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: 2MLYR

Calculation Name: 2D1Y-B-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide

Ligand 3-letter code: NAD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D1Y

Chain ID: B

ChEMBL ID:

UniProt ID: Q5SLC4

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 249
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2934174.407888
FMO2-HF: Nuclear repulsion 2843106.493089
FMO2-HF: Total energy -91067.914799
FMO2-MP2: Total energy -91336.634864


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-137.864-131.79914.775-11.477-9.361-0.136
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.769 / q_NPA : 0.874
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].
3A4PHE00.001-0.0033.38311.70113.000-0.003-0.593-0.704-0.002
4A5ALA0-0.0030.0092.0082.7062.8612.064-0.995-1.224-0.007
5A6GLY00.0070.0103.7108.2478.4730.012-0.083-0.154-0.001
28A29GLU-1-0.838-0.9152.380-86.255-82.7782.704-3.242-2.939-0.032
29A30GLY0-0.012-0.0081.832-48.661-47.8039.996-6.561-4.292-0.094
30A31ALA0-0.0110.0003.5404.5264.5760.002-0.003-0.0480.000
6A7LYS10.8360.9306.71340.56540.5650.0000.0000.0000.000
7A8GLY00.0440.0358.698-1.328-1.3280.0000.0000.0000.000
8A9VAL0-0.040-0.0299.1210.5860.5860.0000.0000.0000.000
9A10LEU00.0340.02612.1660.7230.7230.0000.0000.0000.000
10A11VAL0-0.005-0.00913.918-0.211-0.2110.0000.0000.0000.000
11A12THR00.0660.03316.7650.5720.5720.0000.0000.0000.000
12A13GLY00.0020.00620.553-0.132-0.1320.0000.0000.0000.000
13A14GLY00.006-0.00518.981-0.218-0.2180.0000.0000.0000.000
14A15ALA00.0360.01819.382-0.497-0.4970.0000.0000.0000.000
15A16ARG10.9410.95521.91511.57911.5790.0000.0000.0000.000
16A17GLY0-0.008-0.00521.544-0.115-0.1150.0000.0000.0000.000
17A18ILE00.0510.01718.087-0.727-0.7270.0000.0000.0000.000
18A19GLY00.0510.02917.029-1.101-1.1010.0000.0000.0000.000
19A20ARG10.8470.93916.46413.58413.5840.0000.0000.0000.000
20A21ALA00.0410.01914.836-1.252-1.2520.0000.0000.0000.000
21A22ILE0-0.009-0.01412.724-2.062-2.0620.0000.0000.0000.000
22A23ALA00.0160.01411.502-2.503-2.5030.0000.0000.0000.000
23A24GLN00.0260.00711.039-1.971-1.9710.0000.0000.0000.000
24A25ALA0-0.0070.0058.792-2.861-2.8610.0000.0000.0000.000
25A26PHE00.020-0.0156.887-5.292-5.2920.0000.0000.0000.000
26A27ALA00.0230.0226.104-6.845-6.8450.0000.0000.0000.000
27A28ARG10.7570.8565.68632.34232.3420.0000.0000.0000.000
31A32LEU00.0040.0096.4092.0282.0280.0000.0000.0000.000
32A33VAL0-0.002-0.0029.2791.4461.4460.0000.0000.0000.000
33A34ALA00.0150.01611.7121.2891.2890.0000.0000.0000.000
34A35LEU0-0.039-0.01515.490-0.166-0.1660.0000.0000.0000.000
