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: QK6RY

Calculation Name: 1VCV-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZXK7

Base Structure: X-ray

Registration Date: 2025-10-03

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 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2736170.408687
FMO2-HF: Nuclear repulsion 2651398.071757
FMO2-HF: Total energy -84772.33693
FMO2-MP2: Total energy -85024.097388


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:MET)


Summations of interaction energy for fragment #1(A:1: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.
-98.544-87.23330.255-16.357-25.209-0.171
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.787 / q_NPA : 0.893
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].
3A3HIS00.0160.0083.51513.20414.974-0.009-0.752-1.0090.000
4A4LEU0-0.0270.0022.5314.7676.3350.689-0.585-1.672-0.002
5A5VAL0-0.025-0.0074.2376.2356.450-0.001-0.027-0.1860.000
195A196ARG11.0061.0012.60432.31532.9431.377-0.455-1.550-0.001
196A197GLU-1-0.863-0.9352.510-33.285-32.1621.173-0.736-1.561-0.017
197A198GLN00.0010.0065.267-0.325-0.264-0.001-0.003-0.0570.000
198A199ALA00.0120.0082.8020.669-0.5463.614-0.590-1.8080.003
199A200LYS10.8420.8952.45429.68531.4312.791-1.297-3.240-0.007
200A201ALA00.0320.0173.6731.4190.6690.0461.013-0.309-0.001
202A203VAL0-0.017-0.0112.927-0.3130.5720.237-0.224-0.898-0.001
203A204ASP-1-0.839-0.8986.191-28.881-28.866-0.001-0.003-0.0100.000
209A210GLU-1-0.837-0.9261.875-140.949-139.83618.188-10.742-8.560-0.131
216A217LEU00.005-0.0043.0201.2742.0440.271-0.174-0.8670.000
224A225LEU0-0.113-0.0692.122-1.443-0.5481.578-0.494-1.979-0.001
225A226LEU-1-0.931-0.9472.935-51.515-49.0280.303-1.288-1.503-0.013
6A6ASP-1-0.693-0.8146.735-22.597-22.5970.0000.0000.0000.000
7A7TYR0-0.003-0.00710.3251.0221.0220.0000.0000.0000.000
8A8ALA0-0.021-0.01611.2161.5561.5560.0000.0000.0000.000
9A9LEU0-0.011-0.00214.0690.3080.3080.0000.0000.0000.000
10A10LEU00.0070.00616.7860.4980.4980.0000.0000.0000.000
11A11LYS10.8880.96419.55513.98713.9870.0000.0000.0000.000
12A12PRO00.0150.00222.261-0.035-0.0350.0000.0000.0000.000
13A13TYR00.0250.00422.7480.2350.2350.0000.0000.0000.000
14A14LEU0-0.0410.01020.655-0.007-0.0070.0000.0000.0000.000
15A15THR00.020-0.00924.2390.3370.3370.0000.0000.0000.000
16A16VAL00.0470.00924.598-0.501-0.5010.0000.0000.0000.000
17A17ASP-1-0.875-0.93324.930-11.385-11.3850.0000.0000.0000.000
18A18GLU-1-0.842-0.89821.483-13.056-13.0560.0000.0000.0000.000
19A19ALA0-0.0140.00520.477-0.890-0.8900.0000.0000.0000.000
20A20VAL00.0260.00820.498-0.788-0.7880.0000.0000.0000.000
