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: LV9J9

Calculation Name: 3JVB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JVB

Chain ID: A

ChEMBL ID:

UniProt ID: O37157

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2344711.07238
FMO2-HF: Nuclear repulsion 2254270.941298
FMO2-HF: Total energy -90440.131082
FMO2-MP2: Total energy -90704.970531


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:10:GLY)


Summations of interaction energy for fragment #1(A:10: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.
-6.7310000000001-4.4151.965-2.271-2.009-0.021
Interaction energy analysis for fragmet #1(A:10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.905
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].
3A12THR00.008-0.0083.8431.2322.063-0.011-0.323-0.497-0.001
13A22ASN00.0530.0272.516-13.234-11.7901.979-1.927-1.496-0.020
14A23LEU00.1030.0514.976-2.232-2.193-0.001-0.004-0.0330.000
16A25GLY0-0.022-0.0184.129-0.389-0.350-0.001-0.014-0.0240.000
17A26VAL00.0020.0045.0842.6062.569-0.001-0.0030.0410.000
4A13TYR-1-0.824-0.8895.361-38.946-38.9460.0000.0000.0000.000
5A14VAL0-0.014-0.0249.4400.5270.5270.0000.0000.0000.000
6A15TYR00.0230.02011.5080.4710.4710.0000.0000.0000.000
7A16ASP-1-0.851-0.92715.984-15.256-15.2560.0000.0000.0000.000
8A17ASN0-0.032-0.01718.295-0.021-0.0210.0000.0000.0000.000
9A18ARG10.9450.98816.16616.67216.6720.0000.0000.0000.000
10A19TYR00.0320.00812.071-0.948-0.9480.0000.0000.0000.000
11A20TRP0-0.024-0.00210.0450.2800.2800.0000.0000.0000.000
12A21LYS10.9440.9645.78231.84431.8440.0000.0000.0000.000
15A24GLY00.0590.0317.0501.4651.4650.0000.0000.0000.000
18A27ILE00.0290.0058.1492.3512.3510.0000.0000.0000.000
19A28LYS10.9360.9805.91344.15844.1580.0000.0000.0000.000
20A29ASN00.011-0.0038.3230.2790.2790.0000.0000.0000.000
21A30ALA0-0.005-0.00210.6631.9841.9840.0000.0000.0000.000
22A31LYS10.9420.95613.06320.48420.4840.0000.0000.0000.000
23A32ARG10.8950.93611.82322.86222.8620.0000.0000.0000.000
24A33ARG10.9580.98014.68516.87116.8710.0000.0000.0000.000
25A34LYS10.9050.94416.91517.52017.5200.0000.0000.0000.000
26A35HIS00.0040.03317.3660.4710.4710.0000.0000.0000.000
27A36GLU-1-0.744-0.87316.574-18.345-18.3450.0000.0000.0000.000
28A37GLU-1-0.915-0.93520.142-11.834-11.8340.0000.0000.0000.000
29A38GLU-1-0.844-0.90922.589-11.244-11.2440.0000.0000.0000.000
30A39GLN0-0.041-0.03818.5610.5010.5010.0000.0000.0000.000
31A40GLU-1-0.898-0.93423.375-11.062-11.0620.0000.0000.0000.000
32A41LYS10.7160.82526.11812.30012.3000.0000.0000.0000.000
33A42VAL00.0000.00225.2170.3450.3450.0000.0000.0000.000
34A43GLU-1-0.935-0.95225.256-12.057-12.0570.0000.0000.0000.000
