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: RMV98

Calculation Name: 5A0Q-I-Other547

Preferred Name:

Target Type:

Ligand Name: ada-(ahx)3-(leu)3-vinyl sulfone

Ligand 3-letter code: KNM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5A0Q

Chain ID: I

ChEMBL ID:

UniProt ID: P25786

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2219516.134189
FMO2-HF: Nuclear repulsion 2139572.110343
FMO2-HF: Total energy -79944.023846
FMO2-MP2: Total energy -80171.301406


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:THR)


Summations of interaction energy for fragment #1(A:1: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.
-138.643-140.24443.663-19.457-22.602-0.229
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.671 / q_NPA : 0.811
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].
3A3ILE0-0.024-0.0123.6883.7205.098-0.007-0.465-0.9060.001
17A17ASP-1-0.642-0.7941.786-133.130-134.79017.109-8.873-6.576-0.128
18A18THR0-0.025-0.0044.537-3.962-3.787-0.001-0.015-0.1580.000
19A19ARG10.9050.9533.32654.99555.3490.009-0.073-0.2900.000
20A20ALA00.007-0.0103.967-9.259-8.7090.001-0.129-0.422-0.001
33A33LYS10.8400.9152.43554.06854.7440.351-0.327-0.700-0.001
46A46ALA0-0.015-0.0242.945-7.606-6.6910.121-0.359-0.6780.001
47A47GLY00.0380.0263.1652.7493.6220.036-0.393-0.5150.004
48A48THR0-0.011-0.0095.127-2.466-2.373-0.0010.000-0.0910.000
128A128GLY00.0480.0212.676-7.575-6.8620.327-0.483-0.5560.001
129A129SER0-0.022-0.0161.8424.1751.9667.978-2.091-3.677-0.015
130A130GLY00.0590.0383.0917.8747.7710.0260.398-0.3210.000
166A166ASP-1-0.783-0.8563.786-64.592-63.9800.002-0.321-0.294-0.002
168A168GLY0-0.033-0.0073.0581.7892.2060.058-0.177-0.299-0.001
169A169SER0-0.077-0.0791.897-60.824-63.18717.303-8.236-6.704-0.084
170A170GLY0-0.015-0.0122.80320.34118.2790.3522.087-0.377-0.004
171A171SER0-0.098-0.0555.023-2.523-2.483-0.0010.000-0.0380.000
4A4ALA00.003-0.0105.8521.8301.8300.0000.0000.0000.000
5A5GLY00.0010.0029.4280.4870.4870.0000.0000.0000.000
6A6VAL0-0.007-0.00112.8470.1440.1440.0000.0000.0000.000
7A7VAL0-0.072-0.03616.3730.2940.2940.0000.0000.0000.000
8A8TYR0-0.027-0.04419.649-0.112-0.1120.0000.0000.0000.000
9A9LYS10.7970.89022.43111.11411.1140.0000.0000.0000.000
10A10ASP-1-0.901-0.94725.502-11.289-11.2890.0000.0000.0000.000
11A11GLY0-0.065-0.05522.5050.2000.2000.0000.0000.0000.000
12A12ILE0-0.067-0.02015.983-0.145-0.1450.0000.0000.0000.000
13A13VAL00.0120.01914.7090.1490.1490.0000.0000.0000.000
14A14LEU00.003-0.00611.795-0.769-0.7690.0000.0000.0000.000
15A15GLY00.0350.00610.1201.2421.2420.0000.0000.0000.000
