FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88825

Number of unique PDB entries: 32068

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FMODB ID: VVL31

Calculation Name: 1VCH-D-Xray547

Preferred Name:

Target Type:

Ligand Name: acetic acid | calcium ion | chloride ion

Ligand 3-letter code: ACY | CA | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VCH

Chain ID: D

ChEMBL ID:

UniProt ID: Q5SHW7

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1778968.274514
FMO2-HF: Nuclear repulsion 1711847.980128
FMO2-HF: Total energy -67120.294386
FMO2-MP2: Total energy -67317.720973


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.
-11.77-8.132.246-1.988-3.9-0.014
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 : 0.835 / q_NPA : 0.911
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].
3A3THR0-0.042-0.0242.911-2.2470.7970.241-1.554-1.732-0.012
4A4TYR00.0560.0195.1742.4732.553-0.001-0.007-0.0710.000
16A16PRO00.015-0.0102.205-3.258-3.0382.003-0.375-1.849-0.002
17A17LEU00.0040.0193.9175.3605.6560.003-0.052-0.2480.000
5A5PRO0-0.0160.0098.9470.0070.0070.0000.0000.0000.000
6A6ILE0-0.002-0.00111.2411.4661.4660.0000.0000.0000.000
7A7THR0-0.013-0.02113.220-0.136-0.1360.0000.0000.0000.000
8A8VAL00.0020.00416.5790.5640.5640.0000.0000.0000.000
9A9GLY00.0400.02019.061-0.043-0.0430.0000.0000.0000.000
10A10GLY0-0.019-0.00121.1170.3320.3320.0000.0000.0000.000
11A11VAL0-0.0090.00916.099-0.466-0.4660.0000.0000.0000.000
12A12THR0-0.008-0.00813.750-0.203-0.2030.0000.0000.0000.000
13A13ARG10.7280.81810.09518.75118.7510.0000.0000.0000.000
14A14HIS00.0240.0198.1030.0040.0040.0000.0000.0000.000
15A15VAL00.0100.0175.964-2.948-2.9480.0000.0000.0000.000
18A18ILE0-0.021-0.0095.846-1.945-1.9450.0000.0000.0000.000
19A19GLU-1-0.826-0.9258.441-22.120-22.1200.0000.0000.0000.000
20A20PRO0-0.044-0.00711.0610.8920.8920.0000.0000.0000.000
21A21LEU0-0.015-0.02014.4031.4221.4220.0000.0000.0000.000
22A22PRO0-0.0130.00514.711-0.869-0.8690.0000.0000.0000.000
23A23GLY0-0.009-0.01214.2310.9970.9970.0000.0000.0000.000
24A24ARG10.8920.94514.61914.98414.9840.0000.0000.0000.000
25A25ARG10.8770.9307.71029.33629.3360.0000.0000.0000.000
26A26ILE00.0050.00411.1371.4041.4040.0000.0000.0000.000
27A27PRO00.0040.0008.710-2.174-2.1740.0000.0000.0000.000
28A28LEU0-0.023-0.0075.5821.9891.9890.0000.0000.0000.000
29A29VAL0-0.002-0.0068.612-0.799-0.7990.0000.0000.0000.000
30A30GLU-1-0.769-0.8749.485-18.238-18.2380.0000.0000.0000.000
31A31PHE00.005-0.01011.355-0.156-0.1560.0000.0000.0000.000
32A32LEU0-0.069-0.03712.8990.8610.8610.0000.0000.0000.000
33A33GLY0-0.012-0.00312.748-0.996-0.9960.0000.0000.0000.000
34A34ASP-1-0.791-0.86013.496-18.263-18.2630.0000.0000.0000.000
35A35PRO00.018-0.00115.5750.4130.4130.0000.0000.0000.000
