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: 6735Z

Calculation Name: 2REO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-3'-5'-diphosphate

Ligand 3-letter code: A3P

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2REO

Chain ID: A

ChEMBL ID:

UniProt ID: Q6IMI6

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
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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2997795.217402
FMO2-HF: Nuclear repulsion 2903683.559934
FMO2-HF: Total energy -94111.657468
FMO2-MP2: Total energy -94381.388905


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:42:PHE)


Summations of interaction energy for fragment #1(A:42:PHE)
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.
-48.561-40.8375.088-2.679-10.134-0.005
Interaction energy analysis for fragmet #1(A:42:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.919
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].
3A44ALA00.0830.0582.2380.3283.7512.110-1.681-3.8520.002
4A45LYS10.8020.9003.43535.65635.3820.1250.641-0.4930.001
7A48ASP-1-0.861-0.8973.671-38.642-38.0570.005-0.255-0.336-0.002
9A50ILE0-0.041-0.0374.186-1.565-1.417-0.001-0.016-0.1320.000
31A112GLN0-0.074-0.0624.5900.1480.282-0.001-0.012-0.1200.000
33A114ILE0-0.031-0.0062.350-1.834-1.4181.345-0.403-1.359-0.003
43A124PRO0-0.015-0.0032.546-2.739-1.4751.070-0.518-1.815-0.003
44A125PRO00.051-0.0044.803-0.300-0.170-0.001-0.008-0.1200.000
45A126SER0-0.047-0.0163.3732.0602.4910.014-0.112-0.3330.000
46A127ILE00.0220.0162.6750.2301.5450.424-0.305-1.4350.000
47A128TRP00.0060.0125.3512.6652.754-0.001-0.003-0.0850.000
51A132CYS0-0.0170.0145.741-0.674-0.611-0.001-0.007-0.0540.000
5A46PRO00.0480.0076.530-1.078-1.0780.0000.0000.0000.000
6A47ASP-1-0.870-0.9289.058-20.280-20.2800.0000.0000.0000.000
8A49LEU00.0400.0286.8900.5240.5240.0000.0000.0000.000
10A51LEU00.0170.0208.0681.4871.4870.0000.0000.0000.000
11A52ALA0-0.007-0.00710.389-0.945-0.9450.0000.0000.0000.000
12A53THR00.0170.02311.8951.5641.5640.0000.0000.0000.000
13A54TYR00.0380.02715.270-0.616-0.6160.0000.0000.0000.000
14A55PRO00.0190.00217.3710.4370.4370.0000.0000.0000.000
15A56LYS10.8360.93319.33413.08213.0820.0000.0000.0000.000
16A57SER0-0.007-0.00919.2650.8750.8750.0000.0000.0000.000
17A58GLY00.0440.01920.7470.1240.1240.0000.0000.0000.000
18A59THR0-0.018-0.01714.8320.3640.3640.0000.0000.0000.000
19A60THR0-0.021-0.02616.644-0.633-0.6330.0000.0000.0000.000
20A61TRP0-0.026-0.01218.672-0.113-0.1130.0000.0000.0000.000
21A62MET00.0520.02716.1980.1420.1420.0000.0000.0000.000
22A63HIS00.0370.00812.209-0.766-0.7660.0000.0000.0000.000
23A64GLU-1-0.823-0.92515.752-12.695-12.6950.0000.0000.0000.000
