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: 7YLMK

Calculation Name: 2CB9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetic acid

Ligand 3-letter code: ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CB9

Chain ID: A

ChEMBL ID:

UniProt ID: Q45563

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2675209.700636
FMO2-HF: Nuclear repulsion 2589071.672471
FMO2-HF: Total energy -86138.028165
FMO2-MP2: Total energy -86390.256622


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:6:SER)


Summations of interaction energy for fragment #1(A:6: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.
-352.334-343.56131.607-21.063-19.316-0.205
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.728 / q_NPA : 0.849
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].
3A8ALA0-0.041-0.0273.5278.72010.250-0.012-0.659-0.859-0.001
4A9GLY0-0.0210.0023.0885.6086.9090.257-0.710-0.8480.005
5A10GLU-1-0.832-0.9082.437-65.275-63.0972.743-1.861-3.059-0.020
6A11GLN00.0160.0121.690-27.671-32.58214.401-6.087-3.402-0.056
7A12HIS0-0.046-0.0262.2159.69811.3952.237-1.430-2.505-0.009
51A56ILE0-0.044-0.0094.727-2.070-1.977-0.001-0.015-0.0770.000
53A58GLU-1-0.804-0.8972.220-105.785-100.1015.009-6.128-4.565-0.070
55A60SER0-0.041-0.0154.6601.4301.472-0.001-0.001-0.0400.000
59A64GLN0-0.052-0.0211.898-31.145-29.9866.974-4.172-3.961-0.054
8A13VAL00.0260.0125.7713.3133.3130.0000.0000.0000.000
9A14ILE0-0.035-0.0149.232-0.211-0.2110.0000.0000.0000.000
10A15GLN00.0340.03012.5020.0410.0410.0000.0000.0000.000
11A16LEU0-0.044-0.01915.2580.5930.5930.0000.0000.0000.000
12A17ASN0-0.059-0.02218.3040.2680.2680.0000.0000.0000.000
13A18GLN0-0.022-0.00820.053-0.729-0.7290.0000.0000.0000.000
14A19GLN0-0.023-0.01317.1570.4370.4370.0000.0000.0000.000
15A20GLY00.017-0.00221.6530.5640.5640.0000.0000.0000.000
16A21GLY00.0020.01124.225-0.203-0.2030.0000.0000.0000.000
17A22LYS10.8570.92724.13510.57510.5750.0000.0000.0000.000
18A23ASN0-0.015-0.02218.4500.2230.2230.0000.0000.0000.000
19A24LEU00.0170.00619.5620.2100.2100.0000.0000.0000.000
20A25PHE00.0260.01213.831-0.747-0.7470.0000.0000.0000.000
21A26CYS0-0.0410.00015.8570.7760.7760.0000.0000.0000.000
22A27PHE00.0370.00511.832-1.481-1.4810.0000.0000.0000.000
23A28PRO0-0.0070.00013.2901.3001.3000.0000.0000.0000.000
24A29PRO00.0520.04816.419-0.052-0.0520.0000.0000.0000.000
25A30ILE00.0620.01717.561-0.922-0.9220.0000.0000.0000.000
26A31SER0-0.027-0.01317.649-0.560-0.5600.0000.0000.0000.000
27A32GLY00.0080.00714.237-0.597-0.5970.0000.0000.0000.000
28A33PHE00.008-0.00710.886-2.378-2.3780.0000.0000.0000.000
