FMO DATABASE

FMODB ID: 24VLR

Calculation Name: 1WFD-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WFD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VDV8

Base Structure: SolutionNMR

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-565697.650933
FMO2-HF: Nuclear repulsion	529736.31376
FMO2-HF: Total energy	-35961.337173
FMO2-MP2: Total energy	-36064.026076

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/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.
20.747	21.771	-0.014	-0.405	-0.605	-0.001

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 : 0.877 / q_NPA : 0.926

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	3	SER	0	0.007	0.014	3.848	1.581	2.605	-0.014	-0.405	-0.605	-0.001
4	A	4	GLY	0	0.071	0.027	6.727	3.266	3.266	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.049	-0.013	7.973	-1.965	-1.965	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.024	-0.010	9.388	1.989	1.989	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.046	0.029	7.885	0.858	0.858	0.000	0.000	0.000	0.000
8	A	8	GLN	0	-0.077	-0.051	7.170	1.364	1.364	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.810	-0.903	9.474	-17.401	-17.401	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.069	-0.048	12.876	-0.836	-0.836	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.895	-0.934	15.508	-13.929	-13.929	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.034	-0.010	16.279	0.068	0.068	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.066	-0.016	12.674	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.061	0.041	15.307	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.031	0.021	18.483	0.457	0.457	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.031	-0.024	13.787	0.224	0.224	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.023	-0.013	16.186	0.120	0.120	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.022	0.025	17.476	0.363	0.363	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.021	0.014	20.011	0.538	0.538	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.895	0.949	14.289	18.635	18.635	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.966	0.977	19.674	14.227	14.227	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.021	0.016	22.212	0.469	0.469	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.004	-0.003	22.302	0.434	0.434	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.961	-0.975	21.672	-13.503	-13.503	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.026	-0.024	24.507	0.459	0.459	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.752	-0.885	27.227	-9.917	-9.917	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.034	-0.009	26.896	0.367	0.367	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.933	-0.965	27.829	-10.286	-10.286	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.009	0.002	30.318	0.412	0.412	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.870	0.959	30.127	10.262	10.262	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.074	0.025	31.644	-0.321	-0.321	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.034	0.006	32.819	-0.114	-0.114	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.060	-0.026	29.714	0.047	0.047	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.048	0.026	27.954	-0.308	-0.308	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.010	0.017	28.430	-0.302	-0.302	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.025	0.000	29.124	-0.151	-0.151	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.026	-0.001	24.917	-0.268	-0.268	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.018	-0.007	24.941	-0.464	-0.464	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.037	-0.019	26.691	0.139	0.139	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.887	-0.942	25.528	-11.407	-11.407	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.000	-0.012	22.987	-0.347	-0.347	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.047	-0.030	23.736	-0.308	-0.308	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.910	-0.944	26.354	-10.573	-10.573	0.000	0.000	0.000	0.000
44	A	44	MET	0	0.045	0.019	22.066	-0.302	-0.302	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.029	-0.025	19.970	-0.377	-0.377	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.014	-0.011	23.277	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.022	0.005	24.675	0.129	0.129	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.044	0.019	19.546	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.064	-0.007	22.739	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.911	0.951	24.802	10.368	10.368	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.024	0.032	24.453	0.295	0.295	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.061	-0.038	21.508	-0.803	-0.803	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.971	0.961	23.743	11.442	11.442	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.822	-0.912	19.475	-15.061	-15.061	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.068	0.025	23.112	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.012	0.005	21.031	0.468	0.468	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.921	0.960	15.930	18.237	18.237	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.931	0.966	21.226	11.484	11.484	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.011	0.011	24.832	0.370	0.370	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.027	0.018	19.130	0.158	0.158	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.009	0.004	19.578	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.961	0.975	22.848	10.648	10.648	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.008	-0.003	24.424	0.459	0.459	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.936	0.970	16.986	17.203	17.203	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.005	0.002	23.821	0.245	0.245	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.008	0.000	26.218	0.337	0.337	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.026	0.016	27.048	0.279	0.279	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.012	-0.022	21.075	-0.277	-0.277	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.017	-0.015	27.287	0.208	0.208	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.870	-0.910	30.592	-8.950	-8.950	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.852	0.915	29.081	10.115	10.115	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.014	-0.008	30.150	0.194	0.194	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.864	-0.920	31.920	-8.009	-8.009	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.046	-0.033	34.691	0.405	0.405	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.022	0.009	31.122	0.198	0.198	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.923	0.944	35.152	8.923	8.923	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.820	0.893	37.117	8.240	8.240	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.041	-0.035	36.842	0.024	0.024	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.046	-0.041	35.101	0.078	0.078	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-1.022	-0.995	39.651	-7.152	-7.152	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.016	0.014	42.563	0.014	0.014	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.826	-0.906	40.569	-7.540	-7.540	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.865	0.943	40.610	7.609	7.609	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.857	-0.914	44.639	-6.259	-6.259	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.894	-0.970	46.130	-6.532	-6.532	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.036	-0.012	47.017	0.052	0.052	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.759	0.889	47.634	6.352	6.352	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.027	-0.006	49.919	0.164	0.164	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.020	0.009	50.427	-0.144	-0.144	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.064	-0.022	52.671	0.102	0.102	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.018	-0.038	55.121	0.147	0.147	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.040	-0.015	54.582	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	93	GLY	-1	-0.893	-0.924	48.895	-6.461	-6.461	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY)