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: 3GQQL

Calculation Name: 3BD9-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: 3BD9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IZT8

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3816425.373178
FMO2-HF: Nuclear repulsion 3709168.470902
FMO2-HF: Total energy -107256.902275
FMO2-MP2: Total energy -107574.00273


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:85:SER)


Summations of interaction energy for fragment #1(A:85:SER)
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.
93.93297.8740.444-1.637-2.751-0.005
Interaction energy analysis for fragmet #1(A:85:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / 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].
3A87MET0-0.028-0.0282.395-8.924-6.4500.361-1.124-1.712-0.006
4A88GLN0-0.0320.0035.1753.5103.582-0.001-0.006-0.0650.000
63A147TYR00.0570.0193.458-8.250-7.5200.023-0.312-0.4410.002
64A148PRO0-0.017-0.0153.2313.3283.9940.061-0.195-0.533-0.001
5A89GLN0-0.038-0.0237.2410.5250.5250.0000.0000.0000.000
6A90LEU00.0580.0159.6141.8301.8300.0000.0000.0000.000
7A91PRO0-0.031-0.01612.951-1.050-1.0500.0000.0000.0000.000
8A92LYS10.9140.96010.16727.17627.1760.0000.0000.0000.000
9A93ALA00.0140.01516.3820.8900.8900.0000.0000.0000.000
10A94ILE00.002-0.00119.268-0.535-0.5350.0000.0000.0000.000
11A95ILE0-0.0130.00021.9220.5810.5810.0000.0000.0000.000
12A96ILE00.0370.01925.0170.0840.0840.0000.0000.0000.000
13A97GLY0-0.0170.00027.1800.3850.3850.0000.0000.0000.000
14A98VAL00.0190.03130.103-0.247-0.2470.0000.0000.0000.000
15A99ARG10.9140.92633.1908.6238.6230.0000.0000.0000.000
16A100LYS10.7680.86134.2259.2669.2660.0000.0000.0000.000
17A101GLY00.0390.03134.4110.2100.2100.0000.0000.0000.000
18A102GLY00.0650.02932.7280.0430.0430.0000.0000.0000.000
19A103THR00.0060.00228.355-0.282-0.2820.0000.0000.0000.000
20A104ARG10.8890.93624.52011.70711.7070.0000.0000.0000.000
21A105ALA00.0250.01027.282-0.385-0.3850.0000.0000.0000.000
22A106LEU00.0760.03925.779-0.298-0.2980.0000.0000.0000.000
23A107LEU00.0150.00420.802-0.309-0.3090.0000.0000.0000.000
24A108GLU-1-0.833-0.90822.390-14.146-14.1460.0000.0000.0000.000
25A109MET00.0170.01123.541-0.227-0.2270.0000.0000.0000.000
26A110LEU00.0480.02021.153-0.197-0.1970.0000.0000.0000.000
27A111ASN0-0.038-0.02318.179-1.097-1.0970.0000.0000.0000.000
28A112LEU0-0.0110.00319.615-0.259-0.2590.0000.0000.0000.000
29A113HIS0-0.010-0.00517.014-0.794-0.7940.0000.0000.0000.000
30A114PRO00.0210.01114.213-0.681-0.6810.0000.0000.0000.000
31A115ALA00.002-0.00512.916-1.820-1.8200.0000.0000.0000.000
32A116VAL0-0.033-0.00913.433-0.986-0.9860.0000.0000.0000.000
