FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 7N2ZK

Calculation Name: 3ED5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: formic acid

Ligand 3-letter code: FMT

Ligand of Interest (LOI):

PDB ID: 3ED5

Chain ID: A

ChEMBL ID:

UniProt ID: O06480

Base Structure: X-ray

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3103636.711623
FMO2-HF: Nuclear repulsion 3008931.387424
FMO2-HF: Total energy -94705.3242
FMO2-MP2: Total energy -94983.062128


3D Structure
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.
-195.955-193.5540.084-1.005-1.478-0.003
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 : 0.841 / q_NPA : 0.907
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].
3A3ARG10.8930.9303.66338.91540.6140.018-0.678-1.038-0.001
228A228ASN0-0.065-0.0193.321-10.481-9.7790.066-0.327-0.440-0.002
4A4TYR0-0.033-0.0266.0920.9630.9630.0000.0000.0000.000
5A5ARG10.8950.9449.71827.18027.1800.0000.0000.0000.000
6A6THR0-0.0150.00812.6261.3431.3430.0000.0000.0000.000
7A7LEU00.0150.00812.757-0.856-0.8560.0000.0000.0000.000
8A8LEU0-0.013-0.00716.5061.0101.0100.0000.0000.0000.000
9A9PHE00.0660.01917.847-0.285-0.2850.0000.0000.0000.000
10A10ASP-1-0.762-0.87521.567-10.937-10.9370.0000.0000.0000.000
11A11VAL0-0.033-0.02624.623-0.146-0.1460.0000.0000.0000.000
12A12ASP-1-0.737-0.84527.503-9.640-9.6400.0000.0000.0000.000
13A13ASP-1-0.775-0.87328.343-9.821-9.8210.0000.0000.0000.000
14A14THR0-0.052-0.01622.511-0.453-0.4530.0000.0000.0000.000
15A15ILE0-0.039-0.03623.202-0.410-0.4100.0000.0000.0000.000
16A16LEU0-0.037-0.00925.8250.2080.2080.0000.0000.0000.000
17A17ASP-1-0.857-0.92829.672-9.310-9.3100.0000.0000.0000.000
18A18PHE0-0.034-0.02931.6290.3810.3810.0000.0000.0000.000
19A19GLN0-0.055-0.04232.8760.6140.6140.0000.0000.0000.000
20A20ALA0-0.025-0.01635.0430.3530.3530.0000.0000.0000.000
21A21ALA0-0.0090.00236.1200.2800.2800.0000.0000.0000.000
22A22GLU-1-0.857-0.94537.467-7.860-7.8600.0000.0000.0000.000
23A23ALA0-0.053-0.03139.1470.2720.2720.0000.0000.0000.000
24A24LEU0-0.038-0.01540.8020.2590.2590.0000.0000.0000.000
25A25ALA00.0370.01341.8490.2190.2190.0000.0000.0000.000
26A26LEU0-0.018-0.01342.1220.2120.2120.0000.0000.0000.000
27A27ARG10.8320.90845.0586.8006.8000.0000.0000.0000.000
28A28LEU0-0.016-0.00445.6160.1630.1630.0000.0000.0000.000
29A29LEU0-0.0200.00347.0180.1470.1470.0000.0000.0000.000
30A30PHE0-0.019-0.02648.1270.1290.1290.0000.0000.0000.000
31A31GLU-1-0.844-0.90850.751-6.133-6.1330.0000.0000.0000.000
32A32ASP-1-0.852-0.88552.161-5.804-5.8040.0000.0000.0000.000
33A33GLN0-0.053-0.04753.0590.1530.1530.0000.0000.0000.000
