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: YRNM2

Calculation Name: 2CC0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CC0

Chain ID: A

ChEMBL ID:

UniProt ID: Q54413

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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2014952.172923
FMO2-HF: Nuclear repulsion 1942574.582929
FMO2-HF: Total energy -72377.589994
FMO2-MP2: Total energy -72586.104658


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-34.57-33.23112.973-7.859-6.452-0.09
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.794 / q_NPA : 0.883
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].
3A3CYS00.0150.0123.0726.5948.1770.037-0.703-0.917-0.002
4A4ASN00.0110.0031.749-49.487-49.91312.933-7.120-5.387-0.088
5A5GLY00.0170.0043.8805.9746.1560.003-0.036-0.1480.000
6A6TYR00.0180.0036.833-2.115-2.1150.0000.0000.0000.000
7A7VAL00.0230.01110.0701.3171.3170.0000.0000.0000.000
8A8GLY00.0360.00813.6390.1170.1170.0000.0000.0000.000
9A9LEU0-0.0070.00316.2390.7980.7980.0000.0000.0000.000
10A10THR0-0.033-0.02918.7470.4300.4300.0000.0000.0000.000
11A11PHE00.024-0.00321.4480.0400.0400.0000.0000.0000.000
12A12ASP-1-0.777-0.88925.620-10.831-10.8310.0000.0000.0000.000
13A13ASP-1-0.856-0.93728.998-9.460-9.4600.0000.0000.0000.000
14A14GLY00.0360.05630.8330.2030.2030.0000.0000.0000.000
15A15PRO0-0.038-0.04131.6520.1090.1090.0000.0000.0000.000
16A16SER00.026-0.02532.7850.3610.3610.0000.0000.0000.000
17A17GLY00.0180.00033.834-0.152-0.1520.0000.0000.0000.000
18A18SER0-0.0090.00531.8990.0220.0220.0000.0000.0000.000
19A19THR0-0.024-0.04028.610-0.211-0.2110.0000.0000.0000.000
20A20GLN0-0.002-0.00728.332-0.220-0.2200.0000.0000.0000.000
21A21SER00.0190.00328.297-0.297-0.2970.0000.0000.0000.000
22A22LEU00.0150.02024.592-0.416-0.4160.0000.0000.0000.000
23A23LEU0-0.028-0.01123.990-0.644-0.6440.0000.0000.0000.000
24A24ASN00.0080.02023.298-0.643-0.6430.0000.0000.0000.000
25A25ALA00.0250.01523.406-0.499-0.4990.0000.0000.0000.000
26A26LEU0-0.016-0.00919.609-0.740-0.7400.0000.0000.0000.000
27A27ARG10.9000.95618.90013.14813.1480.0000.0000.0000.000
28A28GLN0-0.041-0.03018.989-0.270-0.2700.0000.0000.0000.000
29A29ASN0-0.060-0.03918.005-0.437-0.4370.0000.0000.0000.000
30A30GLY00.0000.00514.664-1.175-1.1750.0000.0000.0000.000
31A31LEU0-0.060-0.01614.152-1.159-1.1590.0000.0000.0000.000
32A32ARG10.9140.93514.58418.34918.3490.0000.0000.0000.000
33A33ALA00.0420.00017.048-0.432-0.4320.0000.0000.0000.000
34A34THR0-0.046-0.01619.4980.2470.2470.0000.0000.0000.000
35A35MET00.0190.00922.124-0.089-0.0890.0000.0000.0000.000
36A36PHE00.001-0.00923.4550.2080.2080.0000.0000.0000.000
37A37ASN00.015-0.00428.1730.1460.1460.0000.0000.0000.000
38A38GLN0-0.030-0.01531.3010.2700.2700.0000.0000.0000.000
39A39GLY00.004-0.00934.8820.0120.0120.0000.0000.0000.000
40A40GLN0-0.038-0.02637.0130.2600.2600.0000.0000.0000.000
41A41TYR00.0020.01235.3400.0950.0950.0000.0000.0000.000
42A42ALA00.002-0.01433.927-0.054-0.0540.0000.0000.0000.000
