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: 1VVVZ

Calculation Name: 3KV0-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q01494

Base Structure: X-ray

Registration Date: 2025-10-06

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2211443.110944
FMO2-HF: Nuclear repulsion 2134928.303559
FMO2-HF: Total energy -76514.807385
FMO2-MP2: Total energy -76738.888476


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:14:THR)


Summations of interaction energy for fragment #1(A:14:THR)
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.
-230.688-225.62542.436-24.455-23.046-0.199
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.746 / q_NPA : 0.829
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].
3A16LEU00.0080.0242.8396.4139.2540.335-1.325-1.8510.002
4A17GLU-1-0.807-0.8751.847-102.430-102.35317.584-9.122-8.539-0.054
5A18THR0-0.095-0.0544.0686.6497.0810.010-0.118-0.3240.000
158A172LEU0-0.048-0.0203.780-3.511-3.2460.001-0.088-0.1780.000
159A173GLY00.027-0.0052.374-26.236-23.6093.901-3.131-3.397-0.036
160A174ASP-1-0.921-0.9523.658-34.496-34.4240.010-0.051-0.032-0.001
161A175ASP-1-0.890-0.9364.776-29.343-29.364-0.001-0.0100.0320.000
162A176GLU-1-0.948-0.9834.995-26.865-26.770-0.001-0.005-0.0890.000
164A178LYS10.9370.9492.36560.30661.1361.122-0.410-1.5420.001
165A179VAL0-0.027-0.0052.994-3.851-3.0340.191-0.225-0.784-0.001
166A180GLN0-0.027-0.0264.1733.2993.3020.000-0.0110.0080.000
168A182GLU-1-0.792-0.8701.666-102.169-105.14419.284-9.959-6.350-0.110
6A19PHE0-0.053-0.0296.6735.0745.0740.0000.0000.0000.000
7A20LYS10.9600.9828.92521.85221.8520.0000.0000.0000.000
8A21LYS10.8890.96311.75419.91019.9100.0000.0000.0000.000
9A22SER00.0790.0508.528-0.425-0.4250.0000.0000.0000.000
10A23PHE00.014-0.02110.2422.0762.0760.0000.0000.0000.000
11A24VAL0-0.016-0.0109.8111.5471.5470.0000.0000.0000.000
12A25ASP-1-0.899-0.94110.973-22.970-22.9700.0000.0000.0000.000
13A26VAL0-0.040-0.02214.0300.8820.8820.0000.0000.0000.000
14A27PRO0-0.024-0.00617.0150.4170.4170.0000.0000.0000.000
15A28ILE0-0.008-0.01619.3850.3360.3360.0000.0000.0000.000
16A29ASP-1-0.813-0.90622.652-10.412-10.4120.0000.0000.0000.000
17A30ALA0-0.012-0.02525.8590.2650.2650.0000.0000.0000.000
18A31GLU-1-0.944-0.96827.439-9.329-9.3290.0000.0000.0000.000
19A32LYS10.8210.92429.8019.8719.8710.0000.0000.0000.000
20A33GLY00.0070.00830.510-0.014-0.0140.0000.0000.0000.000
21A34ASN0-0.060-0.04325.084-0.385-0.3850.0000.0000.0000.000
22A35ALA00.0330.03925.767-0.263-0.2630.0000.0000.0000.000
23A36ILE0-0.001-0.00121.118-0.339-0.3390.0000.0000.0000.000
24A37SER0-0.021-0.02721.3920.6650.6650.0000.0000.0000.000
25A38THR0-0.011-0.04421.686-0.602-0.6020.0000.0000.0000.000
26A39ALA00.0130.01021.908-0.299-0.2990.0000.0000.0000.000
27A40GLU-1-0.784-0.88517.069-15.088-15.0880.0000.0000.0000.000
28A41PHE00.0340.01517.039-0.882-0.8820.0000.0000.0000.000
29A42LEU0-0.029-0.01918.164-0.483-0.4830.0000.0000.0000.000
30A43GLU-1-0.908-0.95315.663-18.285-18.2850.0000.0000.0000.000
31A44ALA00.0070.02413.558-1.303-1.3030.0000.0000.0000.000
