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: 2M71R

Calculation Name: 1JJV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | mercury (ii) ion

Ligand 3-letter code: ATP | HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JJV

Chain ID: A

ChEMBL ID:

UniProt ID: P44920

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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2274655.571434
FMO2-HF: Nuclear repulsion 2193971.351039
FMO2-HF: Total energy -80684.220395
FMO2-MP2: Total energy -80922.360434


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-155.868-153.024.751-2.126-5.472-0.023
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.798 / q_NPA : 0.896
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].
3A3TYR00.0660.0212.644-7.669-5.0260.801-1.644-1.799-0.016
4A4ILE0-0.037-0.0193.4934.5565.0470.019-0.085-0.4250.000
98A98GLN0-0.099-0.0465.108-2.290-2.199-0.001-0.001-0.0880.000
100A100LEU0-0.0010.0015.416-0.625-0.515-0.001-0.018-0.0910.000
101A101ALA0-0.040-0.0262.350-6.250-6.0153.939-1.733-2.441-0.005
102A102GLU-1-0.907-0.9463.343-25.581-26.500-0.0051.368-0.444-0.002
104A104THR0-0.005-0.0154.534-7.515-7.318-0.001-0.013-0.1840.000
5A5VAL00.0510.0266.3531.8471.8470.0000.0000.0000.000
6A6GLY00.007-0.00310.1860.5940.5940.0000.0000.0000.000
7A7LEU0-0.0100.00912.2570.9950.9950.0000.0000.0000.000
8A8THR0-0.017-0.03715.5620.6020.6020.0000.0000.0000.000
9A9GLY00.0820.03018.6270.2130.2130.0000.0000.0000.000
10A10GLY00.0230.03222.441-0.046-0.0460.0000.0000.0000.000
11A11ILE0-0.025-0.00825.628-0.231-0.2310.0000.0000.0000.000
12A12GLY00.0550.02627.8980.1260.1260.0000.0000.0000.000
13A13SER0-0.081-0.06624.827-0.132-0.1320.0000.0000.0000.000
14A14GLY00.0930.05225.784-0.093-0.0930.0000.0000.0000.000
15A15LYS10.8420.92420.09712.54912.5490.0000.0000.0000.000
16A16THR00.0400.01620.887-0.395-0.3950.0000.0000.0000.000
17A17THR0-0.0020.00622.239-0.227-0.2270.0000.0000.0000.000
18A18ILE00.0250.00919.378-0.122-0.1220.0000.0000.0000.000
19A19ALA00.0200.00217.881-0.531-0.5310.0000.0000.0000.000
20A20ASN0-0.021-0.00718.519-0.879-0.8790.0000.0000.0000.000
21A21LEU00.0350.02920.876-0.168-0.1680.0000.0000.0000.000
22A22PHE00.0110.00615.772-0.175-0.1750.0000.0000.0000.000
23A23THR0-0.066-0.03216.492-0.425-0.4250.0000.0000.0000.000
24A24ASP-1-0.920-0.96418.168-13.152-13.1520.0000.0000.0000.000
25A25LEU0-0.087-0.04117.9910.3650.3650.0000.0000.0000.000
26A26GLY0-0.025-0.01117.104-0.637-0.6370.0000.0000.0000.000
27A27VAL0-0.059-0.01111.954-1.328-1.3280.0000.0000.0000.000
28A28PRO0-0.0010.0079.8121.2871.2870.0000.0000.0000.000
