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

tag_button

FMODB ID: LR5Q9

Calculation Name: 2DT5-A-Xray549

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide

Ligand 3-letter code: NAD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DT5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHS3

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2136174.361729
FMO2-HF: Nuclear repulsion 2056750.756933
FMO2-HF: Total energy -79423.604796
FMO2-MP2: Total energy -79659.000118


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:2:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-35.498-33.471-0.001-0.559-1.467-0.001
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.843 / q_NPA : 1.907
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].
3A4PRO0-0.038-0.0103.759-1.1460.6390.001-0.542-1.244-0.001
4A5GLU-1-0.831-0.9134.710-46.417-46.287-0.001-0.011-0.1180.000
50A51TYR0-0.089-0.0304.744-6.121-6.009-0.001-0.006-0.1050.000
5A6ALA00.0410.0167.8195.7345.7340.0000.0000.0000.000
6A7ALA0-0.042-0.0217.6034.0374.0370.0000.0000.0000.000
7A8ILE00.0220.0057.8883.8553.8550.0000.0000.0000.000
8A9SER00.0210.00110.5834.8274.8270.0000.0000.0000.000
9A10ARG10.8720.9379.76750.70950.7090.0000.0000.0000.000
10A11LEU0-0.0140.00111.6962.8952.8950.0000.0000.0000.000
11A12ILE00.0220.00914.3832.6692.6690.0000.0000.0000.000
12A13THR0-0.010-0.00716.8072.5422.5420.0000.0000.0000.000
13A14TYR0-0.039-0.06214.5572.0802.0800.0000.0000.0000.000
14A15LEU0-0.036-0.00818.2121.4341.4340.0000.0000.0000.000
15A16ARG10.8690.90620.42429.28229.2820.0000.0000.0000.000
16A17ILE00.0170.02021.1741.1841.1840.0000.0000.0000.000
17A18LEU0-0.035-0.02221.0191.0671.0670.0000.0000.0000.000
18A19GLU-1-0.826-0.90324.152-25.217-25.2170.0000.0000.0000.000
19A20GLU-1-0.892-0.94326.696-20.117-20.1170.0000.0000.0000.000
20A21LEU0-0.047-0.02425.7790.8020.8020.0000.0000.0000.000
21A22GLU-1-0.865-0.91828.747-21.035-21.0350.0000.0000.0000.000
22A23ALA0-0.0020.00530.5250.7510.7510.0000.0000.0000.000
23A24GLN0-0.056-0.02330.9180.7370.7370.0000.0000.0000.000
24A25GLY00.0070.01333.8270.4270.4270.0000.0000.0000.000
25A26VAL0-0.056-0.02430.0810.2380.2380.0000.0000.0000.000
26A27HIS00.0210.00530.578-0.624-0.6240.0000.0000.0000.000
27A28ARG10.9150.94528.75918.98518.9850.0000.0000.0000.000
28A29THR00.0480.02024.5380.1490.1490.0000.0000.0000.000
29A30SER00.0430.02225.834-0.875-0.8750.0000.0000.0000.000
30A31SER00.022-0.00721.050-0.299-0.2990.0000.0000.0000.000
31A32GLU-1-0.950-0.97422.412-21.829-21.8290.0000.0000.0000.000
32A33GLN00.0680.06325.133-0.375-0.3750.0000.0000.0000.000
33A34LEU00.017-0.00220.747-0.211-0.2110.0000.0000.0000.000