32A45ALA0-0.007-0.01213.921-0.953-0.9530.0000.0000.0000.000
33A46GLU-1-0.856-0.91916.153-15.813-15.8130.0000.0000.0000.000
34A47SER0-0.011-0.00511.130-0.779-0.7790.0000.0000.0000.000
35A48LEU0-0.0030.01811.632-1.478-1.4780.0000.0000.0000.000
36A49THR0-0.065-0.05612.8490.0380.0380.0000.0000.0000.000
37A50THR0-0.006-0.01210.993-0.263-0.2630.0000.0000.0000.000
38A51MET00.0370.0247.279-0.725-0.7250.0000.0000.0000.000
39A52PHE0-0.010-0.01711.5010.4890.4890.0000.0000.0000.000
40A53ASP-1-0.813-0.87013.770-17.554-17.5540.0000.0000.0000.000
41A54VAL00.0050.0158.6070.7860.7860.0000.0000.0000.000
42A55LEU0-0.064-0.02211.8650.4700.4700.0000.0000.0000.000
43A56GLY00.042-0.00514.2300.6610.6610.0000.0000.0000.000
44A57SER0-0.093-0.03416.9041.2421.2420.0000.0000.0000.000
45A58ILE00.0480.00818.2520.4770.4770.0000.0000.0000.000
46A59ALA00.0120.02520.6790.5260.5260.0000.0000.0000.000
47A60PHE00.027-0.00818.1060.4730.4730.0000.0000.0000.000
48A61SER0-0.0210.00020.2150.0520.0520.0000.0000.0000.000
49A62PRO0-0.014-0.00321.8490.1370.1370.0000.0000.0000.000
50A63VAL0-0.0030.00619.9780.2600.2600.0000.0000.0000.000
51A64LYS10.9100.93617.47916.93916.9390.0000.0000.0000.000
52A65THR0-0.033-0.02820.1480.1020.1020.0000.0000.0000.000
53A66ASP-1-0.910-0.95723.734-11.438-11.4380.0000.0000.0000.000
54A67MET0-0.042-0.00118.015-0.022-0.0220.0000.0000.0000.000
55A68LEU00.0400.01419.2200.1290.1290.0000.0000.0000.000
56A69GLY00.0050.00822.5880.3320.3320.0000.0000.0000.000
57A70ASN0-0.083-0.05924.8830.8370.8370.0000.0000.0000.000
58A71VAL00.0270.01520.2640.2960.2960.0000.0000.0000.000
59A72GLU-1-0.848-0.91623.697-11.477-11.4770.0000.0000.0000.000
60A73LYS10.8760.94426.42610.38410.3840.0000.0000.0000.000
61A74ILE0-0.0060.00224.6620.3570.3570.0000.0000.0000.000
62A75ARG10.8580.90821.12213.93413.9340.0000.0000.0000.000
63A76LYS10.9850.98726.8809.5539.5530.0000.0000.0000.000
64A77ARG10.8870.94930.5189.1499.1490.0000.0000.0000.000
65A78MET0-0.002-0.00825.1750.1000.1000.0000.0000.0000.000
66A79LEU0-0.027-0.02427.8600.1410.1410.0000.0000.0000.000
67A80ALA0-0.035-0.00831.0370.2470.2470.0000.0000.0000.000
68A81ALA00.0050.00933.4350.3180.3180.0000.0000.0000.000
69A82PRO00.0350.03531.079-0.069-0.0690.0000.0000.0000.000
70A83LEU0-0.013-0.01931.545-0.180-0.1800.0000.0000.0000.000
71A84GLU-1-0.900-0.94133.768-8.284-8.2840.0000.0000.0000.000
72A85SER0-0.021-0.02830.087-0.009-0.0090.0000.0000.0000.000
73A86GLN00.0050.01528.001-0.602-0.6020.0000.0000.0000.000
74A87ASN0-0.037-0.01726.181-0.461-0.4610.0000.0000.0000.000
75A88ILE00.0430.01523.7210.3900.3900.0000.0000.0000.000
76A89GLN00.0280.00326.6280.1090.1090.0000.0000.0000.000
77A90ASP-1-0.799-0.88129.942-9.036-9.0360.0000.0000.0000.000
78A91LEU0-0.0290.00327.7750.2740.2740.0000.0000.0000.000
79A92VAL0-0.017-0.00530.0580.2540.2540.0000.0000.0000.000
80A93ARG10.7900.86032.2719.4129.4120.0000.0000.0000.000
81A94ASN0-0.036-0.03134.7650.5330.5330.0000.0000.0000.000
82A95GLU-1-0.745-0.84033.985-8.992-8.9920.0000.0000.0000.000
83A96LEU0-0.028-0.01735.5720.1880.1880.0000.0000.0000.000
84A97LYS10.8570.94438.3558.0488.0480.0000.0000.0000.000
