.0000.0000.0000.0000.0000.000
68A37THR0-0.034-0.09456.0660.0010.0010.0000.0000.0000.000
69A37THR0-0.0650.05154.3680.0000.0000.0000.0000.0000.000
70A38ALA00.114-0.09553.8160.0000.0000.0000.0000.0000.000
71A38ALA0-0.0970.12453.6140.0000.0000.0000.0000.0000.000
72A39THR00.046-0.07654.7310.0000.0000.0000.0000.0000.000
73A39THR0-0.0780.04652.9200.0000.0000.0000.0000.0000.000
74A40ARG00.159-0.04852.855-0.001-0.0010.0000.0000.0000.000
75A40ARG10.7160.95552.1930.0250.0250.0000.0000.0000.000
76A41GLU00.094-0.10350.527-0.002-0.0020.0000.0000.0000.000
77A41GLU-1-0.943-0.80250.465-0.023-0.0230.0000.0000.0000.000
78A42GLU00.091-0.13548.451-0.002-0.0020.0000.0000.0000.000
79A42GLU-1-0.895-0.77548.247-0.021-0.0210.0000.0000.0000.000
80A43ILE00.063-0.08847.589-0.002-0.0020.0000.0000.0000.000
81A43ILE0-0.0330.12449.5590.0000.0000.0000.0000.0000.000
82A44ASP00.095-0.07747.336-0.002-0.0020.0000.0000.0000.000
83A44ASP-1-0.946-0.82847.999-0.029-0.0290.0000.0000.0000.000
84A45TRP00.107-0.06844.474-0.003-0.0030.0000.0000.0000.000
85A45TRP0-0.0660.09740.6720.0010.0010.0000.0000.0000.000
86A46THR0-0.026-0.12843.093-0.003-0.0030.0000.0000.0000.000
87A46THR0-0.0390.07843.8670.0000.0000.0000.0000.0000.000
88A47THR00.051-0.07842.668-0.002-0.0020.0000.0000.0000.000
89A47THR0-0.0690.04944.5770.0000.0000.0000.0000.0000.000
90A48ASN00.070-0.05941.779-0.003-0.0030.0000.0000.0000.000
91A48ASN0-0.1810.02241.616-0.002-0.0020.0000.0000.0000.000
92A49GLU00.129-0.11738.515-0.005-0.0050.0000.0000.0000.000
93A49GLU-1-0.915-0.79837.299-0.047-0.0470.0000.0000.0000.000
94A50LEU00.109-0.09737.626-0.004-0.0040.0000.0000.0000.000
95A50LEU0-0.1070.13038.7360.0000.0000.0000.0000.0000.000
96A51ARG00.086-0.09837.779-0.003-0.0030.0000.0000.0000.000
97A51ARG10.8511.05239.3250.0480.0480.0000.0000.0000.000
98A52ASN00.054-0.08935.653-0.005-0.0050.0000.0000.0000.000
99A52ASN0-0.1280.05634.409-0.005-0.0050.0000.0000.0000.000
100A53ASN00.093-0.07033.289-0.006-0.0060.0000.0000.0000.000
101A53ASN0-0.1420.04233.9340.0000.0000.0000.0000.0000.000
102A54LEU00.092-0.08832.803-0.006-0.0060.0000.0000.0000.000
103A54LEU0-0.0910.08235.6440.0000.0000.0000.0000.0000.000
104A55ARG00.127-0.05833.554-0.004-0.0040.0000.0000.0000.000
105A55ARG10.7701.01232.5700.0670.0670.0000.0000.0000.000
106A56SER00.033-0.07829.599-0.006-0.0060.0000.0000.0000.000
107A56SER0-0.0840.03227.9370.0010.0010.0000.0000.0000.000
108A57ILE00.099-0.07329.091-0.010-0.0100.0000.0000.0000.000
109A57ILE0-0.1360.07930.3980.0010.0010.0000.0000.0000.000
110A58GLU00.104-0.09029.598-0.007-0.0070.0000.0000.0000.000
111A58GLU-1-0.899-0.78932.646-0.073-0.0730.0000.0000.0000.000
112A59TRP00.092-0.06028.438-0.003-0.0030.0000.0000.0000.000
113A59TRP0-0.1160.05423.8480.0070.0070.0000.0000.0000.000
114A60ASP00.041-0.10725.068-0.015-0.0150.0000.0000.0000.000
115A60ASP-1-0.906-0.83625.102-0.121-0.1210.0000.0000.0000.000