29A34GLY00.0740.03212.6131.4111.4110.0000.0000.0000.000
30A35ILE0-0.056-0.04514.1340.9420.9420.0000.0000.0000.000
31A36TYR00.0240.02016.5340.7810.7810.0000.0000.0000.000
32A37PHE00.0380.01616.3430.7740.7740.0000.0000.0000.000
33A38LYS10.8610.93319.73714.83714.8370.0000.0000.0000.000
34A39ASP-1-0.806-0.90621.243-11.400-11.4000.0000.0000.0000.000
35A40LEU00.0370.01221.4100.3770.3770.0000.0000.0000.000
36A41ALA00.0090.00320.4740.2610.2610.0000.0000.0000.000
37A42LEU0-0.052-0.03422.5760.2920.2920.0000.0000.0000.000
38A43GLN00.0160.01225.6460.4620.4620.0000.0000.0000.000
39A44LEU00.0210.01523.7030.4200.4200.0000.0000.0000.000
40A45ASN00.0430.01624.965-0.569-0.5690.0000.0000.0000.000
41A46HIS0-0.082-0.04925.8340.2910.2910.0000.0000.0000.000
42A47LYS10.8620.95226.86710.49310.4930.0000.0000.0000.000
43A48ALA00.0530.02123.8320.1140.1140.0000.0000.0000.000
44A49ALA00.0120.04119.746-0.113-0.1130.0000.0000.0000.000
45A50VAL0-0.004-0.01218.294-0.539-0.5390.0000.0000.0000.000
46A51TYR0-0.013-0.00913.551-0.365-0.3650.0000.0000.0000.000
47A52GLY00.0220.02114.4320.0990.0990.0000.0000.0000.000
48A53PHE00.001-0.0198.261-1.828-1.8280.0000.0000.0000.000
49A54HIS0-0.0020.0057.7453.2593.2590.0000.0000.0000.000
50A55PHE00.0390.0319.560-1.736-1.7360.0000.0000.0000.000
52A57GLU-1-0.746-0.8687.106-27.762-27.7620.0000.0000.0000.000
54A59ASP-1-0.778-0.8956.657-25.613-25.6130.0000.0000.0000.000
56A61ARG10.7840.8756.93127.09527.0950.0000.0000.0000.000
57A62ILE00.0700.0387.851-0.912-0.9120.0000.0000.0000.000
58A63GLU-1-0.789-0.8868.378-24.369-24.3690.0000.0000.0000.000
60A65TYR0-0.024-0.0306.0320.3530.3530.0000.0000.0000.000
61A66VAL00.0550.0309.2071.2211.2210.0000.0000.0000.000
62A67SER0-0.030-0.0137.1931.7651.7650.0000.0000.0000.000
63A68ARG10.8060.8985.33938.23738.2370.0000.0000.0000.000
64A69ILE00.0150.0028.8621.7651.7650.0000.0000.0000.000
65A70THR0-0.024-0.02512.3511.0711.0710.0000.0000.0000.000
66A71GLU-1-0.919-0.9517.908-33.725-33.7250.0000.0000.0000.000
67A72ILE0-0.092-0.03610.9011.1451.1450.0000.0000.0000.000
68A73GLN0-0.052-0.02713.8051.1051.1050.0000.0000.0000.000
69A74PRO00.0010.00316.4320.0020.0020.0000.0000.0000.000
70A75GLU-1-0.934-0.94517.955-13.763-13.7630.0000.0000.0000.000
71A76GLY00.0110.02820.867-0.381-0.3810.0000.0000.0000.000
72A77PRO00.000-0.00122.3830.3680.3680.0000.0000.0000.000
73A78TYR0-0.063-0.06217.330-0.267-0.2670.0000.0000.0000.000
74A79VAL00.0320.01920.4630.4800.4800.0000.0000.0000.000
75A80LEU0-0.025-0.01215.993-0.850-0.8500.0000.0000.0000.000
76A81LEU00.003-0.00218.7020.9040.9040.0000.0000.0000.000
77A82GLY00.0290.00718.445-1.161-1.1610.0000.0000.0000.000
