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: 9QQK2

Calculation Name: 1F8G-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide

Ligand 3-letter code: NAD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F8G

Chain ID: A

ChEMBL ID:

UniProt ID: Q2RSB2

Base Structure: X-ray

Registration Date: 2025-10-06

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 382
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -5661762.173218
FMO2-HF: Nuclear repulsion 5520072.325214
FMO2-HF: Total energy -141689.848004
FMO2-MP2: Total energy -142097.792559


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.
-175.662-162.6121.374-12.338-22.088-0.118
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 : 0.800 / q_NPA : 0.908
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].
3A3ILE0-0.005-0.0013.4481.3003.1460.026-0.792-1.080-0.002
4A4ALA00.0040.0065.2772.0752.077-0.001-0.0010.0010.000
31A31PHE0-0.044-0.0332.734-17.218-15.8115.366-1.473-5.300-0.011
32A32GLU-1-0.825-0.8913.965-44.397-43.787-0.001-0.156-0.4530.000
69A69ASP-1-0.784-0.8792.076-76.628-74.8628.855-5.628-4.993-0.055
70A70VAL0-0.015-0.0033.6564.4045.1880.214-0.190-0.8080.001
345A347VAL0-0.042-0.0112.970-2.657-2.1110.081-0.096-0.5310.000
346A348ASP-1-0.821-0.8694.414-26.852-26.779-0.001-0.008-0.0640.000
347A349LYS10.8780.9204.74520.99321.068-0.001-0.004-0.0710.000
350A352LYS10.8900.9572.88547.71148.9560.149-0.389-1.006-0.002
351A353THR0-0.026-0.0182.572-23.135-19.1412.464-2.822-3.635-0.038
352A354LEU0-0.003-0.0192.253-1.292-0.6764.189-0.961-3.844-0.011
353A355VAL0-0.016-0.0083.5452.2372.3250.0340.182-0.3040.000
5A5ILE0-0.017-0.0078.8251.0791.0790.0000.0000.0000.000
6A6PRO00.0210.01112.3340.2940.2940.0000.0000.0000.000
7A7LYS10.9460.96615.55612.81112.8110.0000.0000.0000.000
8A8GLU-1-0.786-0.87318.422-14.856-14.8560.0000.0000.0000.000
9A9ARG10.8680.91120.78614.11114.1110.0000.0000.0000.000
10A10ARG10.7740.87222.59712.55612.5560.0000.0000.0000.000
11A11PRO00.002-0.01625.597-0.038-0.0380.0000.0000.0000.000
12A12GLY00.0270.01829.1150.0750.0750.0000.0000.0000.000
13A13GLU-1-0.786-0.84022.910-11.967-11.9670.0000.0000.0000.000
14A14ASP-1-0.912-0.94724.933-10.980-10.9800.0000.0000.0000.000
15A15ARG10.7370.83121.77311.87211.8720.0000.0000.0000.000
16A16VAL00.0000.00316.756-0.321-0.3210.0000.0000.0000.000
17A17ALA0-0.0010.00214.4780.2060.2060.0000.0000.0000.000
18A18ILE00.001-0.01312.051-1.280-1.2800.0000.0000.0000.000
19A19SER00.0550.01815.2251.3171.3170.0000.0000.0000.000
20A20PRO00.0640.02015.919-1.105-1.1050.0000.0000.0000.000
21A21GLU-1-0.872-0.91416.584-15.609-15.6090.0000.0000.0000.000
22A22VAL0-0.001-0.01012.128-0.665-0.6650.0000.0000.0000.000