34A35GLY00.0160.00721.102-0.652-0.6520.0000.0000.0000.000
35A36GLY00.0120.00422.090-0.115-0.1150.0000.0000.0000.000
36A37LEU0-0.030-0.02224.6890.3410.3410.0000.0000.0000.000
37A38ALA0-0.030-0.02319.383-0.167-0.1670.0000.0000.0000.000
38A39GLN0-0.0220.00620.707-0.930-0.9300.0000.0000.0000.000
39A40VAL00.0060.01716.456-1.046-1.0460.0000.0000.0000.000
40A41THR00.0660.02518.0200.6970.6970.0000.0000.0000.000
41A42ALA00.0540.01318.978-1.131-1.1310.0000.0000.0000.000
42A43PHE0-0.073-0.04414.595-0.295-0.2950.0000.0000.0000.000
43A44GLN0-0.003-0.00511.446-1.222-1.2220.0000.0000.0000.000
44A45VAL00.0500.03314.780-1.977-1.9770.0000.0000.0000.000
45A46ARG10.9090.94916.26427.10327.1030.0000.0000.0000.000
46A47LYS10.9370.9979.86944.76744.7670.0000.0000.0000.000
47A48ASP-1-0.751-0.84111.217-48.163-48.1630.0000.0000.0000.000
48A49LEU0-0.008-0.00312.190-2.079-2.0790.0000.0000.0000.000
49A50SER0-0.027-0.03514.0460.5200.5200.0000.0000.0000.000
51A52PHE0-0.016-0.0278.453-4.362-4.3620.0000.0000.0000.000
52A53GLY00.0100.02012.1141.2721.2720.0000.0000.0000.000
53A54SER0-0.022-0.02515.0901.7061.7060.0000.0000.0000.000
54A55TYR0-0.013-0.01715.038-0.267-0.2670.0000.0000.0000.000
55A56GLY0-0.003-0.00219.1611.0641.0640.0000.0000.0000.000
56A57THR00.0140.01122.0610.4640.4640.0000.0000.0000.000
57A58ARG10.9300.94922.80824.74624.7460.0000.0000.0000.000
58A59GLY00.0170.01226.5280.5280.5280.0000.0000.0000.000
59A60VAL0-0.0010.00529.0230.4760.4760.0000.0000.0000.000
60A61GLY00.0000.00526.3230.2480.2480.0000.0000.0000.000
61A62TYR0-0.021-0.01618.9760.1520.1520.0000.0000.0000.000
62A63THR00.0210.00024.9691.0541.0540.0000.0000.0000.000
63A64VAL00.0240.02625.677-0.935-0.9350.0000.0000.0000.000
64A65PRO00.0410.02325.450-0.909-0.9090.0000.0000.0000.000
65A66VAL0-0.063-0.02824.198-0.380-0.3800.0000.0000.0000.000
66A67LEU00.0500.01619.020-0.901-0.9010.0000.0000.0000.000
67A68LYS10.8670.92220.78321.31521.3150.0000.0000.0000.000
68A69ARG10.9300.96521.69424.53824.5380.0000.0000.0000.000
69A70GLU-1-0.864-0.91618.722-30.761-30.7610.0000.0000.0000.000
70A71LEU00.0140.00115.630-1.864-1.8640.0000.0000.0000.000
71A72ARG10.9730.97916.98024.85424.8540.0000.0000.0000.000
72A73HIS0-0.041-0.00816.9870.6780.6780.0000.0000.0000.000
73A74ILE0-0.029-0.02112.542-0.941-0.9410.0000.0000.0000.000
74A75LEU0-0.025-0.00312.385-3.265-3.2650.0000.0000.0000.000
75A76GLY00.0030.01014.3300.2540.2540.0000.0000.0000.000
76A77LEU00.0280.01616.1271.5431.5430.0000.0000.0000.000
77A78ASN0-0.061-0.03018.9710.7510.7510.0000.0000.0000.000
78A79ARG10.9030.96716.82032.97932.9790.0000.0000.0000.000
79A80LYS10.8820.95120.62022.82122.8210.0000.0000.0000.000
