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: QLYRY

Calculation Name: 1VK0-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FNG3

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2383291.309702
FMO2-HF: Nuclear repulsion 2303377.627872
FMO2-HF: Total energy -79913.68183
FMO2-MP2: Total energy -80151.872129


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-93.008-91.73-0.009-0.483-0.7860.001
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.908
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].
3A3SER00.0210.0033.8392.0343.312-0.009-0.483-0.7860.001
4A4PHE00.0400.0056.1791.1351.1350.0000.0000.0000.000
5A5ASP-1-0.877-0.9267.636-32.807-32.8070.0000.0000.0000.000
6A6GLY00.0300.0309.6781.2881.2880.0000.0000.0000.000
7A7PRO0-0.0030.01413.252-0.165-0.1650.0000.0000.0000.000
8A8LYS10.9400.98014.66318.43618.4360.0000.0000.0000.000
9A9PHE00.0510.02317.0800.5570.5570.0000.0000.0000.000
10A10LYS10.8880.95720.76011.73411.7340.0000.0000.0000.000
11A11MET00.0210.02921.9820.4760.4760.0000.0000.0000.000
12A12THR00.002-0.01125.2750.0470.0470.0000.0000.0000.000
13A13ASP-1-0.804-0.86525.676-12.046-12.0460.0000.0000.0000.000
14A14GLY0-0.070-0.03726.1410.0560.0560.0000.0000.0000.000
15A15SER0-0.074-0.06621.739-0.606-0.6060.0000.0000.0000.000
16A16TYR0-0.022-0.04018.1540.3660.3660.0000.0000.0000.000
17A17VAL00.0570.05118.118-0.658-0.6580.0000.0000.0000.000
18A18GLN0-0.075-0.04910.5910.6440.6440.0000.0000.0000.000
19A19THR0-0.004-0.02114.450-0.158-0.1580.0000.0000.0000.000
20A20LYS10.8490.9188.59731.59231.5920.0000.0000.0000.000
21A21THR00.0420.02313.2271.0941.0940.0000.0000.0000.000
22A22ILE0-0.048-0.02110.942-1.547-1.5470.0000.0000.0000.000
23A23ASP-1-0.808-0.85514.584-15.794-15.7940.0000.0000.0000.000
24A24VAL0-0.043-0.03215.515-1.189-1.1890.0000.0000.0000.000
25A25GLY00.0480.02616.6771.1431.1430.0000.0000.0000.000
26A26SER0-0.004-0.01817.890-0.669-0.6690.0000.0000.0000.000
27A27SER0-0.024-0.01215.7530.1160.1160.0000.0000.0000.000
28A28THR0-0.0110.01312.289-0.965-0.9650.0000.0000.0000.000
29A29ASP-1-0.789-0.8749.361-27.613-27.6130.0000.0000.0000.000
30A30ILE00.0370.0129.950-2.341-2.3410.0000.0000.0000.000
31A31SER0-0.026-0.01710.625-0.710-0.7100.0000.0000.0000.000
32A32PRO0-0.020-0.0075.631-0.123-0.1230.0000.0000.0000.000
33A33TYR00.0160.0016.669-2.177-2.1770.0000.0000.0000.000
34A34LEU00.0310.0189.6951.3881.3880.0000.0000.0000.000
35A35SER0-0.056-0.0559.6252.3942.3940.0000.0000.0000.000
36A36LEU00.0020.0126.1790.8420.8420.0000.0000.0000.000
37A37ILE00.0200.02310.5211.4411.4410.0000.0000.0000.000
38A38ARG10.8930.94513.22921.89821.8980.0000.0000.0000.000
39A39GLU-1-0.945-0.97010.074-26.374-26.3740.0000.0000.0000.000
40A40ASP-1-0.746-0.82713.640-17.706-17.7060.0000.0000.0000.000
41A41SER00.022-0.01215.1941.2861.2860.0000.0000.0000.000
42A42ILE0-0.091-0.05417.4781.0211.0210.0000.0000.0000.000
43A43LEU0-0.073-0.02814.5600.7860.7860.0000.0000.0000.000
44A44ASN0-0.048-0.03915.7001.1121.1120.0000.0000.0000.000
45A45GLY00.0000.01019.4900.5720.5720.0000.0000.0000.000
46A46ASN00.0410.02121.1800.0990.0990.0000.0000.0000.000
47A47ARG10.8490.91921.78614.28714.2870.0000.0000.0000.000
