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: 9LJM2

Calculation Name: 2C9Y-A-Xray547

Preferred Name: Adenylate kinase 2

Target Type: SINGLE PROTEIN

Ligand Name: bis(adenosine)-5'-tetraphosphate | 1,2-ethanediol

Ligand 3-letter code: B4P | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C9Y

Chain ID: A

ChEMBL ID: CHEMBL4938

UniProt ID: P54819

Base Structure: X-ray

Registration Date: 2025-10-03

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 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2459023.390649
FMO2-HF: Nuclear repulsion 2373240.656107
FMO2-HF: Total energy -85782.734542
FMO2-MP2: Total energy -86029.05311


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:15:GLY)


Summations of interaction energy for fragment #1(A:15: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.
-89.57-83.8719.874-8.511-7.064-0.073
Interaction energy analysis for fragmet #1(A:15:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.912
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].
3A17ARG10.8480.9303.85246.14046.862-0.012-0.249-0.4620.000
25A39PHE0-0.051-0.0222.465-2.260-1.9950.631-0.413-0.483-0.002
26A40CYS0-0.051-0.0222.296-20.068-18.0593.990-3.385-2.615-0.032
27A41VAL0-0.042-0.0052.365-7.219-7.0091.986-1.226-0.970-0.005
28A42CYS0-0.0200.0224.9342.4102.439-0.002-0.009-0.0180.000
79A94ASN0-0.044-0.0362.8581.2531.5650.094-0.174-0.231-0.001
80A95GLY0-0.045-0.0212.400-31.257-29.2043.188-3.051-2.191-0.033
81A96PHE00.023-0.0224.2274.7174.816-0.001-0.004-0.0940.000
4A18ALA00.0140.0146.8293.4113.4110.0000.0000.0000.000
5A19VAL00.0070.0139.5290.7090.7090.0000.0000.0000.000
6A20LEU0-0.022-0.00711.6230.1550.1550.0000.0000.0000.000
7A21LEU00.0090.00214.8761.2411.2410.0000.0000.0000.000
8A22GLY00.0640.01518.549-0.248-0.2480.0000.0000.0000.000
9A23PRO0-0.0310.00721.332-0.016-0.0160.0000.0000.0000.000
10A24PRO00.005-0.02123.342-0.411-0.4110.0000.0000.0000.000
11A25GLY00.0370.01924.3870.3350.3350.0000.0000.0000.000
12A26ALA00.0200.01722.0940.1090.1090.0000.0000.0000.000
13A27GLY00.0530.01620.349-0.100-0.1000.0000.0000.0000.000
14A28LYS10.8460.93316.77115.56915.5690.0000.0000.0000.000
15A29GLY00.0240.00916.090-0.956-0.9560.0000.0000.0000.000
16A30THR0-0.026-0.01117.5320.0290.0290.0000.0000.0000.000
17A31GLN00.0260.01513.854-0.914-0.9140.0000.0000.0000.000
18A32ALA00.0180.01711.933-1.456-1.4560.0000.0000.0000.000
19A33PRO00.0220.01010.996-2.129-2.1290.0000.0000.0000.000
20A34ARG10.8400.89711.40417.10017.1000.0000.0000.0000.000
21A35LEU0-0.0040.0008.393-1.257-1.2570.0000.0000.0000.000
22A36ALA0-0.005-0.0076.700-4.598-4.5980.0000.0000.0000.000
23A37GLU-1-0.939-0.9596.875-30.164-30.1640.0000.0000.0000.000
