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: KV293

Calculation Name: 2ACF-A-Xray547

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ACF

Chain ID: A

ChEMBL ID: CHEMBL5118

UniProt ID: P0C6X7

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1681811.162735
FMO2-HF: Nuclear repulsion 1616516.978841
FMO2-HF: Total energy -65294.183894
FMO2-MP2: Total energy -65482.286831


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:180:HIS)


Summations of interaction energy for fragment #1(A:180:HIS)
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.
-0.2422.851-0.017-1.388-1.686-0.006
Interaction energy analysis for fragmet #1(A:180:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.892
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].
3A182HIS00.0060.0203.4806.0999.027-0.016-1.360-1.551-0.006
4A183MET00.0400.0144.693-7.041-6.876-0.001-0.028-0.1350.000
5A184PRO0-0.0020.0047.4862.4842.4840.0000.0000.0000.000
6A185VAL00.0430.03311.142-0.318-0.3180.0000.0000.0000.000
7A186ASN0-0.003-0.00113.5800.6310.6310.0000.0000.0000.000
8A187GLN0-0.025-0.01212.6880.6250.6250.0000.0000.0000.000
9A188PHE0-0.015-0.00416.0160.0930.0930.0000.0000.0000.000
10A189THR00.0250.00718.4410.7020.7020.0000.0000.0000.000
11A190GLY00.0010.00021.010-0.053-0.0530.0000.0000.0000.000
12A191TYR0-0.078-0.06921.1810.3060.3060.0000.0000.0000.000
13A192LEU00.0140.02526.220-0.018-0.0180.0000.0000.0000.000
14A193LYS10.8680.91729.67210.05310.0530.0000.0000.0000.000
15A194LEU00.0020.00530.7820.2790.2790.0000.0000.0000.000
16A195THR00.0350.00932.8940.2010.2010.0000.0000.0000.000
17A196ASP-1-0.857-0.93231.998-9.888-9.8880.0000.0000.0000.000
18A197ASN0-0.077-0.03130.647-0.105-0.1050.0000.0000.0000.000
19A198VAL00.0180.01729.886-0.291-0.2910.0000.0000.0000.000
20A199ALA00.0350.02726.9080.2130.2130.0000.0000.0000.000
21A200ILE00.0050.00428.097-0.225-0.2250.0000.0000.0000.000
22A201LYS10.8220.89119.93914.27614.2760.0000.0000.0000.000
23A202CYS00.0030.01426.5770.1540.1540.0000.0000.0000.000
24A203VAL0-0.073-0.03420.648-0.230-0.2300.0000.0000.0000.000
25A204ASP-1-0.865-0.93421.100-12.786-12.7860.0000.0000.0000.000
26A205ILE00.0710.01920.540-0.608-0.6080.0000.0000.0000.000
27A206VAL00.0020.00717.283-0.651-0.6510.0000.0000.0000.000
28A207LYS10.9120.95516.09912.39512.3950.0000.0000.0000.000
29A208GLU-1-0.747-0.83515.824-15.912-15.9120.0000.0000.0000.000
30A209ALA0-0.035-0.01616.603-0.762-0.7620.0000.0000.0000.000
31A210GLN0-0.030-0.03412.275-0.845-0.8450.0000.0000.0000.000
32A211SER0-0.056-0.00211.431-1.960-1.9600.0000.0000.0000.000
33A212ALA00.0320.01413.056-1.140-1.1400.0000.0000.0000.000
34A213ASN0-0.045-0.0169.9100.2110.2110.0000.0000.0000.000
35A214PRO00.0200.02412.877-0.142-0.1420.0000.0000.0000.000
