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: 4YJNN

Calculation Name: 1WH4-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WH4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4K2

Base Structure: SolutionNMR

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 127
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -986413.285235
FMO2-HF: Nuclear repulsion 938502.040372
FMO2-HF: Total energy -47911.244863
FMO2-MP2: Total energy -48051.906015


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:GLY)


Summations of interaction energy for fragment #1(A:1: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.
3.13600000000013.699-0.005-0.306-0.2520
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.917
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].
3A3SER0-0.001-0.0073.848-0.0590.504-0.005-0.306-0.2520.000
4A4GLY00.0320.0106.9470.7030.7030.0000.0000.0000.000
5A5SER0-0.039-0.01510.7300.9680.9680.0000.0000.0000.000
6A6SER00.0380.03813.3251.7761.7760.0000.0000.0000.000
7A7GLY00.015-0.00316.218-0.712-0.7120.0000.0000.0000.000
8A8MET0-0.040-0.00519.0280.3130.3130.0000.0000.0000.000
9A9ASN00.0310.00721.4710.7200.7200.0000.0000.0000.000
10A10LYS10.9390.97624.05110.06110.0610.0000.0000.0000.000
11A11PRO00.0140.00824.9950.0360.0360.0000.0000.0000.000
12A12LEU00.0030.01727.3390.3390.3390.0000.0000.0000.000
13A13THR00.0430.01230.703-0.122-0.1220.0000.0000.0000.000
14A14PRO00.0860.03133.0810.1080.1080.0000.0000.0000.000
15A15SER00.0120.00935.0820.0870.0870.0000.0000.0000.000
16A16THR0-0.034-0.00635.1200.2420.2420.0000.0000.0000.000
17A17TYR00.0530.01537.086-0.143-0.1430.0000.0000.0000.000
18A18ILE00.0110.02235.489-0.220-0.2200.0000.0000.0000.000
19A19ARG10.9760.98436.0737.3847.3840.0000.0000.0000.000
20A20ASN0-0.097-0.03836.6580.2540.2540.0000.0000.0000.000
21A21LEU0-0.0200.00431.608-0.247-0.2470.0000.0000.0000.000
22A22ASN00.0640.02630.8120.2250.2250.0000.0000.0000.000
23A23VAL00.0830.03530.851-0.302-0.3020.0000.0000.0000.000
24A24GLY0-0.009-0.00427.513-0.198-0.1980.0000.0000.0000.000
25A25ILE0-0.004-0.00726.645-0.461-0.4610.0000.0000.0000.000
26A26LEU00.0710.03828.248-0.169-0.1690.0000.0000.0000.000
27A27ARG10.9130.97626.55411.46411.4640.0000.0000.0000.000
28A28LYS10.9780.98219.85715.26915.2690.0000.0000.0000.000
29A29LEU00.0340.02325.168-0.239-0.2390.0000.0000.0000.000
30A30SER0-0.053-0.05927.9440.2000.2000.0000.0000.0000.000
31A31ASP-1-0.945-0.97821.969-14.453-14.4530.0000.0000.0000.000
32A32PHE0-0.043-0.02620.403-0.285-0.2850.0000.0000.0000.000
33A33ILE0-0.0180.00125.7340.2030.2030.0000.0000.0000.000
34A34ASP-1-0.871-0.89029.135-9.851-9.8510.0000.0000.0000.000
35A35PRO00.0490.02025.9910.3310.3310.0000.0000.0000.000