24A38ASN00.0490.0296.694-0.810-0.8100.0000.0000.0000.000
29A43HIS00.001-0.0068.417-0.985-0.9850.0000.0000.0000.000
30A44LEU00.004-0.01610.8701.4811.4810.0000.0000.0000.000
31A45ALA00.0680.03913.3580.3320.3320.0000.0000.0000.000
32A46THR00.009-0.00316.7790.5160.5160.0000.0000.0000.000
33A47GLY00.0000.00119.5270.4120.4120.0000.0000.0000.000
34A48ASP-1-0.847-0.93118.668-14.009-14.0090.0000.0000.0000.000
35A49MET0-0.0040.01416.020-0.070-0.0700.0000.0000.0000.000
36A50LEU00.0130.00519.2160.4240.4240.0000.0000.0000.000
37A51ARG10.8720.93922.93112.85612.8560.0000.0000.0000.000
38A52ALA00.0210.01319.9900.4300.4300.0000.0000.0000.000
39A53MET00.0230.01820.3800.3990.3990.0000.0000.0000.000
40A54VAL0-0.0350.00323.0040.4570.4570.0000.0000.0000.000
41A55ALA0-0.025-0.01824.9320.3790.3790.0000.0000.0000.000
42A56SER0-0.030-0.01823.6110.2340.2340.0000.0000.0000.000
43A57GLY00.0250.02225.6640.2000.2000.0000.0000.0000.000
44A58SER00.003-0.00425.1420.4090.4090.0000.0000.0000.000
45A59GLU-1-0.951-0.97727.686-10.079-10.0790.0000.0000.0000.000
46A60LEU00.0400.01422.4930.2560.2560.0000.0000.0000.000
47A61GLY00.0360.02026.4960.0490.0490.0000.0000.0000.000
48A62LYS10.8680.91827.14910.13710.1370.0000.0000.0000.000
49A63LYS10.8560.92826.95311.65011.6500.0000.0000.0000.000
50A64LEU00.0210.01123.9170.1880.1880.0000.0000.0000.000
51A65LYS10.8470.90428.5289.4729.4720.0000.0000.0000.000
52A66ALA00.001-0.00131.0150.2200.2200.0000.0000.0000.000
53A67THR0-0.023-0.02730.6220.2350.2350.0000.0000.0000.000
54A68MET0-0.023-0.01927.2980.0610.0610.0000.0000.0000.000
55A69ASP-1-0.847-0.90232.450-8.938-8.9380.0000.0000.0000.000
56A70ALA0-0.062-0.01935.5210.2620.2620.0000.0000.0000.000
57A71GLY0-0.014-0.00135.9610.1660.1660.0000.0000.0000.000
58A72LYS0-0.048-0.01134.181-0.001-0.0010.0000.0000.0000.000
59A73LEU0-0.017-0.01830.698-0.235-0.2350.0000.0000.0000.000
60A74VAL00.0020.00025.6360.0640.0640.0000.0000.0000.000
61A75SER00.001-0.01827.974-0.089-0.0890.0000.0000.0000.000
62A76ASP-1-0.768-0.88224.421-12.274-12.2740.0000.0000.0000.000
63A77GLU-1-0.779-0.86823.329-11.901-11.9010.0000.0000.0000.000
64A78MET0-0.014-0.00123.635-0.473-0.4730.0000.0000.0000.000
65A79VAL0-0.011-0.00420.163-0.367-0.3670.0000.0000.0000.000
66A80VAL00.0180.01118.851-0.870-0.8700.0000.0000.0000.000
67A81GLU-1-0.780-0.87118.858-13.006-13.0060.0000.0000.0000.000
68A82LEU0-0.045-0.02419.145-0.400-0.4000.0000.0000.0000.000
69A83ILE00.0080.00714.081-0.761-0.7610.0000.0000.0000.000
70A84GLU-1-0.835-0.89014.978-17.345-17.3450.0000.0000.0000.000
71A85LYS10.8290.88515.85714.15714.1570.0000.0000.0000.000
72A86ASN0-0.025-0.01913.563-0.368-0.3680.0000.0000.0000.000