35A44ARG10.9380.96427.9639.5399.5390.0000.0000.0000.000
36A45GLU-1-0.971-0.97330.837-9.728-9.7280.0000.0000.0000.000
37A46PHE00.0200.00925.6330.1800.1800.0000.0000.0000.000
38A47ASP-1-0.765-0.87831.047-8.924-8.9240.0000.0000.0000.000
39A48SER0-0.134-0.08432.9370.4050.4050.0000.0000.0000.000
40A49LEU0-0.018-0.01632.6900.3090.3090.0000.0000.0000.000
41A50ASP-1-0.884-0.94631.249-9.996-9.9960.0000.0000.0000.000
42A51LYS10.7050.85934.7688.9588.9580.0000.0000.0000.000
43A52TYR0-0.081-0.03237.7050.3560.3560.0000.0000.0000.000
44A53LEU00.0170.00736.931-0.194-0.1940.0000.0000.0000.000
45A54VAL0-0.019-0.01135.5420.1840.1840.0000.0000.0000.000
46A55ALA0-0.0060.00137.905-0.064-0.0640.0000.0000.0000.000
47A56GLU-1-0.906-0.95834.561-9.441-9.4410.0000.0000.0000.000
48A57ASP-1-0.817-0.91436.732-8.045-8.0450.0000.0000.0000.000
49A58PRO00.0160.01537.939-0.163-0.1630.0000.0000.0000.000
50A59PHE0-0.039-0.02739.4340.0400.0400.0000.0000.0000.000
51A60CYS0-0.091-0.03933.991-0.188-0.1880.0000.0000.0000.000
52A61GLY00.0620.04934.350-0.287-0.2870.0000.0000.0000.000
53A62PRO0-0.025-0.02535.1730.1240.1240.0000.0000.0000.000
54A63GLY00.0240.01736.9850.2310.2310.0000.0000.0000.000
55A64LYS10.8570.91738.7957.4967.4960.0000.0000.0000.000
56A65ASN00.008-0.01238.3340.2380.2380.0000.0000.0000.000
57A66GLN0-0.042-0.04241.814-0.127-0.1270.0000.0000.0000.000
58A67LYS10.8520.92844.8727.1477.1470.0000.0000.0000.000
59A68LEU00.0590.04646.5770.0370.0370.0000.0000.0000.000
60A69THR0-0.027-0.02348.6860.0460.0460.0000.0000.0000.000
61A70LEU0-0.024-0.00651.0630.0930.0930.0000.0000.0000.000
62A71PHE00.0090.00254.7940.0860.0860.0000.0000.0000.000
63A72LYS10.8470.90650.5786.1996.1990.0000.0000.0000.000
64A73GLU-1-0.804-0.89656.305-5.279-5.2790.0000.0000.0000.000
65A74ILE0-0.014-0.01657.354-0.110-0.1100.0000.0000.0000.000
66A75ARG10.7680.86259.3025.2375.2370.0000.0000.0000.000
67A76ASN0-0.034-0.02060.000-0.090-0.0900.0000.0000.0000.000
68A77ILE0-0.037-0.01858.0870.1090.1090.0000.0000.0000.000
69A78LYS10.8620.92661.5664.9094.9090.0000.0000.0000.000
70A79PRO00.0630.04161.455-0.033-0.0330.0000.0000.0000.000
71A80ASP-1-0.810-0.88861.435-4.972-4.9720.0000.0000.0000.000
72A81THR0-0.095-0.05862.2490.0930.0930.0000.0000.0000.000
73A82MET0-0.0020.00157.289-0.103-0.1030.0000.0000.0000.000
74A83LYS10.8540.91560.7315.1225.1220.0000.0000.0000.000
75A84LEU00.0030.01660.605-0.112-0.1120.0000.0000.0000.000
76A85ILE0-0.040-0.01556.3710.0220.0220.0000.0000.0000.000
77A86VAL0-0.015-0.01258.499-0.028-0.0280.0000.0000.0000.000
78A87ASN00.0140.00060.9240.0180.0180.0000.0000.0000.000
79A88TRP0-0.0060.00956.8050.0620.0620.0000.0000.0000.000