16A16ALA00.017-0.0055.639-2.236-2.2360.0000.0000.0000.000
21A21THR0-0.013-0.0145.1341.0641.0640.0000.0000.0000.000
22A22GLU-1-0.909-0.9476.855-22.100-22.1000.0000.0000.0000.000
23A23GLY0-0.007-0.0118.5642.2352.2350.0000.0000.0000.000
24A24MET0-0.001-0.0078.255-3.466-3.4660.0000.0000.0000.000
25A25VAL00.0050.01710.7750.0810.0810.0000.0000.0000.000
26A26VAL0-0.044-0.0347.332-2.243-2.2430.0000.0000.0000.000
27A27ALA00.0380.0349.2342.0372.0370.0000.0000.0000.000
28A28ASP-1-0.825-0.9198.677-26.749-26.7490.0000.0000.0000.000
29A29LYS10.8700.9247.81618.93218.9320.0000.0000.0000.000
30A30ASN00.016-0.0019.728-0.945-0.9450.0000.0000.0000.000
31A31CYS0-0.0050.0316.3141.4021.4020.0000.0000.0000.000
32A32SER00.0250.0047.215-2.969-2.9690.0000.0000.0000.000
34A34ILE0-0.0090.0017.7450.0870.0870.0000.0000.0000.000
35A35HIS00.0040.0039.741-0.009-0.0090.0000.0000.0000.000
36A36PHE0-0.003-0.00812.9170.4220.4220.0000.0000.0000.000
37A37ILE0-0.0180.00415.1430.2560.2560.0000.0000.0000.000
38A38SER00.019-0.02318.2941.0431.0430.0000.0000.0000.000
39A39PRO0-0.021-0.00420.617-0.516-0.5160.0000.0000.0000.000
40A40ASN00.0130.01422.185-0.302-0.3020.0000.0000.0000.000
41A41ILE0-0.037-0.03117.402-0.154-0.1540.0000.0000.0000.000
42A42TYR00.0790.03714.2700.1140.1140.0000.0000.0000.000
43A43CYS0-0.026-0.01710.9350.5130.5130.0000.0000.0000.000
44A44CYS0-0.0250.0167.3240.0290.0290.0000.0000.0000.000
45A45GLY00.0680.0366.8081.6701.6700.0000.0000.0000.000
49A49ALA00.0540.0136.8571.0441.0440.0000.0000.0000.000
50A50ALA00.0290.0148.0351.1331.1330.0000.0000.0000.000
51A51ASP-1-0.774-0.90010.449-19.362-19.3620.0000.0000.0000.000
52A52THR0-0.0150.0086.8710.8620.8620.0000.0000.0000.000
53A53ASP-1-0.838-0.9039.949-19.259-19.2590.0000.0000.0000.000
54A54MET00.0060.00912.1421.4521.4520.0000.0000.0000.000
55A55THR0-0.031-0.02913.3131.4061.4060.0000.0000.0000.000
56A56THR0-0.025-0.03312.1210.9210.9210.0000.0000.0000.000
57A57GLN0-0.026-0.01414.8871.7181.7180.0000.0000.0000.000
58A58LEU00.0100.01817.6850.8340.8340.0000.0000.0000.000
59A59ILE0-0.005-0.01417.3190.7920.7920.0000.0000.0000.000
60A60SER00.013-0.00218.3310.3720.3720.0000.0000.0000.000
61A61SER0-0.080-0.03920.0450.7370.7370.0000.0000.0000.000
62A62ASN00.0270.00622.3570.8010.8010.0000.0000.0000.000
63A63LEU0-0.012-0.01720.5820.5140.5140.0000.0000.0000.000
64A64GLU00.0240.03622.5480.2650.2650.0000.0000.0000.000
65A65LEU00.0310.02925.6360.4070.4070.0000.0000.0000.000
66A66HIS0-0.029-0.00526.9840.4540.4540.0000.0000.0000.000
67A67SER0-0.015-0.04126.7190.3300.3300.0000.0000.0000.000
68A68LEU0-0.0220.00129.2640.2900.2900.0000.0000.0000.000
69A69SER0-0.039-0.02631.3940.3860.3860.0000.0000.0000.000