80A81TRP0-0.019-0.01814.044-0.107-0.1070.0000.0000.0000.000
81A82GLY00.0240.00619.7700.8570.8570.0000.0000.0000.000
82A83LEU0-0.019-0.01618.084-1.518-1.5180.0000.0000.0000.000
83A84CYS0-0.029-0.00220.2781.0411.0410.0000.0000.0000.000
84A85ILE00.0230.02520.808-1.221-1.2210.0000.0000.0000.000
85A86VAL00.0340.01021.5071.0401.0400.0000.0000.0000.000
86A87GLY00.0560.02322.755-0.739-0.7390.0000.0000.0000.000
87A88MET0-0.0210.02025.580-0.596-0.5960.0000.0000.0000.000
88A89GLY00.0370.01327.9090.8790.8790.0000.0000.0000.000
89A90ARG10.9340.95729.34419.02519.0250.0000.0000.0000.000
90A91LEU00.0450.03122.2890.2800.2800.0000.0000.0000.000
91A92GLY00.0910.04524.900-0.308-0.3080.0000.0000.0000.000
92A93SER0-0.028-0.03425.8750.2840.2840.0000.0000.0000.000
93A94ALA00.0090.00027.8000.1370.1370.0000.0000.0000.000
94A95LEU0-0.022-0.01221.476-0.102-0.1020.0000.0000.0000.000
95A96ALA00.0180.00625.449-0.306-0.3060.0000.0000.0000.000
96A97ASP-1-0.862-0.91027.507-18.251-18.2510.0000.0000.0000.000
97A98TYR0-0.0180.00822.8960.1050.1050.0000.0000.0000.000
98A99PRO0-0.023-0.01926.487-0.488-0.4880.0000.0000.0000.000
99A100GLY0-0.017-0.00724.1780.0540.0540.0000.0000.0000.000
100A101PHE0-0.023-0.00920.773-1.185-1.1850.0000.0000.0000.000
101A102GLY00.0080.00922.104-0.904-0.9040.0000.0000.0000.000
102A103GLU-1-0.932-0.97024.556-22.723-22.7230.0000.0000.0000.000
103A104SER0-0.036-0.03120.1120.4300.4300.0000.0000.0000.000
104A105PHE0-0.021-0.01115.850-0.998-0.9980.0000.0000.0000.000
105A106GLU-1-0.792-0.88821.071-21.105-21.1050.0000.0000.0000.000
106A107LEU0-0.0100.01123.177-0.428-0.4280.0000.0000.0000.000
107A108ARG10.7920.89423.02324.70824.7080.0000.0000.0000.000
108A109GLY00.0320.01226.0040.5430.5430.0000.0000.0000.000
109A110PHE00.0140.00425.423-0.970-0.9700.0000.0000.0000.000
110A111PHE00.0250.01624.4630.5340.5340.0000.0000.0000.000
111A112ASP-1-0.778-0.90626.831-20.316-20.3160.0000.0000.0000.000
112A113VAL00.002-0.00629.0840.0610.0610.0000.0000.0000.000
113A114ASP-1-0.814-0.88630.866-16.457-16.4570.0000.0000.0000.000
114A115PRO00.0180.00233.924-0.135-0.1350.0000.0000.0000.000
115A116GLU-1-0.899-0.94036.917-14.519-14.5190.0000.0000.0000.000
116A117LYS10.6610.81331.67118.32018.3200.0000.0000.0000.000
117A118VAL0-0.021-0.01832.665-0.133-0.1330.0000.0000.0000.000
118A119GLY00.0060.01234.9240.4670.4670.0000.0000.0000.000
119A120ARG10.9130.96832.36817.98117.9810.0000.0000.0000.000
120A121PRO00.0040.00034.901-0.506-0.5060.0000.0000.0000.000
121A122VAL0-0.022-0.02430.493-0.078-0.0780.0000.0000.0000.000
122A123ARG10.8470.89930.50918.70418.7040.0000.0000.0000.000
123A124GLY00.0150.01030.567-0.579-0.5790.0000.0000.0000.000