48A48ALA00.0590.04622.8250.2870.2870.0000.0000.0000.000
49A49VAL0-0.052-0.01819.254-0.953-0.9530.0000.0000.0000.000
50A50ILE00.0080.02221.7520.5370.5370.0000.0000.0000.000
51A51PHE0-0.044-0.04121.997-0.893-0.8930.0000.0000.0000.000
52A52ASP-1-0.787-0.87823.921-11.209-11.2090.0000.0000.0000.000
53A53VAL0-0.027-0.01424.327-0.786-0.7860.0000.0000.0000.000
54A54TYR0-0.046-0.03223.6870.1400.1400.0000.0000.0000.000
55A55TRP0-0.011-0.03227.311-0.372-0.3720.0000.0000.0000.000
56A56ASP-1-0.897-0.94129.988-10.158-10.1580.0000.0000.0000.000
57A57VAL0-0.0070.00831.7200.0270.0270.0000.0000.0000.000
58A58GLY00.0410.02835.1160.1810.1810.0000.0000.0000.000
59A59PHE00.013-0.01736.3030.1700.1700.0000.0000.0000.000
60A60PRO0-0.018-0.00537.4750.2290.2290.0000.0000.0000.000
61A61GLU-1-0.743-0.84839.481-7.789-7.7890.0000.0000.0000.000
62A62THR0-0.073-0.05241.1560.2800.2800.0000.0000.0000.000
63A63GLU-1-0.806-0.85642.358-7.016-7.0160.0000.0000.0000.000
64A64THR0-0.061-0.04644.8200.0410.0410.0000.0000.0000.000
65A65LYS10.7940.87642.5987.3597.3590.0000.0000.0000.000
66A66THR00.0160.00840.3290.1340.1340.0000.0000.0000.000
67A67LYS10.8660.93541.2847.0417.0410.0000.0000.0000.000
68A68THR00.0520.04037.900-0.080-0.0800.0000.0000.0000.000
69A69SER0-0.023-0.01836.740-0.259-0.2590.0000.0000.0000.000
70A70GLY0-0.060-0.02636.019-0.170-0.1700.0000.0000.0000.000
71A71TRP0-0.020-0.01133.604-0.312-0.3120.0000.0000.0000.000
72A72SER0-0.028-0.00329.739-0.252-0.2520.0000.0000.0000.000
73A73LEU00.0210.00124.393-0.106-0.1060.0000.0000.0000.000
74A74SER0-0.026-0.00325.908-0.487-0.4870.0000.0000.0000.000
75A75SER0-0.021-0.03321.802-0.698-0.6980.0000.0000.0000.000
76A76VAL00.0020.01419.9410.5160.5160.0000.0000.0000.000
77A77LYS10.8530.94020.26912.13212.1320.0000.0000.0000.000
78A78LEU0-0.038-0.02216.9690.3770.3770.0000.0000.0000.000
79A79SER00.012-0.02318.182-0.697-0.6970.0000.0000.0000.000
80A80THR0-0.042-0.04416.7730.3400.3400.0000.0000.0000.000
81A81ARG10.8500.90619.33512.66612.6660.0000.0000.0000.000
82A82ASN0-0.020-0.02715.8500.9140.9140.0000.0000.0000.000
83A83LEU0-0.032-0.00412.150-0.978-0.9780.0000.0000.0000.000
84A84CYS0-0.0160.00815.6471.4551.4550.0000.0000.0000.000
85A85LEU0-0.056-0.01912.570-1.180-1.1800.0000.0000.0000.000
86A86PHE00.0460.01415.7511.2071.2070.0000.0000.0000.000
87A87LEU0-0.023-0.01614.170-1.278-1.2780.0000.0000.0000.000
88A88ARG10.8850.89617.72516.88616.8860.0000.0000.0000.000
89A89LEU0-0.010-0.00419.367-0.892-0.8920.0000.0000.0000.000
90A90PRO0-0.0160.01020.3970.4960.4960.0000.0000.0000.000
91A91LYS10.9000.92923.28811.04011.0400.0000.0000.0000.000
92A92PRO0-0.046-0.01225.5800.2550.2550.0000.0000.0000.000
93A93PHE00.0500.01423.274-0.588-0.5880.0000.0000.0000.000
94A94HIS00.0360.00920.8660.0190.0190.0000.0000.0000.000
95A95ASP-1-0.832-0.93120.616-13.591-13.5910.0000.0000.0000.000
96A96ASN0-0.045-0.03315.4850.8640.8640.0000.0000.0000.000
97A97LEU00.0460.02216.624-0.837-0.8370.0000.0000.0000.000
98A98LYS10.8490.92819.03713.49613.4960.0000.0000.0000.000
99A99ASP-1-0.837-0.90415.086-18.926-18.9260.0000.0000.0000.000
100A100LEU00.0230.01817.254-0.150-0.1500.0000.0000.0000.000
101A101TYR0-0.033-0.02818.7830.2220.2220.0000.0000.0000.000