33A117VAL0-0.0150.00111.431-0.033-0.0330.0000.0000.0000.000
34A118LYS10.8340.91614.77414.97914.9790.0000.0000.0000.000
35A119ALA00.0360.00916.978-0.667-0.6670.0000.0000.0000.000
36A120SER0-0.076-0.03917.8591.0951.0950.0000.0000.0000.000
37A121GLN0-0.030-0.01820.331-0.177-0.1770.0000.0000.0000.000
38A122GLU-1-0.851-0.93622.747-11.607-11.6070.0000.0000.0000.000
39A123ILE0-0.014-0.01819.6910.1090.1090.0000.0000.0000.000
40A124HIS0-0.083-0.04823.1740.1930.1930.0000.0000.0000.000
41A125PHE00.0240.01820.9300.0110.0110.0000.0000.0000.000
42A126PHE00.032-0.00120.6430.2180.2180.0000.0000.0000.000
43A127ASP-1-0.807-0.90526.152-10.902-10.9020.0000.0000.0000.000
44A128ASN00.0190.01028.2280.5030.5030.0000.0000.0000.000
45A129ASP-1-0.770-0.86928.258-10.351-10.3510.0000.0000.0000.000
46A130GLU-1-0.848-0.90128.855-11.224-11.2240.0000.0000.0000.000
47A131ASN0-0.068-0.04124.661-0.391-0.3910.0000.0000.0000.000
48A132TYR00.023-0.00623.823-0.441-0.4410.0000.0000.0000.000
49A133GLY00.0020.00224.879-0.341-0.3410.0000.0000.0000.000
50A134LYS10.7860.89822.64711.98211.9820.0000.0000.0000.000
51A135GLY00.0150.01521.582-0.633-0.6330.0000.0000.0000.000
52A136ILE00.028-0.01216.161-0.450-0.4500.0000.0000.0000.000
53A137GLU-1-0.781-0.88213.347-24.177-24.1770.0000.0000.0000.000
54A138TRP0-0.0120.00715.849-1.005-1.0050.0000.0000.0000.000
55A139TYR0-0.013-0.04117.515-0.777-0.7770.0000.0000.0000.000
56A140ARG10.8490.9128.22829.04529.0450.0000.0000.0000.000
57A141LYS10.8770.93613.07420.16820.1680.0000.0000.0000.000
58A142LYS10.9220.97714.37616.55016.5500.0000.0000.0000.000
59A143MET0-0.0260.00612.7010.7780.7780.0000.0000.0000.000
60A144PRO0-0.0070.00212.716-0.972-0.9720.0000.0000.0000.000
61A145PHE0-0.006-0.0156.575-1.285-1.2850.0000.0000.0000.000
62A146SER0-0.0190.0027.3792.7632.7630.0000.0000.0000.000
65A149GLN00.0160.0075.8111.6031.6030.0000.0000.0000.000
66A150GLN0-0.0160.0118.5790.2890.2890.0000.0000.0000.000
67A151ILE0-0.006-0.00810.544-0.757-0.7570.0000.0000.0000.000
68A152THR00.0280.01611.9860.2200.2200.0000.0000.0000.000
69A153ILE00.0060.00114.0900.8670.8670.0000.0000.0000.000
70A154GLU-1-0.696-0.79517.896-14.537-14.5370.0000.0000.0000.000
71A155LYS10.8060.91220.19812.53712.5370.0000.0000.0000.000
72A156SER00.023-0.00123.8760.1260.1260.0000.0000.0000.000
73A157PRO0-0.058-0.03326.2980.2390.2390.0000.0000.0000.000
74A158ALA00.0310.02629.7770.3660.3660.0000.0000.0000.000
75A159TYR0-0.019-0.01723.2890.4150.4150.0000.0000.0000.000
76A160PHE00.0050.01429.4180.2810.2810.0000.0000.0000.000
77A161ILE0-0.020-0.02331.6610.2740.2740.0000.0000.0000.000
78A162THR00.0020.00031.5440.3240.3240.0000.0000.0000.000