36A36GLN0-0.007-0.02425.2680.3310.3310.0000.0000.0000.000
37A37GLU-1-0.840-0.91630.459-8.498-8.4980.0000.0000.0000.000
38A38GLY00.0130.01331.3920.2400.2400.0000.0000.0000.000
39A39TRP00.0500.00632.3680.3830.3830.0000.0000.0000.000
40A40LYS10.8220.92734.9288.6228.6220.0000.0000.0000.000
41A41LYS10.9150.96532.6039.9219.9210.0000.0000.0000.000
42A42LEU00.0340.02534.4850.1630.1630.0000.0000.0000.000
43A43ALA0-0.010-0.02036.6680.2060.2060.0000.0000.0000.000
44A44VAL0-0.021-0.01739.9440.2030.2030.0000.0000.0000.000
45A45ALA0-0.0050.01038.3740.1620.1620.0000.0000.0000.000
46A46ILE0-0.0190.00038.9960.1370.1370.0000.0000.0000.000
47A47LYS10.9440.98542.0767.5507.5500.0000.0000.0000.000
48A48LYS10.8950.94945.4846.2826.2820.0000.0000.0000.000
49A49PRO00.006-0.00948.306-0.011-0.0110.0000.0000.0000.000
50A50SER0-0.029-0.02549.3830.0150.0150.0000.0000.0000.000
51A51GLY0-0.0010.00548.8880.0760.0760.0000.0000.0000.000
52A52ASP-1-0.886-0.93649.274-6.262-6.2620.0000.0000.0000.000
53A53ASP-1-0.860-0.93646.995-6.946-6.9460.0000.0000.0000.000
54A54ARG10.8380.92444.9197.1497.1490.0000.0000.0000.000
55A55TYR0-0.053-0.03242.7470.0840.0840.0000.0000.0000.000
56A56ASN00.0490.03244.749-0.049-0.0490.0000.0000.0000.000
57A57GLN00.0690.01544.480-0.169-0.1690.0000.0000.0000.000
58A58PHE0-0.040-0.01346.839-0.053-0.0530.0000.0000.0000.000
59A59HIS00.015-0.00445.688-0.048-0.0480.0000.0000.0000.000
60A60ILE00.0150.02241.090-0.145-0.1450.0000.0000.0000.000
61A61ARG10.9260.94942.6026.9536.9530.0000.0000.0000.000
62A62ARG10.9310.96844.3336.6186.6180.0000.0000.0000.000
63A63PHE00.0430.01739.465-0.062-0.0620.0000.0000.0000.000
64A64GLU-1-0.820-0.92139.607-7.909-7.9090.0000.0000.0000.000
65A65ALA0-0.015-0.00840.110-0.119-0.1190.0000.0000.0000.000
66A66LEU0-0.0460.00938.315-0.028-0.0280.0000.0000.0000.000
67A67LEU00.0700.03434.923-0.105-0.1050.0000.0000.0000.000
68A68GLN0-0.063-0.03036.288-0.259-0.2590.0000.0000.0000.000
69A69THR0-0.069-0.04438.5540.0930.0930.0000.0000.0000.000
70A70GLY00.0240.02134.885-0.043-0.0430.0000.0000.0000.000
71A71LYS10.7800.89034.5338.0458.0450.0000.0000.0000.000
72A72SER0-0.015-0.04132.0740.0190.0190.0000.0000.0000.000
73A73PRO00.007-0.00534.0790.1570.1570.0000.0000.0000.000
74A74THR00.0280.01430.8990.2560.2560.0000.0000.0000.000
75A75CYS0-0.039-0.01333.2720.1000.1000.0000.0000.0000.000
76A76GLU-1-0.823-0.90634.686-7.912-7.9120.0000.0000.0000.000
77A77LEU0-0.0160.00936.4820.1880.1880.0000.0000.0000.000
78A78LEU0-0.006-0.01532.4980.1270.1270.0000.0000.0000.000
79A79PHE0-0.028-0.01436.9400.1110.1110.0000.0000.0000.000
80A80ASP-1-0.874-0.93139.047-7.193-7.1930.0000.0000.0000.000
81A81TRP00.059-0.00236.1830.0880.0880.0000.0000.0000.000
82A82GLY0-0.010-0.02040.4520.0530.0530.0000.0000.0000.000
