FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 97ZJ2

Calculation Name: 5LXQ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | zinc ion

Ligand 3-letter code: ATP | ZN

Ligand of Interest (LOI):

PDB ID: 5LXQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q3TWN3

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 151
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1515628.460624
FMO2-HF: Nuclear repulsion 1454884.158784
FMO2-HF: Total energy -60744.30184
FMO2-MP2: Total energy -60920.235981


3D Structure
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:9:PRO)


Summations of interaction energy for fragment #1(A:9:PRO)
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.
-6.0733.41399999999997.219-7.026-9.682-0.07
Interaction energy analysis for fragmet #1(A:9:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.903
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].
3A11GLU-1-0.804-0.8813.844-28.672-27.101-0.022-0.612-0.938-0.001
12A20LEU0-0.012-0.0043.195-3.702-3.0390.109-0.202-0.571-0.001
13A21ILE00.0240.0194.6091.8532.083-0.001-0.062-0.1670.000
14A22THR0-0.065-0.0472.396-27.221-23.9103.415-3.586-3.141-0.034
15A23HIS00.0260.0172.400-9.165-8.0833.328-1.465-2.945-0.023
16A24ASN00.0740.0214.8700.1840.297-0.001-0.004-0.1070.000
28A36GLU-1-0.831-0.9144.511-43.425-43.307-0.001-0.024-0.0940.000
32A40TYR0-0.021-0.0152.839-7.804-5.9150.372-0.880-1.381-0.010
129A137ARG10.8790.9383.38048.04548.5550.020-0.191-0.338-0.001
4A12VAL0-0.036-0.0276.6682.1152.1150.0000.0000.0000.000
5A13THR00.0190.0129.8780.5820.5820.0000.0000.0000.000
6A14TYR0-0.027-0.02412.9910.8460.8460.0000.0000.0000.000
7A15LYS10.9350.97416.53413.47613.4760.0000.0000.0000.000
8A16ASN00.0200.01418.935-0.230-0.2300.0000.0000.0000.000
9A17MET0-0.0410.00815.8310.1710.1710.0000.0000.0000.000
10A18ARG10.7890.8809.55724.61224.6120.0000.0000.0000.000
11A19PHE00.0530.0129.3620.6430.6430.0000.0000.0000.000
17A25PRO0-0.039-0.0087.733-0.161-0.1610.0000.0000.0000.000
18A26THR00.0290.0089.1392.7602.7600.0000.0000.0000.000
19A27ASN00.050-0.01212.401-0.468-0.4680.0000.0000.0000.000
20A28ALA00.0320.02915.1390.2750.2750.0000.0000.0000.000
21A29THR0-0.050-0.0259.690-0.410-0.4100.0000.0000.0000.000
22A30LEU00.0220.01710.775-1.939-1.9390.0000.0000.0000.000
23A31ASN00.0060.00812.105-0.900-0.9000.0000.0000.0000.000
24A32LYS10.8570.9086.07333.28233.2820.0000.0000.0000.000
25A33PHE0-0.010-0.0026.339-2.411-2.4110.0000.0000.0000.000
26A34ILE00.0480.0197.890-1.874-1.8740.0000.0000.0000.000
27A35GLU-1-0.834-0.8968.835-29.644-29.6440.0000.0000.0000.000
29A37LEU0-0.026-0.0106.474-1.143-1.1430.0000.0000.0000.000
30A38LYS10.9260.9607.32918.98318.9830.0000.0000.0000.000
31A39LYS10.8240.9136.96233.70533.7050.0000.0000.0000.000
33A41GLY00.0340.0288.1320.8580.8580.0000.0000.0000.000
34A42VAL0-0.060-0.0319.2670.7160.7160.0000.0000.0000.000
35A43THR00.0490.02611.2791.1401.1400.0000.0000.0000.000
36A44THR0-0.038-0.02613.2761.1931.1930.0000.0000.0000.000
37A45ILE0-0.009-0.0049.858-2.042-2.0420.0000.0000.0000.000
38A46VAL0-0.012-0.00911.5681.7171.7170.0000.0000.0000.000
39A47ARG10.8280.90411.65817.29617.2960.0000.0000.0000.000
40A48VAL0-0.003-0.01712.3961.4771.4770.0000.0000.0000.000
41A49CYS-1-0.907-0.89113.387-21.974-21.9740.0000.0000.0000.000