73A87LEU00.0150.0049.826-1.488-1.4880.0000.0000.0000.000
74A88GLU-1-0.862-0.90312.023-17.589-17.5890.0000.0000.0000.000
75A89THR0-0.049-0.02512.582-0.056-0.0560.0000.0000.0000.000
76A90PRO0-0.003-0.02511.260-2.166-2.1660.0000.0000.0000.000
77A91LEU00.001-0.0029.728-2.173-2.1730.0000.0000.0000.000
78A93LYS10.9500.9976.94631.51031.5100.0000.0000.0000.000
82A97LEU00.0090.0176.698-0.411-0.4110.0000.0000.0000.000
83A98LEU00.0040.0019.0961.9481.9480.0000.0000.0000.000
84A99ASP-1-0.811-0.91212.556-17.017-17.0170.0000.0000.0000.000
85A100GLY0-0.029-0.01715.7600.5570.5570.0000.0000.0000.000
86A101PHE0-0.002-0.00517.5531.0061.0060.0000.0000.0000.000
87A102PRO00.0570.03616.702-1.027-1.0270.0000.0000.0000.000
88A103ARG10.7750.86219.81013.42213.4220.0000.0000.0000.000
89A104THR00.0180.00723.2340.3260.3260.0000.0000.0000.000
90A105VAL00.0600.02323.327-0.516-0.5160.0000.0000.0000.000
91A106ARG10.8790.93323.65510.87710.8770.0000.0000.0000.000
92A107GLN0-0.009-0.02121.553-0.660-0.6600.0000.0000.0000.000
93A108ALA0-0.020-0.00919.258-0.745-0.7450.0000.0000.0000.000
94A109GLU-1-0.909-0.95519.333-13.074-13.0740.0000.0000.0000.000
95A110MET00.0170.00420.894-0.261-0.2610.0000.0000.0000.000
96A111LEU0-0.037-0.01014.101-0.397-0.3970.0000.0000.0000.000
97A112ASP-1-0.746-0.83416.319-20.012-20.0120.0000.0000.0000.000
98A113ASP-1-0.869-0.93017.671-14.497-14.4970.0000.0000.0000.000
99A114LEU0-0.075-0.03215.283-0.152-0.1520.0000.0000.0000.000
100A115MET0-0.082-0.03611.742-1.909-1.9090.0000.0000.0000.000
101A116GLU-1-0.865-0.93714.750-18.025-18.0250.0000.0000.0000.000
102A117LYS10.7820.87217.40415.29315.2930.0000.0000.0000.000
103A118ARG10.7640.85510.70725.34525.3450.0000.0000.0000.000
104A119LYS10.9160.96913.93415.90415.9040.0000.0000.0000.000
105A120GLU-1-0.786-0.8499.655-32.883-32.8830.0000.0000.0000.000
106A121LYS10.9110.9349.82631.54831.5480.0000.0000.0000.000
107A122LEU0-0.016-0.0109.690-3.016-3.0160.0000.0000.0000.000
108A123ASP-1-0.821-0.9076.863-41.455-41.4550.0000.0000.0000.000
109A124SER00.007-0.00210.1772.2852.2850.0000.0000.0000.000
110A125VAL0-0.020-0.01511.807-0.542-0.5420.0000.0000.0000.000
111A126ILE00.0210.02112.4191.2241.2240.0000.0000.0000.000
112A127GLU-1-0.838-0.91815.425-13.367-13.3670.0000.0000.0000.000
113A128PHE0-0.014-0.02815.2650.2120.2120.0000.0000.0000.000
114A129SER0-0.0040.00220.0990.8910.8910.0000.0000.0000.000
115A130ILE0-0.014-0.01423.3880.0040.0040.0000.0000.0000.000
116A131PRO00.0370.02026.2270.1540.1540.0000.0000.0000.000
117A132ASP-1-0.800-0.88330.059-10.131-10.1310.0000.0000.0000.000
118A133SER0-0.007-0.01131.658-0.029-0.0290.0000.0000.0000.000
119A134LEU0-0.0170.00128.7950.2110.2110.0000.0000.0000.000