35A36CYS0-0.023-0.00217.6190.6060.6060.0000.0000.0000.000
36A37ASP-1-0.795-0.92421.381-13.232-13.2320.0000.0000.0000.000
37A38LEU00.0380.04924.2560.1290.1290.0000.0000.0000.000
38A39ARG10.8450.93425.86511.47611.4760.0000.0000.0000.000
39A40PRO00.0380.02125.644-0.510-0.5100.0000.0000.0000.000
40A41GLU-1-0.788-0.90425.437-11.819-11.8190.0000.0000.0000.000
41A42GLY0-0.013-0.02821.715-0.611-0.6110.0000.0000.0000.000
42A43LYS10.8160.90320.55213.27413.2740.0000.0000.0000.000
43A44GLU-1-0.861-0.93520.659-13.256-13.2560.0000.0000.0000.000
44A45VAL0-0.067-0.02916.749-0.792-0.7920.0000.0000.0000.000
45A46ALA0-0.010-0.00216.094-1.222-1.2220.0000.0000.0000.000
46A47GLU-1-0.850-0.91915.912-15.171-15.1710.0000.0000.0000.000
47A48ALA0-0.037-0.01716.905-0.591-0.5910.0000.0000.0000.000
48A49ILE0-0.080-0.04411.656-1.129-1.1290.0000.0000.0000.000
49A50GLY0-0.0220.00511.726-2.100-2.1000.0000.0000.0000.000
50A51GLY0-0.0150.00413.393-0.843-0.8430.0000.0000.0000.000
51A52ALA0-0.023-0.01714.0411.4281.4280.0000.0000.0000.000
52A53PHE0-0.019-0.02717.112-0.421-0.4210.0000.0000.0000.000
53A54PHE0-0.0040.00118.9290.3310.3310.0000.0000.0000.000
54A55GLN0-0.039-0.03022.889-0.096-0.0960.0000.0000.0000.000
55A56VAL0-0.018-0.02224.4710.1810.1810.0000.0000.0000.000
56A57ASP-1-0.860-0.92927.174-10.146-10.1460.0000.0000.0000.000
57A58LEU0-0.024-0.02624.382-0.131-0.1310.0000.0000.0000.000
58A59GLU-1-0.881-0.94128.788-8.894-8.8940.0000.0000.0000.000
59A60ASP-1-0.830-0.90231.911-9.282-9.2820.0000.0000.0000.000
60A61GLU-1-0.935-0.97830.941-9.470-9.4700.0000.0000.0000.000
61A62ARG10.9200.94430.9928.8798.8790.0000.0000.0000.000
62A63GLU-1-0.881-0.93928.971-10.679-10.6790.0000.0000.0000.000
63A64ARG10.7720.85726.5699.9879.9870.0000.0000.0000.000
64A65VAL0-0.041-0.02325.928-0.482-0.4820.0000.0000.0000.000
65A66ARG10.9560.99326.20310.04810.0480.0000.0000.0000.000
66A67PHE00.0490.02018.926-0.416-0.4160.0000.0000.0000.000
67A68VAL0-0.014-0.01120.982-0.717-0.7170.0000.0000.0000.000
68A69GLU-1-0.947-0.97121.726-11.782-11.7820.0000.0000.0000.000
69A70GLU-1-0.912-0.97522.898-12.385-12.3850.0000.0000.0000.000
70A71ALA00.0020.00218.158-0.526-0.5260.0000.0000.0000.000
71A72ALA0-0.016-0.00918.038-1.020-1.0200.0000.0000.0000.000
72A73TYR0-0.070-0.02918.871-0.384-0.3840.0000.0000.0000.000
73A74ALA0-0.037-0.02118.788-0.344-0.3440.0000.0000.0000.000
74A75LEU0-0.050-0.02013.133-0.877-0.8770.0000.0000.0000.000
75A76GLY0-0.0250.00414.548-1.264-1.2640.0000.0000.0000.000
76A77ARG10.7790.84611.66725.38325.3830.0000.0000.0000.000
77A78VAL00.0250.00414.629-0.541-0.5410.0000.0000.0000.000