78A83TYR0-0.027-0.04319.8620.5560.5560.0000.0000.0000.000
79A84SER0-0.014-0.01120.790-0.821-0.8210.0000.0000.0000.000
80A85ALA00.0150.00019.518-0.151-0.1510.0000.0000.0000.000
81A86GLY00.0400.02417.384-0.551-0.5510.0000.0000.0000.000
82A87GLY0-0.055-0.03118.322-0.418-0.4180.0000.0000.0000.000
83A88ASN0-0.009-0.01820.6310.0040.0040.0000.0000.0000.000
84A89LEU00.0030.00912.726-0.314-0.3140.0000.0000.0000.000
85A90ALA00.000-0.00916.235-0.715-0.7150.0000.0000.0000.000
86A91PHE00.0140.02117.244-0.042-0.0420.0000.0000.0000.000
87A92GLU-1-0.773-0.89216.029-16.096-16.0960.0000.0000.0000.000
88A93VAL0-0.064-0.02913.012-0.809-0.8090.0000.0000.0000.000
89A94VAL00.0020.00515.424-0.117-0.1170.0000.0000.0000.000
90A95GLN0-0.001-0.00518.828-0.262-0.2620.0000.0000.0000.000
91A96ALA0-0.014-0.00814.6410.2220.2220.0000.0000.0000.000
92A97MET0-0.069-0.03315.552-0.324-0.3240.0000.0000.0000.000
93A98GLU-1-0.751-0.86517.386-12.888-12.8880.0000.0000.0000.000
94A99GLN0-0.041-0.01618.8580.7150.7150.0000.0000.0000.000
95A100LYS10.7780.87312.80022.32622.3260.0000.0000.0000.000
96A101GLY0-0.036-0.01118.7780.0770.0770.0000.0000.0000.000
97A102LEU0-0.057-0.02815.9710.2950.2950.0000.0000.0000.000
98A103GLU-1-0.921-0.96520.506-11.629-11.6290.0000.0000.0000.000
99A104VAL0-0.004-0.00919.620-0.407-0.4070.0000.0000.0000.000
100A105SER00.000-0.02122.3860.2890.2890.0000.0000.0000.000
101A106ASP-1-0.790-0.85024.342-10.808-10.8080.0000.0000.0000.000
102A107PHE00.014-0.00120.018-0.766-0.7660.0000.0000.0000.000
103A108ILE0-0.018-0.01123.0680.5620.5620.0000.0000.0000.000
104A109ILE00.0030.00623.114-0.633-0.6330.0000.0000.0000.000
105A110VAL0-0.015-0.01324.0680.5520.5520.0000.0000.0000.000
106A111ASP-1-0.733-0.87325.162-10.847-10.8470.0000.0000.0000.000
107A112ALA00.0010.02023.721-0.097-0.0970.0000.0000.0000.000
108A113TYR0-0.055-0.03325.7100.3950.3950.0000.0000.0000.000
109A114LYS10.8250.92626.29110.63910.6390.0000.0000.0000.000
110A115LYS10.7790.89222.91813.76613.7660.0000.0000.0000.000
111A116ASP-1-0.842-0.91625.880-10.811-10.8110.0000.0000.0000.000
112A117GLN0-0.070-0.03727.9850.1880.1880.0000.0000.0000.000
113A118SER00.0030.01824.700-0.178-0.1780.0000.0000.0000.000
114A119ILE0-0.047-0.02325.1260.5480.5480.0000.0000.0000.000
115A120THR0-0.012-0.02225.026-0.415-0.4150.0000.0000.0000.000
116A121ALA00.0330.01621.782-0.102-0.1020.0000.0000.0000.000
117A122ASP-1-0.835-0.89922.444-12.785-12.7850.0000.0000.0000.000
118A123THR0-0.067-0.05222.607-0.448-0.4480.0000.0000.0000.000
119A124GLU-1-0.856-0.91424.884-10.116-10.1160.0000.0000.0000.000
120A125ASN0-0.086-0.04125.779-0.361-0.3610.0000.0000.0000.000