80A89SER00.1240.06464.544-0.016-0.0160.0000.0000.0000.000
81A90GLY00.0880.02263.898-0.080-0.0800.0000.0000.0000.000
82A91LYS10.9040.95063.8804.6714.6710.0000.0000.0000.000
83A92GLU-1-0.813-0.87164.048-5.013-5.0130.0000.0000.0000.000
84A93PHE00.0140.00756.714-0.059-0.0590.0000.0000.0000.000
85A94LEU00.0120.02359.698-0.087-0.0870.0000.0000.0000.000
86A95ARG10.7390.84360.5855.0855.0850.0000.0000.0000.000
87A96GLU-1-0.809-0.87658.168-5.496-5.4960.0000.0000.0000.000
88A97THR00.005-0.01855.066-0.124-0.1240.0000.0000.0000.000
89A98TRP0-0.025-0.01555.956-0.064-0.0640.0000.0000.0000.000
90A99THR0-0.036-0.04257.236-0.030-0.0300.0000.0000.0000.000
91A100ARG10.8050.89354.1085.7355.7350.0000.0000.0000.000
92A101PHE00.0410.02549.339-0.061-0.0610.0000.0000.0000.000
93A102MET0-0.048-0.01152.678-0.133-0.1330.0000.0000.0000.000
94A103GLU-1-1.012-1.00854.620-5.998-5.9980.0000.0000.0000.000
95A104ASP-1-0.843-0.90948.751-6.776-6.7760.0000.0000.0000.000
96A105SER0-0.017-0.01949.507-0.179-0.1790.0000.0000.0000.000
97A106PHE0-0.075-0.01950.432-0.027-0.0270.0000.0000.0000.000
98A107PRO0-0.068-0.03250.4950.0090.0090.0000.0000.0000.000
99A108ILE00.0430.00549.629-0.134-0.1340.0000.0000.0000.000
100A109VAL0-0.061-0.02246.3020.0700.0700.0000.0000.0000.000
101A110ASN0-0.026-0.03143.9900.0410.0410.0000.0000.0000.000
102A111ASP-1-0.870-0.92547.150-6.509-6.5090.0000.0000.0000.000
103A112GLN0-0.042-0.04346.122-0.166-0.1660.0000.0000.0000.000
104A113GLU-1-0.845-0.89246.250-6.897-6.8970.0000.0000.0000.000
105A114VAL0-0.002-0.00746.455-0.165-0.1650.0000.0000.0000.000
106A115MET0-0.069-0.02740.8300.0120.0120.0000.0000.0000.000
107A116ASP-1-0.726-0.83846.550-6.653-6.6530.0000.0000.0000.000
108A117VAL0-0.044-0.02247.989-0.071-0.0710.0000.0000.0000.000
109A118PHE00.0420.01045.3420.0670.0670.0000.0000.0000.000
110A119LEU00.0130.01249.1030.0050.0050.0000.0000.0000.000
111A120VAL0-0.033-0.01846.423-0.052-0.0520.0000.0000.0000.000
112A121ILE00.0040.01149.5980.0930.0930.0000.0000.0000.000
113A122ASN0-0.017-0.02145.709-0.024-0.0240.0000.0000.0000.000
114A123MET0-0.0150.00649.0840.1910.1910.0000.0000.0000.000
115A124ARG10.9130.94347.2616.5386.5380.0000.0000.0000.000
116A125SER00.0510.02750.8730.1770.1770.0000.0000.0000.000
117A126THR0-0.063-0.06452.520-0.106-0.1060.0000.0000.0000.000
118A127LYS10.8470.93354.7925.5155.5150.0000.0000.0000.000
119A128PRO00.0380.02651.245-0.088-0.0880.0000.0000.0000.000
120A129ASN0-0.049-0.05150.5070.1050.1050.0000.0000.0000.000
121A130ARG10.8610.95451.7765.6865.6860.0000.0000.0000.000
122A131CYS0-0.053-0.03949.792-0.173-0.1730.0000.0000.0000.000
123A132PHE00.0140.01750.9520.0830.0830.0000.0000.0000.000