21A21ALA0-0.021-0.00720.524-0.523-0.5230.0000.0000.0000.000
22A22GLY00.006-0.00616.647-0.858-0.8580.0000.0000.0000.000
23A23ALA0-0.004-0.01016.000-1.232-1.2320.0000.0000.0000.000
24A24ARG10.9210.95617.32113.36213.3620.0000.0000.0000.000
25A25LYS10.9030.94012.61120.37120.3710.0000.0000.0000.000
26A26ALA0-0.007-0.00412.581-1.935-1.9350.0000.0000.0000.000
27A27GLU-1-0.738-0.86912.407-21.862-21.8620.0000.0000.0000.000
28A28GLU-1-0.990-0.98413.331-20.690-20.6900.0000.0000.0000.000
29A29LEU00.0080.0059.045-1.001-1.0010.0000.0000.0000.000
30A30GLY0-0.034-0.0058.337-4.321-4.3210.0000.0000.0000.000
31A31VAL0-0.057-0.0267.900-3.742-3.7420.0000.0000.0000.000
32A32ALA0-0.0190.0008.2092.1712.1710.0000.0000.0000.000
33A33ALA0-0.025-0.0219.8402.9812.9810.0000.0000.0000.000
34A34TYR0-0.022-0.01411.901-1.470-1.4700.0000.0000.0000.000
35A35CYS0-0.098-0.04114.5111.3621.3620.0000.0000.0000.000
36A36VAL00.0640.02516.2500.1410.1410.0000.0000.0000.000
37A37ASN00.035-0.00619.6210.1900.1900.0000.0000.0000.000
38A38PRO00.019-0.00222.9900.0700.0700.0000.0000.0000.000
39A39ILE0-0.0050.00725.4040.0880.0880.0000.0000.0000.000
40A40TYR0-0.025-0.04523.3300.3130.3130.0000.0000.0000.000
41A41ALA00.0210.01923.430-0.321-0.3210.0000.0000.0000.000
42A42PRO00.002-0.01024.466-0.232-0.2320.0000.0000.0000.000
43A43VAL00.0060.00725.3470.0240.0240.0000.0000.0000.000
44A44VAL00.0160.00619.976-0.242-0.2420.0000.0000.0000.000
45A45ARG10.8160.90020.05814.24414.2440.0000.0000.0000.000
46A46PRO0-0.021-0.01423.125-0.346-0.3460.0000.0000.0000.000
47A47LEU0-0.057-0.01820.9390.0400.0400.0000.0000.0000.000
48A48LEU0-0.076-0.01117.010-0.749-0.7490.0000.0000.0000.000
49A49ARG10.8770.93017.76017.67317.6730.0000.0000.0000.000
50A50LYS10.9150.95910.78925.56125.5610.0000.0000.0000.000
51A51VAL0-0.034-0.00911.944-0.476-0.4760.0000.0000.0000.000
52A52LYS10.9220.95313.95321.98421.9840.0000.0000.0000.000
53A53LEU0-0.0090.00016.051-0.511-0.5110.0000.0000.0000.000
54A55VAL00.0200.01017.8290.3860.3860.0000.0000.0000.000
55A56VAL0-0.0200.00219.205-0.169-0.1690.0000.0000.0000.000
56A57ALA00.022-0.00321.5370.5530.5530.0000.0000.0000.000
57A58ASP-1-0.784-0.89024.810-10.363-10.3630.0000.0000.0000.000
58A59PHE00.0260.03819.675-0.190-0.1900.0000.0000.0000.000
59A60PRO0-0.016-0.01522.9720.2520.2520.0000.0000.0000.000
60A61PHE00.025-0.02124.405-0.115-0.1150.0000.0000.0000.000
61A62GLY00.0030.02327.1900.0870.0870.0000.0000.0000.000
62A63ALA0-0.029-0.02828.0070.2280.2280.0000.0000.0000.000
63A64LEU0-0.024-0.00230.7010.3460.3460.0000.0000.0000.000
64A65PRO00.0390.00633.296-0.065-0.0650.0000.0000.0000.000
65A66THR00.031-0.00633.232-0.038-0.0380.0000.0000.0000.000