43A43ALA0-0.014-0.01335.4360.0190.0190.0000.0000.0000.000
44A44GLN0-0.029-0.00838.9440.0310.0310.0000.0000.0000.000
45A45ASN0-0.039-0.01335.6940.1550.1550.0000.0000.0000.000
46A46PRO00.0710.02934.958-0.315-0.3150.0000.0000.0000.000
47A47SER00.008-0.00133.869-0.323-0.3230.0000.0000.0000.000
48A48LEU00.0240.00831.860-0.269-0.2690.0000.0000.0000.000
49A49VAL0-0.0190.00030.160-0.398-0.3980.0000.0000.0000.000
50A50ARG10.8120.89027.78410.03810.0380.0000.0000.0000.000
51A51ALA00.0530.03328.155-0.387-0.3870.0000.0000.0000.000
52A52GLN00.008-0.00925.832-0.409-0.4090.0000.0000.0000.000
53A53VAL00.0100.01524.146-0.574-0.5740.0000.0000.0000.000
54A54ASP-1-0.834-0.89623.524-11.283-11.2830.0000.0000.0000.000
55A55ALA0-0.035-0.02823.323-0.434-0.4340.0000.0000.0000.000
56A56GLY00.0120.01019.727-0.706-0.7060.0000.0000.0000.000
57A57MET0-0.074-0.00719.260-1.101-1.1010.0000.0000.0000.000
58A58TRP00.0170.00815.3470.2970.2970.0000.0000.0000.000
59A59VAL00.0080.00422.5650.1090.1090.0000.0000.0000.000
60A60ALA0-0.038-0.01625.552-0.041-0.0410.0000.0000.0000.000
61A61ASN0-0.032-0.03927.5910.3450.3450.0000.0000.0000.000
62A62HIS10.8640.93330.5399.6429.6420.0000.0000.0000.000
63A63SER0-0.010-0.00832.5460.3290.3290.0000.0000.0000.000
64A64TYR0-0.0020.00436.205-0.080-0.0800.0000.0000.0000.000
65A65THR00.003-0.03038.9240.0440.0440.0000.0000.0000.000
66A66HIS00.0290.03534.854-0.193-0.1930.0000.0000.0000.000
67A67PRO00.0300.03038.3820.0670.0670.0000.0000.0000.000
68A68HIS10.8780.89739.2407.6857.6850.0000.0000.0000.000
69A69MET00.0030.01036.9590.2150.2150.0000.0000.0000.000
70A70THR0-0.016-0.00938.4290.1880.1880.0000.0000.0000.000
71A71GLN0-0.012-0.00741.0560.1900.1900.0000.0000.0000.000
72A72LEU0-0.0330.00641.8180.1730.1730.0000.0000.0000.000
73A73GLY00.0690.03144.983-0.013-0.0130.0000.0000.0000.000
74A74GLN00.0460.00642.3150.0110.0110.0000.0000.0000.000
75A75ALA00.0350.00843.485-0.146-0.1460.0000.0000.0000.000
76A76GLN00.0260.01644.935-0.067-0.0670.0000.0000.0000.000
77A77MET00.0000.01339.783-0.200-0.2000.0000.0000.0000.000
78A78ASP-1-0.766-0.86639.816-7.696-7.6960.0000.0000.0000.000
79A79SER00.0260.04440.812-0.159-0.1590.0000.0000.0000.000
80A80GLU-1-0.762-0.87339.293-7.752-7.7520.0000.0000.0000.000
81A81ILE00.0120.02435.037-0.178-0.1780.0000.0000.0000.000
82A82SER0-0.007-0.02336.716-0.151-0.1510.0000.0000.0000.000
83A83ARG10.8650.91838.5417.2247.2240.0000.0000.0000.000
84A84THR0-0.002-0.01433.846-0.021-0.0210.0000.0000.0000.000
85A85GLN0-0.013-0.00331.700-0.291-0.2910.0000.0000.0000.000
86A86GLN00.001-0.00435.031-0.042-0.0420.0000.0000.0000.000
87A87ALA00.0030.01336.7680.0070.0070.0000.0000.0000.000
88A88ILE0-0.010-0.00530.223-0.052-0.0520.0000.0000.0000.000
89A89ALA0-0.028-0.00832.907-0.139-0.1390.0000.0000.0000.000
90A90GLY0-0.017-0.00734.076-0.007-0.0070.0000.0000.0000.000
91A91ALA0-0.027-0.00434.0530.0960.0960.0000.0000.0000.000
92A92GLY00.0060.00732.789-0.144-0.1440.0000.0000.0000.000
93A93GLY00.005-0.00429.169-0.319-0.3190.0000.0000.0000.000