124A125GLY0-0.023-0.01331.545-0.280-0.2800.0000.0000.0000.000
125A126VAL0-0.0150.00032.1520.4450.4450.0000.0000.0000.000
126A127ILE0-0.037-0.00330.315-0.679-0.6790.0000.0000.0000.000
127A128GLU-1-0.806-0.87829.855-18.157-18.1570.0000.0000.0000.000
128A129HIS00.0750.02330.408-0.609-0.6090.0000.0000.0000.000
129A130VAL0-0.020-0.02025.130-0.311-0.3110.0000.0000.0000.000
130A131ASP-1-0.874-0.94626.855-19.743-19.7430.0000.0000.0000.000
131A132LEU0-0.040-0.01829.2390.0780.0780.0000.0000.0000.000
132A133LEU0-0.0030.01422.415-0.274-0.2740.0000.0000.0000.000
133A134PRO00.0340.00424.958-0.466-0.4660.0000.0000.0000.000
134A135GLN0-0.023-0.00925.929-0.016-0.0160.0000.0000.0000.000
135A136ARG10.7840.86226.46719.25519.2550.0000.0000.0000.000
136A137VAL00.0410.03620.114-0.042-0.0420.0000.0000.0000.000
137A138PRO00.0240.01322.721-0.565-0.5650.0000.0000.0000.000
138A139GLY0-0.039-0.01622.8230.8010.8010.0000.0000.0000.000
139A140ARG10.8000.90023.49021.64521.6450.0000.0000.0000.000
140A141ILE0-0.003-0.00519.6390.0910.0910.0000.0000.0000.000
141A142GLU-1-0.874-0.92516.140-28.357-28.3570.0000.0000.0000.000
142A143ILE00.012-0.00413.900-2.009-2.0090.0000.0000.0000.000
143A144ALA00.0350.01415.9022.0042.0040.0000.0000.0000.000
144A145LEU0-0.031-0.01216.412-1.911-1.9110.0000.0000.0000.000
145A146LEU0-0.025-0.00417.2711.6611.6610.0000.0000.0000.000
146A147THR0-0.010-0.03319.147-0.749-0.7490.0000.0000.0000.000
147A148VAL0-0.0290.00521.7561.2761.2760.0000.0000.0000.000
148A149PRO00.001-0.00422.909-0.784-0.7840.0000.0000.0000.000
149A150ARG10.9340.95121.63523.00023.0000.0000.0000.0000.000
150A151GLU-1-0.844-0.91922.444-23.145-23.1450.0000.0000.0000.000
151A152ALA0-0.004-0.00424.4420.3850.3850.0000.0000.0000.000
152A153ALA0-0.019-0.00219.099-0.270-0.2700.0000.0000.0000.000
153A154GLN00.0390.00716.337-1.559-1.5590.0000.0000.0000.000
154A155LYS10.9841.00119.41722.38022.3800.0000.0000.0000.000
155A156ALA00.008-0.01021.3180.3660.3660.0000.0000.0000.000
156A157ALA00.0220.01415.935-0.152-0.1520.0000.0000.0000.000
157A158ASP-1-0.844-0.91917.879-28.656-28.6560.0000.0000.0000.000
158A159LEU0-0.060-0.03319.5860.4090.4090.0000.0000.0000.000
159A160LEU00.002-0.00317.7860.3720.3720.0000.0000.0000.000
160A161VAL0-0.014-0.01214.876-0.271-0.2710.0000.0000.0000.000
161A162ALA0-0.033-0.01417.5860.1970.1970.0000.0000.0000.000
162A163ALA0-0.039-0.00520.9260.8770.8770.0000.0000.0000.000
163A164GLY00.0090.00218.6580.5000.5000.0000.0000.0000.000
164A165ILE0-0.080-0.02814.675-0.484-0.4840.0000.0000.0000.000
165A166LYS10.9230.95012.95930.90130.9010.0000.0000.0000.000
166A167GLY0-0.0020.00711.202-3.993-3.9930.0000.0000.0000.000