29A29LEU00.019-0.00311.765-0.779-0.7790.0000.0000.0000.000
30A30VAL0-0.053-0.0249.2770.5160.5160.0000.0000.0000.000
31A31ASP-1-0.814-0.91012.518-15.127-15.1270.0000.0000.0000.000
32A32ALA00.021-0.00815.8720.0730.0730.0000.0000.0000.000
33A33ASP-1-0.872-0.93716.885-12.882-12.8820.0000.0000.0000.000
34A34VAL0-0.089-0.04317.6610.6930.6930.0000.0000.0000.000
35A35VAL00.0090.00113.2340.3870.3870.0000.0000.0000.000
36A36ALA0-0.008-0.01416.4430.3630.3630.0000.0000.0000.000
37A37ARG10.8420.91719.35213.23013.2300.0000.0000.0000.000
38A38GLU-1-0.739-0.86615.632-16.053-16.0530.0000.0000.0000.000
39A39VAL0-0.0110.00516.2720.1170.1170.0000.0000.0000.000
40A40VAL0-0.045-0.02418.7670.3670.3670.0000.0000.0000.000
41A41ALA00.0130.01221.8340.4300.4300.0000.0000.0000.000
42A42LYS10.8750.91723.6109.2559.2550.0000.0000.0000.000
43A43ASP-1-0.882-0.92625.428-9.703-9.7030.0000.0000.0000.000
44A44SER0-0.015-0.01321.072-0.299-0.2990.0000.0000.0000.000
45A45PRO00.011-0.02020.7250.3510.3510.0000.0000.0000.000
46A46LEU0-0.041-0.01819.1440.1960.1960.0000.0000.0000.000
47A47LEU00.0070.02023.3490.3660.3660.0000.0000.0000.000
48A48SER00.0090.00426.0980.2200.2200.0000.0000.0000.000
49A49LYS11.0201.01422.90011.38711.3870.0000.0000.0000.000
50A50ILE0-0.015-0.00324.9860.2550.2550.0000.0000.0000.000
51A51VAL0-0.038-0.01728.7650.3320.3320.0000.0000.0000.000
52A52GLU-1-0.890-0.94930.261-8.921-8.9210.0000.0000.0000.000
53A53HIS10.8160.91430.9198.9728.9720.0000.0000.0000.000
54A54PHE0-0.043-0.03029.3650.1570.1570.0000.0000.0000.000
55A55GLY00.0280.01234.1890.2330.2330.0000.0000.0000.000
56A56ALA0-0.030-0.03134.4540.1390.1390.0000.0000.0000.000
57A57GLN0-0.0060.01135.4510.0770.0770.0000.0000.0000.000
58A58ILE00.000-0.00635.948-0.184-0.1840.0000.0000.0000.000
59A59LEU00.0180.01832.573-0.177-0.1770.0000.0000.0000.000
60A60THR0-0.044-0.01533.8900.2610.2610.0000.0000.0000.000
61A61GLU-1-0.786-0.88635.714-7.725-7.7250.0000.0000.0000.000
62A62GLN0-0.037-0.01835.264-0.230-0.2300.0000.0000.0000.000
63A63GLY0-0.055-0.02032.079-0.243-0.2430.0000.0000.0000.000
64A64GLU-1-0.762-0.88126.372-10.835-10.8350.0000.0000.0000.000
65A65LEU00.0240.02326.6390.3070.3070.0000.0000.0000.000
66A66ASN00.0460.02629.934-0.231-0.2310.0000.0000.0000.000
67A67ARG10.7800.87723.49011.15311.1530.0000.0000.0000.000
68A68ALA0-0.053-0.01929.922-0.181-0.1810.0000.0000.0000.000
69A69ALA00.0870.03733.0510.0280.0280.0000.0000.0000.000
70A70LEU00.0060.01027.7530.0630.0630.0000.0000.0000.000
71A71ARG10.9030.94829.2799.4739.4730.0000.0000.0000.000
72A72GLU-1-0.918-0.95632.080-7.612-7.6120.0000.0000.0000.000