94A94GLY0-0.0090.00728.266-0.380-0.3800.0000.0000.0000.000
95A95THR00.002-0.01529.8020.3370.3370.0000.0000.0000.000
96A96PRO0-0.0110.00628.025-0.312-0.3120.0000.0000.0000.000
97A97LYS10.9430.96825.36110.71010.7100.0000.0000.0000.000
98A98LEU00.0020.02021.875-0.011-0.0110.0000.0000.0000.000
99A99PHE00.026-0.00526.5470.3100.3100.0000.0000.0000.000
100A100ARG10.7960.88023.64611.89411.8940.0000.0000.0000.000
101A101PRO00.0210.01729.4470.2340.2340.0000.0000.0000.000
102A102PRO00.0220.01732.263-0.245-0.2450.0000.0000.0000.000
103A103TYR0-0.049-0.04134.1610.1000.1000.0000.0000.0000.000
104A104GLY00.0110.01931.442-0.086-0.0860.0000.0000.0000.000
105A105GLU-1-0.913-0.91832.206-8.156-8.1560.0000.0000.0000.000
106A106THR0-0.019-0.05532.6330.1740.1740.0000.0000.0000.000
107A107ASN00.0530.01335.6620.0490.0490.0000.0000.0000.000
108A108ALA00.0460.01737.369-0.130-0.1300.0000.0000.0000.000
109A109THR00.0170.01738.849-0.046-0.0460.0000.0000.0000.000
110A110LEU00.0610.03535.2670.0010.0010.0000.0000.0000.000
111A111ARG10.8220.89931.2539.5909.5900.0000.0000.0000.000
112A112SER0-0.034-0.02435.347-0.063-0.0630.0000.0000.0000.000
113A113VAL00.0040.00437.5930.0180.0180.0000.0000.0000.000
114A114GLU0-0.028-0.05832.206-0.110-0.1100.0000.0000.0000.000
115A115ALA00.0130.01133.567-0.146-0.1460.0000.0000.0000.000
116A116LYS10.8000.91234.5787.4287.4280.0000.0000.0000.000
117A117TYR0-0.050-0.05334.7440.1110.1110.0000.0000.0000.000
118A118GLY0-0.025-0.00531.922-0.220-0.2200.0000.0000.0000.000
119A119LEU0-0.107-0.05429.426-0.366-0.3660.0000.0000.0000.000
120A120THR00.004-0.02324.5410.3580.3580.0000.0000.0000.000
121A121GLU-1-0.765-0.81227.215-9.942-9.9420.0000.0000.0000.000
122A122VAL0-0.031-0.01422.893-0.431-0.4310.0000.0000.0000.000
123A123ILE00.0250.02525.5500.2380.2380.0000.0000.0000.000
124A124TRP00.021-0.00723.034-0.320-0.3200.0000.0000.0000.000
125A125ASP-1-0.779-0.86219.955-15.036-15.0360.0000.0000.0000.000
126A126VAL0-0.038-0.01720.6870.2860.2860.0000.0000.0000.000
127A127ASP-1-0.761-0.85823.364-10.971-10.9710.0000.0000.0000.000
128A128SER0-0.038-0.05024.552-0.013-0.0130.0000.0000.0000.000
129A129GLN0-0.037-0.02425.9950.3660.3660.0000.0000.0000.000
130A130ASP-1-0.733-0.84327.843-10.870-10.8700.0000.0000.0000.000
131A131TRP0-0.058-0.05129.8770.4590.4590.0000.0000.0000.000
132A132ASN0-0.068-0.04032.6180.5540.5540.0000.0000.0000.000
133A133ASN0-0.015-0.00834.1450.1140.1140.0000.0000.0000.000
134A134ALA00.0220.03729.4150.0090.0090.0000.0000.0000.000
135A135SER00.0580.02730.202-0.164-0.1640.0000.0000.0000.000
136A136THR00.0500.00626.061-0.220-0.2200.0000.0000.0000.000
137A137ASP-1-0.818-0.88125.687-12.407-12.4070.0000.0000.0000.000
138A138ALA0-0.022-0.00525.175-0.525-0.5250.0000.0000.0000.000
139A139ILE00.0090.00823.727-0.414-0.4140.0000.0000.0000.000
140A140VAL0-0.004-0.00320.318-0.612-0.6120.0000.0000.0000.000
141A141GLN00.0210.01420.633-1.027-1.0270.0000.0000.0000.000
142A142ALA0-0.039-0.01021.830-0.311-0.3110.0000.0000.0000.000