23A23VAL00.0140.02011.736-1.857-1.8570.0000.0000.0000.000
24A24LYS10.9951.01011.37814.61614.6160.0000.0000.0000.000
25A25LYS10.8990.95911.67017.27117.2710.0000.0000.0000.000
26A26LEU00.0200.0186.758-1.166-1.1660.0000.0000.0000.000
27A27VAL00.0390.0207.084-4.380-4.3800.0000.0000.0000.000
28A28GLY0-0.018-0.0048.865-1.527-1.5270.0000.0000.0000.000
29A29LEU0-0.062-0.0405.6371.7711.7710.0000.0000.0000.000
30A30GLY00.0210.0195.272-3.303-3.3030.0000.0000.0000.000
33A33VAL00.0120.0016.008-1.958-1.9580.0000.0000.0000.000
34A34ILE0-0.0020.0068.4172.3262.3260.0000.0000.0000.000
35A35VAL00.0160.00110.4260.0610.0610.0000.0000.0000.000
36A36GLU-1-0.810-0.87813.508-15.275-15.2750.0000.0000.0000.000
37A37GLN0-0.018-0.00916.5260.6510.6510.0000.0000.0000.000
38A38GLY00.0380.00219.8000.3890.3890.0000.0000.0000.000
39A39ALA0-0.057-0.03517.8090.4960.4960.0000.0000.0000.000
40A40GLY00.001-0.00419.7980.1890.1890.0000.0000.0000.000
41A41VAL00.0040.00921.0520.4460.4460.0000.0000.0000.000
42A42GLY00.0370.02124.6410.4050.4050.0000.0000.0000.000
43A43ALA0-0.025-0.01022.4280.3390.3390.0000.0000.0000.000
44A44SER0-0.036-0.02224.5320.1640.1640.0000.0000.0000.000
45A45ILE0-0.060-0.02519.444-0.134-0.1340.0000.0000.0000.000
46A46THR00.0430.00622.181-0.329-0.3290.0000.0000.0000.000
47A47ASP-1-0.757-0.88219.654-15.363-15.3630.0000.0000.0000.000
48A48ASP-1-0.883-0.92319.777-14.011-14.0110.0000.0000.0000.000
49A49ALA0-0.033-0.01221.250-0.393-0.3930.0000.0000.0000.000
50A50LEU0-0.021-0.02015.782-0.652-0.6520.0000.0000.0000.000
51A51THR00.016-0.00516.333-1.330-1.3300.0000.0000.0000.000
52A52ALA0-0.027-0.01317.197-0.646-0.6460.0000.0000.0000.000
53A53ALA0-0.116-0.06216.1630.2430.2430.0000.0000.0000.000
54A54GLY0-0.001-0.00313.458-0.862-0.8620.0000.0000.0000.000
55A55ALA0-0.055-0.02212.010-2.302-2.3020.0000.0000.0000.000
56A56THR0-0.013-0.02110.9391.2341.2340.0000.0000.0000.000
57A57ILE0-0.0090.00113.537-0.428-0.4280.0000.0000.0000.000
58A58ALA00.0030.00714.0280.0350.0350.0000.0000.0000.000
59A59SER00.003-0.01516.0990.6350.6350.0000.0000.0000.000
60A60THR00.012-0.00317.9720.6830.6830.0000.0000.0000.000
61A61ALA00.0330.02116.238-1.097-1.0970.0000.0000.0000.000
62A62ALA00.0410.01615.142-1.067-1.0670.0000.0000.0000.000
63A63GLN00.0000.00414.558-0.989-0.9890.0000.0000.0000.000
64A64ALA00.003-0.00212.378-1.670-1.6700.0000.0000.0000.000
65A65LEU0-0.006-0.01410.533-2.451-2.4510.0000.0000.0000.000
66A66SER0-0.019-0.00210.653-1.967-1.9670.0000.0000.0000.000
67A67GLN00.018-0.0097.463-2.115-2.1150.0000.0000.0000.000
68A68ALA0-0.0400.0086.105-5.681-5.6810.0000.0000.0000.000
71A71VAL00.0160.0085.627-0.959-0.9590.0000.0000.0000.000