78A79ASP-1-0.760-0.84211.454-25.377-25.3770.0000.0000.0000.000
79A80VAL0-0.038-0.02510.8030.2930.2930.0000.0000.0000.000
80A81LEU00.0030.01713.7770.2260.2260.0000.0000.0000.000
81A82VAL0-0.014-0.01014.0670.0570.0570.0000.0000.0000.000
82A83ASN0-0.011-0.01217.2120.4340.4340.0000.0000.0000.000
83A84ASN0-0.013-0.03418.8480.2600.2600.0000.0000.0000.000
84A85ALA0-0.036-0.00320.8460.4910.4910.0000.0000.0000.000
85A86ALA0-0.014-0.02024.0330.1760.1760.0000.0000.0000.000
86A87ILE0-0.0310.00027.1390.0540.0540.0000.0000.0000.000
87A88ALA00.0290.01130.667-0.023-0.0230.0000.0000.0000.000
88A89ALA00.000-0.01033.5110.0650.0650.0000.0000.0000.000
89A90PRO0-0.024-0.00137.0530.0680.0680.0000.0000.0000.000
90A91GLY00.0600.02739.4050.1660.1660.0000.0000.0000.000
91A92SER00.0330.02141.273-0.142-0.1420.0000.0000.0000.000
92A93ALA00.000-0.01943.7780.0090.0090.0000.0000.0000.000
93A94LEU0-0.026-0.00845.0850.0920.0920.0000.0000.0000.000
94A95THR0-0.020-0.00845.5880.0550.0550.0000.0000.0000.000
95A96VAL0-0.0160.01440.479-0.024-0.0240.0000.0000.0000.000
96A97ARG10.8730.89342.0487.5997.5990.0000.0000.0000.000
97A98LEU00.0420.00342.941-0.195-0.1950.0000.0000.0000.000
98A99PRO0-0.023-0.02742.424-0.155-0.1550.0000.0000.0000.000
99A100GLU-1-0.779-0.84239.278-7.941-7.9410.0000.0000.0000.000
100A101TRP00.0470.02138.009-0.271-0.2710.0000.0000.0000.000
101A102ARG10.9380.96337.7847.2167.2160.0000.0000.0000.000
102A103ARG10.9380.97734.8168.4108.4100.0000.0000.0000.000
103A104VAL00.0030.00233.159-0.297-0.2970.0000.0000.0000.000
104A105LEU0-0.018-0.01132.713-0.333-0.3330.0000.0000.0000.000
105A106GLU-1-0.806-0.87632.744-9.891-9.8910.0000.0000.0000.000
106A107VAL00.012-0.00528.767-0.334-0.3340.0000.0000.0000.000
107A108ASN0-0.021-0.02628.272-0.712-0.7120.0000.0000.0000.000
108A109LEU0-0.038-0.01828.414-0.291-0.2910.0000.0000.0000.000
109A110THR0-0.024-0.01629.550-0.269-0.2690.0000.0000.0000.000
110A111ALA00.0270.02427.330-0.216-0.2160.0000.0000.0000.000
111A112PRO0-0.0010.00224.693-0.373-0.3730.0000.0000.0000.000
112A113MET0-0.0100.03125.133-0.478-0.4780.0000.0000.0000.000
113A114HIS00.0220.01827.040-0.284-0.2840.0000.0000.0000.000
114A115LEU00.0250.00522.719-0.146-0.1460.0000.0000.0000.000
115A116SER0-0.006-0.02622.339-0.791-0.7910.0000.0000.0000.000
116A117ALA0-0.006-0.00423.341-0.263-0.2630.0000.0000.0000.000
117A118LEU0-0.071-0.02424.5190.0790.0790.0000.0000.0000.000
118A119ALA00.0640.02719.192-0.137-0.1370.0000.0000.0000.000
119A120ALA00.0390.01520.399-0.543-0.5430.0000.0000.0000.000
120A121ARG10.8690.92722.22111.50011.5000.0000.0000.0000.000
121A122GLU-1-0.801-0.88119.388-14.110-14.1100.0000.0000.0000.000