66A67ALA00.003-0.00134.004-0.166-0.1660.0000.0000.0000.000
67A68SER0-0.017-0.01434.5280.0520.0520.0000.0000.0000.000
68A69ARG10.6940.81627.08410.31610.3160.0000.0000.0000.000
69A70ILE00.0260.00830.157-0.306-0.3060.0000.0000.0000.000
70A71ALA00.0240.01531.653-0.154-0.1540.0000.0000.0000.000
71A72LEU0-0.060-0.02227.919-0.069-0.0690.0000.0000.0000.000
72A73VAL00.019-0.00125.922-0.249-0.2490.0000.0000.0000.000
73A74SER00.0260.02127.770-0.315-0.3150.0000.0000.0000.000
74A75ARG10.9580.97430.0519.0499.0490.0000.0000.0000.000
75A76LEU0-0.050-0.02724.864-0.172-0.1720.0000.0000.0000.000
76A77ALA00.0060.01525.665-0.475-0.4750.0000.0000.0000.000
77A78GLU-1-0.893-0.93126.744-9.932-9.9320.0000.0000.0000.000
78A79VAL0-0.039-0.02525.953-0.155-0.1550.0000.0000.0000.000
79A80ALA0-0.012-0.00821.829-0.486-0.4860.0000.0000.0000.000
80A81ASP-1-0.831-0.89718.570-15.743-15.7430.0000.0000.0000.000
81A82GLU-1-0.790-0.87314.711-21.566-21.5660.0000.0000.0000.000
82A83ILE00.0060.00319.0930.2280.2280.0000.0000.0000.000
83A84ASP-1-0.731-0.85316.048-18.537-18.5370.0000.0000.0000.000
84A85VAL00.0140.00619.3450.4330.4330.0000.0000.0000.000
85A86VAL0-0.0200.00722.233-0.359-0.3590.0000.0000.0000.000
86A87ALA00.0600.03723.7000.4780.4780.0000.0000.0000.000
87A88PRO00.0260.01625.5640.0850.0850.0000.0000.0000.000
88A89ILE00.0500.02024.9560.3010.3010.0000.0000.0000.000
89A90GLY00.0410.02128.7420.1740.1740.0000.0000.0000.000
90A91LEU0-0.0020.00532.2390.2370.2370.0000.0000.0000.000
91A92VAL0-0.009-0.00427.6360.1910.1910.0000.0000.0000.000
92A93LYS10.7910.87728.96310.02610.0260.0000.0000.0000.000
93A94SER0-0.051-0.02332.4060.3000.3000.0000.0000.0000.000
94A95ARG10.7910.87232.0939.2959.2950.0000.0000.0000.000
95A96ARG10.9300.98734.8447.8207.8200.0000.0000.0000.000
96A97TRP00.0550.01729.042-0.106-0.1060.0000.0000.0000.000
97A98ALA0-0.020-0.01433.997-0.117-0.1170.0000.0000.0000.000
98A99GLU-1-0.918-0.97335.900-7.934-7.9340.0000.0000.0000.000
99A100VAL00.0160.00629.465-0.122-0.1220.0000.0000.0000.000
100A101ARG10.9860.99330.8118.6598.6590.0000.0000.0000.000
101A102ARG10.9600.98832.0927.8927.8920.0000.0000.0000.000
102A103ASP-1-0.786-0.84229.941-10.028-10.0280.0000.0000.0000.000
103A104LEU00.0440.01025.792-0.149-0.1490.0000.0000.0000.000
104A105ILE00.0300.01828.358-0.270-0.2700.0000.0000.0000.000
105A106SER0-0.042-0.02730.5130.0240.0240.0000.0000.0000.000
106A107VAL0-0.065-0.04126.845-0.051-0.0510.0000.0000.0000.000
107A108VAL0-0.011-0.00324.387-0.292-0.2920.0000.0000.0000.000
108A109GLY00.0300.02326.710-0.180-0.1800.0000.0000.0000.000
109A110ALA0-0.051-0.03329.6870.0470.0470.0000.0000.0000.000
