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: M85JZ

Calculation Name: 6PX3-C-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6PX3

Chain ID: C

ChEMBL ID:

UniProt ID: P06897

Base Structure: ElectronMicroscopy

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1653513.29641
FMO2-HF: Nuclear repulsion 1585404.439565
FMO2-HF: Total energy -68108.856845
FMO2-MP2: Total energy -68312.289457


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:-71:MET)


Summations of interaction energy for fragment #1(A:-71: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.
-63.987-58.88126.06-10.562-20.601-0.134
Interaction energy analysis for fragmet #1(A:-71:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.778 / q_NPA : 0.894
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].
3A-69ILE0-0.0140.0012.4970.4113.5610.977-1.346-2.781-0.008
4A-68PHE00.004-0.0024.6821.2001.250-0.001-0.015-0.0330.000
16A-56GLU-1-0.924-0.9533.785-61.714-61.2550.000-0.123-0.3360.000
17A-55VAL0-0.018-0.0132.3689.02410.9981.606-1.103-2.476-0.004
18A-54GLU-1-0.871-0.9321.785-101.065-100.46112.942-7.707-5.839-0.100
19A-53SER0-0.003-0.0163.1973.8854.7480.215-0.140-0.938-0.002
20A-52SER00.010-0.0023.9513.9504.0410.006-0.010-0.0870.000
56A-16LEU0-0.001-0.0103.0730.4741.0440.110-0.120-0.559-0.001
57A-15SER00.017-0.0015.2060.0740.152-0.001-0.002-0.0750.000
61A-11ILE0-0.0210.0032.9010.3790.8220.085-0.099-0.4280.000
62A-10GLN00.0150.0052.501-7.835-7.7903.498-0.989-2.554-0.013
63A-9LYS10.9470.9482.38539.27036.8786.549-0.016-4.142-0.006
64A-8GLU-1-0.855-0.9083.228-33.175-34.0040.0741.108-0.3530.000
5A-67VAL00.0220.0178.5030.4590.4590.0000.0000.0000.000
6A-66LYS10.9170.96711.12817.19817.1980.0000.0000.0000.000
7A-65THR00.0380.03214.6260.7710.7710.0000.0000.0000.000
8A-64LEU00.023-0.00417.6150.2960.2960.0000.0000.0000.000
9A-63THR0-0.051-0.02720.6910.5120.5120.0000.0000.0000.000
10A-62GLY0-0.027-0.00819.8260.4000.4000.0000.0000.0000.000
11A-61LYS10.8500.91917.64116.87416.8740.0000.0000.0000.000
12A-60THR00.014-0.00813.3800.0220.0220.0000.0000.0000.000
13A-59ILE0-0.0110.00711.8790.6770.6770.0000.0000.0000.000
14A-58THR00.0190.0027.9880.1390.1390.0000.0000.0000.000
15A-57LEU0-0.022-0.0057.1481.8341.8340.0000.0000.0000.000
21A-51ASP-1-0.790-0.8785.524-42.174-42.1740.0000.0000.0000.000
22A-50THR00.004-0.0267.2760.8780.8780.0000.0000.0000.000
23A-49ILE0-0.022-0.0088.550-2.012-2.0120.0000.0000.0000.000
24A-48ASP-1-0.845-0.92210.722-18.368-18.3680.0000.0000.0000.000
25A-47ASN0-0.0060.0149.585-0.483-0.4830.0000.0000.0000.000
26A-46VAL00.0090.0156.954-0.643-0.6430.0000.0000.0000.000
27A-45LYS10.8350.9119.79017.92517.9250.0000.0000.0000.000
28A-44SER0-0.037-0.02013.0080.9100.9100.0000.0000.0000.000
29A-43LYS10.8420.9006.02645.01945.0190.0000.0000.0000.000
30A-42ILE0-0.015-0.01311.1850.4420.4420.0000.0000.0000.000