124A133ARG10.8550.91346.6936.6336.6330.0000.0000.0000.000
125A134PHE00.0170.00449.5020.1530.1530.0000.0000.0000.000
126A135LEU0-0.039-0.01351.516-0.100-0.1000.0000.0000.0000.000
127A136ALA00.014-0.00152.8780.0800.0800.0000.0000.0000.000
128A137GLN00.0380.01554.842-0.055-0.0550.0000.0000.0000.000
129A138HIS00.0410.03453.9850.0110.0110.0000.0000.0000.000
130A139ALA00.0030.00957.8560.0370.0370.0000.0000.0000.000
131A140LEU00.0070.00454.791-0.018-0.0180.0000.0000.0000.000
132A141ARG10.9210.95559.4975.1715.1710.0000.0000.0000.000
133A142CYS0-0.0390.01063.2750.0170.0170.0000.0000.0000.000
134A143ASP-1-0.843-0.93066.224-4.526-4.5260.0000.0000.0000.000
135A144PRO0-0.034-0.03669.300-0.035-0.0350.0000.0000.0000.000
136A145ASP-1-0.916-0.94670.914-4.359-4.3590.0000.0000.0000.000
137A146TYR0-0.089-0.03967.1160.0310.0310.0000.0000.0000.000
138A147VAL0-0.0090.00069.414-0.081-0.0810.0000.0000.0000.000
139A148PRO0-0.0320.00665.7660.0530.0530.0000.0000.0000.000
140A149HIS00.0100.00167.6830.0590.0590.0000.0000.0000.000
141A150GLU-1-0.774-0.87466.607-4.993-4.9930.0000.0000.0000.000
142A151ILE0-0.074-0.04665.472-0.086-0.0860.0000.0000.0000.000
143A152ILE0-0.0030.01761.7540.0850.0850.0000.0000.0000.000
144A153ARG10.8390.88664.6274.8294.8290.0000.0000.0000.000
145A154ILE0-0.0270.00358.510-0.040-0.0400.0000.0000.0000.000
146A155VAL0-0.009-0.01261.1320.0480.0480.0000.0000.0000.000
147A156GLU-1-0.950-0.97057.890-5.578-5.5780.0000.0000.0000.000
148A157PRO0-0.0320.00355.277-0.032-0.0320.0000.0000.0000.000
149A158SER00.0290.01250.713-0.129-0.1290.0000.0000.0000.000
150A159TYR00.031-0.00249.5090.0400.0400.0000.0000.0000.000
151A160VAL0-0.0020.00847.680-0.154-0.1540.0000.0000.0000.000
152A161GLY00.0160.02144.296-0.057-0.0570.0000.0000.0000.000
153A162ASN0-0.032-0.02141.8300.0220.0220.0000.0000.0000.000
154A163ASN0-0.022-0.03344.4490.0260.0260.0000.0000.0000.000
155A164GLU-1-0.796-0.87744.190-7.208-7.2080.0000.0000.0000.000
156A165TYR0-0.047-0.02746.784-0.104-0.1040.0000.0000.0000.000
157A166ARG10.8380.91140.3547.7227.7220.0000.0000.0000.000
158A167ILE00.000-0.00248.063-0.039-0.0390.0000.0000.0000.000
159A168SER0-0.072-0.05848.3730.0580.0580.0000.0000.0000.000
160A169LEU0-0.059-0.04850.0960.1520.1520.0000.0000.0000.000
161A170ALA-1-0.947-0.94151.349-5.991-5.9910.0000.0000.0000.000
162A186THR00.0600.01357.332-0.029-0.0290.0000.0000.0000.000
163A187ASN0-0.031-0.01759.258-0.065-0.0650.0000.0000.0000.000
164A188SER00.020-0.00961.3180.0460.0460.0000.0000.0000.000
165A189PHE00.0520.03062.8460.0080.0080.0000.0000.0000.000
166A190GLU-1-0.938-0.98363.722-4.600-4.6000.0000.0000.0000.000
167A191HIS00.0130.01263.697-0.043-0.0430.0000.0000.0000.000
168A192PHE00.0200.02157.856-0.012-0.0120.0000.0000.0000.000
169A193ILE00.0120.01063.0980.0060.0060.0000.0000.0000.000
170A194ASN0-0.023-0.01163.279-0.008-0.0080.0000.0000.0000.000
171A195LYS10.8830.93060.6375.2085.2080.0000.0000.0000.000
172A196VAL00.0220.01563.9210.0180.0180.0000.0000.0000.000
173A197ILE0-0.0260.00265.3050.0210.0210.0000.0000.0000.000
174A198TRP00.0540.01562.7640.0720.0720.0000.0000.0000.000
175A199GLU-1-0.803-0.91359.282-5.476-5.4760.0000.0000.0000.000
176A200ASN0-0.066-0.04063.701-0.011-0.0110.0000.0000.0000.000
177A201PHE0-0.032-0.00765.9240.0490.0490.0000.0000.0000.000
178A202TYR0-0.047-0.03560.2860.0310.0310.0000.0000.0000.000
179A203LYS0-0.020-0.00260.697-0.043-0.0430.0000.0000.0000.000
180A204PRO0-0.0040.01956.6770.0480.0480.0000.0000.0000.000
181A205ILE00.0130.01459.1540.0260.0260.0000.0000.0000.000
182A206VAL00.005-0.01654.991-0.063-0.0630.0000.0000.0000.000
183A207TYR0-0.028-0.02458.3570.0680.0680.0000.0000.0000.000
184A208ILE00.011-0.01153.523-0.129-0.1290.0000.0000.0000.000
185A209GLY00.0370.01556.5080.1380.1380.0000.0000.0000.000
186A210THR0-0.046-0.01454.789-0.106-0.1060.0000.0000.0000.000
187A211ASP-1-0.822-0.90452.552-6.051-6.0510.0000.0000.0000.000
188A212SER0-0.033-0.04055.9800.0400.0400.0000.0000.0000.000
189A213ALA0-0.009-0.00957.4620.0860.0860.0000.0000.0000.000
190A214GLU-1-0.919-0.96458.407-5.358-5.3580.0000.0000.0000.000
191A215ASP-1-0.852-0.92761.052-5.058-5.0580.0000.0000.0000.000
192A216GLU-1-0.746-0.83756.888-5.738-5.7380.0000.0000.0000.000
193A217GLU-1-0.830-0.87658.766-5.316-5.3160.0000.0000.0000.000
194A218VAL0-0.018-0.00454.124-0.126-0.1260.0000.0000.0000.000
195A219LEU0-0.022-0.01152.5210.0950.0950.0000.0000.0000.000
196A220PHE00.033-0.00653.320-0.132-0.1320.0000.0000.0000.000
197A221GLU-1-0.859-0.91548.156-6.661-6.6610.0000.0000.0000.000
198A222VAL00.0230.03551.675-0.097-0.0970.0000.0000.0000.000
199A223SER0-0.016-0.02449.245-0.027-0.0270.0000.0000.0000.000
200A224LEU00.0210.02750.9620.0150.0150.0000.0000.0000.000
201A225VAL0-0.029-0.02043.997-0.055-0.0550.0000.0000.0000.000
202A226PHE00.0490.02947.2660.0280.0280.0000.0000.0000.000
203A227LYS10.7920.90339.0577.9867.9860.0000.0000.0000.000
204A228ILE0-0.0070.00543.3980.1290.1290.0000.0000.0000.000
205A229LYS10.8380.89641.3907.0867.0860.0000.0000.0000.000
206A230GLU-1-0.833-0.90541.665-7.368-7.3680.0000.0000.0000.000
207A231PHE0-0.043-0.02941.252-0.243-0.2430.0000.0000.0000.000
208A232ALA00.0100.01140.3740.1460.1460.0000.0000.0000.000
209A233PRO0-0.023-0.00340.667-0.179-0.1790.0000.0000.0000.000
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