73A73ARG10.8260.91534.0898.0708.0700.0000.0000.0000.000
74A74VAL0-0.009-0.00929.6020.0630.0630.0000.0000.0000.000
75A75PHE0-0.034-0.01332.952-0.013-0.0130.0000.0000.0000.000
76A76ASN0-0.062-0.04135.3450.1960.1960.0000.0000.0000.000
77A77HIS00.0920.04736.3000.1340.1340.0000.0000.0000.000
78A78ASP-1-0.857-0.94132.800-8.919-8.9190.0000.0000.0000.000
79A79GLU-1-0.949-0.95631.913-8.106-8.1060.0000.0000.0000.000
80A80ASP-1-0.756-0.89131.899-8.589-8.5890.0000.0000.0000.000
81A81LYS10.7980.90929.5918.4118.4110.0000.0000.0000.000
82A82LEU00.0090.01127.450-0.435-0.4350.0000.0000.0000.000
83A83TRP0-0.037-0.01126.887-0.385-0.3850.0000.0000.0000.000
84A84LEU00.0360.00825.597-0.286-0.2860.0000.0000.0000.000
85A85ASN0-0.002-0.00623.536-0.553-0.5530.0000.0000.0000.000
86A86ASN0-0.021-0.01622.095-0.776-0.7760.0000.0000.0000.000
87A87LEU0-0.0300.00021.968-0.357-0.3570.0000.0000.0000.000
88A88LEU0-0.016-0.01120.246-0.505-0.5050.0000.0000.0000.000
89A89HIS00.0310.02118.451-0.880-0.8800.0000.0000.0000.000
90A90PRO0-0.007-0.00715.794-0.986-0.9860.0000.0000.0000.000
91A91ALA00.0300.01814.489-0.970-0.9700.0000.0000.0000.000
92A92ILE00.001-0.00514.225-0.836-0.8360.0000.0000.0000.000
93A93ARG10.9850.99810.72018.77918.7790.0000.0000.0000.000
94A94GLU-1-0.818-0.9119.605-23.655-23.6550.0000.0000.0000.000
95A95ARG10.8950.9429.23815.69815.6980.0000.0000.0000.000
96A96MET0-0.034-0.00510.189-0.761-0.7610.0000.0000.0000.000
97A97LYS10.8420.9165.96823.53223.5320.0000.0000.0000.000
99A99LYS10.9140.9416.27517.12317.1230.0000.0000.0000.000
103A103GLN0-0.082-0.0335.8672.7512.7510.0000.0000.0000.000
105A105ALA00.0160.0266.7190.7170.7170.0000.0000.0000.000
106A106PRO00.0430.0296.724-5.863-5.8630.0000.0000.0000.000
107A107TYR00.015-0.0236.985-4.809-4.8090.0000.0000.0000.000
108A108THR0-0.010-0.0156.7812.8062.8060.0000.0000.0000.000
109A109LEU0-0.0070.0188.624-0.033-0.0330.0000.0000.0000.000
110A110PHE00.007-0.0199.4660.1980.1980.0000.0000.0000.000
111A111VAL00.0300.02611.5190.8430.8430.0000.0000.0000.000
112A112VAL00.009-0.00514.0820.3350.3350.0000.0000.0000.000
113A113PRO0-0.011-0.01416.9390.2700.2700.0000.0000.0000.000
114A114LEU0-0.0100.00819.9160.4450.4450.0000.0000.0000.000
115A115LEU00.0330.02113.597-0.109-0.1090.0000.0000.0000.000
116A116ILE00.0150.01217.229-0.465-0.4650.0000.0000.0000.000
117A117GLU-1-0.824-0.91719.636-12.730-12.7300.0000.0000.0000.000
118A118ASN0-0.031-0.02718.8620.6450.6450.0000.0000.0000.000
119A119LYS10.9070.95417.63312.72712.7270.0000.0000.0000.000
120A120LEU00.003-0.00113.134-0.666-0.6660.0000.0000.0000.000
121A121THR00.0090.00812.453-1.467-1.4670.0000.0000.0000.000