121A126ASP-1-0.847-0.91423.319-13.176-13.1760.0000.0000.0000.000
122A127ASP-1-0.813-0.91725.517-10.660-10.6600.0000.0000.0000.000
123A128SER0-0.031-0.02126.657-0.289-0.2890.0000.0000.0000.000
124A129ALA0-0.034-0.00727.7100.0280.0280.0000.0000.0000.000
125A130ALA0-0.0200.00725.9470.2080.2080.0000.0000.0000.000
126A131TYR0-0.054-0.04425.697-0.340-0.3400.0000.0000.0000.000
127A132LEU0-0.033-0.01020.394-0.009-0.0090.0000.0000.0000.000
128A133PRO00.0180.00223.7750.1960.1960.0000.0000.0000.000
129A134GLU-1-0.742-0.83123.365-13.306-13.3060.0000.0000.0000.000
130A135ALA00.0450.02621.254-0.419-0.4190.0000.0000.0000.000
131A136VAL0-0.043-0.01718.971-0.904-0.9040.0000.0000.0000.000
132A137ARG10.7980.86318.86412.42112.4210.0000.0000.0000.000
133A138GLU-1-0.927-0.96518.097-15.774-15.7740.0000.0000.0000.000
134A139THR0-0.024-0.02714.100-0.981-0.9810.0000.0000.0000.000
135A140VAL0-0.066-0.03614.623-1.246-1.2460.0000.0000.0000.000
136A141MET0-0.039-0.01815.913-0.602-0.6020.0000.0000.0000.000
137A142GLN0-0.039-0.00610.7321.2711.2710.0000.0000.0000.000
138A143LYS10.8220.9058.04431.30631.3060.0000.0000.0000.000
139A144LYS10.9280.97612.84714.30314.3030.0000.0000.0000.000
140A145ARG10.7990.86416.36914.92814.9280.0000.0000.0000.000
141A146CYS00.0390.03312.269-0.306-0.3060.0000.0000.0000.000
142A147TYR0-0.020-0.02014.041-0.144-0.1440.0000.0000.0000.000
143A148GLN0-0.019-0.02215.1310.2950.2950.0000.0000.0000.000
144A149GLU-1-0.955-0.96716.852-16.764-16.7640.0000.0000.0000.000
145A150TYR00.0260.00114.5210.3130.3130.0000.0000.0000.000
146A151TRP00.005-0.01816.6530.6530.6530.0000.0000.0000.000
147A152ALA0-0.0120.00019.1700.6540.6540.0000.0000.0000.000
148A153GLN0-0.052-0.04617.9860.8510.8510.0000.0000.0000.000
149A154LEU0-0.050-0.00418.1820.2730.2730.0000.0000.0000.000
150A155ILE0-0.008-0.00320.7290.6930.6930.0000.0000.0000.000
151A156ASN0-0.051-0.02820.868-0.038-0.0380.0000.0000.0000.000
152A157GLU-1-0.917-0.95923.426-11.844-11.8440.0000.0000.0000.000
153A158GLY0-0.033-0.01624.963-0.223-0.2230.0000.0000.0000.000
154A159ARG10.8640.91926.74610.08810.0880.0000.0000.0000.000
155A160ILE00.0030.02522.438-0.530-0.5300.0000.0000.0000.000
156A161LYS10.9240.95625.31611.34211.3420.0000.0000.0000.000
157A162SER0-0.011-0.00923.9300.2840.2840.0000.0000.0000.000
158A163ASN0-0.077-0.04426.0350.3700.3700.0000.0000.0000.000
159A164ILE0-0.019-0.01226.639-0.454-0.4540.0000.0000.0000.000
160A165HIS00.010-0.01127.3560.7110.7110.0000.0000.0000.000
161A166PHE00.0120.00327.767-0.334-0.3340.0000.0000.0000.000
162A167ILE0-0.013-0.01227.7020.4260.4260.0000.0000.0000.000