34A34ASN0-0.079-0.03155.2960.1310.1310.0000.0000.0000.000
35A35ILE00.0070.01753.7140.0830.0830.0000.0000.0000.000
36A36PRO0-0.010-0.01853.587-0.107-0.1070.0000.0000.0000.000
37A37LEU00.0170.02146.077-0.031-0.0310.0000.0000.0000.000
38A38THR0-0.003-0.00849.650-0.104-0.1040.0000.0000.0000.000
39A39ASN0-0.004-0.02746.985-0.192-0.1920.0000.0000.0000.000
40A40ASP-1-0.868-0.92146.542-6.345-6.3450.0000.0000.0000.000
41A41MET0-0.0020.01547.514-0.090-0.0900.0000.0000.0000.000
42A42LYS10.9400.97643.3966.7996.7990.0000.0000.0000.000
43A43ALA0-0.0100.00142.891-0.205-0.2050.0000.0000.0000.000
44A44GLN0-0.0040.00343.158-0.238-0.2380.0000.0000.0000.000
45A45TYR0-0.0110.00340.501-0.029-0.0290.0000.0000.0000.000
46A46LYS10.9380.97238.0197.7547.7540.0000.0000.0000.000
47A47THR0-0.024-0.01139.645-0.234-0.2340.0000.0000.0000.000
48A48ILE0-0.014-0.00541.127-0.109-0.1090.0000.0000.0000.000
49A49ASN00.0260.01737.7570.0140.0140.0000.0000.0000.000
50A50GLN00.0320.01733.053-0.125-0.1250.0000.0000.0000.000
51A51GLY0-0.009-0.00637.320-0.161-0.1610.0000.0000.0000.000
52A52LEU0-0.010-0.00239.555-0.049-0.0490.0000.0000.0000.000
53A53TRP00.014-0.01034.605-0.162-0.1620.0000.0000.0000.000
54A54ARG10.7710.87432.7589.0369.0360.0000.0000.0000.000
55A55ALA00.0300.01435.796-0.117-0.1170.0000.0000.0000.000
56A56PHE0-0.001-0.00234.727-0.028-0.0280.0000.0000.0000.000
57A57GLU-1-0.806-0.89331.251-10.109-10.1090.0000.0000.0000.000
58A58GLU-1-0.862-0.91533.382-8.815-8.8150.0000.0000.0000.000
59A59GLY0-0.0020.00435.5430.0870.0870.0000.0000.0000.000
60A60LYS10.7950.89337.7088.2938.2930.0000.0000.0000.000
61A61MET0-0.0300.00840.2020.1880.1880.0000.0000.0000.000
62A62THR00.0310.01740.125-0.217-0.2170.0000.0000.0000.000
63A63ARG10.8780.92135.5408.6868.6860.0000.0000.0000.000
64A64ASP-1-0.877-0.93839.942-7.424-7.4240.0000.0000.0000.000
65A65GLU-1-0.885-0.94943.335-6.812-6.8120.0000.0000.0000.000
66A66VAL00.0150.02039.0940.1230.1230.0000.0000.0000.000
67A67VAL0-0.065-0.03040.4000.0690.0690.0000.0000.0000.000
68A68ASN00.002-0.01743.0210.1860.1860.0000.0000.0000.000
69A69THR0-0.038-0.02645.7250.1610.1610.0000.0000.0000.000
70A70ARG10.8530.92039.7287.7387.7380.0000.0000.0000.000
71A71PHE00.0170.00443.8430.1010.1010.0000.0000.0000.000
72A72SER0-0.035-0.02548.3630.1320.1320.0000.0000.0000.000
73A73ALA0-0.040-0.02348.0100.1270.1270.0000.0000.0000.000
74A74LEU00.0250.01247.2140.0900.0900.0000.0000.0000.000
75A75LEU0-0.007-0.01449.8320.1050.1050.0000.0000.0000.000
76A76LYS10.9751.00952.9875.9705.9700.0000.0000.0000.000
77A77GLU-1-0.904-0.95649.823-6.211-6.2110.0000.0000.0000.000
78A78TYR0-0.045-0.03550.4040.0310.0310.0000.0000.0000.000