24A65ILE0-0.018-0.02018.8060.1760.1760.0000.0000.0000.000
25A66LEU0-0.002-0.01813.4590.1020.1020.0000.0000.0000.000
26A67ASP-1-0.959-0.96715.418-15.098-15.0980.0000.0000.0000.000
27A68MET00.0340.02216.2730.6600.6600.0000.0000.0000.000
28A69ILE0-0.024-0.01018.1590.3090.3090.0000.0000.0000.000
29A70LEU0-0.059-0.03212.604-0.102-0.1020.0000.0000.0000.000
30A71ASN-1-0.976-0.95516.980-12.156-12.1560.0000.0000.0000.000
32A113LEU00.0480.0407.487-1.287-1.2870.0000.0000.0000.000
34A115LYS10.9200.9686.64919.56319.5630.0000.0000.0000.000
35A116THR0-0.024-0.0177.969-0.863-0.8630.0000.0000.0000.000
36A117HIS0-0.018-0.02410.0771.7281.7280.0000.0000.0000.000
37A118LEU0-0.0140.0147.3730.9690.9690.0000.0000.0000.000
38A119PRO00.0370.03311.4590.6370.6370.0000.0000.0000.000
39A120SER00.0420.00411.314-1.728-1.7280.0000.0000.0000.000
40A121HIS00.0290.00210.947-1.687-1.6870.0000.0000.0000.000
41A122LEU0-0.034-0.0229.874-0.282-0.2820.0000.0000.0000.000
42A123ILE0-0.0140.0175.778-3.642-3.6420.0000.0000.0000.000
48A129LYS10.9280.9608.54127.73027.7300.0000.0000.0000.000
49A130GLU0-0.057-0.0646.0372.1362.1360.0000.0000.0000.000
50A131ASN0-0.0020.0029.3071.0421.0420.0000.0000.0000.000
52A133LYS00.0170.0348.1500.4600.4600.0000.0000.0000.000
53A134ILE0-0.037-0.0228.299-1.185-1.1850.0000.0000.0000.000
54A135VAL00.0360.02010.6931.4621.4620.0000.0000.0000.000
55A136TYR0-0.063-0.04913.034-0.452-0.4520.0000.0000.0000.000
56A137VAL0-0.004-0.00415.0660.8600.8600.0000.0000.0000.000
57A138ALA00.0150.01418.105-0.294-0.2940.0000.0000.0000.000
58A139ARG10.8730.93220.69711.38911.3890.0000.0000.0000.000
59A140ASN0-0.037-0.05023.900-0.015-0.0150.0000.0000.0000.000
60A141PRO00.0250.00526.790-0.068-0.0680.0000.0000.0000.000
61A142LYS10.7910.88527.7618.6048.6040.0000.0000.0000.000
62A143ASP-1-0.762-0.87628.827-9.332-9.3320.0000.0000.0000.000
63A144CYS0-0.101-0.01823.490-0.195-0.1950.0000.0000.0000.000
64A145LEU00.0550.03326.433-0.127-0.1270.0000.0000.0000.000
65A146VAL00.0300.01328.621-0.027-0.0270.0000.0000.0000.000
66A147SER0-0.083-0.04526.6110.0560.0560.0000.0000.0000.000
67A148TYR0-0.038-0.04420.867-0.204-0.2040.0000.0000.0000.000
68A149TYR00.0300.03026.748-0.139-0.1390.0000.0000.0000.000
69A150HIS00.015-0.00730.1540.0030.0030.0000.0000.0000.000
70A151PHE00.002-0.00622.233-0.013-0.0130.0000.0000.0000.000
71A152HIS0-0.043-0.04824.621-0.336-0.3360.0000.0000.0000.000
72A153ARG10.8920.95227.8508.7658.7650.0000.0000.0000.000
73A154MET0-0.0490.00427.1140.0060.0060.0000.0000.0000.000
74A155ALA00.0180.00724.865-0.009-0.0090.0000.0000.0000.000
75A156SER0-0.012-0.02726.967-0.026-0.0260.0000.0000.0000.000
76A157PHE0-0.035-0.01320.737-0.039-0.0390.0000.0000.0000.000