70A70THR0-0.098-0.04931.2170.2600.2600.0000.0000.0000.000
71A71GLY00.0170.02733.3950.2140.2140.0000.0000.0000.000
72A72ARG10.8380.92429.0799.9169.9160.0000.0000.0000.000
73A73LEU00.0510.02026.120-0.159-0.1590.0000.0000.0000.000
74A74PRO00.0300.02123.9690.2420.2420.0000.0000.0000.000
75A75ARG10.9010.94925.1629.6739.6730.0000.0000.0000.000
76A76VAL00.0360.02719.652-0.058-0.0580.0000.0000.0000.000
77A77VAL00.0410.01921.169-0.287-0.2870.0000.0000.0000.000
78A78THR0-0.045-0.02123.0820.0990.0990.0000.0000.0000.000
79A79ALA00.0790.04319.0380.0670.0670.0000.0000.0000.000
80A80ASN00.0250.01216.9780.1410.1410.0000.0000.0000.000
81A81ARG10.9160.97119.41210.57510.5750.0000.0000.0000.000
82A82MET00.0170.00620.5190.0640.0640.0000.0000.0000.000
83A83LEU00.0360.02014.889-0.012-0.0120.0000.0000.0000.000
84A84LYS10.9200.97017.70013.06713.0670.0000.0000.0000.000
85A85GLN0-0.013-0.01819.3600.0090.0090.0000.0000.0000.000
86A86MET0-0.0190.01818.0790.4040.4040.0000.0000.0000.000
87A87LEU0-0.005-0.00613.5070.1060.1060.0000.0000.0000.000
88A88PHE00.0160.02117.0400.1000.1000.0000.0000.0000.000
89A89ARG10.8460.91119.98812.47512.4750.0000.0000.0000.000
90A90TYR00.014-0.01017.7800.6820.6820.0000.0000.0000.000
91A91GLN0-0.031-0.00719.888-0.013-0.0130.0000.0000.0000.000
92A92GLY00.0450.02615.6980.0930.0930.0000.0000.0000.000
93A93TYR0-0.068-0.03315.464-0.374-0.3740.0000.0000.0000.000
94A94ILE0-0.0410.00112.850-0.341-0.3410.0000.0000.0000.000
95A95GLY00.0550.02111.5670.2620.2620.0000.0000.0000.000
96A96ALA0-0.110-0.0488.114-1.674-1.6740.0000.0000.0000.000
97A97ALA0-0.019-0.0057.3971.9481.9480.0000.0000.0000.000
98A98LEU00.000-0.0227.563-1.773-1.7730.0000.0000.0000.000
99A99VAL00.005-0.0028.2121.2741.2740.0000.0000.0000.000
100A100LEU0-0.0050.00410.443-0.020-0.0200.0000.0000.0000.000
101A101GLY00.0450.01413.8470.5160.5160.0000.0000.0000.000
102A102GLY00.021-0.00416.0930.0450.0450.0000.0000.0000.000
103A103VAL00.0190.01319.6740.2430.2430.0000.0000.0000.000
104A104ASP-1-0.758-0.89023.360-10.537-10.5370.0000.0000.0000.000
105A105VAL0-0.007-0.00826.472-0.015-0.0150.0000.0000.0000.000
106A106THR0-0.086-0.06127.616-0.010-0.0100.0000.0000.0000.000
107A107GLY00.0220.02826.8490.0450.0450.0000.0000.0000.000
108A108PRO00.0260.01321.996-0.162-0.1620.0000.0000.0000.000
109A109HIS0-0.057-0.04620.701-0.119-0.1190.0000.0000.0000.000
110A110LEU00.0540.03413.325-0.378-0.3780.0000.0000.0000.000
111A111TYR0-0.047-0.03515.6000.8120.8120.0000.0000.0000.000
112A112SER00.0460.02511.457-1.692-1.6920.0000.0000.0000.000
113A113ILE0-0.036-0.03411.5021.9171.9170.0000.0000.0000.000