72A72TRP00.001-0.0129.0380.8890.8890.0000.0000.0000.000
73A73LYS10.8400.89111.46815.29215.2920.0000.0000.0000.000
74A74VAL0-0.031-0.01315.1410.0440.0440.0000.0000.0000.000
75A75GLN0-0.016-0.03518.6110.3140.3140.0000.0000.0000.000
76A76ARG10.8930.95419.24610.80010.8000.0000.0000.0000.000
77A77PRO0-0.0130.00516.7710.3900.3900.0000.0000.0000.000
78A78MET0-0.039-0.02219.2610.4030.4030.0000.0000.0000.000
79A79THR00.0610.02321.514-0.476-0.4760.0000.0000.0000.000
80A80ALA00.006-0.01023.8150.2560.2560.0000.0000.0000.000
81A81GLU-1-0.940-0.96126.279-9.725-9.7250.0000.0000.0000.000
82A82GLU-1-0.786-0.85625.178-11.150-11.1500.0000.0000.0000.000
83A83GLY00.0310.02428.0780.0430.0430.0000.0000.0000.000
84A84THR0-0.077-0.05822.466-0.094-0.0940.0000.0000.0000.000
85A85ASP-1-0.817-0.90821.080-13.602-13.6020.0000.0000.0000.000
86A86GLU-1-0.841-0.93418.033-14.997-14.9970.0000.0000.0000.000
87A87VAL0-0.019-0.01416.706-1.076-1.0760.0000.0000.0000.000
88A88ALA0-0.008-0.01716.534-0.879-0.8790.0000.0000.0000.000
89A89LEU0-0.047-0.02315.802-0.539-0.5390.0000.0000.0000.000
90A90ILE0-0.056-0.00610.987-1.443-1.4430.0000.0000.0000.000
91A91LYS10.8340.9175.54740.80840.8080.0000.0000.0000.000
92A92GLU-1-0.895-0.96411.175-17.470-17.4700.0000.0000.0000.000
93A93GLY0-0.017-0.00310.420-1.641-1.6410.0000.0000.0000.000
94A94ALA0-0.050-0.0027.227-1.569-1.5690.0000.0000.0000.000
95A95VAL0-0.013-0.0156.4702.7682.7680.0000.0000.0000.000
96A96LEU0-0.001-0.0028.447-1.015-1.0150.0000.0000.0000.000
97A97MET0-0.054-0.0098.3090.7670.7670.0000.0000.0000.000
98A98CYS00.0020.00912.702-0.091-0.0910.0000.0000.0000.000
99A99HIS00.0270.02116.2400.1090.1090.0000.0000.0000.000
100A100LEU00.025-0.01817.3090.1730.1730.0000.0000.0000.000
101A101GLY00.0200.01420.6390.4300.4300.0000.0000.0000.000
102A102ALA00.0430.01421.0350.3920.3920.0000.0000.0000.000
103A103LEU0-0.029-0.02323.1530.2590.2590.0000.0000.0000.000
104A104THR0-0.047-0.01726.3310.4400.4400.0000.0000.0000.000
105A105ASN0-0.076-0.03624.7510.2800.2800.0000.0000.0000.000
106A106ARG10.9440.96924.6729.8489.8480.0000.0000.0000.000
107A107PRO00.1060.05124.936-0.415-0.4150.0000.0000.0000.000
108A108VAL00.0010.00619.959-0.348-0.3480.0000.0000.0000.000
109A109VAL00.0310.01220.075-0.630-0.6300.0000.0000.0000.000
110A110GLU-1-0.794-0.85820.693-11.459-11.4590.0000.0000.0000.000
111A111ALA00.0040.00021.397-0.273-0.2730.0000.0000.0000.000
112A112LEU0-0.019-0.01815.410-0.548-0.5480.0000.0000.0000.000
113A113THR0-0.015-0.00516.761-0.781-0.7810.0000.0000.0000.000
114A114LYS10.8610.91118.53411.32611.3260.0000.0000.0000.000
115A115ARG10.8760.96515.23017.52817.5280.0000.0000.0000.000