31A-41GLN0-0.034-0.01513.8980.7290.7290.0000.0000.0000.000
32A-40ASP-1-0.892-0.94114.105-20.456-20.4560.0000.0000.0000.000
33A-39LYS10.8150.90612.07023.37323.3730.0000.0000.0000.000
34A-38GLU-1-0.835-0.91115.586-16.638-16.6380.0000.0000.0000.000
35A-37GLY00.0140.02118.5920.9870.9870.0000.0000.0000.000
36A-36ILE0-0.047-0.02617.5340.7030.7030.0000.0000.0000.000
37A-35PRO00.0300.01718.978-0.836-0.8360.0000.0000.0000.000
38A-34PRO00.0500.01517.4520.1360.1360.0000.0000.0000.000
39A-33ASP-1-0.865-0.93418.745-13.008-13.0080.0000.0000.0000.000
40A-32GLN00.0030.00521.6170.1190.1190.0000.0000.0000.000
41A-31GLN0-0.014-0.00614.800-0.757-0.7570.0000.0000.0000.000
42A-30ARG10.7880.88917.22313.43513.4350.0000.0000.0000.000
43A-29LEU00.0420.02510.6590.0860.0860.0000.0000.0000.000
44A-28ILE00.0010.00413.7350.4680.4680.0000.0000.0000.000
45A-27PHE00.029-0.0038.454-0.998-0.9980.0000.0000.0000.000
46A-26ALA0-0.0090.00711.6030.7970.7970.0000.0000.0000.000
47A-25GLY00.0300.01513.3290.6650.6650.0000.0000.0000.000
48A-24LYS10.9290.97513.52116.95516.9550.0000.0000.0000.000
49A-23GLN00.022-0.00414.642-0.774-0.7740.0000.0000.0000.000
50A-22LEU0-0.073-0.0379.374-0.025-0.0250.0000.0000.0000.000
51A-21GLU-1-0.903-0.96813.411-14.995-14.9950.0000.0000.0000.000
52A-20ASP-1-0.837-0.90513.181-17.927-17.9270.0000.0000.0000.000
53A-19GLY00.0620.02613.418-1.122-1.1220.0000.0000.0000.000
54A-18ARG10.8160.92711.33017.61717.6170.0000.0000.0000.000
55A-17THR00.008-0.0107.805-1.733-1.7330.0000.0000.0000.000
58A-14ASP-1-0.866-0.9116.362-19.238-19.2380.0000.0000.0000.000
59A-13TYR00.0030.0067.8691.6541.6540.0000.0000.0000.000
60A-12ASN0-0.063-0.0306.540-0.451-0.4510.0000.0000.0000.000
65A-7SER0-0.026-0.0125.0574.6004.6000.0000.0000.0000.000
66A-6THR0-0.032-0.0176.923-1.451-1.4510.0000.0000.0000.000
67A-5LEU00.0010.0076.4701.6471.6470.0000.0000.0000.000
68A-4HIS0-0.019-0.01410.1360.4930.4930.0000.0000.0000.000
69A-3LEU0-0.0050.00113.929-0.113-0.1130.0000.0000.0000.000
70A-2VAL0-0.024-0.01715.6370.7470.7470.0000.0000.0000.000
71A-1LEU00.0250.01018.991-0.380-0.3800.0000.0000.0000.000
72A0ARG10.7860.88319.15714.36114.3610.0000.0000.0000.000
73A1LEU00.0110.00623.509-0.068-0.0680.0000.0000.0000.000
74A2ARG10.8810.93726.17310.73010.7300.0000.0000.0000.000
75A3GLY-1-0.866-0.92428.986-9.241-9.2410.0000.0000.0000.000
76A16GLY00.0950.03843.9890.0510.0510.0000.0000.0000.000
77A17ARG10.9120.95642.4156.5576.5570.0000.0000.0000.000
78A18SER0-0.004-0.02738.5230.0190.0190.0000.0000.0000.000
79A19SER00.0170.00637.932-0.147-0.1470.0000.0000.0000.000
80A20ARG10.9400.96438.2007.0467.0460.0000.0000.0000.000
81A21ALA0-0.038-0.01636.024-0.005-0.0050.0000.0000.0000.000
82A22GLY00.1130.07333.525-0.202-0.2020.0000.0000.0000.000
83A23LEU0-0.077-0.02532.396-0.154-0.1540.0000.0000.0000.000
84A24GLN00.0690.02132.8100.4060.4060.0000.0000.0000.000