122A122ALA0-0.020-0.00711.367-0.925-0.9250.0000.0000.0000.000
123A123LEU0-0.071-0.0357.976-1.416-1.4160.0000.0000.0000.000
124A124CYS0-0.063-0.0237.367-1.718-1.7180.0000.0000.0000.000
125A125ASP-1-0.822-0.8955.306-43.287-43.2870.0000.0000.0000.000
126A126ARG10.7910.8858.44720.77720.7770.0000.0000.0000.000
127A127ILE0-0.022-0.02011.718-0.462-0.4620.0000.0000.0000.000
128A128LEU00.0110.02014.5680.9320.9320.0000.0000.0000.000
129A129VAL0-0.026-0.02816.6520.1210.1210.0000.0000.0000.000
130A130VAL0-0.019-0.00320.0920.2540.2540.0000.0000.0000.000
131A131ASP-1-0.869-0.93422.685-10.675-10.6750.0000.0000.0000.000
132A132VAL0-0.018-0.00725.8110.1360.1360.0000.0000.0000.000
133A133SER0-0.004-0.00929.3560.0600.0600.0000.0000.0000.000
134A134PRO00.029-0.00932.512-0.010-0.0100.0000.0000.0000.000
135A135GLN0-0.010-0.00533.7250.0950.0950.0000.0000.0000.000
136A136THR00.0150.00331.8510.2320.2320.0000.0000.0000.000
137A137GLN0-0.042-0.01528.975-0.035-0.0350.0000.0000.0000.000
138A138LEU00.0070.01231.983-0.001-0.0010.0000.0000.0000.000
139A139ALA0-0.0090.00835.3700.0580.0580.0000.0000.0000.000
140A140ARG0-0.087-0.04630.676-0.116-0.1160.0000.0000.0000.000
141A141SER0-0.024-0.01732.191-0.336-0.3360.0000.0000.0000.000
142A142ALA0-0.030-0.02033.8170.2010.2010.0000.0000.0000.000
143A143GLN0-0.043-0.05336.2730.0200.0200.0000.0000.0000.000
144A144ARG10.8270.91536.6098.0728.0720.0000.0000.0000.000
145A145ASP-1-0.798-0.88842.432-6.623-6.6230.0000.0000.0000.000
146A146ASN0-0.039-0.02642.867-0.146-0.1460.0000.0000.0000.000
147A147ASN00.008-0.01241.544-0.238-0.2380.0000.0000.0000.000
148A148ASN00.0240.01738.637-0.058-0.0580.0000.0000.0000.000
149A149PHE00.0480.01138.086-0.242-0.2420.0000.0000.0000.000
150A150GLU-1-0.840-0.89438.640-7.290-7.2900.0000.0000.0000.000
151A151GLN0-0.062-0.02635.405-0.348-0.3480.0000.0000.0000.000
152A152ILE00.0230.01132.808-0.248-0.2480.0000.0000.0000.000
153A153GLN00.0430.01033.644-0.186-0.1860.0000.0000.0000.000
154A154ARG10.8530.91035.0827.5487.5480.0000.0000.0000.000
155A155ILE00.0080.01429.402-0.164-0.1640.0000.0000.0000.000
156A156MET0-0.048-0.00630.381-0.270-0.2700.0000.0000.0000.000
157A157ASN0-0.015-0.00430.972-0.209-0.2090.0000.0000.0000.000
158A158SER0-0.084-0.03829.792-0.031-0.0310.0000.0000.0000.000
159A159GLN00.0050.01025.900-0.275-0.2750.0000.0000.0000.000
160A160VAL0-0.023-0.00723.5590.3350.3350.0000.0000.0000.000
161A161SER00.0440.01326.6260.0010.0010.0000.0000.0000.000
162A162GLN00.019-0.01927.172-0.056-0.0560.0000.0000.0000.000
163A163GLN00.0060.00127.113-0.353-0.3530.0000.0000.0000.000
