FMO DATABASE

FMODB ID: VV6N1

Calculation Name: 1HKF-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HKF

Chain ID: A

ChEMBL ID:

UniProt ID: O95944

Base Structure: X-ray

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-861909.761238
FMO2-HF: Nuclear repulsion	818076.051338
FMO2-HF: Total energy	-43833.7099
FMO2-MP2: Total energy	-43959.097356

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
54.362	59.781	1.931	-2.625	-4.725	-0.007

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.935

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 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	7	ALA	0	0.002	0.018	3.749	-0.800	0.587	0.003	-0.545	-0.846	-0.001
4	A	8	GLN	0	-0.008	-0.012	5.458	2.423	2.574	-0.001	-0.010	-0.140	0.000
85	A	90	TRP	0	-0.082	-0.077	2.960	-8.655	-7.085	0.618	-0.915	-1.273	-0.005
99	A	105	VAL	0	-0.046	-0.024	4.758	-3.339	-3.268	-0.001	-0.002	-0.068	0.000
100	A	106	ARG	1	0.787	0.880	2.534	55.609	57.791	1.313	-1.143	-2.352	-0.001
101	A	107	PHE	0	0.040	-0.005	4.361	-0.599	-0.541	-0.001	-0.010	-0.046	0.000
5	A	9	VAL	0	0.015	0.006	8.237	0.253	0.253	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.034	-0.009	11.465	1.091	1.091	0.000	0.000	0.000	0.000
7	A	11	GLN	0	0.015	0.005	13.892	-0.696	-0.696	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.028	-0.015	17.403	0.697	0.697	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.021	0.016	20.587	-0.189	-0.189	0.000	0.000	0.000	0.000
10	A	14	ALA	0	0.047	0.005	23.712	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.019	-0.001	25.477	0.369	0.369	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.056	-0.013	23.521	0.161	0.161	0.000	0.000	0.000	0.000
13	A	17	THR	0	-0.009	-0.016	22.515	-0.075	-0.075	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.010	0.006	14.912	-0.166	-0.166	0.000	0.000	0.000	0.000
15	A	19	THR	0	-0.004	-0.004	18.491	0.299	0.299	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.000	0.002	11.754	-0.543	-0.543	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.930	0.975	14.197	15.409	15.409	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.085	-0.009	7.886	0.669	0.669	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.060	0.036	12.928	1.419	1.419	0.000	0.000	0.000	0.000
20	A	24	TYR	0	-0.078	-0.083	13.255	-1.802	-1.802	0.000	0.000	0.000	0.000
21	A	25	PRO	0	0.023	0.025	14.979	0.691	0.691	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.039	0.004	17.978	-0.078	-0.078	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.001	-0.009	19.285	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	28	GLY	0	0.000	0.005	22.101	0.331	0.331	0.000	0.000	0.000	0.000
25	A	29	SER	0	0.005	-0.002	25.818	-0.135	-0.135	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.010	0.010	23.480	0.058	0.058	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.023	-0.025	20.837	-0.427	-0.427	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.812	-0.894	16.844	-17.328	-17.328	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.903	0.970	18.735	13.126	13.126	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.813	0.905	15.454	14.489	14.489	0.000	0.000	0.000	0.000
31	A	35	GLY	0	-0.004	-0.010	14.231	1.066	1.066	0.000	0.000	0.000	0.000
32	A	36	TRP	0	0.017	0.003	10.374	-2.129	-2.129	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.071	-0.034	9.826	-0.537	-0.537	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.939	0.983	11.196	17.417	17.417	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.823	-0.879	5.699	-45.803	-45.803	0.000	0.000	0.000	0.000
36	A	40	ALA	0	0.017	0.014	10.637	1.103	1.103	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.019	-0.005	11.588	0.486	0.486	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.004	0.000	7.590	-1.178	-1.178	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.003	0.004	8.101	-2.667	-2.667	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.024	0.000	10.877	1.676	1.676	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.056	0.031	11.796	0.932	0.932	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.857	0.914	14.997	17.305	17.305	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.030	0.004	15.414	0.708	0.708	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.063	0.043	17.179	0.745	0.745	0.000	0.000	0.000	0.000
45	A	50	THR	0	-0.034	-0.029	17.188	-1.283	-1.283	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.006	0.018	18.784	0.950	0.950	0.000	0.000	0.000	0.000