122A123MET00.0080.01916.197-0.041-0.0410.0000.0000.0000.000
123A124ARG10.9270.96618.67012.51112.5110.0000.0000.0000.000
124A125LYS10.7360.85019.96314.48214.4820.0000.0000.0000.000
125A126VAL0-0.028-0.00415.0870.0150.0150.0000.0000.0000.000
126A127GLY0-0.0230.00116.647-0.781-0.7810.0000.0000.0000.000
127A128GLY0-0.020-0.01518.1310.3080.3080.0000.0000.0000.000
128A129GLY00.0170.00114.935-0.673-0.6730.0000.0000.0000.000
129A130ALA0-0.063-0.01914.0300.4880.4880.0000.0000.0000.000
130A131ILE00.0350.01416.009-0.334-0.3340.0000.0000.0000.000
131A132VAL0-0.030-0.01014.8980.3140.3140.0000.0000.0000.000
132A133ASN00.017-0.00717.929-0.192-0.1920.0000.0000.0000.000
133A134VAL00.0170.01419.189-0.183-0.1830.0000.0000.0000.000
134A135ALA00.0100.01521.6520.7080.7080.0000.0000.0000.000
135A136SER0-0.003-0.01724.6240.0110.0110.0000.0000.0000.000
136A137VAL00.0430.02426.3590.1640.1640.0000.0000.0000.000
137A138GLN0-0.012-0.01828.6520.4470.4470.0000.0000.0000.000
138A139GLY00.0250.00729.4750.2020.2020.0000.0000.0000.000
139A140LEU0-0.099-0.04627.4940.0260.0260.0000.0000.0000.000
140A141PHE00.0050.00231.5980.3130.3130.0000.0000.0000.000
141A142ALA0-0.028-0.01833.860-0.176-0.1760.0000.0000.0000.000
142A143GLU-1-0.811-0.89034.937-9.037-9.0370.0000.0000.0000.000
143A144GLN0-0.041-0.03137.7640.2420.2420.0000.0000.0000.000
144A145GLU-1-0.957-0.98539.741-7.304-7.3040.0000.0000.0000.000
145A146ASN00.0460.02433.597-0.046-0.0460.0000.0000.0000.000
146A147ALA00.0240.01336.622-0.215-0.2150.0000.0000.0000.000
147A148ALA00.0140.00037.061-0.083-0.0830.0000.0000.0000.000
148A149TYR00.0060.02727.887-0.390-0.3900.0000.0000.0000.000
149A150ASN00.004-0.00732.625-0.006-0.0060.0000.0000.0000.000
150A151ALA0-0.0070.00433.872-0.152-0.1520.0000.0000.0000.000
151A152SER0-0.017-0.02032.187-0.245-0.2450.0000.0000.0000.000
152A153LYS10.8840.94925.37211.82511.8250.0000.0000.0000.000
153A154GLY00.0380.02329.481-0.307-0.3070.0000.0000.0000.000
154A155GLY0-0.025-0.01331.702-0.050-0.0500.0000.0000.0000.000
155A156LEU0-0.0050.00224.726-0.149-0.1490.0000.0000.0000.000
156A157VAL0-0.0030.00727.018-0.452-0.4520.0000.0000.0000.000
157A158ASN00.0050.00228.028-0.292-0.2920.0000.0000.0000.000
158A159LEU00.0160.01127.366-0.009-0.0090.0000.0000.0000.000
159A160THR0-0.014-0.01823.064-0.411-0.4110.0000.0000.0000.000
160A161ARG10.9120.95325.37410.44910.4490.0000.0000.0000.000
161A162SER0-0.033-0.00727.8080.1150.1150.0000.0000.0000.000
162A163LEU00.0210.00224.572-0.090-0.0900.0000.0000.0000.000
163A164ALA0-0.0140.00423.985-0.329-0.3290.0000.0000.0000.000