79A79GLY0-0.022-0.00355.3910.0730.0730.0000.0000.0000.000
80A80TYR0-0.043-0.02956.1880.1200.1200.0000.0000.0000.000
81A81GLU-1-0.938-0.97656.693-5.424-5.4240.0000.0000.0000.000
82A82ALA0-0.018-0.00753.7840.0100.0100.0000.0000.0000.000
83A83ASP-1-0.863-0.93053.710-5.965-5.9650.0000.0000.0000.000
84A84GLY00.018-0.00350.497-0.058-0.0580.0000.0000.0000.000
85A85ALA00.0550.03149.088-0.152-0.1520.0000.0000.0000.000
86A86LEU0-0.043-0.01949.815-0.085-0.0850.0000.0000.0000.000
87A87LEU0-0.021-0.01349.612-0.054-0.0540.0000.0000.0000.000
88A88GLU-1-0.709-0.82643.051-7.533-7.5330.0000.0000.0000.000
89A89GLN0-0.045-0.02446.004-0.046-0.0460.0000.0000.0000.000
90A90LYS10.8060.88347.6895.8985.8980.0000.0000.0000.000
91A91TYR00.0190.00239.771-0.058-0.0580.0000.0000.0000.000
92A92ARG10.8160.88138.3187.7007.7000.0000.0000.0000.000
93A93ARG10.8910.93242.5076.4946.4940.0000.0000.0000.000
94A94PHE00.007-0.00243.671-0.056-0.0560.0000.0000.0000.000
95A95LEU00.0020.00237.557-0.109-0.1090.0000.0000.0000.000
96A96GLU-1-0.828-0.88138.862-8.023-8.0230.0000.0000.0000.000
97A97GLU-1-0.885-0.91840.142-6.980-6.9800.0000.0000.0000.000
98A98GLY0-0.0120.00538.583-0.023-0.0230.0000.0000.0000.000
99A99HIS0-0.025-0.01134.666-0.353-0.3530.0000.0000.0000.000
100A100GLN00.0490.02433.603-0.235-0.2350.0000.0000.0000.000
101A101LEU00.0180.01928.017-0.183-0.1830.0000.0000.0000.000
102A102ILE0-0.0160.00525.1910.2250.2250.0000.0000.0000.000
103A103ASP-1-0.891-0.95526.088-10.617-10.6170.0000.0000.0000.000
104A104GLY0-0.009-0.01423.292-0.463-0.4630.0000.0000.0000.000
105A105ALA0-0.008-0.00222.726-0.504-0.5040.0000.0000.0000.000
106A106PHE0-0.015-0.01323.223-0.361-0.3610.0000.0000.0000.000
107A107ASP-1-0.871-0.93922.310-12.059-12.0590.0000.0000.0000.000
108A108LEU0-0.031-0.00216.477-0.596-0.5960.0000.0000.0000.000
109A109ILE0-0.008-0.00718.883-0.740-0.7400.0000.0000.0000.000
110A110SER0-0.0020.00220.611-0.243-0.2430.0000.0000.0000.000
111A111ASN0-0.034-0.04716.814-0.179-0.1790.0000.0000.0000.000
112A112LEU0-0.066-0.03414.126-1.148-1.1480.0000.0000.0000.000
113A113GLN00.0370.02016.488-0.847-0.8470.0000.0000.0000.000
114A114GLN0-0.081-0.02716.9310.0600.0600.0000.0000.0000.000
115A115GLN0-0.079-0.04511.575-1.969-1.9690.0000.0000.0000.000
116A116PHE0-0.044-0.0219.885-1.986-1.9860.0000.0000.0000.000
117A117ASP-1-0.863-0.92415.173-15.752-15.7520.0000.0000.0000.000
118A118LEU00.0070.00917.576-0.481-0.4810.0000.0000.0000.000
119A119TYR00.009-0.00819.4770.8920.8920.0000.0000.0000.000
120A120ILE00.0020.01822.175-0.242-0.2420.0000.0000.0000.000
121A121VAL0-0.006-0.00322.4560.1690.1690.0000.0000.0000.000