36A215MET00.003-0.02116.056-1.044-1.0440.0000.0000.0000.000
37A216VAL00.006-0.00417.6340.1710.1710.0000.0000.0000.000
38A217ILE0-0.0140.00719.4580.0450.0450.0000.0000.0000.000
39A218VAL00.0130.00921.3670.2480.2480.0000.0000.0000.000
40A219ASN0-0.034-0.04324.979-0.009-0.0090.0000.0000.0000.000
41A220ALA0-0.0100.00526.5730.2510.2510.0000.0000.0000.000
42A221ALA0-0.0030.00629.8200.0840.0840.0000.0000.0000.000
43A222ASN00.017-0.01731.4420.3430.3430.0000.0000.0000.000
44A223ILE00.0610.01934.053-0.248-0.2480.0000.0000.0000.000
45A224HIS00.0090.01335.828-0.103-0.1030.0000.0000.0000.000
46A225LEU0-0.0130.00129.579-0.164-0.1640.0000.0000.0000.000
47A226LYS10.8520.93330.6249.2219.2210.0000.0000.0000.000
48A227HIS00.002-0.01227.1360.3330.3330.0000.0000.0000.000
49A228GLY0-0.010-0.00728.768-0.211-0.2110.0000.0000.0000.000
50A229GLY00.0150.00230.1290.2100.2100.0000.0000.0000.000
51A230GLY00.0220.00929.908-0.152-0.1520.0000.0000.0000.000
52A231VAL00.0270.00725.274-0.205-0.2050.0000.0000.0000.000
53A232ALA00.0640.04825.513-0.443-0.4430.0000.0000.0000.000
54A233GLY00.0060.00225.692-0.352-0.3520.0000.0000.0000.000
55A234ALA0-0.045-0.02023.422-0.267-0.2670.0000.0000.0000.000
56A235LEU00.0370.01020.754-0.547-0.5470.0000.0000.0000.000
57A236ASN00.0890.03120.834-0.857-0.8570.0000.0000.0000.000
58A237LYS10.9420.98121.50311.37311.3730.0000.0000.0000.000
59A238ALA0-0.0090.00217.416-0.304-0.3040.0000.0000.0000.000
60A239THR0-0.038-0.00416.933-0.688-0.6880.0000.0000.0000.000
61A240ASN0-0.045-0.02818.6020.3370.3370.0000.0000.0000.000
62A241GLY00.0150.01420.3060.2590.2590.0000.0000.0000.000
63A242ALA0-0.011-0.00519.6690.3930.3930.0000.0000.0000.000
64A243MET00.0320.02521.1690.3880.3880.0000.0000.0000.000
65A244GLN0-0.032-0.02523.1290.4480.4480.0000.0000.0000.000
66A245LYS10.9130.96124.23112.51912.5190.0000.0000.0000.000
67A246GLU-1-0.770-0.88022.755-13.830-13.8300.0000.0000.0000.000
68A247SER00.009-0.00425.7250.3060.3060.0000.0000.0000.000
69A248ASP-1-0.815-0.87628.383-9.573-9.5730.0000.0000.0000.000
70A249ASP-1-0.909-0.95827.358-10.936-10.9360.0000.0000.0000.000
71A250TYR0-0.011-0.01028.8950.0910.0910.0000.0000.0000.000
72A251ILE0-0.020-0.00930.7860.2990.2990.0000.0000.0000.000
73A252LYS10.9130.95633.0529.7149.7140.0000.0000.0000.000
74A253LEU0-0.059-0.01431.0870.1810.1810.0000.0000.0000.000
75A254ASN0-0.036-0.03434.1970.1170.1170.0000.0000.0000.000
76A255GLY00.0320.03636.0730.2720.2720.0000.0000.0000.000
77A256PRO0-0.032-0.02536.204-0.277-0.2770.0000.0000.0000.000
78A257LEU0-0.005-0.00332.7060.0360.0360.0000.0000.0000.000
79A258THR00.018-0.00136.6520.1610.1610.0000.0000.0000.000
80A259VAL00.0240.00337.493-0.238-0.2380.0000.0000.0000.000
81A260GLY0-0.0080.00237.5610.1890.1890.0000.0000.0000.000