163A168GLU-1-0.758-0.85729.300-9.244-9.2440.0000.0000.0000.000
164A169ALA00.018-0.01931.3490.1200.1200.0000.0000.0000.000
165A170GLY00.0080.01232.6510.2400.2400.0000.0000.0000.000
166A171ILE0-0.101-0.05035.2620.3230.3230.0000.0000.0000.000
167A172GLN00.0150.01034.818-0.169-0.1690.0000.0000.0000.000
168A173THR0-0.013-0.01436.9960.1900.1900.0000.0000.0000.000
169A174GLU-1-0.959-0.97735.316-8.739-8.7390.0000.0000.0000.000
170A175THR0-0.006-0.01036.258-0.154-0.1540.0000.0000.0000.000
171A176SER0-0.0010.00236.2040.2630.2630.0000.0000.0000.000
172A177GLY00.010-0.00937.358-0.132-0.1320.0000.0000.0000.000
173A178ALA00.006-0.00335.141-0.035-0.0350.0000.0000.0000.000
174A179MET00.0300.01732.064-0.237-0.2370.0000.0000.0000.000
175A180VAL0-0.012-0.00633.678-0.147-0.1470.0000.0000.0000.000
176A181LEU0-0.034-0.01835.8820.0030.0030.0000.0000.0000.000
177A182GLN00.0270.03230.317-0.240-0.2400.0000.0000.0000.000
178A183LYS10.8100.90230.3518.5298.5290.0000.0000.0000.000
179A184TRP00.021-0.01023.437-0.023-0.0230.0000.0000.0000.000
180A185GLN0-0.0310.00230.3400.0360.0360.0000.0000.0000.000
181A186ASP-1-0.894-0.94831.059-10.264-10.2640.0000.0000.0000.000
182A187ALA0-0.010-0.01027.332-0.079-0.0790.0000.0000.0000.000
183A188ALA00.0570.03927.984-0.424-0.4240.0000.0000.0000.000
184A189GLU-1-0.990-0.99728.876-10.650-10.6500.0000.0000.0000.000
185A190GLU-1-0.925-0.96930.972-9.804-9.8040.0000.0000.0000.000
186A191GLY00.0030.01631.4140.3170.3170.0000.0000.0000.000
187A192TYR0-0.043-0.05131.116-0.230-0.2300.0000.0000.0000.000
188A193ALA0-0.043-0.01232.1230.3750.3750.0000.0000.0000.000
189A194GLU-1-0.865-0.91832.110-9.110-9.1100.0000.0000.0000.000
190A195TYR0-0.073-0.05531.4220.4150.4150.0000.0000.0000.000
191A196THR0-0.047-0.03033.428-0.164-0.1640.0000.0000.0000.000
192A197GLY00.0140.01632.5520.0830.0830.0000.0000.0000.000
193A198TYR0-0.053-0.04632.7650.3480.3480.0000.0000.0000.000
194A199GLY00.0620.03132.389-0.316-0.3160.0000.0000.0000.000
195A200ALA00.0150.00633.1880.0610.0610.0000.0000.0000.000
196A201HIS00.0500.01726.282-0.562-0.5620.0000.0000.0000.000
197A202LYS10.8390.90927.2519.6379.6370.0000.0000.0000.000
198A203ASP-1-0.819-0.88427.358-10.126-10.1260.0000.0000.0000.000
199A204MET0-0.076-0.00127.521-0.110-0.1100.0000.0000.0000.000
200A205LEU0-0.005-0.00822.7680.0460.0460.0000.0000.0000.000
201A206GLU-1-0.910-0.94524.575-12.570-12.5700.0000.0000.0000.000
202A207GLY00.005-0.00727.2870.4190.4190.0000.0000.0000.000
203A208GLU-1-0.985-1.00630.497-8.572-8.5720.0000.0000.0000.000
204A209PHE0-0.022-0.01430.8090.2220.2220.0000.0000.0000.000
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