122A122THR00.0370.01625.4520.1910.1910.0000.0000.0000.000
123A123ASN00.0690.01728.658-0.011-0.0110.0000.0000.0000.000
124A124GLY00.0000.01431.7860.3680.3680.0000.0000.0000.000
125A125VAL0-0.040-0.02633.829-0.051-0.0510.0000.0000.0000.000
126A126SER00.0540.02234.852-0.111-0.1110.0000.0000.0000.000
127A127HIS0-0.054-0.03935.633-0.120-0.1200.0000.0000.0000.000
128A128THR0-0.019-0.03336.268-0.018-0.0180.0000.0000.0000.000
129A129GLN0-0.004-0.00531.3840.1530.1530.0000.0000.0000.000
130A130TYR00.011-0.00532.296-0.141-0.1410.0000.0000.0000.000
131A131LYS10.7530.86034.3067.8547.8540.0000.0000.0000.000
132A132ARG10.8230.88732.9889.1519.1510.0000.0000.0000.000
133A133LEU00.0490.03928.369-0.122-0.1220.0000.0000.0000.000
134A134ARG10.8480.94031.4188.8508.8500.0000.0000.0000.000
135A135ASP-1-0.855-0.90733.970-8.274-8.2740.0000.0000.0000.000
136A136SER0-0.018-0.02431.234-0.050-0.0500.0000.0000.0000.000
137A137GLY0-0.022-0.01730.824-0.234-0.2340.0000.0000.0000.000
138A138LEU00.0260.00825.659-0.297-0.2970.0000.0000.0000.000
139A139PHE0-0.001-0.01727.090-0.309-0.3090.0000.0000.0000.000
140A140PRO0-0.037-0.03328.323-0.183-0.1830.0000.0000.0000.000
141A141PHE0-0.0100.01423.060-0.193-0.1930.0000.0000.0000.000
142A142PHE0-0.019-0.00622.261-0.736-0.7360.0000.0000.0000.000
143A143LYS10.8030.90820.65615.64815.6480.0000.0000.0000.000
144A144ASP-1-0.866-0.93124.731-10.898-10.8980.0000.0000.0000.000
145A145ILE0-0.057-0.03726.020-0.363-0.3630.0000.0000.0000.000
146A146PHE00.0310.01823.7890.4080.4080.0000.0000.0000.000
147A147VAL00.0320.02528.577-0.137-0.1370.0000.0000.0000.000
148A148SER00.0190.00231.5340.0480.0480.0000.0000.0000.000
149A149GLU-1-0.831-0.89132.668-8.546-8.5460.0000.0000.0000.000
150A150ASP-1-0.895-0.94133.584-9.083-9.0830.0000.0000.0000.000
151A151THR0-0.088-0.05930.665-0.040-0.0400.0000.0000.0000.000
152A152GLY0-0.027-0.00633.9750.0120.0120.0000.0000.0000.000
153A153PHE0-0.049-0.02332.4110.1310.1310.0000.0000.0000.000
154A154GLN0-0.006-0.01431.7420.0970.0970.0000.0000.0000.000
155A155LYS10.7480.87525.49111.74311.7430.0000.0000.0000.000
156A156PRO0-0.021-0.01226.9860.3880.3880.0000.0000.0000.000
157A157MET0-0.040-0.02227.177-0.242-0.2420.0000.0000.0000.000
158A158LYS10.9860.99226.35610.36810.3680.0000.0000.0000.000
159A159GLU-1-0.885-0.95227.223-10.596-10.5960.0000.0000.0000.000
160A160TYR0-0.045-0.02425.844-0.116-0.1160.0000.0000.0000.000
161A161PHE00.0260.00822.779-0.142-0.1420.0000.0000.0000.000
162A162ASN0-0.005-0.00224.885-0.712-0.7120.0000.0000.0000.000
163A163TYR0-0.010-0.00126.758-0.023-0.0230.0000.0000.0000.000
164A164VAL00.0220.01422.806-0.001-0.0010.0000.0000.0000.000