102A102ARG10.8210.87717.01716.98116.9810.0000.0000.0000.000
103A103PHE0-0.040-0.01116.1810.1490.1490.0000.0000.0000.000
104A104PHE00.1000.04019.2870.2370.2370.0000.0000.0000.000
105A105ALA00.0140.02122.6210.6170.6170.0000.0000.0000.000
106A106SER0-0.0140.00120.8130.6330.6330.0000.0000.0000.000
107A107LYS10.9760.97522.99110.94310.9430.0000.0000.0000.000
108A108PHE0-0.081-0.03519.1760.2050.2050.0000.0000.0000.000
109A109VAL00.0450.03420.054-0.211-0.2110.0000.0000.0000.000
110A110THR00.0130.02123.4210.4790.4790.0000.0000.0000.000
111A111PHE0-0.030-0.01520.825-0.412-0.4120.0000.0000.0000.000
112A112VAL00.0150.00925.5950.5500.5500.0000.0000.0000.000
113A113GLY00.0540.02726.620-0.494-0.4940.0000.0000.0000.000
114A114VAL0-0.012-0.01929.0400.3510.3510.0000.0000.0000.000
115A115GLN0-0.053-0.04632.109-0.047-0.0470.0000.0000.0000.000
116A116ILE0-0.0020.01329.4680.0160.0160.0000.0000.0000.000
117A117GLU-1-0.981-0.98632.641-8.286-8.2860.0000.0000.0000.000
118A118GLU-1-0.855-0.94135.387-8.305-8.3050.0000.0000.0000.000
119A119ASP-1-0.824-0.90330.214-10.362-10.3620.0000.0000.0000.000
120A120LEU0-0.050-0.03929.804-0.293-0.2930.0000.0000.0000.000
121A121ASP-1-0.812-0.87632.114-8.767-8.7670.0000.0000.0000.000
122A122LEU00.0400.01732.969-0.056-0.0560.0000.0000.0000.000
123A123LEU0-0.046-0.02826.705-0.252-0.2520.0000.0000.0000.000
124A124ARG10.7810.88330.0539.0249.0240.0000.0000.0000.000
125A125GLU-1-0.920-0.96832.249-8.371-8.3710.0000.0000.0000.000
126A126ASN0-0.052-0.04432.1520.2450.2450.0000.0000.0000.000
127A127HIS0-0.0040.01027.244-0.021-0.0210.0000.0000.0000.000
128A128GLY00.0200.04028.436-0.346-0.3460.0000.0000.0000.000
129A129LEU0-0.083-0.04023.359-0.253-0.2530.0000.0000.0000.000
130A130VAL0-0.016-0.01927.2900.2970.2970.0000.0000.0000.000
131A131ILE00.0290.01925.314-0.377-0.3770.0000.0000.0000.000
132A132ARG10.7730.86725.71212.03412.0340.0000.0000.0000.000
133A133ASN0-0.057-0.02626.9670.7430.7430.0000.0000.0000.000
134A134ALA00.0200.01227.393-0.494-0.4940.0000.0000.0000.000
135A135ILE00.0230.01729.4640.3720.3720.0000.0000.0000.000
136A136ASN00.0370.01931.095-0.422-0.4220.0000.0000.0000.000
137A137VAL00.0240.00030.9460.3190.3190.0000.0000.0000.000
138A138GLY00.0620.03133.5430.1480.1480.0000.0000.0000.000
139A139LYS10.8760.93236.5768.3338.3330.0000.0000.0000.000
140A140LEU00.0300.01533.7240.1630.1630.0000.0000.0000.000
141A141ALA00.0350.01436.2020.1340.1340.0000.0000.0000.000
142A142ALA0-0.049-0.01737.9380.1910.1910.0000.0000.0000.000
143A143GLU-1-0.964-0.99340.709-7.584-7.5840.0000.0000.0000.000
144A144ALA0-0.0030.00538.7860.1790.1790.0000.0000.0000.000
145A145ARG10.7840.87537.5338.4448.4440.0000.0000.0000.000
146A146GLY00.0100.02642.3700.1810.1810.0000.0000.0000.000
147A147THR0-0.103-0.05343.1740.2050.2050.0000.0000.0000.000
148A148LEU00.039-0.00843.597-0.144-0.1440.0000.0000.0000.000
149A149VAL0-0.002-0.00743.649-0.083-0.0830.0000.0000.0000.000
150A150LEU00.000-0.00739.256-0.104-0.1040.0000.0000.0000.000
151A151GLU-1-0.833-0.89539.025-7.994-7.9940.0000.0000.0000.000
152A152PHE0-0.050-0.00939.579-0.142-0.1420.0000.0000.0000.000
153A153LEU0-0.049-0.00138.0770.0580.0580.0000.0000.0000.000
154A154GLY00.0710.03835.719-0.182-0.1820.0000.0000.0000.000