77A158MET0-0.087-0.01822.066-0.811-0.8110.0000.0000.0000.000
78A159PRO0-0.035-0.03024.0130.3560.3560.0000.0000.0000.000
79A160ASP-1-0.777-0.89227.264-9.209-9.2090.0000.0000.0000.000
80A161PRO0-0.084-0.04330.143-0.080-0.0800.0000.0000.0000.000
81A162GLN0-0.064-0.03631.4990.1520.1520.0000.0000.0000.000
82A163ASN00.0140.02235.2860.2350.2350.0000.0000.0000.000
83A164LEU0-0.0050.00433.857-0.297-0.2970.0000.0000.0000.000
84A165GLU-1-0.865-0.95035.057-8.171-8.1710.0000.0000.0000.000
85A166GLU-1-0.860-0.92634.582-8.592-8.5920.0000.0000.0000.000
86A167PHE0-0.031-0.02326.872-0.340-0.3400.0000.0000.0000.000
87A168TYR00.004-0.00530.721-0.425-0.4250.0000.0000.0000.000
88A169GLU-1-0.827-0.89731.829-9.813-9.8130.0000.0000.0000.000
89A170LYS10.9831.00126.46610.83510.8350.0000.0000.0000.000
90A171PHE0-0.010-0.01925.200-0.469-0.4690.0000.0000.0000.000
91A172MET0-0.040-0.01427.148-0.515-0.5150.0000.0000.0000.000
92A173SER0-0.026-0.00928.6680.0060.0060.0000.0000.0000.000
93A174GLY0-0.020-0.00724.451-0.284-0.2840.0000.0000.0000.000
94A175LYS10.7840.89723.4849.4649.4640.0000.0000.0000.000
95A176VAL0-0.013-0.01422.5970.2990.2990.0000.0000.0000.000
96A177VAL00.0660.03418.656-0.632-0.6320.0000.0000.0000.000
97A178GLY00.0080.01217.0560.2010.2010.0000.0000.0000.000
98A179GLY0-0.0080.01518.142-0.421-0.4210.0000.0000.0000.000
99A180SER00.007-0.02520.4130.6300.6300.0000.0000.0000.000
100A181TRP00.0420.01820.698-0.479-0.4790.0000.0000.0000.000
101A182PHE00.0460.01121.661-0.285-0.2850.0000.0000.0000.000
102A183ASP-1-0.843-0.92620.277-13.270-13.2700.0000.0000.0000.000
103A184HIS0-0.0260.00214.5900.0870.0870.0000.0000.0000.000
104A185VAL00.0180.01217.784-0.442-0.4420.0000.0000.0000.000
105A186LYS10.8780.95220.18712.11212.1120.0000.0000.0000.000
106A187GLY00.0270.02317.5440.0260.0260.0000.0000.0000.000
107A188TRP0-0.008-0.0299.346-0.771-0.7710.0000.0000.0000.000
108A189TRP0-0.038-0.01716.292-0.105-0.1050.0000.0000.0000.000
109A190ALA0-0.011-0.01419.1150.1560.1560.0000.0000.0000.000
110A191ALA0-0.012-0.00214.019-0.065-0.0650.0000.0000.0000.000
111A192LYS10.9060.95415.85812.55812.5580.0000.0000.0000.000
112A193ASP-1-0.965-0.96317.217-12.470-12.4700.0000.0000.0000.000
113A194MET0-0.056-0.02216.1870.4130.4130.0000.0000.0000.000
114A195HIS0-0.010-0.00612.171-0.883-0.8830.0000.0000.0000.000
115A196ARG0-0.056-0.02912.4660.5060.5060.0000.0000.0000.000
116A197ILE0-0.039-0.02512.469-0.953-0.9530.0000.0000.0000.000
117A198LEU00.0040.02114.3321.0221.0220.0000.0000.0000.000
118A199TYR0-0.049-0.04416.402-0.260-0.2600.0000.0000.0000.000
119A200LEU0-0.0120.00118.4930.7000.7000.0000.0000.0000.000
120A201PHE00.0290.00920.680-0.350-0.3500.0000.0000.0000.000