120A135LEU00.0000.00126.589-0.016-0.0160.0000.0000.0000.000
121A136ILE00.022-0.00529.814-0.015-0.0150.0000.0000.0000.000
122A137ARG10.9020.97733.1069.0379.0370.0000.0000.0000.000
123A138ARG10.8500.92823.52512.40012.4000.0000.0000.0000.000
124A139ILE0-0.060-0.02628.482-0.235-0.2350.0000.0000.0000.000
125A140THR00.015-0.00331.1210.0580.0580.0000.0000.0000.000
126A141GLY00.0090.01934.9340.0460.0460.0000.0000.0000.000
127A142ARG10.7320.85426.77110.87910.8790.0000.0000.0000.000
128A143LEU00.0350.01033.3750.2990.2990.0000.0000.0000.000
129A144ILE0-0.050-0.02130.841-0.437-0.4370.0000.0000.0000.000
130A145HIS00.1020.06231.0900.1010.1010.0000.0000.0000.000
131A146PRO0-0.062-0.04132.301-0.222-0.2220.0000.0000.0000.000
132A147LYS10.8520.92133.3638.5328.5320.0000.0000.0000.000
133A148SER0-0.019-0.02227.989-0.264-0.2640.0000.0000.0000.000
134A149GLY00.0100.01527.758-0.381-0.3810.0000.0000.0000.000
135A150ARG10.8410.89225.77510.77610.7760.0000.0000.0000.000
136A151SER0-0.022-0.02027.4040.4140.4140.0000.0000.0000.000
137A152TYR00.0370.00528.157-0.491-0.4910.0000.0000.0000.000
138A153HIS00.008-0.02230.5740.1070.1070.0000.0000.0000.000
139A154GLU-1-0.872-0.93832.335-8.699-8.6990.0000.0000.0000.000
140A155GLU-1-0.894-0.93833.847-8.750-8.7500.0000.0000.0000.000
141A156PHE0-0.054-0.04328.968-0.233-0.2330.0000.0000.0000.000
142A157ASN0-0.097-0.05026.462-0.672-0.6720.0000.0000.0000.000
143A158PRO00.0610.04628.9770.0260.0260.0000.0000.0000.000
144A159PRO0-0.0340.00130.727-0.304-0.3040.0000.0000.0000.000
145A160LYS10.8620.90427.72910.92310.9230.0000.0000.0000.000
146A161GLU-1-0.900-0.94833.401-7.698-7.6980.0000.0000.0000.000
147A162PRO00.0420.02636.179-0.165-0.1650.0000.0000.0000.000
148A163MET0-0.041-0.03337.3310.1130.1130.0000.0000.0000.000
149A164LYS10.9380.98635.7317.9647.9640.0000.0000.0000.000
150A165ASP-1-0.740-0.82230.216-10.592-10.5920.0000.0000.0000.000
151A166ASP-1-0.796-0.89328.511-10.331-10.3310.0000.0000.0000.000
152A167ILE0-0.078-0.02625.725-0.109-0.1090.0000.0000.0000.000
153A168THR0-0.045-0.03729.1800.1910.1910.0000.0000.0000.000
154A169GLY00.0970.04832.766-0.004-0.0040.0000.0000.0000.000
155A170GLU-1-0.877-0.91735.350-8.549-8.5490.0000.0000.0000.000
156A171PRO0-0.016-0.01936.481-0.137-0.1370.0000.0000.0000.000
157A172LEU0-0.043-0.00433.031-0.163-0.1630.0000.0000.0000.000
158A173ILE0-0.033-0.01336.5730.2940.2940.0000.0000.0000.000
159A174ARG10.9920.98136.7517.1817.1810.0000.0000.0000.000
160A175ARG10.9410.97329.03610.20510.2050.0000.0000.0000.000
161A176SER0-0.024-0.03236.3860.0960.0960.0000.0000.0000.000
162A177ASP-1-0.876-0.92436.183-8.075-8.0750.0000.0000.0000.000