82A261GLY00.0010.01935.961-0.102-0.1020.0000.0000.0000.000
83A262SER0-0.043-0.05330.411-0.262-0.2620.0000.0000.0000.000
84A263CYS0-0.0200.00829.7940.0980.0980.0000.0000.0000.000
85A264LEU0-0.0050.00523.754-0.262-0.2620.0000.0000.0000.000
86A265LEU0-0.0070.00524.165-0.102-0.1020.0000.0000.0000.000
87A266SER0-0.016-0.02518.460-0.900-0.9000.0000.0000.0000.000
88A267GLY0-0.0080.00517.7520.7080.7080.0000.0000.0000.000
89A268HIS0-0.064-0.05416.304-0.673-0.6730.0000.0000.0000.000
90A269ASN0-0.024-0.02512.404-0.710-0.7100.0000.0000.0000.000
91A270LEU0-0.052-0.01513.185-0.332-0.3320.0000.0000.0000.000
92A271ALA00.0280.01515.245-0.026-0.0260.0000.0000.0000.000
93A272LYS10.9390.98315.21919.59319.5930.0000.0000.0000.000
94A273LYS10.9060.94216.16615.49915.4990.0000.0000.0000.000
95A274CYS00.0120.00819.892-0.077-0.0770.0000.0000.0000.000
96A275LEU0-0.0030.01322.3090.3250.3250.0000.0000.0000.000
97A276HIS00.0450.00924.4920.4890.4890.0000.0000.0000.000
98A277VAL00.009-0.00228.0980.2600.2600.0000.0000.0000.000
99A278VAL0-0.0330.00331.1170.0090.0090.0000.0000.0000.000
100A279GLY00.0250.01434.3470.1680.1680.0000.0000.0000.000
101A280PRO00.0030.00635.9980.0110.0110.0000.0000.0000.000
102A281ASN00.006-0.00138.5310.0130.0130.0000.0000.0000.000
103A282LEU00.0260.01639.9150.1790.1790.0000.0000.0000.000
104A283ASN0-0.067-0.03839.6400.3200.3200.0000.0000.0000.000
105A284ALA0-0.051-0.01941.9060.0870.0870.0000.0000.0000.000
106A285GLY0-0.0130.00343.7650.1100.1100.0000.0000.0000.000
107A286GLU-1-0.902-0.94440.600-7.711-7.7110.0000.0000.0000.000
108A287ASP-1-0.831-0.92944.444-6.867-6.8670.0000.0000.0000.000
109A288ILE00.0230.00041.297-0.194-0.1940.0000.0000.0000.000
110A289GLN00.001-0.00442.367-0.250-0.2500.0000.0000.0000.000
111A290LEU0-0.011-0.00640.908-0.131-0.1310.0000.0000.0000.000
112A291LEU0-0.020-0.01236.203-0.262-0.2620.0000.0000.0000.000
113A292LYS10.9400.98337.4887.8957.8950.0000.0000.0000.000
114A293ALA0-0.006-0.00337.840-0.184-0.1840.0000.0000.0000.000
115A294ALA00.0330.01134.908-0.240-0.2400.0000.0000.0000.000
116A295TYR00.025-0.02031.692-0.454-0.4540.0000.0000.0000.000
117A296GLU-1-0.821-0.88933.214-9.061-9.0610.0000.0000.0000.000
118A297ASN0-0.037-0.01131.419-0.250-0.2500.0000.0000.0000.000
119A298PHE00.0310.00829.006-0.407-0.4070.0000.0000.0000.000
120A299ASN0-0.044-0.03529.055-0.609-0.6090.0000.0000.0000.000
121A300SER0-0.041-0.01129.293-0.056-0.0560.0000.0000.0000.000
122A301GLN0-0.030-0.02624.594-0.902-0.9020.0000.0000.0000.000
123A302ASP-1-0.865-0.90223.753-12.705-12.7050.0000.0000.0000.000
124A303ILE0-0.044-0.03321.2200.0350.0350.0000.0000.0000.000
125A304LEU0-0.063-0.00922.377-0.498-0.4980.0000.0000.0000.000
126A305LEU00.0000.01919.1100.1620.1620.0000.0000.0000.000
127A306ALA00.018-0.00822.3630.0360.0360.0000.0000.0000.000