79A163GLU-1-0.913-0.96832.669-8.724-8.7240.0000.0000.0000.000
80A164GLU-1-0.823-0.89530.889-9.703-9.7030.0000.0000.0000.000
81A165VAL0-0.017-0.01526.838-0.324-0.3240.0000.0000.0000.000
82A166PRO0-0.033-0.01127.496-0.456-0.4560.0000.0000.0000.000
83A167GLU-1-0.868-0.93627.637-10.211-10.2110.0000.0000.0000.000
84A168ARG10.7390.85826.03110.07210.0720.0000.0000.0000.000
85A169ILE0-0.027-0.01222.293-0.589-0.5890.0000.0000.0000.000
86A170TYR0-0.004-0.00122.783-0.646-0.6460.0000.0000.0000.000
87A171LYS10.9420.96723.98111.11111.1110.0000.0000.0000.000
88A172MET0-0.066-0.00817.995-0.554-0.5540.0000.0000.0000.000
89A173ASN0-0.005-0.02617.490-0.521-0.5210.0000.0000.0000.000
90A174SER00.0720.05120.2430.0550.0550.0000.0000.0000.000
91A175SER00.0000.01420.1470.5580.5580.0000.0000.0000.000
92A176ILE0-0.072-0.01818.825-0.513-0.5130.0000.0000.0000.000
93A177LYS10.8560.92719.61815.66515.6650.0000.0000.0000.000
94A178LEU0-0.024-0.01222.366-0.321-0.3210.0000.0000.0000.000
95A179LEU0-0.009-0.00922.6300.3580.3580.0000.0000.0000.000
96A180ILE00.004-0.00126.2830.0720.0720.0000.0000.0000.000
97A181ILE0-0.066-0.01829.8940.0440.0440.0000.0000.0000.000
98A182VAL0-0.014-0.00231.8130.1120.1120.0000.0000.0000.000
99A183ARG10.8580.94235.6428.2538.2530.0000.0000.0000.000
100A184GLU-1-0.693-0.80538.590-7.009-7.0090.0000.0000.0000.000
101A185PRO00.0120.01142.182-0.009-0.0090.0000.0000.0000.000
102A186THR0-0.013-0.01143.1870.0080.0080.0000.0000.0000.000
103A187THR0-0.035-0.03942.7060.0160.0160.0000.0000.0000.000
104A188ARG10.7210.82637.7138.1178.1170.0000.0000.0000.000
105A189ALA00.0130.00441.334-0.108-0.1080.0000.0000.0000.000
106A190ILE00.0220.01543.733-0.003-0.0030.0000.0000.0000.000
107A191SER00.0140.00640.244-0.102-0.1020.0000.0000.0000.000
108A192ASP-1-0.802-0.88439.443-8.237-8.2370.0000.0000.0000.000
109A193TYR0-0.033-0.04441.067-0.050-0.0500.0000.0000.0000.000
110A194THR00.0440.00743.1910.1280.1280.0000.0000.0000.000
111A195GLN00.0320.01235.399-0.071-0.0710.0000.0000.0000.000
112A196VAL0-0.081-0.03440.940-0.047-0.0470.0000.0000.0000.000
113A197LEU0-0.0160.00443.0560.0690.0690.0000.0000.0000.000
114A198GLU-1-0.887-0.93941.629-7.700-7.7000.0000.0000.0000.000
115A199GLY0-0.037-0.02142.066-0.008-0.0080.0000.0000.0000.000
116A200LYS10.8760.94942.7196.9386.9380.0000.0000.0000.000
117A201GLU-1-0.859-0.93446.266-6.608-6.6080.0000.0000.0000.000
118A202ARG10.9220.95837.7988.2328.2320.0000.0000.0000.000
119A203LYS0-0.058-0.03144.228-0.088-0.0880.0000.0000.0000.000
120A204ASN0-0.040-0.01846.5960.1120.1120.0000.0000.0000.000
121A205LYS00.0150.02546.2640.1140.1140.0000.0000.0000.000