163A178ASP-1-0.945-0.96032.858-9.593-9.5930.0000.0000.0000.000
164A179ASN00.009-0.01136.0010.1470.1470.0000.0000.0000.000
165A180GLU-1-0.820-0.91737.054-8.265-8.2650.0000.0000.0000.000
166A181LYS10.9220.97337.6017.4447.4440.0000.0000.0000.000
167A182ALA00.002-0.00936.335-0.068-0.0680.0000.0000.0000.000
168A183LEU00.0210.01730.956-0.211-0.2110.0000.0000.0000.000
169A184LYS10.9790.97233.1837.9397.9390.0000.0000.0000.000
170A185ILE0-0.0170.00334.982-0.028-0.0280.0000.0000.0000.000
171A186ARG10.9410.96727.66410.57410.5740.0000.0000.0000.000
172A187LEU00.0150.00928.844-0.356-0.3560.0000.0000.0000.000
173A188GLN00.0500.02830.482-0.379-0.3790.0000.0000.0000.000
174A189ALA00.0020.01231.463-0.082-0.0820.0000.0000.0000.000
175A190TYR00.0220.00822.925-0.383-0.3830.0000.0000.0000.000
176A191HIS00.0330.00027.265-0.624-0.6240.0000.0000.0000.000
177A192THR0-0.036-0.01329.093-0.065-0.0650.0000.0000.0000.000
178A193GLN0-0.024-0.01026.589-0.413-0.4130.0000.0000.0000.000
179A194THR0-0.001-0.01922.772-0.430-0.4300.0000.0000.0000.000
180A195THR00.0130.01124.962-0.365-0.3650.0000.0000.0000.000
181A196PRO0-0.007-0.00826.788-0.211-0.2110.0000.0000.0000.000
182A197LEU0-0.0190.00520.700-0.235-0.2350.0000.0000.0000.000
183A198ILE00.0210.01322.069-0.697-0.6970.0000.0000.0000.000
184A199GLU-1-0.799-0.89422.920-11.992-11.9920.0000.0000.0000.000
185A200TYR0-0.055-0.05119.5380.3150.3150.0000.0000.0000.000
186A201TYR00.0900.01116.879-0.164-0.1640.0000.0000.0000.000
187A202ARG10.8240.91319.48711.47111.4710.0000.0000.0000.000
188A203LYS10.8540.92422.03911.72611.7260.0000.0000.0000.000
189A204ARG10.7880.88115.07719.01019.0100.0000.0000.0000.000
190A205GLY00.0020.00718.231-0.838-0.8380.0000.0000.0000.000
191A206ILE0-0.0070.00413.983-0.564-0.5640.0000.0000.0000.000
192A207HIS0-0.055-0.03315.243-1.161-1.1610.0000.0000.0000.000
193A208SER0-0.022-0.01415.547-0.220-0.2200.0000.0000.0000.000
194A209ALA0-0.0030.02317.410-0.479-0.4790.0000.0000.0000.000
195A210ILE0-0.038-0.01316.053-0.140-0.1400.0000.0000.0000.000
196A211ASP-1-0.759-0.84019.399-12.072-12.0720.0000.0000.0000.000
197A212ALA0-0.006-0.01020.829-0.312-0.3120.0000.0000.0000.000
198A213SER0-0.104-0.09022.0960.4090.4090.0000.0000.0000.000
199A214GLN0-0.028-0.01222.2680.4240.4240.0000.0000.0000.000
200A215THR00.0560.02323.542-0.289-0.2890.0000.0000.0000.000
201A216PRO00.0390.00620.078-0.577-0.5770.0000.0000.0000.000
202A217ASP-1-0.807-0.89317.918-16.405-16.4050.0000.0000.0000.000
203A218VAL00.0180.02117.758-0.828-0.8280.0000.0000.0000.000
204A219VAL0-0.031-0.00817.255-0.690-0.6900.0000.0000.0000.000
205A220PHE00.0030.00410.863-0.796-0.7960.0000.0000.0000.000
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