164A165LEU0-0.038-0.01524.969-0.137-0.1370.0000.0000.0000.000
165A166ASP-1-0.861-0.93928.191-10.607-10.6070.0000.0000.0000.000
166A167LEU0-0.045-0.02823.093-0.007-0.0070.0000.0000.0000.000
167A168ALA00.0550.04423.458-0.524-0.5240.0000.0000.0000.000
168A169PRO0-0.042-0.02724.255-0.326-0.3260.0000.0000.0000.000
169A170LEU0-0.061-0.02523.1630.0400.0400.0000.0000.0000.000
170A171ARG10.9090.95518.61615.38415.3840.0000.0000.0000.000
171A172ILE0-0.0250.00618.813-1.116-1.1160.0000.0000.0000.000
172A173ARG10.7830.90713.84321.38321.3830.0000.0000.0000.000
173A174VAL0-0.002-0.00418.801-0.668-0.6680.0000.0000.0000.000
174A175ASN00.005-0.01417.7481.2441.2440.0000.0000.0000.000
175A176ALA00.0130.00920.473-0.095-0.0950.0000.0000.0000.000
176A177VAL00.0120.02417.132-0.079-0.0790.0000.0000.0000.000
177A178ALA00.001-0.01520.3060.4190.4190.0000.0000.0000.000
178A179PRO0-0.020-0.00520.9500.2480.2480.0000.0000.0000.000
179A180GLY00.0500.02723.4580.5450.5450.0000.0000.0000.000
180A181ALA0-0.023-0.00126.097-0.124-0.1240.0000.0000.0000.000
181A182ILE0-0.016-0.00421.307-0.255-0.2550.0000.0000.0000.000
182A183ALA00.0400.02123.9580.3310.3310.0000.0000.0000.000
183A184THR0-0.051-0.03422.299-0.392-0.3920.0000.0000.0000.000
184A185GLU-1-0.835-0.92124.540-12.336-12.3360.0000.0000.0000.000
185A186ALA00.0150.01327.0590.3640.3640.0000.0000.0000.000
186A187VAL0-0.0100.00727.7540.3800.3800.0000.0000.0000.000
187A188LEU0-0.003-0.00626.3280.3630.3630.0000.0000.0000.000
188A189GLU-1-0.923-0.97230.312-9.922-9.9220.0000.0000.0000.000
189A190ALA0-0.022-0.00332.6550.3240.3240.0000.0000.0000.000
190A191ILE0-0.040-0.03830.9500.2800.2800.0000.0000.0000.000
191A192ALA0-0.005-0.01231.8580.0610.0610.0000.0000.0000.000
192A193LEU0-0.049-0.01433.8350.1460.1460.0000.0000.0000.000
193A194SER0-0.007-0.00635.7380.2500.2500.0000.0000.0000.000
194A195PRO00.0050.01337.2320.0910.0910.0000.0000.0000.000
195A196ASP-1-0.876-0.96034.381-9.088-9.0880.0000.0000.0000.000
196A197PRO00.0150.00537.265-0.026-0.0260.0000.0000.0000.000
197A198GLU-1-0.907-0.93040.191-7.115-7.1150.0000.0000.0000.000
198A199ARG10.8530.91140.2677.7547.7540.0000.0000.0000.000
199A200THR00.0450.01336.876-0.099-0.0990.0000.0000.0000.000
200A201ARG10.7760.92530.6049.5499.5490.0000.0000.0000.000
201A202ARG10.8820.92233.5727.6657.6650.0000.0000.0000.000
202A203ASP-1-0.853-0.90735.021-8.110-8.1100.0000.0000.0000.000
203A204TRP00.028-0.00931.814-0.046-0.0460.0000.0000.0000.000
204A205GLU-1-0.858-0.92030.042-10.403-10.4030.0000.0000.0000.000
205A206ASP-1-0.827-0.91231.408-8.912-8.9120.0000.0000.0000.000
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