83A83THR0-0.048-0.03641.1870.1190.1190.0000.0000.0000.000
84A84THR0-0.059-0.01543.7450.2640.2640.0000.0000.0000.000
85A85ASN0-0.128-0.05044.1530.1170.1170.0000.0000.0000.000
86A86CYS00.0300.03840.2950.1090.1090.0000.0000.0000.000
87A87THR0-0.023-0.03838.201-0.027-0.0270.0000.0000.0000.000
88A88VAL00.007-0.00231.819-0.088-0.0880.0000.0000.0000.000
89A89GLY0-0.013-0.01033.774-0.235-0.2350.0000.0000.0000.000
90A90ASP-1-0.776-0.87035.574-8.153-8.1530.0000.0000.0000.000
91A91LEU0-0.023-0.01532.056-0.062-0.0620.0000.0000.0000.000
92A92VAL0-0.029-0.01830.071-0.206-0.2060.0000.0000.0000.000
93A93ASP-1-0.875-0.93732.464-8.982-8.9820.0000.0000.0000.000
94A94LEU0-0.049-0.03435.291-0.028-0.0280.0000.0000.0000.000
95A95LEU0-0.039-0.03529.416-0.051-0.0510.0000.0000.0000.000
96A96VAL0-0.009-0.00530.136-0.242-0.2420.0000.0000.0000.000
97A97GLN0-0.045-0.01232.0970.1330.1330.0000.0000.0000.000
98A98ILE0-0.085-0.03732.3340.2100.2100.0000.0000.0000.000
99A99GLU-1-0.884-0.95229.043-10.489-10.4890.0000.0000.0000.000
100A100LEU0-0.0300.00327.707-0.521-0.5210.0000.0000.0000.000
101A101PHE00.0360.00225.445-0.244-0.2440.0000.0000.0000.000
102A102ALA00.0030.02622.077-0.210-0.2100.0000.0000.0000.000
103A103PRO00.010-0.00623.644-0.277-0.2770.0000.0000.0000.000
104A104ALA00.0460.03125.9030.1430.1430.0000.0000.0000.000
105A105THR0-0.006-0.02621.6500.0130.0130.0000.0000.0000.000
106A106LEU0-0.088-0.04222.067-0.309-0.3090.0000.0000.0000.000
107A107LEU0-0.064-0.02323.9380.0690.0690.0000.0000.0000.000
108A108LEU0-0.001-0.02527.2580.1860.1860.0000.0000.0000.000
109A109PRO0-0.022-0.01123.1310.1510.1510.0000.0000.0000.000
110A110ASP-1-0.972-0.96825.114-11.355-11.3550.0000.0000.0000.000
111A111ALA0-0.018-0.00427.8240.2520.2520.0000.0000.0000.000
112A112VAL00.0220.00326.0240.2510.2510.0000.0000.0000.000
113A113PRO00.0050.01527.715-0.282-0.2820.0000.0000.0000.000
114A114GLN00.0080.00824.910-0.028-0.0280.0000.0000.0000.000
115A115THR00.0000.00422.441-0.356-0.3560.0000.0000.0000.000
116A116VAL0-0.049-0.03018.602-0.742-0.7420.0000.0000.0000.000
117A117LYS10.9860.98718.43215.72115.7210.0000.0000.0000.000
118A118SER0-0.019-0.01313.093-1.233-1.2330.0000.0000.0000.000
119A119LEU00.0000.01910.8031.2411.2410.0000.0000.0000.000
120A120PRO00.0110.00312.958-1.511-1.5110.0000.0000.0000.000
121A121PRO00.005-0.0029.299-0.350-0.3500.0000.0000.0000.000
122A122SER0-0.005-0.01810.6571.9361.9360.0000.0000.0000.000
123A123GLY00.0290.00311.079-2.336-2.3360.0000.0000.0000.000
124A124PRO0-0.050-0.00413.3590.8200.8200.0000.0000.0000.000
125A125SER0-0.013-0.00815.4580.4520.4520.0000.0000.0000.000
126A126SER0-0.042-0.03217.2200.7890.7890.0000.0000.0000.000
127A127GLY-1-0.909-0.93520.180-13.266-13.2660.0000.0000.0000.000