110A111ALA0-0.004-0.00224.8040.0130.0130.0000.0000.0000.000
111A112GLY00.0030.00426.231-0.341-0.3410.0000.0000.0000.000
112A113GLY0-0.010-0.00525.2710.0330.0330.0000.0000.0000.000
113A114ARG10.8110.92022.20112.50712.5070.0000.0000.0000.000
114A115VAL0-0.027-0.01116.0050.1370.1370.0000.0000.0000.000
115A116VAL00.0170.00819.423-0.177-0.1770.0000.0000.0000.000
116A117LYS10.7720.86413.58519.76219.7620.0000.0000.0000.000
117A118VAL00.0310.01818.2420.3850.3850.0000.0000.0000.000
118A119ILE0-0.055-0.03518.352-0.547-0.5470.0000.0000.0000.000
119A120THR00.023-0.00219.1570.8110.8110.0000.0000.0000.000
120A121GLU-1-0.773-0.85120.408-12.925-12.9250.0000.0000.0000.000
121A122GLU-1-0.750-0.85517.980-13.261-13.2610.0000.0000.0000.000
122A123PRO0-0.032-0.00219.6580.4520.4520.0000.0000.0000.000
123A124TYR00.0310.01822.3600.4460.4460.0000.0000.0000.000
124A125LEU0-0.0090.02623.0680.5130.5130.0000.0000.0000.000
125A126ARG10.9590.99025.5209.3689.3680.0000.0000.0000.000
126A127ASP-1-0.775-0.88725.349-11.672-11.6720.0000.0000.0000.000
127A128GLU-1-0.857-0.93327.361-9.529-9.5290.0000.0000.0000.000
128A129GLU-1-0.824-0.88327.831-9.701-9.7010.0000.0000.0000.000
129A130ARG10.7800.86621.95012.10512.1050.0000.0000.0000.000
130A131TYR00.0190.01022.173-0.467-0.4670.0000.0000.0000.000
131A132THR0-0.0060.00325.624-0.016-0.0160.0000.0000.0000.000
132A133LEU0-0.012-0.01124.3900.1200.1200.0000.0000.0000.000
133A134TYR0-0.057-0.08020.302-0.270-0.2700.0000.0000.0000.000
134A135ASP-1-0.774-0.84823.635-11.225-11.2250.0000.0000.0000.000
135A136ILE0-0.0100.00226.6690.0720.0720.0000.0000.0000.000
136A137ILE0-0.022-0.01521.149-0.001-0.0010.0000.0000.0000.000
137A138ALA0-0.0090.00123.722-0.297-0.2970.0000.0000.0000.000
138A139GLU-1-0.946-0.97424.718-9.515-9.5150.0000.0000.0000.000
139A140ALA0-0.063-0.03726.1990.2260.2260.0000.0000.0000.000
140A141GLY0-0.0060.00925.2480.0100.0100.0000.0000.0000.000
141A142ALA0-0.041-0.01221.239-0.242-0.2420.0000.0000.0000.000
142A143HIS00.0600.03617.539-0.267-0.2670.0000.0000.0000.000
143A144PHE0-0.037-0.02411.589-0.793-0.7930.0000.0000.0000.000
144A145ILE00.0180.03616.3950.9490.9490.0000.0000.0000.000
145A146LYS10.8210.91514.40216.17416.1740.0000.0000.0000.000
146A147SER00.0150.00214.2450.8460.8460.0000.0000.0000.000
147A148SER0-0.011-0.00815.9160.9910.9910.0000.0000.0000.000
148A149THR0-0.011-0.05816.986-0.830-0.8300.0000.0000.0000.000
149A150GLY0-0.031-0.01317.498-0.488-0.4880.0000.0000.0000.000
150A151PHE0-0.074-0.06218.0910.2120.2120.0000.0000.0000.000
151A152ALA00.0100.03021.4750.5000.5000.0000.0000.0000.000
152A153GLU-1-0.857-0.93323.367-9.651-9.6510.0000.0000.0000.000