85A98THR0-0.045-0.02439.2470.0290.0290.0000.0000.0000.000
86A100SER0-0.057-0.03936.3220.1660.1660.0000.0000.0000.000
87A101HIS10.9210.96635.8628.3268.3260.0000.0000.0000.000
88A102THR0-0.0140.00233.064-0.139-0.1390.0000.0000.0000.000
89A103ALA00.005-0.00430.074-0.287-0.2870.0000.0000.0000.000
90A104THR0-0.002-0.00629.611-0.390-0.3900.0000.0000.0000.000
91A105GLU-1-0.930-0.97030.835-9.080-9.0800.0000.0000.0000.000
92A106GLY0-0.016-0.01428.756-0.190-0.1900.0000.0000.0000.000
93A107LEU00.0290.01024.992-0.459-0.4590.0000.0000.0000.000
94A108LEU0-0.0030.00226.361-0.319-0.3190.0000.0000.0000.000
95A109TRP0-0.024-0.02227.286-0.235-0.2350.0000.0000.0000.000
96A110LEU00.0170.01720.438-0.372-0.3720.0000.0000.0000.000
97A111VAL00.0180.00822.197-0.622-0.6220.0000.0000.0000.000
98A112ARG10.9400.98422.7059.8689.8680.0000.0000.0000.000
99A113GLY00.0140.01021.941-0.226-0.2260.0000.0000.0000.000
100A114LEU0-0.0070.00116.941-0.749-0.7490.0000.0000.0000.000
101A115GLU-1-0.800-0.88618.301-12.691-12.6910.0000.0000.0000.000
102A116PHE0-0.065-0.03120.054-0.348-0.3480.0000.0000.0000.000
103A117THR00.023-0.00214.456-0.233-0.2330.0000.0000.0000.000
104A118CYS00.0390.02915.531-1.045-1.0450.0000.0000.0000.000
105A119ILE00.0000.01016.448-0.431-0.4310.0000.0000.0000.000
106A120ALA0-0.024-0.00317.3080.0500.0500.0000.0000.0000.000
107A121LEU00.0200.00411.187-0.015-0.0150.0000.0000.0000.000
108A122SER00.0290.00214.236-0.649-0.6490.0000.0000.0000.000
109A123LYS10.8100.90215.81313.38713.3870.0000.0000.0000.000
110A124ASN0-0.0230.01114.796-0.641-0.6410.0000.0000.0000.000
111A125ILE00.0530.02810.9930.4870.4870.0000.0000.0000.000
112A126GLY0-0.0220.00814.3320.0670.0670.0000.0000.0000.000
113A127SER0-0.071-0.04917.5691.1641.1640.0000.0000.0000.000
114A128THR00.0280.00217.976-0.724-0.7240.0000.0000.0000.000
115A129GLU-1-0.798-0.84720.060-13.089-13.0890.0000.0000.0000.000
116A130GLU-1-0.703-0.85318.621-16.847-16.8470.0000.0000.0000.000
117A131LEU00.0270.01213.6770.3820.3820.0000.0000.0000.000
118A132ALA00.0280.01318.0160.1810.1810.0000.0000.0000.000
119A133ASP-1-0.880-0.93021.342-11.740-11.7400.0000.0000.0000.000
120A134SER0-0.023-0.02918.4820.1070.1070.0000.0000.0000.000
121A135PHE00.0250.00715.4080.3200.3200.0000.0000.0000.000
122A136ARG10.8670.89120.65112.24912.2490.0000.0000.0000.000
123A137GLY0-0.064-0.04323.6650.5460.5460.0000.0000.0000.000
124A138SER00.001-0.01120.5000.6300.6300.0000.0000.0000.000
125A139TYR00.020-0.01123.0320.5720.5720.0000.0000.0000.000
126A140ARG10.8720.92925.16311.16611.1660.0000.0000.0000.000
127A141VAL00.0080.00625.5140.4190.4190.0000.0000.0000.000
128A142THR00.0090.02023.2410.0470.0470.0000.0000.0000.000
129A143LEU00.0120.00223.8810.3250.3250.0000.0000.0000.000
130A144LYS10.9280.97727.73110.00010.0000.0000.0000.0000.000
131A145PRO0-0.051-0.04230.1510.3330.3330.0000.0000.0000.000
132A146HIS00.0130.01530.1580.4670.4670.0000.0000.0000.000
133A147HIS00.0670.06326.6940.2320.2320.0000.0000.0000.000
134A148SER00.0480.01432.3070.1810.1810.0000.0000.0000.000