42A50GLU-1-0.772-0.91315.331-16.644-16.6440.0000.0000.0000.000
43A51ALA00.0180.00615.783-1.098-1.0980.0000.0000.0000.000
44A52THR00.0040.01613.2960.5380.5380.0000.0000.0000.000
45A53TYR0-0.086-0.06111.3810.4700.4700.0000.0000.0000.000
46A54ASP-1-0.783-0.85916.183-14.817-14.8170.0000.0000.0000.000
47A55THR0-0.025-0.01717.011-0.835-0.8350.0000.0000.0000.000
48A56THR0-0.045-0.04518.149-0.068-0.0680.0000.0000.0000.000
49A57LEU0-0.014-0.01516.7520.1710.1710.0000.0000.0000.000
50A58VAL0-0.013-0.01313.059-0.406-0.4060.0000.0000.0000.000
51A59GLU-1-0.786-0.88315.667-15.364-15.3640.0000.0000.0000.000
52A60LYS10.9200.97118.32513.45613.4560.0000.0000.0000.000
53A61GLU-1-0.944-0.97315.390-16.118-16.1180.0000.0000.0000.000
54A62GLY0-0.019-0.00316.870-0.318-0.3180.0000.0000.0000.000
55A63ILE0-0.058-0.01911.827-0.279-0.2790.0000.0000.0000.000
56A64HIS10.8690.92715.25815.46915.4690.0000.0000.0000.000
57A65VAL00.0220.00314.516-1.211-1.2110.0000.0000.0000.000
58A66LEU0-0.058-0.02815.6201.2981.2980.0000.0000.0000.000
59A67ASP-1-0.791-0.88016.096-18.337-18.3370.0000.0000.0000.000
60A68TRP0-0.036-0.03017.1220.6700.6700.0000.0000.0000.000
61A69PRO00.0240.01418.064-0.465-0.4650.0000.0000.0000.000
62A70PHE0-0.013-0.01716.1730.6610.6610.0000.0000.0000.000
63A71ASP-1-0.876-0.93419.080-13.601-13.6010.0000.0000.0000.000
64A72ASP-1-0.869-0.94616.585-18.402-18.4020.0000.0000.0000.000
65A73GLY0-0.060-0.02417.5100.7210.7210.0000.0000.0000.000
66A74ALA00.0100.01018.8770.5170.5170.0000.0000.0000.000
67A75PRO0-0.038-0.02819.355-0.830-0.8300.0000.0000.0000.000
68A76PRO00.0040.02118.5320.4070.4070.0000.0000.0000.000
69A77SER00.0500.00920.8690.3710.3710.0000.0000.0000.000
70A78ASN00.013-0.01523.610-0.504-0.5040.0000.0000.0000.000
71A79GLN0-0.0090.00125.2380.2820.2820.0000.0000.0000.000
72A80ILE00.0690.05419.134-0.176-0.1760.0000.0000.0000.000
73A81VAL0-0.027-0.01120.465-0.679-0.6790.0000.0000.0000.000
74A82ASP-1-0.841-0.91521.779-11.753-11.7530.0000.0000.0000.000
75A83ASP-1-0.824-0.88922.016-12.378-12.3780.0000.0000.0000.000
76A84TRP0-0.002-0.01312.497-0.331-0.3310.0000.0000.0000.000
77A85LEU0-0.011-0.01819.112-0.245-0.2450.0000.0000.0000.000
78A86SER0-0.055-0.02921.1260.5010.5010.0000.0000.0000.000
79A87LEU00.0040.00716.2440.1460.1460.0000.0000.0000.000
80A88VAL00.0080.00316.052-0.136-0.1360.0000.0000.0000.000
81A89LYS10.8370.92218.47311.71111.7110.0000.0000.0000.000
82A90ILE0-0.003-0.00521.9400.4190.4190.0000.0000.0000.000
83A91LYS10.9120.96217.19815.51415.5140.0000.0000.0000.000
84A92PHE0-0.016-0.01413.5850.0080.0080.0000.0000.0000.000
85A93ARG10.8050.89219.29012.01812.0180.0000.0000.0000.000
86A94GLU-1-0.907-0.94121.698-13.525-13.5250.0000.0000.0000.000
87A95GLU-1-0.899-0.95518.611-15.560-15.5600.0000.0000.0000.000
88A96PRO0-0.006-0.00318.736-0.986-0.9860.0000.0000.0000.000
89A97GLY0-0.0050.00516.7700.0990.0990.0000.0000.0000.000
90A98CYS0-0.0330.01114.603-1.461-1.4610.0000.0000.0000.000
91A99CYS0-0.057-0.0258.315-0.845-0.8450.0000.0000.0000.000
92A100ILE00.0170.00411.0280.9890.9890.0000.0000.0000.000
93A101ALA00.0200.0007.271-2.215-2.2150.0000.0000.0000.000
94A102VAL0-0.025-0.0047.3033.0663.0660.0000.0000.0000.000
95A103HIS00.0080.0097.039-4.660-4.6600.0000.0000.0000.000
96A104CYS-1-0.815-0.8908.597-24.858-24.8580.0000.0000.0000.000