165A165PHE0-0.002-0.01520.687-0.318-0.3180.0000.0000.0000.000
166A166GLU-1-0.965-0.98023.389-12.401-12.4010.0000.0000.0000.000
167A167ARG10.8460.93125.52911.16611.1660.0000.0000.0000.000
168A168ILE0-0.0120.01419.525-0.101-0.1010.0000.0000.0000.000
169A169PRO0-0.021-0.02221.787-0.296-0.2960.0000.0000.0000.000
170A170GLN0-0.049-0.03017.641-0.137-0.1370.0000.0000.0000.000
171A171PHE00.0490.03917.085-1.509-1.5090.0000.0000.0000.000
172A172SER00.001-0.00613.341-0.890-0.8900.0000.0000.0000.000
173A173ALA00.0410.03514.624-0.873-0.8730.0000.0000.0000.000
174A174GLU-1-0.909-0.9498.579-33.299-33.2990.0000.0000.0000.000
175A175HIS0-0.042-0.0278.742-5.564-5.5640.0000.0000.0000.000
176A176THR00.026-0.00411.2480.5770.5770.0000.0000.0000.000
177A177LEU0-0.036-0.00211.938-0.640-0.6400.0000.0000.0000.000
178A178ILE0-0.030-0.00514.2520.7760.7760.0000.0000.0000.000
179A179ILE0-0.020-0.01415.849-0.533-0.5330.0000.0000.0000.000
180A180GLY00.0500.01218.8460.5760.5760.0000.0000.0000.000
181A181ASP-1-0.823-0.90422.001-11.565-11.5650.0000.0000.0000.000
182A182SER00.0200.02724.7260.1340.1340.0000.0000.0000.000
183A183LEU00.0130.00723.577-0.293-0.2930.0000.0000.0000.000
184A184THR0-0.071-0.05425.574-0.151-0.1510.0000.0000.0000.000
185A185ALA00.0360.01827.3720.0990.0990.0000.0000.0000.000
186A186ASP-1-0.725-0.86522.202-12.696-12.6960.0000.0000.0000.000
187A187ILE0-0.0120.00819.527-0.540-0.5400.0000.0000.0000.000
188A188LYS10.8900.93921.51810.34210.3420.0000.0000.0000.000
189A189GLY00.0380.01323.927-0.019-0.0190.0000.0000.0000.000
190A190GLY00.013-0.00419.535-0.155-0.1550.0000.0000.0000.000
191A191GLN0-0.0040.00619.450-0.476-0.4760.0000.0000.0000.000
192A192LEU0-0.083-0.05120.4520.0000.0000.0000.0000.0000.000
193A193ALA0-0.051-0.01321.4350.1850.1850.0000.0000.0000.000
194A194GLY0-0.021-0.00318.161-0.376-0.3760.0000.0000.0000.000
195A195LEU0-0.048-0.02115.778-1.187-1.1870.0000.0000.0000.000
196A196ASP-1-0.796-0.85110.309-27.166-27.1660.0000.0000.0000.000
197A197THR00.007-0.00613.8920.9680.9680.0000.0000.0000.000
198A198CYS0-0.045-0.02014.726-0.530-0.5300.0000.0000.0000.000
199A199TRP0-0.029-0.02416.5080.5520.5520.0000.0000.0000.000
200A200MET0-0.0070.00119.912-0.429-0.4290.0000.0000.0000.000
201A201ASN00.011-0.00521.8791.0421.0420.0000.0000.0000.000
202A202PRO00.0700.03524.1190.0560.0560.0000.0000.0000.000
203A203ASP-1-0.917-0.96625.795-9.816-9.8160.0000.0000.0000.000
204A204MET0-0.090-0.03925.1700.3010.3010.0000.0000.0000.000
205A205LYS10.9250.96727.08110.21610.2160.0000.0000.0000.000
206A206PRO00.0200.01127.300-0.346-0.3460.0000.0000.0000.000
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