128A307PRO0-0.0040.01425.5200.0290.0290.0000.0000.0000.000
129A308LEU00.0100.00727.8050.1060.1060.0000.0000.0000.000
130A309LEU00.0050.01130.5150.0610.0610.0000.0000.0000.000
131A310SER00.020-0.02133.1270.1520.1520.0000.0000.0000.000
132A311ALA00.0060.02433.3350.2590.2590.0000.0000.0000.000
133A312GLY00.004-0.00534.052-0.132-0.1320.0000.0000.0000.000
134A313ILE0-0.009-0.01333.6560.2060.2060.0000.0000.0000.000
135A314PHE0-0.0200.01433.4970.1580.1580.0000.0000.0000.000
136A315GLY00.0360.02737.5340.1680.1680.0000.0000.0000.000
137A316ALA0-0.004-0.00338.4840.2000.2000.0000.0000.0000.000
138A317LYS10.9440.96738.7137.1357.1350.0000.0000.0000.000
139A318PRO00.0390.01735.354-0.036-0.0360.0000.0000.0000.000
140A319LEU00.0740.03636.639-0.174-0.1740.0000.0000.0000.000
141A320GLN00.0070.00938.806-0.009-0.0090.0000.0000.0000.000
142A321SER0-0.013-0.02635.328-0.097-0.0970.0000.0000.0000.000
143A322LEU00.0260.01132.970-0.164-0.1640.0000.0000.0000.000
144A323GLN00.0110.01335.848-0.001-0.0010.0000.0000.0000.000
145A324VAL00.0260.01238.009-0.023-0.0230.0000.0000.0000.000
146A325CYS0-0.0340.00231.814-0.153-0.1530.0000.0000.0000.000
147A326VAL00.0210.00635.119-0.112-0.1120.0000.0000.0000.000
148A327GLN0-0.049-0.01736.4090.0260.0260.0000.0000.0000.000
149A328THR0-0.089-0.04935.8050.2290.2290.0000.0000.0000.000
150A329VAL0-0.060-0.02030.412-0.087-0.0870.0000.0000.0000.000
151A330ARG10.8830.92333.6179.1879.1870.0000.0000.0000.000
152A331THR0-0.030-0.02727.915-0.082-0.0820.0000.0000.0000.000
153A332GLN0-0.015-0.00525.3350.2940.2940.0000.0000.0000.000
154A333VAL0-0.041-0.03125.943-0.350-0.3500.0000.0000.0000.000
155A334TYR00.0280.01922.9370.2040.2040.0000.0000.0000.000
156A335ILE00.007-0.01124.738-0.228-0.2280.0000.0000.0000.000
157A336ALA00.0140.00223.499-0.021-0.0210.0000.0000.0000.000
158A337VAL0-0.017-0.01825.6250.3350.3350.0000.0000.0000.000
159A338ASN0-0.003-0.01826.856-0.001-0.0010.0000.0000.0000.000
160A339ASP-1-0.861-0.90928.070-8.594-8.5940.0000.0000.0000.000
161A340LYS10.9090.92329.8549.5789.5780.0000.0000.0000.000
162A341ALA00.0210.01532.0510.0720.0720.0000.0000.0000.000
163A342LEU0-0.021-0.01632.8600.1340.1340.0000.0000.0000.000
164A343TYR0-0.047-0.02629.3080.0360.0360.0000.0000.0000.000
165A344GLU-1-0.787-0.90733.053-9.049-9.0490.0000.0000.0000.000
166A345GLN0-0.085-0.03535.6960.2000.2000.0000.0000.0000.000
167A346VAL0-0.007-0.01834.1080.0720.0720.0000.0000.0000.000
168A347VAL0-0.041-0.01733.841-0.036-0.0360.0000.0000.0000.000
169A348MET0-0.026-0.02236.3690.0910.0910.0000.0000.0000.000
170A349ASP-1-0.885-0.93739.408-7.477-7.4770.0000.0000.0000.000
171A350TYR0-0.114-0.05735.310-0.028-0.0280.0000.0000.0000.000
172A351LEU-1-0.973-0.96038.394-7.378-7.3780.0000.0000.0000.000