36A36GLU-1-0.838-0.88917.506-15.234-15.2340.0000.0000.0000.000
37A37PHE00.005-0.00512.8830.4540.4540.0000.0000.0000.000
38A38THR0-0.018-0.02516.9980.4210.4210.0000.0000.0000.000
39A39ARG10.8890.95218.91311.38211.3820.0000.0000.0000.000
40A40ALA00.0440.02519.8190.4660.4660.0000.0000.0000.000
41A41ALA00.0020.00018.6790.2660.2660.0000.0000.0000.000
42A42ALA00.012-0.00220.8180.4140.4140.0000.0000.0000.000
43A43GLU-1-0.984-1.00923.835-10.442-10.4420.0000.0000.0000.000
44A44ALA0-0.012-0.00523.0400.3680.3680.0000.0000.0000.000
45A45LEU00.0190.00522.7600.2480.2480.0000.0000.0000.000
46A46ARG10.9440.97926.0669.8689.8680.0000.0000.0000.000
47A47PRO0-0.070-0.04128.5570.3480.3480.0000.0000.0000.000
48A48LEU0-0.0070.00726.7810.2330.2330.0000.0000.0000.000
49A49VAL0-0.029-0.00330.3380.0680.0680.0000.0000.0000.000
50A50PRO00.0090.01932.6600.1670.1670.0000.0000.0000.000
51A51LYS10.9150.94436.2527.8227.8220.0000.0000.0000.000
52A52GLU-1-0.896-0.95738.961-7.411-7.4110.0000.0000.0000.000
53A53ALA0-0.023-0.01134.6140.0310.0310.0000.0000.0000.000
54A54GLU-1-0.859-0.92336.739-7.083-7.0830.0000.0000.0000.000
55A55ILE0-0.048-0.02432.933-0.035-0.0350.0000.0000.0000.000
56A56LEU00.0070.01828.299-0.085-0.0850.0000.0000.0000.000
57A57PHE00.040-0.01327.4410.0880.0880.0000.0000.0000.000
58A58THR00.015-0.01222.887-0.343-0.3430.0000.0000.0000.000
59A59THR0-0.008-0.00320.9300.2700.2700.0000.0000.0000.000
60A60GLU-1-0.782-0.87520.051-11.928-11.9280.0000.0000.0000.000
61A61THR0-0.034-0.03316.1580.0780.0780.0000.0000.0000.000
62A62SER00.0370.00012.8390.6510.6510.0000.0000.0000.000
63A63PRO00.0340.02615.6780.0760.0760.0000.0000.0000.000
64A64ILE0-0.0160.01119.0160.5520.5520.0000.0000.0000.000
65A65PRO0-0.015-0.00717.2980.5340.5340.0000.0000.0000.000
66A66LEU00.0360.02219.3250.3980.3980.0000.0000.0000.000
67A67THR00.005-0.01321.1550.5250.5250.0000.0000.0000.000
68A68HIS00.0190.02923.7350.3840.3840.0000.0000.0000.000
69A69VAL00.007-0.00623.0450.3750.3750.0000.0000.0000.000
70A70LEU0-0.0140.00225.3120.2910.2910.0000.0000.0000.000
71A71ALA0-0.015-0.01427.0880.3310.3310.0000.0000.0000.000
72A72GLU-1-0.917-0.96028.645-9.613-9.6130.0000.0000.0000.000
73A73ALA0-0.045-0.02529.2400.2840.2840.0000.0000.0000.000
74A74LEU0-0.062-0.03030.6430.2170.2170.0000.0000.0000.000
75A75GLY0-0.0150.01033.3300.2630.2630.0000.0000.0000.000
76A76LEU0-0.038-0.00732.9450.2040.2040.0000.0000.0000.000
77A77PRO0-0.011-0.00232.705-0.221-0.2210.0000.0000.0000.000
78A78TYR0-0.029-0.04325.846-0.190-0.1900.0000.0000.0000.000
79A79VAL0-0.055-0.01229.5820.1420.1420.0000.0000.0000.000
80A80VAL0-0.006-0.00923.830-0.305-0.3050.0000.0000.0000.000
81A81ALA0-0.021-0.00326.0830.2330.2330.0000.0000.0000.000
82A82ARG10.8340.89723.39710.30810.3080.0000.0000.0000.000
83A83ARG10.8780.90519.27113.21113.2110.0000.0000.0000.000