116A116LYS10.9020.93414.45114.66114.6610.0000.0000.0000.000
117A117ILE0-0.0400.00111.786-0.866-0.8660.0000.0000.0000.000
118A118THR0-0.007-0.01510.1131.4951.4950.0000.0000.0000.000
119A119ALA0-0.0180.00111.283-1.133-1.1330.0000.0000.0000.000
120A120TYR00.007-0.0059.8001.2201.2200.0000.0000.0000.000
121A121ALA00.0360.02214.467-0.243-0.2430.0000.0000.0000.000
122A122MET00.0150.01314.5940.0490.0490.0000.0000.0000.000
123A123GLU-1-0.819-0.92017.693-12.906-12.9060.0000.0000.0000.000
124A124LEU0-0.064-0.02820.2820.6260.6260.0000.0000.0000.000
125A125MET00.0180.03915.5320.0670.0670.0000.0000.0000.000
126A126PRO00.0130.00719.1530.6060.6060.0000.0000.0000.000
127A127ARG10.7800.86622.33110.95110.9510.0000.0000.0000.000
128A128ILE00.0240.02219.9640.3720.3720.0000.0000.0000.000
129A129SER00.0420.00123.004-0.343-0.3430.0000.0000.0000.000
130A130ARG10.7760.86616.22013.74413.7440.0000.0000.0000.000
131A131ALA00.0600.02718.647-0.613-0.6130.0000.0000.0000.000
132A132GLN0-0.035-0.01719.6980.0330.0330.0000.0000.0000.000
133A133SER0-0.0080.00117.907-0.035-0.0350.0000.0000.0000.000
134A134MET0-0.0080.01214.663-0.597-0.5970.0000.0000.0000.000
135A135ASP-1-0.742-0.81117.189-12.015-12.0150.0000.0000.0000.000
136A136ILE00.0120.00818.1810.3330.3330.0000.0000.0000.000
137A137LEU0-0.0260.00020.9440.3900.3900.0000.0000.0000.000
138A138SER0-0.029-0.03424.0820.3480.3480.0000.0000.0000.000
139A139SER0-0.017-0.02721.3390.4660.4660.0000.0000.0000.000
140A140GLN00.0030.00022.6950.3540.3540.0000.0000.0000.000
141A141SER00.009-0.01625.8670.4660.4660.0000.0000.0000.000
142A142ASN0-0.0040.01028.1180.6170.6170.0000.0000.0000.000
143A143LEU00.0130.01226.3660.3210.3210.0000.0000.0000.000
144A144ALA00.0290.01430.1050.2600.2600.0000.0000.0000.000
145A145GLY00.0350.00632.0590.2840.2840.0000.0000.0000.000
146A146TYR0-0.009-0.00433.0580.3190.3190.0000.0000.0000.000
147A147ARG10.8270.88533.3228.8938.8930.0000.0000.0000.000
148A148ALA00.0040.00435.4020.1980.1980.0000.0000.0000.000
149A149VAL0-0.0020.00537.9990.2410.2410.0000.0000.0000.000
150A150ILE0-0.0230.00037.0270.1950.1950.0000.0000.0000.000
151A151ASP-1-0.758-0.83737.115-8.128-8.1280.0000.0000.0000.000
152A152GLY00.010-0.00340.3500.1750.1750.0000.0000.0000.000
153A153ALA0-0.045-0.03742.9530.1920.1920.0000.0000.0000.000
154A154TYR0-0.064-0.01342.1620.1110.1110.0000.0000.0000.000
155A155GLU-1-0.838-0.91443.317-6.822-6.8220.0000.0000.0000.000
156A156PHE0-0.0040.01045.9560.1870.1870.0000.0000.0000.000
157A157ALA00.0110.01148.899-0.007-0.0070.0000.0000.0000.000
158A158ARG10.7480.84551.5375.9075.9070.0000.0000.0000.000
159A159ALA00.0220.01550.385-0.133-0.1330.0000.0000.0000.000