116A61LEU00.024-0.11124.972-0.018-0.0180.0000.0000.0000.000
117A61LEU0-0.0990.08227.3150.0020.0020.0000.0000.0000.000
118A62GLU00.079-0.10926.8750.0040.0040.0000.0000.0000.000
119A62GLU-1-0.985-0.84727.120-0.120-0.1200.0000.0000.0000.000
120A63ASP00.142-0.09222.644-0.006-0.0060.0000.0000.0000.000
121A63ASP-1-0.958-0.81721.619-0.203-0.2030.0000.0000.0000.000
122A64LEU00.058-0.12621.584-0.030-0.0300.0000.0000.0000.000
123A64LEU0-0.0710.10420.9200.0020.0020.0000.0000.0000.000
124A65ASP00.094-0.08922.327-0.015-0.0150.0000.0000.0000.000
125A65ASP-1-0.841-0.76826.208-0.129-0.1290.0000.0000.0000.000
126A66GLU00.074-0.14222.6580.0030.0030.0000.0000.0000.000
127A66GLU-1-0.973-0.80121.950-0.204-0.2040.0000.0000.0000.000
128A67THR0-0.034-0.11418.831-0.017-0.0170.0000.0000.0000.000
129A67THR0-0.0880.02717.936-0.007-0.0070.0000.0000.0000.000
130A68ILE00.096-0.08819.162-0.031-0.0310.0000.0000.0000.000
131A68ILE0-0.1030.10022.1010.0040.0040.0000.0000.0000.000
132A69SER00.026-0.10021.600-0.004-0.0040.0000.0000.0000.000
133A69SER0-0.0490.07823.0310.0080.0080.0000.0000.0000.000
134A70ILE00.070-0.07918.4080.0160.0160.0000.0000.0000.000
135A70ILE0-0.1030.08116.459-0.014-0.0140.0000.0000.0000.000
136A71VAL00.003-0.14017.436-0.036-0.0360.0000.0000.0000.000
137A71VAL0-0.0840.09616.4740.0000.0000.0000.0000.0000.000
138A72GLU00.078-0.12918.430-0.008-0.0080.0000.0000.0000.000
139A72GLU-1-0.877-0.76522.641-0.135-0.1350.0000.0000.0000.000
140A73ALA00.091-0.10621.0850.0210.0210.0000.0000.0000.000
141A73ALA0-0.0790.11920.245-0.001-0.0010.0000.0000.0000.000
142A74ASN0-0.016-0.10817.0390.0090.0090.0000.0000.0000.000
143A74ASN0-0.1320.05315.198-0.003-0.0030.0000.0000.0000.000
144A75PRO00.100-0.06416.325-0.045-0.0450.0000.0000.0000.000
145A76ARG00.0690.01415.6910.0000.0000.0000.0000.0000.000
146A76ARG10.8431.05413.9860.1650.1650.0000.0000.0000.000
147A77LYS00.091-0.08911.9760.0150.0150.0000.0000.0000.000
148A77LYS10.8351.0539.9830.8400.8400.0000.0000.0000.000
149A78PHE00.021-0.10311.298-0.125-0.1250.0000.0000.0000.000
150A78PHE0-0.0600.09612.523-0.031-0.0310.0000.0000.0000.000
151A79ASN00.141-0.03513.5930.0170.0170.0000.0000.0000.000
152A79ASN0-0.1790.02213.5310.0090.0090.0000.0000.0000.000
153A80LEU00.056-0.12315.2290.0380.0380.0000.0000.0000.000
154A80LEU0-0.0310.12515.657-0.001-0.0010.0000.0000.0000.000
155A81ASP00.098-0.06617.7420.0050.0050.0000.0000.0000.000
156A81ASP-1-0.852-0.80221.083-0.050-0.0500.0000.0000.0000.000
157A82ALA00.127-0.08921.052-0.017-0.0170.0000.0000.0000.000
158A82ALA0-0.0770.11124.3910.0020.0020.0000.0000.0000.000
159A83THR0-0.066-0.09924.121-0.007-0.0070.0000.0000.0000.000
160A83THR0-0.0230.04825.5360.0030.0030.0000.0000.0000.000
161A84GLU00.149-0.06822.0640.0020.0020.0000.0000.0000.000
162A84GLU-1-0.918-0.78719.458-0.139-0.1390.0000.0000.0000.000