155A155THR0-0.004-0.00929.3630.2190.2190.0000.0000.0000.000
156A156ARG10.8530.89032.7588.6648.6640.0000.0000.0000.000
157A157GLU-1-0.799-0.87833.935-7.987-7.9870.0000.0000.0000.000
158A158LEU00.0120.00533.3830.1710.1710.0000.0000.0000.000
159A159ALA00.0390.01331.9020.0510.0510.0000.0000.0000.000
160A160HIS0-0.110-0.06033.8110.1710.1710.0000.0000.0000.000
161A161ARG10.8460.90936.9237.6887.6880.0000.0000.0000.000
162A162VAL00.0150.01934.6060.1920.1920.0000.0000.0000.000
163A163LEU0-0.009-0.01331.1320.0790.0790.0000.0000.0000.000
164A164TRP0-0.095-0.03435.5230.1780.1780.0000.0000.0000.000
165A165SER0-0.0040.00832.1080.1660.1660.0000.0000.0000.000
166A166ASP-1-0.899-0.95833.537-8.957-8.9570.0000.0000.0000.000
167A167LEU00.0210.00332.105-0.371-0.3710.0000.0000.0000.000
168A168GLY00.0250.01833.709-0.060-0.0600.0000.0000.0000.000
169A169GLN0-0.050-0.04827.5330.4960.4960.0000.0000.0000.000
170A170LEU0-0.0190.00228.956-0.137-0.1370.0000.0000.0000.000
171A171ASP-1-0.775-0.85631.308-8.834-8.8340.0000.0000.0000.000
172A172SER0-0.065-0.02733.1670.1990.1990.0000.0000.0000.000
173A173ILE0-0.028-0.01127.8390.0860.0860.0000.0000.0000.000
174A174GLU0-0.062-0.07531.3930.1880.1880.0000.0000.0000.000
175A175ALA0-0.027-0.01033.8650.1670.1670.0000.0000.0000.000
176A176LYS10.7970.90031.86410.02510.0250.0000.0000.0000.000
177A177TRP00.0890.04827.971-0.163-0.1630.0000.0000.0000.000
178A178GLU-1-0.900-0.96632.770-8.877-8.8770.0000.0000.0000.000
179A179LYS10.8360.91134.4798.1658.1650.0000.0000.0000.000
180A180ALA0-0.0260.01929.990-0.092-0.0920.0000.0000.0000.000
181A181GLY00.0210.01628.064-0.093-0.0930.0000.0000.0000.000
182A182PRO00.000-0.02023.743-0.144-0.1440.0000.0000.0000.000
183A183GLU-1-0.923-0.96621.008-15.282-15.2820.0000.0000.0000.000
184A184GLU-1-0.759-0.87523.400-10.708-10.7080.0000.0000.0000.000
185A185GLN0-0.035-0.01626.293-0.320-0.3200.0000.0000.0000.000
186A186LEU0-0.026-0.00818.618-0.110-0.1100.0000.0000.0000.000
187A187GLU-1-0.851-0.91122.524-12.428-12.4280.0000.0000.0000.000
188A188ALA00.0060.00023.547-0.011-0.0110.0000.0000.0000.000
189A189ALA00.0170.01623.7400.0920.0920.0000.0000.0000.000
190A190ALA00.021-0.00920.653-0.153-0.1530.0000.0000.0000.000
191A191ILE0-0.021-0.01022.406-0.021-0.0210.0000.0000.0000.000
192A192GLU-1-0.802-0.90425.315-10.478-10.4780.0000.0000.0000.000
193A193GLY0-0.0080.00422.9990.1660.1660.0000.0000.0000.000
194A194TRP00.0280.00622.7190.3190.3190.0000.0000.0000.000
195A195LEU0-0.0250.00124.2010.3280.3280.0000.0000.0000.000
196A196ILE00.0130.00027.0710.3210.3210.0000.0000.0000.000
197A197VAL0-0.039-0.01222.3950.0610.0610.0000.0000.0000.000
198A198ASN00.005-0.00325.6990.3820.3820.0000.0000.0000.000
199A199VAL0-0.024-0.00128.4850.3210.3210.0000.0000.0000.000
200A200TRP00.002-0.00826.9870.3560.3560.0000.0000.0000.000
201A201ASP-1-0.821-0.92125.843-12.140-12.1400.0000.0000.0000.000
202A202GLN0-0.029-0.00128.9940.3460.3460.0000.0000.0000.000
203A203LEU0-0.011-0.01432.7830.1750.1750.0000.0000.0000.000
204A204SER0-0.081-0.03830.4410.0580.0580.0000.0000.0000.000
205A205ASP-1-1.046-1.02031.273-10.024-10.0240.0000.0000.0000.000
206A206GLU-2-1.769-1.84434.347-16.527-16.5270.0000.0000.0000.000