84A84ARG10.9570.98221.80611.71111.7110.0000.0000.0000.000
85A85ARG10.9250.96725.1738.5008.5000.0000.0000.0000.000
86A86ARG10.9300.97226.8598.9928.9920.0000.0000.0000.000
87A87PRO00.021-0.01127.8290.2720.2720.0000.0000.0000.000
88A88TYR0-0.007-0.03031.057-0.038-0.0380.0000.0000.0000.000
89A89MET0-0.0840.00528.6640.0410.0410.0000.0000.0000.000
90A90GLU-1-0.872-0.93232.943-7.235-7.2350.0000.0000.0000.000
91A91ASP-1-0.839-0.91035.422-7.380-7.3800.0000.0000.0000.000
92A92PRO0-0.0080.00932.417-0.014-0.0140.0000.0000.0000.000
93A93ILE00.0130.00733.6700.1080.1080.0000.0000.0000.000
94A94ILE00.0210.01430.729-0.282-0.2820.0000.0000.0000.000
95A95GLN0-0.059-0.04430.3420.5270.5270.0000.0000.0000.000
96A96GLU-1-0.838-0.89128.251-9.719-9.7190.0000.0000.0000.000
97A97VAL0-0.015-0.00123.9620.2200.2200.0000.0000.0000.000
98A98GLN0-0.027-0.00626.9890.2010.2010.0000.0000.0000.000
99A99THR00.010-0.02125.478-0.567-0.5670.0000.0000.0000.000
100A100LEU00.0100.00122.8970.1700.1700.0000.0000.0000.000
101A101THR0-0.005-0.02126.2110.2400.2400.0000.0000.0000.000
102A102LEU00.0080.01421.7830.0040.0040.0000.0000.0000.000
103A103GLY0-0.0380.00526.3780.1910.1910.0000.0000.0000.000
104A104VAL00.0200.00926.8620.2650.2650.0000.0000.0000.000
105A105GLY0-0.014-0.00825.625-0.358-0.3580.0000.0000.0000.000
106A106GLU-1-0.871-0.91719.686-12.778-12.7780.0000.0000.0000.000
107A107VAL0-0.025-0.01823.4850.2380.2380.0000.0000.0000.000
108A108LEU00.0200.00723.757-0.176-0.1760.0000.0000.0000.000
109A109TRP00.003-0.01826.5530.6020.6020.0000.0000.0000.000
110A110LEU0-0.0040.00328.387-0.243-0.2430.0000.0000.0000.000
111A111ASP-1-0.839-0.92930.721-8.155-8.1550.0000.0000.0000.000
112A112ARG10.9010.94132.6827.3537.3530.0000.0000.0000.000
113A113ARG10.9580.98035.0467.3967.3960.0000.0000.0000.000
114A114PHE0-0.061-0.04028.504-0.009-0.0090.0000.0000.0000.000
115A115ALA00.008-0.00233.9460.0430.0430.0000.0000.0000.000
116A116GLU-1-0.856-0.94435.994-7.072-7.0720.0000.0000.0000.000
117A117LYS10.8900.95234.1658.1778.1770.0000.0000.0000.000
118A118LEU00.000-0.00433.070-0.093-0.0930.0000.0000.0000.000
119A119LEU00.0120.03337.2460.0460.0460.0000.0000.0000.000
120A120ASN0-0.064-0.04740.9960.1170.1170.0000.0000.0000.000
121A121GLN0-0.0320.00037.9610.0020.0020.0000.0000.0000.000
122A122ARG10.9260.96838.2506.8706.8700.0000.0000.0000.000
123A123VAL0-0.021-0.01732.064-0.149-0.1490.0000.0000.0000.000
124A124VAL00.0270.01329.4310.0180.0180.0000.0000.0000.000
125A125LEU0-0.036-0.02027.633-0.172-0.1720.0000.0000.0000.000
126A126VAL00.0310.01423.345-0.053-0.0530.0000.0000.0000.000
127A127SER0-0.023-0.01420.210-0.104-0.1040.0000.0000.0000.000
128A128ASP-1-0.786-0.90515.939-15.193-15.1930.0000.0000.0000.000
129A129VAL0-0.019-0.01514.930-0.092-0.0920.0000.0000.0000.000