85A25PHE00.0340.02633.7260.2800.2800.0000.0000.0000.000
86A26PRO00.0020.01836.8240.1100.1100.0000.0000.0000.000
87A27VAL00.0770.02538.5250.1680.1680.0000.0000.0000.000
88A28GLY0-0.018-0.00740.9270.1190.1190.0000.0000.0000.000
89A29ARG10.9320.96342.7846.9726.9720.0000.0000.0000.000
90A30VAL00.0660.03838.9700.1300.1300.0000.0000.0000.000
91A31HIS00.0440.02042.3790.1140.1140.0000.0000.0000.000
92A32ARG10.9160.96145.0406.3306.3300.0000.0000.0000.000
93A33LEU0-0.018-0.01943.1210.1290.1290.0000.0000.0000.000
94A34LEU00.0360.01341.2680.0740.0740.0000.0000.0000.000
95A35ARG10.9220.95445.4816.1166.1160.0000.0000.0000.000
96A36LYS10.9220.95649.1075.6575.6570.0000.0000.0000.000
97A37GLY00.0120.01747.4520.0750.0750.0000.0000.0000.000
98A38ASN0-0.048-0.01648.412-0.006-0.0060.0000.0000.0000.000
99A39TYR00.0200.01644.472-0.020-0.0200.0000.0000.0000.000
100A40ALA00.0120.00446.689-0.043-0.0430.0000.0000.0000.000
101A41GLU-1-0.898-0.93448.591-5.593-5.5930.0000.0000.0000.000
102A42ARG10.9210.95449.7285.9565.9560.0000.0000.0000.000
103A43VAL0-0.0010.00344.507-0.121-0.1210.0000.0000.0000.000
104A44GLY00.0300.01844.4350.0720.0720.0000.0000.0000.000
105A45ALA00.005-0.02043.796-0.100-0.1000.0000.0000.0000.000
106A46GLY00.0620.02940.250-0.061-0.0610.0000.0000.0000.000
107A47ALA00.0120.01938.878-0.187-0.1870.0000.0000.0000.000
108A48PRO0-0.034-0.03238.775-0.122-0.1220.0000.0000.0000.000
109A49VAL0-0.0080.00136.125-0.077-0.0770.0000.0000.0000.000
110A50TYR00.0590.03330.934-0.147-0.1470.0000.0000.0000.000
111A51LEU00.0240.01133.841-0.190-0.1900.0000.0000.0000.000
112A52ALA0-0.033-0.02534.702-0.104-0.1040.0000.0000.0000.000
113A53ALA00.0530.02931.116-0.129-0.1290.0000.0000.0000.000
114A54VAL00.0190.01029.946-0.264-0.2640.0000.0000.0000.000
115A55LEU0-0.021-0.01730.134-0.148-0.1480.0000.0000.0000.000
116A56GLU-1-0.978-0.97129.289-9.942-9.9420.0000.0000.0000.000
117A57TYR00.0890.04921.865-0.302-0.3020.0000.0000.0000.000
118A58LEU0-0.012-0.01126.327-0.298-0.2980.0000.0000.0000.000
119A59THR0-0.062-0.04427.6670.0090.0090.0000.0000.0000.000
120A60ALA00.005-0.00225.773-0.055-0.0550.0000.0000.0000.000
121A61GLU-1-0.843-0.91620.651-13.264-13.2640.0000.0000.0000.000
122A62ILE0-0.020-0.01123.609-0.208-0.2080.0000.0000.0000.000
123A63LEU0-0.019-0.02326.0690.0260.0260.0000.0000.0000.000
124A64GLU-1-0.817-0.88919.488-13.692-13.6920.0000.0000.0000.000
125A65LEU0-0.021-0.00819.225-0.224-0.2240.0000.0000.0000.000
126A66ALA0-0.002-0.00722.444-0.031-0.0310.0000.0000.0000.000
127A67GLY00.011-0.00525.5470.1950.1950.0000.0000.0000.000
128A68ASN00.0130.01119.656-0.058-0.0580.0000.0000.0000.000
129A69ALA00.0380.02622.334-0.027-0.0270.0000.0000.0000.000
130A70ALA0-0.023-0.01023.8280.1550.1550.0000.0000.0000.000
131A71ARG10.8600.92419.53213.55413.5540.0000.0000.0000.000