160A160PHE00.0370.01144.2570.0420.0420.0000.0000.0000.000
161A161PRO00.0370.03748.0370.0720.0720.0000.0000.0000.000
162A162MET0-0.039-0.01950.3790.1070.1070.0000.0000.0000.000
163A163MET0-0.0010.00053.374-0.078-0.0780.0000.0000.0000.000
164A164MET00.0180.01355.7190.1190.1190.0000.0000.0000.000
165A165THR00.001-0.01158.354-0.072-0.0720.0000.0000.0000.000
166A166ALA00.0070.00460.8170.0610.0610.0000.0000.0000.000
167A167ALA0-0.0110.00363.6690.0770.0770.0000.0000.0000.000
168A168GLY00.0170.01464.0120.0550.0550.0000.0000.0000.000
169A169THR0-0.032-0.02558.853-0.090-0.0900.0000.0000.0000.000
170A170VAL00.0100.01155.6800.0560.0560.0000.0000.0000.000
171A171PRO00.002-0.00256.850-0.062-0.0620.0000.0000.0000.000
172A172PRO00.0500.03551.552-0.033-0.0330.0000.0000.0000.000
173A173ALA00.0060.02249.1140.0900.0900.0000.0000.0000.000
174A174ARG10.8190.89650.5095.7155.7150.0000.0000.0000.000
175A175VAL00.0390.01344.128-0.024-0.0240.0000.0000.0000.000
176A176LEU0-0.0070.00346.6490.0460.0460.0000.0000.0000.000
177A177VAL0-0.019-0.00839.912-0.068-0.0680.0000.0000.0000.000
178A178PHE00.025-0.00442.1930.1020.1020.0000.0000.0000.000
179A179GLY00.0140.01338.752-0.161-0.1610.0000.0000.0000.000
180A180VAL0-0.049-0.04237.629-0.070-0.0700.0000.0000.0000.000
181A181GLY00.0850.04933.694-0.072-0.0720.0000.0000.0000.000
182A182VAL0-0.017-0.02528.5770.1020.1020.0000.0000.0000.000
183A183ALA00.0370.02031.8120.0420.0420.0000.0000.0000.000
184A184GLY00.0630.03333.4540.1400.1400.0000.0000.0000.000
185A185LEU00.001-0.00433.6310.1620.1620.0000.0000.0000.000
186A186GLN0-0.025-0.01932.2140.3260.3260.0000.0000.0000.000
187A187ALA00.0220.02935.2440.1020.1020.0000.0000.0000.000
188A188ILE00.010-0.00238.1110.1970.1970.0000.0000.0000.000
189A189ALA00.0120.00936.9890.1560.1560.0000.0000.0000.000
190A190THR0-0.028-0.03036.8310.0510.0510.0000.0000.0000.000
191A191ALA00.0230.00739.3020.1310.1310.0000.0000.0000.000
192A192LYS10.8250.91442.2706.7246.7240.0000.0000.0000.000
193A193ARG10.9290.96436.2728.1658.1650.0000.0000.0000.000
194A194LEU0-0.025-0.00242.2300.0830.0830.0000.0000.0000.000
195A195GLY00.009-0.00244.8990.1420.1420.0000.0000.0000.000
196A196ALA0-0.0020.00946.4780.1580.1580.0000.0000.0000.000
197A197VAL0-0.056-0.03948.091-0.013-0.0130.0000.0000.0000.000
198A198VAL0-0.015-0.00143.5970.0080.0080.0000.0000.0000.000
199A199MET0-0.020-0.00447.0590.0770.0770.0000.0000.0000.000
200A200ALA00.0140.00242.733-0.134-0.1340.0000.0000.0000.000
201A201THR0-0.033-0.01643.8020.1230.1230.0000.0000.0000.000
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203A203VAL00.0070.00640.7230.1360.1360.0000.0000.0000.000
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