121A202TYR00.0140.00123.2820.3750.3750.0000.0000.0000.000
122A203GLU-1-0.777-0.90524.288-10.570-10.5700.0000.0000.0000.000
123A204ASP-1-0.865-0.91525.589-9.769-9.7690.0000.0000.0000.000
124A205ILE00.007-0.00221.2270.2690.2690.0000.0000.0000.000
125A206LYS10.8800.94525.7719.5069.5060.0000.0000.0000.000
126A207LYS10.8160.92028.8279.5749.5740.0000.0000.0000.000
127A208ASP-1-0.857-0.94329.456-8.754-8.7540.0000.0000.0000.000
128A209PRO00.0300.01426.885-0.259-0.2590.0000.0000.0000.000
129A210LYS10.8490.92426.5858.7198.7190.0000.0000.0000.000
130A211ARG10.9410.97727.0828.9878.9870.0000.0000.0000.000
131A212GLU-1-0.819-0.91123.550-11.226-11.2260.0000.0000.0000.000
132A213ILE00.0260.01422.626-0.535-0.5350.0000.0000.0000.000
133A214GLU-1-0.824-0.90823.028-10.047-10.0470.0000.0000.0000.000
134A215LYS10.7100.83921.92810.94910.9490.0000.0000.0000.000
135A216ILE0-0.002-0.00717.554-0.406-0.4060.0000.0000.0000.000
136A217LEU00.0230.02119.144-0.494-0.4940.0000.0000.0000.000
137A218LYS10.9610.97821.00110.38010.3800.0000.0000.0000.000
138A219PHE0-0.057-0.03213.702-0.008-0.0080.0000.0000.0000.000
139A220LEU0-0.005-0.00814.322-0.722-0.7220.0000.0000.0000.000
140A221GLU-1-0.889-0.93117.281-13.962-13.9620.0000.0000.0000.000
141A222LYS0-0.045-0.01018.5940.3390.3390.0000.0000.0000.000
142A223ASP-1-0.951-0.97521.367-9.666-9.6660.0000.0000.0000.000
143A224ILE00.016-0.00522.515-0.155-0.1550.0000.0000.0000.000
144A225SER00.0300.02526.1330.1900.1900.0000.0000.0000.000
145A226GLU-1-0.788-0.90629.150-8.853-8.8530.0000.0000.0000.000
146A227GLU-1-0.971-0.97831.528-8.266-8.2660.0000.0000.0000.000
147A228ILE00.0420.01925.434-0.003-0.0030.0000.0000.0000.000
148A229LEU00.0190.01226.079-0.211-0.2110.0000.0000.0000.000
149A230ASN0-0.021-0.02127.743-0.126-0.1260.0000.0000.0000.000
150A231LYS10.8410.91525.25410.28610.2860.0000.0000.0000.000
151A232ILE00.0290.01822.290-0.097-0.0970.0000.0000.0000.000
152A233ILE0-0.0090.01925.739-0.132-0.1320.0000.0000.0000.000
153A234TYR0-0.008-0.00427.8430.0170.0170.0000.0000.0000.000
154A235HIS0-0.045-0.02023.5250.3590.3590.0000.0000.0000.000
155A236THR0-0.024-0.03122.282-0.147-0.1470.0000.0000.0000.000
156A237SER00.000-0.00325.0780.0010.0010.0000.0000.0000.000
157A238PHE0-0.013-0.02127.518-0.145-0.1450.0000.0000.0000.000
158A239ASP-1-0.882-0.94928.733-8.680-8.6800.0000.0000.0000.000
159A240VAL0-0.0040.01027.9760.0730.0730.0000.0000.0000.000
160A241MET0-0.0100.00021.290-0.184-0.1840.0000.0000.0000.000
161A242LYS10.8590.93926.5448.8938.8930.0000.0000.0000.000
162A243GLN0-0.019-0.01329.006-0.001-0.0010.0000.0000.0000.000
163A244ASN00.0650.05523.7280.1470.1470.0000.0000.0000.000
164A245PRO00.012-0.00526.088-0.313-0.3130.0000.0000.0000.000