167A168ILE0-0.0010.00011.5413.3483.3480.0000.0000.0000.000
168A169LEU00.0000.01111.977-2.945-2.9450.0000.0000.0000.000
169A170ASN00.007-0.02513.5584.8054.8050.0000.0000.0000.000
170A171PHE00.0410.00315.340-0.850-0.8500.0000.0000.0000.000
171A172ALA0-0.0020.01718.2631.2811.2810.0000.0000.0000.000
172A173PRO0-0.045-0.02417.562-1.547-1.5470.0000.0000.0000.000
173A174VAL0-0.036-0.02816.3841.3971.3970.0000.0000.0000.000
174A175VAL0-0.0060.00011.371-1.853-1.8530.0000.0000.0000.000
175A176LEU0-0.025-0.00712.7461.9531.9530.0000.0000.0000.000
176A177GLU-1-0.937-0.96012.125-36.470-36.4700.0000.0000.0000.000
177A178VAL00.002-0.00510.0372.1932.1930.0000.0000.0000.000
178A179PRO00.0080.01011.684-1.876-1.8760.0000.0000.0000.000
179A180LYS10.8900.9317.77942.24842.2480.0000.0000.0000.000
180A181GLU-1-0.891-0.9457.880-46.388-46.3880.0000.0000.0000.000
181A182VAL0-0.043-0.00910.2011.2211.2210.0000.0000.0000.000
182A183ALA0-0.018-0.0057.130-3.559-3.5590.0000.0000.0000.000
183A184VAL00.003-0.0157.2535.6755.6750.0000.0000.0000.000
184A185GLU-1-0.919-0.9456.767-73.453-73.4530.0000.0000.0000.000
185A186ASN0-0.013-0.0089.7656.7606.7600.0000.0000.0000.000
186A187VAL00.0170.01412.240-1.266-1.2660.0000.0000.0000.000
187A188ASP-1-0.840-0.91615.037-33.804-33.8040.0000.0000.0000.000
188A189PHE00.0190.00117.480-0.270-0.2700.0000.0000.0000.000
189A190LEU00.004-0.00218.7481.3211.3210.0000.0000.0000.000
190A191ALA00.0490.03315.9480.7710.7710.0000.0000.0000.000
191A192GLY0-0.036-0.01718.0050.3040.3040.0000.0000.0000.000
192A193LEU00.017-0.00321.0480.9020.9020.0000.0000.0000.000
193A194THR0-0.022-0.01719.2541.0441.0440.0000.0000.0000.000
194A195ARG10.9620.98216.43833.54533.5450.0000.0000.0000.000
195A196LEU00.0110.00921.9290.8680.8680.0000.0000.0000.000
196A197SER0-0.021-0.00424.6221.0861.0860.0000.0000.0000.000
197A198PHE00.0310.01422.9290.6360.6360.0000.0000.0000.000
198A199ALA00.0410.01124.9840.7040.7040.0000.0000.0000.000
199A200ILE0-0.044-0.02926.9500.8050.8050.0000.0000.0000.000
200A201LEU0-0.029-0.00727.5240.7540.7540.0000.0000.0000.000
201A202ASN0-0.081-0.02726.7550.7610.7610.0000.0000.0000.000
202A203PRO00.0270.01528.665-0.392-0.3920.0000.0000.0000.000
203A204LYS10.8840.92930.75017.60317.6030.0000.0000.0000.000
204A205TRP00.0160.01420.4130.0510.0510.0000.0000.0000.000
205A206ARG10.8530.89624.95121.77521.7750.0000.0000.0000.000
206A207GLU-1-0.893-0.93818.144-31.010-31.0100.0000.0000.0000.000
207A208GLU-1-0.793-0.89721.648-23.854-23.8540.0000.0000.0000.000
208A209MET0-0.126-0.05523.5500.8390.8390.0000.0000.0000.000
209A210MET0-0.082-0.04017.8250.1350.1350.0000.0000.0000.000
210A211GLY-1-0.960-0.95220.661-27.332-27.3320.0000.0000.0000.000