143A143VAL00.0440.00816.797-0.467-0.4670.0000.0000.0000.000
144A144SER0-0.066-0.04017.111-1.071-1.0710.0000.0000.0000.000
145A145ARG10.9380.97817.09512.68112.6810.0000.0000.0000.000
146A146LEU0-0.0410.00915.468-0.064-0.0640.0000.0000.0000.000
147A147GLY00.0490.01513.536-1.449-1.4490.0000.0000.0000.000
148A148ASN00.027-0.0099.957-0.638-0.6380.0000.0000.0000.000
149A149GLY00.0290.02611.8161.4721.4720.0000.0000.0000.000
150A150GLN0-0.063-0.01513.9400.9700.9700.0000.0000.0000.000
151A151VAL00.0040.00016.400-0.712-0.7120.0000.0000.0000.000
152A152ILE00.0100.00019.0170.4460.4460.0000.0000.0000.000
153A153LEU0-0.0240.03021.306-0.028-0.0280.0000.0000.0000.000
154A154MET0-0.0140.01720.7960.0110.0110.0000.0000.0000.000
155A155HIS10.8290.90225.77910.66610.6660.0000.0000.0000.000
156A156ASP-1-0.780-0.86028.074-10.492-10.4920.0000.0000.0000.000
157A157TRP00.0700.02429.469-0.078-0.0780.0000.0000.0000.000
158A158PRO0-0.0300.00829.7410.1980.1980.0000.0000.0000.000
159A159ALA00.0480.01630.161-0.361-0.3610.0000.0000.0000.000
160A160ASN0-0.011-0.02229.770-0.156-0.1560.0000.0000.0000.000
161A161THR00.015-0.01725.354-0.388-0.3880.0000.0000.0000.000
162A162LEU0-0.027-0.00525.460-0.561-0.5610.0000.0000.0000.000
163A163ALA0-0.015-0.00926.230-0.346-0.3460.0000.0000.0000.000
164A164ALA0-0.0020.00123.483-0.334-0.3340.0000.0000.0000.000
165A165ILE0-0.0150.00420.605-0.803-0.8030.0000.0000.0000.000
166A166PRO00.0420.01819.807-0.934-0.9340.0000.0000.0000.000
167A167ARG10.8710.91818.99012.49112.4910.0000.0000.0000.000
168A168ILE0-0.0100.01517.392-0.867-0.8670.0000.0000.0000.000
169A169ALA00.0320.01915.225-1.216-1.2160.0000.0000.0000.000
170A170GLN0-0.008-0.01114.194-1.539-1.5390.0000.0000.0000.000
171A171THR0-0.033-0.02514.322-1.158-1.1580.0000.0000.0000.000
172A172LEU0-0.044-0.01611.848-0.899-0.8990.0000.0000.0000.000
173A173ALA00.0490.0259.852-2.822-2.8220.0000.0000.0000.000
174A174GLY0-0.015-0.0039.345-3.318-3.3180.0000.0000.0000.000
175A175LYS10.8160.90510.13622.19422.1940.0000.0000.0000.000
176A176GLY00.0010.0125.994-2.715-2.7150.0000.0000.0000.000
177A177LEU0-0.069-0.0326.095-4.784-4.7840.0000.0000.0000.000
178A179SER00.0230.0219.6761.1451.1450.0000.0000.0000.000
179A180GLY00.004-0.00412.280-0.946-0.9460.0000.0000.0000.000
180A181MET0-0.0400.01013.2331.7611.7610.0000.0000.0000.000
181A182ILE0-0.006-0.01815.802-0.699-0.6990.0000.0000.0000.000
182A183SER00.0090.00617.4890.7890.7890.0000.0000.0000.000
183A184PRO00.026-0.00319.1270.4870.4870.0000.0000.0000.000
184A185GLN00.0210.02819.9020.6600.6600.0000.0000.0000.000
185A186THR0-0.011-0.01118.3050.2650.2650.0000.0000.0000.000
186A187GLY00.0350.03421.3890.0010.0010.0000.0000.0000.000
187A188ARG10.8140.88916.87716.36016.3600.0000.0000.0000.000
188A189ALA0-0.047-0.01414.1570.1180.1180.0000.0000.0000.000
189A190VAL0-0.018-0.01512.220-0.796-0.7960.0000.0000.0000.000
190A191ALA00.0160.0009.355-0.200-0.2000.0000.0000.0000.000
191A192PRO-1-0.948-0.95910.586-18.594-18.5940.0000.0000.0000.000