122A206THR00.0200.00650.592-0.055-0.0550.0000.0000.0000.000
123A207TYR00.007-0.01846.327-0.105-0.1050.0000.0000.0000.000
124A208TYR0-0.0040.00751.4440.1280.1280.0000.0000.0000.000
125A209LYS11.0241.02051.6535.4895.4890.0000.0000.0000.000
126A210PHE00.0690.03046.7890.0050.0050.0000.0000.0000.000
127A211GLU-1-0.779-0.90551.075-6.010-6.0100.0000.0000.0000.000
128A212LYS10.9030.95354.1675.5625.5620.0000.0000.0000.000
129A213LEU0-0.0330.00149.0790.0050.0050.0000.0000.0000.000
130A214ALA0-0.012-0.01749.645-0.065-0.0650.0000.0000.0000.000
131A215ILE0-0.0220.00651.049-0.027-0.0270.0000.0000.0000.000
132A216ASP-1-0.823-0.88554.699-5.558-5.5580.0000.0000.0000.000
133A217PRO0-0.035-0.03156.6650.0760.0760.0000.0000.0000.000
134A218ASN0-0.0250.00259.9360.0570.0570.0000.0000.0000.000
135A219THR00.001-0.03258.8940.0440.0440.0000.0000.0000.000
136A220CYS0-0.041-0.00759.4680.0460.0460.0000.0000.0000.000
137A221GLU-1-0.896-0.93956.483-5.609-5.6090.0000.0000.0000.000
138A222VAL0-0.004-0.00850.193-0.056-0.0560.0000.0000.0000.000
139A223ASN00.0140.00651.477-0.036-0.0360.0000.0000.0000.000
140A224THR0-0.004-0.01247.618-0.119-0.1190.0000.0000.0000.000
141A225LYS10.9460.97247.4635.9795.9790.0000.0000.0000.000
142A226TYR00.0420.03446.099-0.206-0.2060.0000.0000.0000.000
143A227LYS10.9720.98638.6638.0558.0550.0000.0000.0000.000
144A228ALA00.0060.02541.968-0.174-0.1740.0000.0000.0000.000
145A229VAL00.0720.04042.993-0.110-0.1100.0000.0000.0000.000
146A230ARG10.9080.93441.7477.0677.0670.0000.0000.0000.000
147A231THR0-0.047-0.03137.181-0.171-0.1710.0000.0000.0000.000
148A232SER00.0010.00138.908-0.272-0.2720.0000.0000.0000.000
149A233ILE0-0.0500.00841.2860.0480.0480.0000.0000.0000.000
150A234TYR00.001-0.04037.422-0.156-0.1560.0000.0000.0000.000
151A235THR00.0340.01237.799-0.226-0.2260.0000.0000.0000.000
152A236LYS10.9360.97539.1257.2037.2030.0000.0000.0000.000
153A237HIS0-0.032-0.02635.648-0.123-0.1230.0000.0000.0000.000
154A238LEU00.0390.02933.157-0.213-0.2130.0000.0000.0000.000
155A239GLU-1-0.828-0.92735.165-8.013-8.0130.0000.0000.0000.000
156A240ARG10.7330.85533.7059.0669.0660.0000.0000.0000.000
157A241TRP0-0.011-0.01126.640-0.270-0.2700.0000.0000.0000.000
158A242LEU00.0240.00731.597-0.244-0.2440.0000.0000.0000.000
159A243LYS10.8820.96233.8008.4818.4810.0000.0000.0000.000
160A244TYR0-0.019-0.00129.1740.0230.0230.0000.0000.0000.000
161A245PHE0-0.031-0.01624.456-0.272-0.2720.0000.0000.0000.000
162A246PRO00.0730.03827.9040.3710.3710.0000.0000.0000.000
163A247ILE00.0360.01329.654-0.303-0.3030.0000.0000.0000.000
164A248GLU-1-0.862-0.94328.627-10.098-10.0980.0000.0000.0000.000
165A249GLN0-0.095-0.06224.065-0.233-0.2330.0000.0000.0000.000