164A164GLU-1-0.845-0.91325.680-11.037-11.0370.0000.0000.0000.000
165A165ARG10.8890.94322.37711.28111.2810.0000.0000.0000.000
166A166LEU00.0110.00122.170-0.567-0.5670.0000.0000.0000.000
167A167LYS10.8250.90023.20210.22710.2270.0000.0000.0000.000
168A168TRP00.002-0.00816.500-0.513-0.5130.0000.0000.0000.000
169A169ALA0-0.047-0.01018.321-0.840-0.8400.0000.0000.0000.000
170A170ASP-1-0.838-0.90114.789-18.733-18.7330.0000.0000.0000.000
171A171ASP-1-0.776-0.84115.841-17.761-17.7610.0000.0000.0000.000
172A172VAL0-0.003-0.01518.8520.0470.0470.0000.0000.0000.000
173A173ILE0-0.0130.00121.0980.1660.1660.0000.0000.0000.000
174A174ASN0-0.067-0.04123.4140.2070.2070.0000.0000.0000.000
175A175ASN00.016-0.01126.434-0.171-0.1710.0000.0000.0000.000
176A176ASP-1-0.719-0.81928.382-9.389-9.3890.0000.0000.0000.000
177A177ALA0-0.053-0.00831.8670.3190.3190.0000.0000.0000.000
178A178GLU-1-0.835-0.92932.285-9.023-9.0230.0000.0000.0000.000
179A179LEU00.0320.00229.006-0.011-0.0110.0000.0000.0000.000
180A180ALA0-0.028-0.01132.746-0.066-0.0660.0000.0000.0000.000
181A181GLN0-0.014-0.01235.5910.0300.0300.0000.0000.0000.000
182A182ASN00.0180.00529.714-0.005-0.0050.0000.0000.0000.000
183A183LEU00.0100.02027.810-0.321-0.3210.0000.0000.0000.000
184A184PRO00.0310.00928.645-0.387-0.3870.0000.0000.0000.000
185A185HIS00.0170.01328.864-0.498-0.4980.0000.0000.0000.000
186A186LEU0-0.031-0.00725.663-0.420-0.4200.0000.0000.0000.000
187A187GLN00.019-0.00124.325-0.308-0.3080.0000.0000.0000.000
188A188GLN0-0.035-0.01624.104-0.414-0.4140.0000.0000.0000.000
189A189LYS10.8800.93422.26212.29912.2990.0000.0000.0000.000
190A190VAL00.0310.00319.102-0.626-0.6260.0000.0000.0000.000
191A191LEU00.0040.00519.376-0.936-0.9360.0000.0000.0000.000
192A192GLU-1-0.851-0.91020.252-13.001-13.0010.0000.0000.0000.000
193A193LEU0-0.028-0.01617.037-0.580-0.5800.0000.0000.0000.000
194A194HIS00.0530.05615.653-1.850-1.8500.0000.0000.0000.000
195A195GLN0-0.034-0.02115.614-0.962-0.9620.0000.0000.0000.000
196A196PHE0-0.030-0.00616.010-0.932-0.9320.0000.0000.0000.000
197A197TYR0-0.026-0.06311.617-1.012-1.0120.0000.0000.0000.000
198A198LEU0-0.018-0.00511.400-2.651-2.6510.0000.0000.0000.000
199A199GLN0-0.020-0.00712.246-0.631-0.6310.0000.0000.0000.000
200A200GLN0-0.050-0.03210.914-0.201-0.2010.0000.0000.0000.000
201A201ALA0-0.036-0.0187.988-2.459-2.4590.0000.0000.0000.000
202A202GLU-1-0.951-0.9668.046-28.655-28.6550.0000.0000.0000.000
203A203ASN0-0.037-0.02610.3950.3530.3530.0000.0000.0000.000
204A204LYS10.7770.8895.29442.20842.2080.0000.0000.0000.000
205A205ASN-1-0.962-0.9536.390-34.640-34.6400.0000.0000.0000.000