114A114TYR00.0830.04510.310-1.071-1.0710.0000.0000.0000.000
115A115PRO00.0140.00510.7401.1771.1770.0000.0000.0000.000
116A116HIS00.0430.02312.9970.8230.8230.0000.0000.0000.000
117A117GLY00.0020.00615.7730.9020.9020.0000.0000.0000.000
118A118SER0-0.063-0.02316.0950.9040.9040.0000.0000.0000.000
119A119THR0-0.065-0.05615.678-0.547-0.5470.0000.0000.0000.000
120A120ASP-1-0.864-0.91516.229-14.308-14.3080.0000.0000.0000.000
121A121LYS10.9010.96216.50912.34412.3440.0000.0000.0000.000
122A122LEU00.0160.00717.0160.8150.8150.0000.0000.0000.000
123A123PRO0-0.019-0.01617.729-0.592-0.5920.0000.0000.0000.000
124A124TYR00.0700.04815.326-0.126-0.1260.0000.0000.0000.000
125A125VAL0-0.009-0.00211.1580.4080.4080.0000.0000.0000.000
126A126THR0-0.014-0.0208.465-0.809-0.8090.0000.0000.0000.000
127A127MET0-0.042-0.0115.5492.1222.1220.0000.0000.0000.000
131A131SER0-0.075-0.0225.1136.3876.3870.0000.0000.0000.000
132A132LEU00.0580.0306.9663.0803.0800.0000.0000.0000.000
133A133ALA00.0290.0179.1711.9981.9980.0000.0000.0000.000
134A134ALA00.0210.0098.5221.8241.8240.0000.0000.0000.000
135A135MET0-0.029-0.02210.4432.6222.6220.0000.0000.0000.000
136A136ALA00.0580.03812.5941.6281.6280.0000.0000.0000.000
137A137VAL0-0.0120.00013.6071.3031.3030.0000.0000.0000.000
138A138PHE0-0.004-0.03111.5130.7770.7770.0000.0000.0000.000
139A139GLU-1-0.989-0.98616.098-15.295-15.2950.0000.0000.0000.000
140A140ASP-1-0.875-0.92718.440-14.066-14.0660.0000.0000.0000.000
141A141LYS10.7770.87818.11115.75715.7570.0000.0000.0000.000
142A142PHE0-0.012-0.00219.0620.5120.5120.0000.0000.0000.000
143A143ARG10.7970.88820.87812.66312.6630.0000.0000.0000.000
144A144PRO00.003-0.00724.012-0.220-0.2200.0000.0000.0000.000
145A145ASP-1-0.845-0.93125.830-10.516-10.5160.0000.0000.0000.000
146A146MET0-0.0320.02819.928-0.089-0.0890.0000.0000.0000.000
147A147GLU-1-0.828-0.92925.418-11.165-11.1650.0000.0000.0000.000
148A148GLU-1-0.853-0.91323.366-13.350-13.3500.0000.0000.0000.000
149A149GLU-1-0.874-0.94522.292-14.589-14.5890.0000.0000.0000.000
150A150GLU-1-0.756-0.86221.669-13.711-13.7110.0000.0000.0000.000
151A151ALA00.0320.00618.934-0.762-0.7620.0000.0000.0000.000
152A152LYS10.7790.88017.14513.49613.4960.0000.0000.0000.000
153A153ASN0-0.077-0.04316.583-0.514-0.5140.0000.0000.0000.000
154A154LEU00.0260.03416.8210.0120.0120.0000.0000.0000.000
155A155VAL0-0.017-0.01511.880-1.554-1.5540.0000.0000.0000.000
156A156SER0-0.069-0.04811.852-2.695-2.6950.0000.0000.0000.000
157A157GLU-1-0.752-0.86711.892-21.231-21.2310.0000.0000.0000.000
158A158ALA00.0350.02911.996-0.959-0.9590.0000.0000.0000.000
159A159ILE0-0.052-0.0346.307-3.547-3.5470.0000.0000.0000.000