165A246MET0-0.0120.00221.096-0.143-0.1430.0000.0000.0000.000
166A247THR0-0.013-0.01120.333-0.462-0.4620.0000.0000.0000.000
167A248ASN00.0100.01722.430-0.496-0.4960.0000.0000.0000.000
168A249TYR0-0.029-0.02818.585-0.133-0.1330.0000.0000.0000.000
169A250THR0-0.040-0.03724.2900.1780.1780.0000.0000.0000.000
170A251THR0-0.0070.00523.2160.2330.2330.0000.0000.0000.000
171A252LEU0-0.012-0.01521.585-0.478-0.4780.0000.0000.0000.000
172A253PRO00.0010.01325.5140.3790.3790.0000.0000.0000.000
173A254THR00.0450.01228.216-0.227-0.2270.0000.0000.0000.000
174A255SER00.0150.00130.113-0.092-0.0920.0000.0000.0000.000
175A256ILE0-0.039-0.00123.422-0.189-0.1890.0000.0000.0000.000
176A257MET00.002-0.01421.911-0.339-0.3390.0000.0000.0000.000
177A258ASP-1-0.790-0.88227.543-8.691-8.6910.0000.0000.0000.000
178A259HIS0-0.040-0.04326.8810.2790.2790.0000.0000.0000.000
179A260SER0-0.049-0.01331.6840.2100.2100.0000.0000.0000.000
180A261ILE0-0.040-0.00233.2400.1890.1890.0000.0000.0000.000
181A262SER00.025-0.01530.7590.1500.1500.0000.0000.0000.000
182A263PRO0-0.0150.00630.572-0.271-0.2710.0000.0000.0000.000
183A264PHE00.0190.00620.863-0.165-0.1650.0000.0000.0000.000
184A265MET0-0.0350.00223.409-0.092-0.0920.0000.0000.0000.000
185A266ARG10.8170.90427.9679.7619.7610.0000.0000.0000.000
186A267LYS10.9170.91830.5848.5868.5860.0000.0000.0000.000
187A268GLY00.0120.02528.6480.1240.1240.0000.0000.0000.000
188A269MET0-0.024-0.02129.6990.0410.0410.0000.0000.0000.000
189A270PRO00.0010.00829.276-0.098-0.0980.0000.0000.0000.000
190A271GLY00.0100.00031.4850.2600.2600.0000.0000.0000.000
191A272ASP-1-0.823-0.87432.728-8.525-8.5250.0000.0000.0000.000
192A273TRP00.007-0.03132.8270.2350.2350.0000.0000.0000.000
193A274LYS10.8590.92134.6997.8747.8740.0000.0000.0000.000
194A275ASN0-0.085-0.03537.2690.3710.3710.0000.0000.0000.000
195A276TYR0-0.038-0.02835.507-0.013-0.0130.0000.0000.0000.000
196A277PHE00.0090.00733.031-0.026-0.0260.0000.0000.0000.000
197A278THR00.0380.02838.5430.1900.1900.0000.0000.0000.000
198A279VAL00.022-0.00441.059-0.147-0.1470.0000.0000.0000.000
199A280ALA00.0630.03642.351-0.096-0.0960.0000.0000.0000.000
200A281GLN00.0720.03036.5620.0030.0030.0000.0000.0000.000
201A282ASN00.0050.01137.436-0.433-0.4330.0000.0000.0000.000
202A283GLU-1-0.937-0.96538.382-7.085-7.0850.0000.0000.0000.000
203A284GLU-1-0.952-0.98237.994-8.159-8.1590.0000.0000.0000.000
204A285PHE00.0380.00330.247-0.242-0.2420.0000.0000.0000.000
205A286ASP-1-0.818-0.89634.757-8.649-8.6490.0000.0000.0000.000
206A287LYS10.8290.92236.1608.1328.1320.0000.0000.0000.000
207A288ASP-1-0.797-0.89633.314-8.741-8.7410.0000.0000.0000.000
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