166A250PHE0-0.054-0.03125.763-0.458-0.4580.0000.0000.0000.000
167A251HIS00.0070.01126.7300.1070.1070.0000.0000.0000.000
168A252VAL0-0.0030.00228.571-0.099-0.0990.0000.0000.0000.000
169A253VAL0-0.029-0.02028.1750.0830.0830.0000.0000.0000.000
170A254ASP-1-0.772-0.89431.351-8.340-8.3400.0000.0000.0000.000
171A255GLY00.025-0.01834.195-0.168-0.1680.0000.0000.0000.000
172A256ASP-1-0.816-0.90835.086-7.920-7.9200.0000.0000.0000.000
173A257ARG10.9250.97535.8858.1918.1910.0000.0000.0000.000
174A258LEU0-0.031-0.01629.574-0.087-0.0870.0000.0000.0000.000
175A259ILE0-0.049-0.02433.719-0.134-0.1340.0000.0000.0000.000
176A260THR0-0.024-0.02836.4230.0770.0770.0000.0000.0000.000
177A261GLU-1-0.945-0.97036.174-8.427-8.4270.0000.0000.0000.000
178A262PRO00.0300.01431.284-0.173-0.1730.0000.0000.0000.000
179A263LEU00.0160.00927.912-0.284-0.2840.0000.0000.0000.000
180A264PRO0-0.008-0.01529.822-0.325-0.3250.0000.0000.0000.000
181A265GLU-1-0.720-0.81930.589-9.832-9.8320.0000.0000.0000.000
182A266LEU0-0.010-0.00825.712-0.367-0.3670.0000.0000.0000.000
183A267GLN00.0330.01525.599-0.489-0.4890.0000.0000.0000.000
184A268LEU0-0.056-0.02426.641-0.173-0.1730.0000.0000.0000.000
185A269VAL00.0040.00522.798-0.268-0.2680.0000.0000.0000.000
186A270GLU-1-0.760-0.89021.678-13.601-13.6010.0000.0000.0000.000
187A271LYS10.9610.98621.62810.27110.2710.0000.0000.0000.000
188A272PHE00.0150.02623.357-0.407-0.4070.0000.0000.0000.000
189A273LEU0-0.029-0.02018.851-0.390-0.3900.0000.0000.0000.000
190A274ASN0-0.042-0.01418.523-1.163-1.1630.0000.0000.0000.000
191A275LEU0-0.0040.00815.872-0.725-0.7250.0000.0000.0000.000
192A276PRO0-0.0040.00517.3780.8030.8030.0000.0000.0000.000
193A277PRO00.0330.02020.235-0.423-0.4230.0000.0000.0000.000
194A278ARG10.8370.89917.00215.04515.0450.0000.0000.0000.000
195A279ILE0-0.0150.01121.8140.1740.1740.0000.0000.0000.000
196A280SER00.021-0.00324.0220.5150.5150.0000.0000.0000.000
197A281GLN00.030-0.00527.0640.1130.1130.0000.0000.0000.000
198A282TYR00.0260.03425.4630.1680.1680.0000.0000.0000.000
199A283ASN00.0010.01123.9680.0440.0440.0000.0000.0000.000
200A284LEU00.0190.00927.417-0.147-0.1470.0000.0000.0000.000
201A285TYR00.0170.01030.5730.1370.1370.0000.0000.0000.000
202A286PHE00.0400.02834.043-0.100-0.1000.0000.0000.0000.000
203A287ASN0-0.015-0.01836.4080.3280.3280.0000.0000.0000.000
204A288ALA00.0580.01438.4160.0190.0190.0000.0000.0000.000
205A289THR0-0.0130.00941.2910.1630.1630.0000.0000.0000.000
206A290ARG10.8330.90434.6158.8948.8940.0000.0000.0000.000
207A291GLY00.0360.02640.2540.0040.0040.0000.0000.0000.000
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