160A160ALA0-0.019-0.0127.582-4.457-4.4570.0000.0000.0000.000
161A161ALA00.0170.0139.875-0.739-0.7390.0000.0000.0000.000
162A162GLY00.0290.0206.3240.3680.3680.0000.0000.0000.000
163A163ILE0-0.095-0.0595.771-3.609-3.6090.0000.0000.0000.000
164A164PHE0-0.051-0.0236.8221.8121.8120.0000.0000.0000.000
165A165ASN0-0.056-0.0289.1273.2033.2030.0000.0000.0000.000
167A167LEU0-0.006-0.0056.712-0.116-0.1160.0000.0000.0000.000
172A172ASN00.0280.0197.870-0.373-0.3730.0000.0000.0000.000
173A173ILE00.0120.0317.874-4.335-4.3350.0000.0000.0000.000
174A174ASP-1-0.826-0.9188.746-26.566-26.5660.0000.0000.0000.000
175A175LEU0-0.023-0.02010.372-1.538-1.5380.0000.0000.0000.000
176A176CYS0-0.088-0.04513.0671.3761.3760.0000.0000.0000.000
177A177VAL00.0180.02215.114-0.470-0.4700.0000.0000.0000.000
178A178ILE0-0.013-0.00117.7080.5300.5300.0000.0000.0000.000
179A179SER00.0690.02420.0360.3010.3010.0000.0000.0000.000
180A180LYS10.8930.93423.69910.54810.5480.0000.0000.0000.000
181A181ASN0-0.0430.00326.9040.3350.3350.0000.0000.0000.000
182A182LYS10.9090.92923.93813.29913.2990.0000.0000.0000.000
183A183LEU0-0.0130.01720.511-0.399-0.3990.0000.0000.0000.000
184A184ASP-1-0.811-0.88219.677-13.601-13.6010.0000.0000.0000.000
185A185PHE00.0220.00113.398-1.005-1.0050.0000.0000.0000.000
186A186LEU0-0.019-0.00115.5860.7300.7300.0000.0000.0000.000
187A187ARG10.8800.92111.39023.67823.6780.0000.0000.0000.000
188A188PRO0-0.053-0.01212.851-1.579-1.5790.0000.0000.0000.000
189A189TYR00.0420.02213.0811.1101.1100.0000.0000.0000.000
190A190THR00.0240.01612.7681.3231.3230.0000.0000.0000.000
191A191VAL0-0.004-0.01012.292-1.966-1.9660.0000.0000.0000.000
192A192PRO00.0470.03710.3191.3031.3030.0000.0000.0000.000
193A193ASN00.0390.0279.4371.3051.3050.0000.0000.0000.000
194A194LYS10.8470.91611.58222.25822.2580.0000.0000.0000.000
195A195LYS10.9210.95013.14917.04717.0470.0000.0000.0000.000
196A196GLY00.0590.03415.2760.9450.9450.0000.0000.0000.000
197A197THR00.0230.00615.5730.9300.9300.0000.0000.0000.000
198A198ARG10.8800.93618.60212.80712.8070.0000.0000.0000.000
199A199LEU00.0930.05321.5680.3460.3460.0000.0000.0000.000
200A200GLY00.0530.03224.1880.5310.5310.0000.0000.0000.000
201A201ARG10.8540.91324.20712.09712.0970.0000.0000.0000.000
202A202TYR00.0610.05028.1560.3060.3060.0000.0000.0000.000
203A203ARG10.8520.89429.4738.9668.9660.0000.0000.0000.000
204A204CYS00.0090.01229.1620.0080.0080.0000.0000.0000.000
205A205GLU-1-0.833-0.91231.973-8.792-8.7920.0000.0000.0000.000
206A206LYS10.8930.95835.5938.4438.4430.0000.0000.0000.000
207A207GLY-1-0.887-0.93137.429-7.678-7.6780.0000.0000.0000.000