153A154GLU-1-0.912-0.97824.090-10.637-10.6370.0000.0000.0000.000
154A155ALA00.0820.04625.5690.0750.0750.0000.0000.0000.000
155A156TYR0-0.049-0.03428.1440.1840.1840.0000.0000.0000.000
156A157ALA00.0240.00523.7920.0770.0770.0000.0000.0000.000
157A158ALA00.0150.01725.9200.0400.0400.0000.0000.0000.000
158A159ARG10.8660.92227.4999.1429.1420.0000.0000.0000.000
159A160GLN0-0.055-0.01227.1400.2440.2440.0000.0000.0000.000
160A161GLY0-0.0190.00727.0550.0160.0160.0000.0000.0000.000
161A162ASN0-0.086-0.05621.919-0.502-0.5020.0000.0000.0000.000
162A163PRO00.0280.02018.7960.2710.2710.0000.0000.0000.000
163A164VAL00.0370.00219.216-0.131-0.1310.0000.0000.0000.000
164A165HIS0-0.043-0.01914.945-0.966-0.9660.0000.0000.0000.000
165A166SER0-0.010-0.02411.8660.2820.2820.0000.0000.0000.000
166A167THR0-0.049-0.05012.827-0.279-0.2790.0000.0000.0000.000
167A168PRO00.0550.01810.296-0.265-0.2650.0000.0000.0000.000
168A169GLU-1-0.789-0.87412.109-16.099-16.0990.0000.0000.0000.000
169A170ARG10.8880.96115.52413.93813.9380.0000.0000.0000.000
170A171ALA00.026-0.01111.4040.1970.1970.0000.0000.0000.000
171A172ALA00.0260.00813.4400.1110.1110.0000.0000.0000.000
172A173ALA0-0.058-0.02215.0220.5920.5920.0000.0000.0000.000
173A174ILE0-0.005-0.00115.4420.4020.4020.0000.0000.0000.000
174A175ALA00.0240.01313.6320.3090.3090.0000.0000.0000.000
175A176ARG10.8900.97015.72914.54814.5480.0000.0000.0000.000
176A177TYR00.0560.01418.9780.3160.3160.0000.0000.0000.000
177A178ILE0-0.004-0.01116.4690.4170.4170.0000.0000.0000.000
178A179LYS10.8480.93115.33218.07518.0750.0000.0000.0000.000
179A180GLU-1-0.928-0.97419.972-12.582-12.5820.0000.0000.0000.000
180A181LYS10.8300.93623.11511.46511.4650.0000.0000.0000.000
181A182GLY00.0020.01422.9820.3010.3010.0000.0000.0000.000
182A183TYR0-0.070-0.06321.3930.0640.0640.0000.0000.0000.000
183A184ARG10.9140.94020.00013.68213.6820.0000.0000.0000.000
184A185LEU00.0280.02918.120-0.065-0.0650.0000.0000.0000.000
185A186GLY00.0270.01313.921-0.465-0.4650.0000.0000.0000.000
186A187VAL0-0.032-0.02011.6671.1961.1960.0000.0000.0000.000
187A188LYS10.7390.83810.55719.22819.2280.0000.0000.0000.000
188A189MET0-0.0060.0289.4352.1452.1450.0000.0000.0000.000
189A190ALA00.0280.00410.265-1.674-1.6740.0000.0000.0000.000
190A191GLY00.0590.05812.4251.0961.0960.0000.0000.0000.000
191A192GLY00.0490.01213.292-0.274-0.2740.0000.0000.0000.000
192A193ILE0-0.039-0.0096.8870.0100.0100.0000.0000.0000.000
193A194ARG10.9440.9789.00518.36518.3650.0000.0000.0000.000
194A195THR00.0210.0026.7180.4800.4800.0000.0000.0000.000
201A202ILE0-0.009-0.0126.3701.7141.7140.0000.0000.0000.000
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