135A149PHE00.001-0.02734.137-0.258-0.2580.0000.0000.0000.000
136A150LEU00.0280.02135.333-0.038-0.0380.0000.0000.0000.000
137A151VAL00.0230.01629.381-0.161-0.1610.0000.0000.0000.000
138A152LYS10.9070.96829.8768.6808.6800.0000.0000.0000.000
139A153PRO0-0.018-0.01329.899-0.296-0.2960.0000.0000.0000.000
140A154ILE00.0320.03326.830-0.213-0.2130.0000.0000.0000.000
141A155PHE00.0690.02623.379-0.399-0.3990.0000.0000.0000.000
142A156SER0-0.048-0.01825.184-0.449-0.4490.0000.0000.0000.000
143A157ALA00.0050.01026.630-0.186-0.1860.0000.0000.0000.000
144A158ALA00.0120.00922.305-0.259-0.2590.0000.0000.0000.000
145A159MET0-0.023-0.00821.396-0.521-0.5210.0000.0000.0000.000
146A160SER0-0.054-0.04522.277-0.156-0.1560.0000.0000.0000.000
147A161ALA0-0.0280.00622.6290.1600.1600.0000.0000.0000.000
148A162CYS0-0.088-0.01418.495-0.703-0.7030.0000.0000.0000.000
149A163PRO0-0.0010.02114.9520.5500.5500.0000.0000.0000.000
150A164TYR00.0210.00917.4960.2470.2470.0000.0000.0000.000
151A165ARG10.8000.86514.53516.65016.6500.0000.0000.0000.000
152A166LYS10.9130.95713.04115.98815.9880.0000.0000.0000.000
153A167ASP-1-0.825-0.92012.551-19.532-19.5320.0000.0000.0000.000
154A168PHE0-0.060-0.0339.993-1.479-1.4790.0000.0000.0000.000
155A169TYR0-0.004-0.0458.240-2.080-2.0800.0000.0000.0000.000
156A170ALA00.0630.0437.164-3.908-3.9080.0000.0000.0000.000
157A171LYS10.8640.9406.92820.21520.2150.0000.0000.0000.000
163A177GLN0-0.057-0.0287.4731.2511.2510.0000.0000.0000.000
167A181GLU-1-0.934-0.9627.075-23.709-23.7090.0000.0000.0000.000
169A183LEU0-0.007-0.0115.9983.2463.2460.0000.0000.0000.000
170A184ARG10.8860.9337.59924.25224.2520.0000.0000.0000.000
171A185GLU-1-0.924-0.9518.599-25.406-25.4060.0000.0000.0000.000
172A186TYR00.013-0.0017.6012.1022.1020.0000.0000.0000.000
173A187LEU0-0.030-0.0299.7022.0042.0040.0000.0000.0000.000
174A188VAL00.0130.01512.6431.6911.6910.0000.0000.0000.000
175A189ALA0-0.0130.00512.8171.3541.3540.0000.0000.0000.000
176A190LEU0-0.030-0.01313.6331.1141.1140.0000.0000.0000.000
177A191ASP-1-0.850-0.93915.404-13.227-13.2270.0000.0000.0000.000
178A192LYS10.9480.98517.91315.19915.1990.0000.0000.0000.000
179A193ILE00.000-0.00416.4910.9450.9450.0000.0000.0000.000
180A194VAL00.0100.00119.1020.7520.7520.0000.0000.0000.000
181A195ASN0-0.051-0.03721.3831.1551.1550.0000.0000.0000.000
182A196ILE0-0.104-0.04322.0240.6660.6660.0000.0000.0000.000
183A197LEU00.0160.00522.2680.5680.5680.0000.0000.0000.000
184A198LYS10.8400.91324.88011.80711.8070.0000.0000.0000.000
185A199ARG10.9911.00525.65311.41811.4180.0000.0000.0000.000
186A200PHE0-0.0080.00928.7460.3340.3340.0000.0000.0000.000
187A201LEU00.0220.02427.4760.3680.3680.0000.0000.0000.000
188A202GLU-1-0.949-0.98230.095-9.666-9.6660.0000.0000.0000.000
189A203SER0-0.070-0.04433.3100.4780.4780.0000.0000.0000.000
190A204LYS10.9360.93435.3647.4887.4880.0000.0000.0000.000
191A205GLU-1-0.837-0.88634.584-8.618-8.6180.0000.0000.0000.000
192A206ALA00.0180.01832.691-0.004-0.0040.0000.0000.0000.000
193A207LYS10.8180.90934.7228.3598.3590.0000.0000.0000.000
194A208TRP-1-0.897-0.94533.529-7.725-7.7250.0000.0000.0000.000