130A130VAL0-0.0120.00618.3280.5650.5650.0000.0000.0000.000
131A131ALA00.0790.03519.186-0.269-0.2690.0000.0000.0000.000
132A132SER00.0400.01321.2230.3620.3620.0000.0000.0000.000
133A133GLY00.0650.03023.8740.4370.4370.0000.0000.0000.000
134A134GLU-1-0.909-0.97524.968-9.678-9.6780.0000.0000.0000.000
135A135THR00.0070.00322.1340.1280.1280.0000.0000.0000.000
136A136MET00.0510.02423.9560.3160.3160.0000.0000.0000.000
137A137ARG10.9070.95527.1529.6579.6570.0000.0000.0000.000
138A138ALA0-0.042-0.01127.3500.3450.3450.0000.0000.0000.000
139A139MET00.0210.00825.5250.1770.1770.0000.0000.0000.000
140A140GLU-1-0.798-0.87029.397-8.379-8.3790.0000.0000.0000.000
141A141LYS10.9320.97331.7089.0989.0980.0000.0000.0000.000
142A142MET0-0.082-0.02629.1430.1220.1220.0000.0000.0000.000
143A143VAL00.0140.01632.5050.1760.1760.0000.0000.0000.000
144A144LEU0-0.0040.00735.0140.2100.2100.0000.0000.0000.000
145A145ARG10.7880.88134.2998.1988.1980.0000.0000.0000.000
146A146ALA0-0.032-0.00636.4270.1100.1100.0000.0000.0000.000
147A147GLY00.0110.01138.4570.1070.1070.0000.0000.0000.000
148A148GLY00.0390.03438.1530.1310.1310.0000.0000.0000.000
149A149HIS0-0.071-0.05938.1140.0850.0850.0000.0000.0000.000
150A150VAL0-0.012-0.00132.695-0.068-0.0680.0000.0000.0000.000
151A151VAL00.0030.00735.2060.1370.1370.0000.0000.0000.000
152A152ALA00.0230.01332.0020.0060.0060.0000.0000.0000.000
153A153ARG10.7730.84828.4498.8898.8890.0000.0000.0000.000
154A154LEU00.0280.02326.300-0.045-0.0450.0000.0000.0000.000
155A155ALA0-0.026-0.01721.230-0.165-0.1650.0000.0000.0000.000
156A156VAL00.0050.01618.4950.2270.2270.0000.0000.0000.000
157A157PHE00.005-0.01215.507-0.107-0.1070.0000.0000.0000.000
158A158ARG10.8720.91619.08112.60412.6040.0000.0000.0000.000
159A159GLN00.0170.01017.130-0.311-0.3110.0000.0000.0000.000
160A160GLY00.0290.02319.4950.3970.3970.0000.0000.0000.000
161A161THR0-0.012-0.01422.4430.4120.4120.0000.0000.0000.000
162A162PRO0-0.0080.00924.1540.0650.0650.0000.0000.0000.000
163A163GLY00.0030.00926.2900.3230.3230.0000.0000.0000.000
164A164LEU0-0.063-0.03528.3670.3740.3740.0000.0000.0000.000
165A165ALA00.0140.01729.226-0.237-0.2370.0000.0000.0000.000
166A166VAL00.001-0.01825.3300.1190.1190.0000.0000.0000.000
167A167ASP-1-0.894-0.92027.779-9.630-9.6300.0000.0000.0000.000
168A168THR0-0.058-0.05723.154-0.373-0.3730.0000.0000.0000.000
169A169VAL0-0.0170.01222.0380.2400.2400.0000.0000.0000.000
170A170ALA0-0.0040.00219.3760.0270.0270.0000.0000.0000.000
171A171GLU-1-0.875-0.92119.786-13.111-13.1110.0000.0000.0000.000
172A172LEU0-0.049-0.02912.807-0.532-0.5320.0000.0000.0000.000
173A173PRO0-0.017-0.00513.9790.5150.5150.0000.0000.0000.000
174A174VAL0-0.009-0.03014.601-0.821-0.8210.0000.0000.0000.000
175A175LEU-1-0.915-0.94711.095-20.500-20.5000.0000.0000.0000.000