97A105VAL0-0.026-0.0289.383-2.813-2.8130.0000.0000.0000.000
98A106ALA0-0.0200.01211.426-0.195-0.1950.0000.0000.0000.000
99A107GLY00.0630.0098.179-1.936-1.9360.0000.0000.0000.000
100A108LEU0-0.106-0.0787.5582.1722.1720.0000.0000.0000.000
101A109GLY00.0650.0389.9441.6161.6160.0000.0000.0000.000
102A110ARG10.7940.88612.80218.96618.9660.0000.0000.0000.000
103A111ALA00.0550.0088.9800.5850.5850.0000.0000.0000.000
104A112PRO0-0.022-0.0189.594-0.009-0.0090.0000.0000.0000.000
105A113VAL00.0070.00511.3221.4031.4030.0000.0000.0000.000
106A114LEU00.0430.03213.3931.0661.0660.0000.0000.0000.000
107A115VAL00.0080.0129.5340.8400.8400.0000.0000.0000.000
108A116ALA00.0110.00013.0040.9730.9730.0000.0000.0000.000
109A117LEU00.0010.00015.6491.0191.0190.0000.0000.0000.000
110A118ALA0-0.0020.00215.4380.9130.9130.0000.0000.0000.000
111A119LEU0-0.021-0.02013.8070.5790.5790.0000.0000.0000.000
112A120ILE0-0.033-0.01217.4840.7890.7890.0000.0000.0000.000
113A121GLU-1-0.783-0.86720.644-11.622-11.6220.0000.0000.0000.000
114A122GLY00.0140.01020.5620.5210.5210.0000.0000.0000.000
115A123GLY0-0.053-0.02921.5550.1990.1990.0000.0000.0000.000
116A124MET0-0.0350.01717.447-0.100-0.1000.0000.0000.0000.000
117A125LYS10.9030.92821.75012.09912.0990.0000.0000.0000.000
118A126TYR00.0290.01121.309-0.667-0.6670.0000.0000.0000.000
119A127GLU-1-0.814-0.90720.871-13.120-13.1200.0000.0000.0000.000
120A128ASP-1-0.921-0.95520.374-15.687-15.6870.0000.0000.0000.000
121A129ALA00.0380.01117.375-1.027-1.0270.0000.0000.0000.000
122A130VAL0-0.025-0.01216.079-1.503-1.5030.0000.0000.0000.000
123A131GLN0-0.004-0.01115.937-1.721-1.7210.0000.0000.0000.000
124A132PHE00.0100.00313.605-1.615-1.6150.0000.0000.0000.000
125A133ILE0-0.0050.00010.769-2.202-2.2020.0000.0000.0000.000
126A134ARG10.8720.91911.07916.31116.3110.0000.0000.0000.000
127A135GLN0-0.035-0.00712.682-1.483-1.4830.0000.0000.0000.000
128A136LYS10.9000.9707.84227.63227.6320.0000.0000.0000.000
130A138ARG11.0301.0199.22921.77621.7760.0000.0000.0000.000
131A139GLY00.0170.00811.717-1.136-1.1360.0000.0000.0000.000
132A140ALA0-0.018-0.01710.7781.1831.1830.0000.0000.0000.000
133A141PHE00.0870.04512.1740.0190.0190.0000.0000.0000.000
134A142ASN0-0.0030.00615.6210.7320.7320.0000.0000.0000.000
135A143SER00.036-0.00718.640-0.009-0.0090.0000.0000.0000.000
136A144LYS10.9510.98321.76912.19712.1970.0000.0000.0000.000
137A145GLN00.0260.01015.7310.0060.0060.0000.0000.0000.000
138A146LEU00.0130.00718.8130.0290.0290.0000.0000.0000.000
139A147LEU00.0580.03221.0490.2350.2350.0000.0000.0000.000
140A148TYR0-0.031-0.01121.0730.5660.5660.0000.0000.0000.000
141A149LEU0-0.025-0.02517.2410.1990.1990.0000.0000.0000.000
142A150GLU-1-0.979-0.97221.893-11.407-11.4070.0000.0000.0000.000
143A151LYS10.9650.97724.87310.38810.3880.0000.0000.0000.000
144A152TYR0-0.012-0.01123.7680.5110.5110.0000.0000.0000.000
145A153ARG10.8270.90925.85210.70710.7070.0000.0000.0000.000
146A154PRO00.0160.01925.030-0.021-0.0210.0000.0000.0000.000
147A155LYS10.8470.89526.48711.66011.6600.0000.0000.0000.000
148A156MET0-0.026-0.00526.8940.4560.4560.0000.0000.0000.000
149A157ARG10.8210.89724.57612.11712.1170.0000.0000.0000.000
150A158LEU00.0210.01220.4540.0210.0210.0000.0000.0000.000
151A159ARG00.1360.07824.469-1.426-1.4260.0000.0000.0000.000