163A85LEU00.133-0.09122.436-0.002-0.0020.0000.0000.0000.000
164A85LEU0-0.0980.10820.830-0.002-0.0020.0000.0000.0000.000
165A86SER00.041-0.10223.057-0.007-0.0070.0000.0000.0000.000
166A86SER0-0.0670.05126.9400.0030.0030.0000.0000.0000.000
167A87ILE00.065-0.08926.1580.0010.0010.0000.0000.0000.000
168A87ILE0-0.1250.08325.5950.0020.0020.0000.0000.0000.000
169A88ARG00.032-0.11823.4410.0090.0090.0000.0000.0000.000
170A88ARG10.6540.91416.8950.2050.2050.0000.0000.0000.000
171A89LYS00.157-0.06724.817-0.001-0.0010.0000.0000.0000.000
172A89LYS10.7450.99025.7240.1270.1270.0000.0000.0000.000
173A90ALA00.109-0.07327.5140.0010.0010.0000.0000.0000.000
174A90ALA0-0.0770.09929.7350.0020.0020.0000.0000.0000.000
175A91PHE00.048-0.05927.6830.0080.0080.0000.0000.0000.000
176A91PHE0-0.0580.07225.6060.0010.0010.0000.0000.0000.000
177A92ILE00.115-0.07327.8760.0080.0080.0000.0000.0000.000
178A92ILE0-0.0640.12524.5160.0000.0000.0000.0000.0000.000
179A93THR00.045-0.09428.8850.0020.0020.0000.0000.0000.000
180A93THR0-0.0890.04230.8900.0000.0000.0000.0000.0000.000
181A94SER00.028-0.07532.2690.0030.0030.0000.0000.0000.000
182A94SER0-0.0850.04032.1450.0010.0010.0000.0000.0000.000
183A95THR0-0.024-0.10631.3860.0060.0060.0000.0000.0000.000
184A95THR0-0.0270.06030.5040.0010.0010.0000.0000.0000.000
185A96ARG00.085-0.07832.5110.0030.0030.0000.0000.0000.000
186A96ARG10.7100.96028.7670.1120.1120.0000.0000.0000.000
187A97GLN00.134-0.06633.8980.0010.0010.0000.0000.0000.000
188A97GLN0-0.1360.05837.415-0.003-0.0030.0000.0000.0000.000
189A98VAL00.108-0.08136.3330.0030.0030.0000.0000.0000.000
190A98VAL0-0.1240.07435.6530.0000.0000.0000.0000.0000.000
191A99VAL00.077-0.11335.6450.0050.0050.0000.0000.0000.000
192A99VAL0-0.0900.10433.6030.0000.0000.0000.0000.0000.000
193A100ARG00.099-0.08936.9060.0020.0020.0000.0000.0000.000
194A100ARG10.7661.02838.5370.0550.0550.0000.0000.0000.000
195A101ASP00.066-0.10539.5070.0010.0010.0000.0000.0000.000
196A101ASP-1-0.932-0.82540.866-0.045-0.0450.0000.0000.0000.000
197A102MET00.091-0.08340.7220.0030.0030.0000.0000.0000.000
198A102MET0-0.0930.09137.0810.0010.0010.0000.0000.0000.000
199A103LYS00.085-0.08840.8640.0030.0030.0000.0000.0000.000
200A103LYS10.7340.97237.2830.0670.0670.0000.0000.0000.000
201A104ASP00.140-0.05842.1160.0010.0010.0000.0000.0000.000
202A104ASP-1-0.964-0.83443.812-0.049-0.0490.0000.0000.0000.000
203A105GLN00.044-0.12645.0080.0020.0020.0000.0000.0000.000
204A105GLN0-0.0870.08545.5190.0000.0000.0000.0000.0000.000
205A106MET00.072-0.09445.1610.0030.0030.0000.0000.0000.000
206A106MET0-0.1310.07443.145-0.001-0.0010.0000.0000.0000.000
207A107SER0-0.043-0.10345.9960.0020.0020.0000.0000.0000.000
208A107SER0-0.0680.05444.480-0.001-0.0010.0000.0000.0000.000
209A108THR0-0.194-0.18547.1580.0010.0010.0000.0000.0000.000
210A108THR00.0570.05049.9340.0010.0010.0000.0000.0000.000