132A72ASP-1-0.834-0.90519.862-13.728-13.7280.0000.0000.0000.000
133A73ASN0-0.092-0.05123.1980.2800.2800.0000.0000.0000.000
134A74LYS10.9500.97425.53111.66611.6660.0000.0000.0000.000
135A75LYS10.8330.91028.1299.9639.9630.0000.0000.0000.000
136A76THR00.0450.02129.169-0.245-0.2450.0000.0000.0000.000
137A77ARG10.9130.95431.3528.4548.4540.0000.0000.0000.000
138A78ILE00.0550.04028.439-0.090-0.0900.0000.0000.0000.000
139A79ILE00.0030.00531.3640.3260.3260.0000.0000.0000.000
140A80PRO00.0550.01031.848-0.283-0.2830.0000.0000.0000.000
141A81ARG10.8610.92330.1719.1429.1420.0000.0000.0000.000
142A82HIS00.0430.01927.616-0.112-0.1120.0000.0000.0000.000
143A83LEU00.0320.02227.152-0.321-0.3210.0000.0000.0000.000
144A84GLN0-0.021-0.00828.197-0.171-0.1710.0000.0000.0000.000
145A85LEU0-0.018-0.01624.900-0.167-0.1670.0000.0000.0000.000
146A86ALA0-0.0140.00623.545-0.410-0.4100.0000.0000.0000.000
147A87VAL00.000-0.00623.625-0.267-0.2670.0000.0000.0000.000
148A88ARG10.8570.91824.8059.1189.1180.0000.0000.0000.000
149A89ASN0-0.031-0.01320.437-0.090-0.0900.0000.0000.0000.000
150A90ASP00.0170.02619.364-0.508-0.5080.0000.0000.0000.000
151A91GLU-1-0.868-0.94117.660-12.794-12.7940.0000.0000.0000.000
152A92GLU-1-0.917-0.95218.612-13.153-13.1530.0000.0000.0000.000
153A93LEU00.003-0.01122.1580.6170.6170.0000.0000.0000.000
154A94ASN0-0.006-0.01023.9960.8370.8370.0000.0000.0000.000
155A95LYS10.9270.96624.38110.29110.2910.0000.0000.0000.000
156A96LEU0-0.040-0.01326.1800.3720.3720.0000.0000.0000.000
157A97LEU0-0.021-0.01828.2790.4050.4050.0000.0000.0000.000
158A98GLY00.0460.03629.5630.1680.1680.0000.0000.0000.000
159A99ARG10.8930.93630.4187.9877.9870.0000.0000.0000.000
160A100VAL00.0100.02432.3150.2750.2750.0000.0000.0000.000
161A101THR00.0090.00333.708-0.218-0.2180.0000.0000.0000.000
162A102ILE00.0030.01131.1280.1510.1510.0000.0000.0000.000
163A103ALA00.0310.00835.3000.0140.0140.0000.0000.0000.000
164A104GLN00.021-0.00537.202-0.169-0.1690.0000.0000.0000.000
165A105GLY00.0200.02833.531-0.144-0.1440.0000.0000.0000.000
166A106GLY00.0190.00832.640-0.228-0.2280.0000.0000.0000.000
167A107VAL00.0420.01331.311-0.095-0.0950.0000.0000.0000.000
168A108LEU00.0350.02024.3600.0660.0660.0000.0000.0000.000
169A109PRO0-0.031-0.02026.2870.2550.2550.0000.0000.0000.000
170A110ASN0-0.0010.00526.252-0.451-0.4510.0000.0000.0000.000
171A111ILE00.0210.01527.4670.3670.3670.0000.0000.0000.000
172A112GLN00.0260.01527.785-0.278-0.2780.0000.0000.0000.000
173A113SER00.0570.01726.3920.2910.2910.0000.0000.0000.000
174A114VAL00.0170.00228.4930.0870.0870.0000.0000.0000.000
175A115LEU0-0.040-0.01731.9470.2380.2380.0000.0000.0000.000
176A116LEU0-0.0180.01227.7290.1300.1300.0000.0000.0000.000
177A117PRO0-0.007-0.02032.1700.1840.1840.0000.0000.0000.000
178A118LYS10.9050.95832.3907.9327.9320.0000.0000.0000.000
179A119LYS00.0650.04730.4470.2750.2750.0000.0000.0000.000