47	A	52	SER	0	0.023	-0.022	20.258	-0.414	-0.414	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.974	0.977	22.952	10.451	10.451	0.000	0.000	0.000	0.000
49	A	54	PRO	0	0.022	0.035	23.631	-0.208	-0.208	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.817	0.885	24.380	11.121	11.121	0.000	0.000	0.000	0.000
51	A	56	THR	0	-0.058	-0.020	25.080	0.393	0.393	0.000	0.000	0.000	0.000
52	A	57	MET	0	0.037	0.012	25.412	-0.426	-0.426	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.041	-0.014	22.416	0.170	0.170	0.000	0.000	0.000	0.000
54	A	59	TRP	0	0.110	0.051	23.327	-0.523	-0.523	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.040	-0.030	22.271	-0.739	-0.739	0.000	0.000	0.000	0.000
56	A	61	SER	0	0.040	0.008	23.580	-0.405	-0.405	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.766	0.853	21.431	13.812	13.812	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.015	-0.002	19.343	-0.523	-0.523	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.006	0.005	20.534	0.520	0.520	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.052	-0.039	16.588	-0.901	-0.901	0.000	0.000	0.000	0.000
61	A	66	TRP	0	0.057	0.047	20.309	0.654	0.654	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.711	-0.846	19.490	-15.386	-15.386	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.805	-0.892	20.947	-10.830	-10.830	0.000	0.000	0.000	0.000
64	A	69	PRO	0	-0.017	-0.014	21.564	-0.274	-0.274	0.000	0.000	0.000	0.000
65	A	70	ASP	-1	-0.849	-0.902	22.611	-10.934	-10.934	0.000	0.000	0.000	0.000
66	A	71	ALA	0	-0.025	-0.006	22.707	0.173	0.173	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.021	0.024	20.323	-0.306	-0.306	0.000	0.000	0.000	0.000
68	A	73	PHE	0	-0.054	-0.044	16.915	-1.089	-1.089	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.019	-0.003	12.495	0.562	0.562	0.000	0.000	0.000	0.000
70	A	75	THR	0	-0.005	-0.021	16.232	-0.762	-0.762	0.000	0.000	0.000	0.000
71	A	76	VAL	0	-0.008	0.002	14.046	0.670	0.670	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.006	-0.011	17.149	0.008	0.008	0.000	0.000	0.000	0.000
73	A	78	MET	0	-0.028	0.012	16.430	-0.368	-0.368	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.045	0.012	20.115	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	80	ASP	-1	-0.813	-0.897	23.654	-11.629	-11.629	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.038	-0.004	19.385	-0.378	-0.378	0.000	0.000	0.000	0.000
77	A	82	ARG	1	0.920	0.941	22.084	12.860	12.860	0.000	0.000	0.000	0.000
78	A	83	GLU	-1	-0.861	-0.914	21.195	-14.037	-14.037	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.859	-0.934	19.703	-14.187	-14.187	0.000	0.000	0.000	0.000
80	A	85	ASP	-1	-0.824	-0.878	18.041	-15.815	-15.815	0.000	0.000	0.000	0.000
81	A	86	SER	0	0.014	0.017	15.781	-1.589	-1.589	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.004	0.006	12.538	0.336	0.336	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.023	-0.011	7.077	-3.574	-3.574	0.000	0.000	0.000	0.000
84	A	89	TYR	0	-0.001	-0.026	8.535	2.154	2.154	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.913	0.933	7.267	28.848	28.848	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.013	0.023	10.642	1.693	1.693	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.040	-0.020	13.049	-1.582	-1.582	0.000	0.000	0.000	0.000
89	A	95	ARG	1	0.965	0.971	14.135	19.925	19.925	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.020	-0.029	18.381	0.094	0.094	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.057	-0.027	20.795	0.316	0.316	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.755	-0.853	19.142	-15.695	-15.695	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.053	-0.014	17.458	-0.198	-0.198	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.002	-0.008	15.286	-1.328	-1.328	0.000	0.000	0.000	0.000
95	A	101	VAL	0	-0.020	-0.022	9.122	0.424	0.424	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.053	-0.032	12.422	-0.873	-0.873	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.946	0.974	8.697	25.445	25.445	0.000	0.000	0.000	0.000
98	A	104	SER	0	-0.009	-0.009	5.519	1.634	1.634	0.000	0.000	0.000	0.000
102	A	108	TYR	0	-0.011	-0.018	7.632	-1.949	-1.949	0.000	0.000	0.000	0.000
103	A	109	LEU	0	-0.016	0.009	9.991	1.087	1.087	0.000	0.000	0.000	0.000
104	A	110	VAL	0	0.014	-0.005	13.580	-0.249	-0.249	0.000	0.000	0.000	0.000
105	A	111	VAL	0	-0.011	-0.010	16.638	0.307	0.307	0.000	0.000	0.000	0.000
106	A	112	SER	-1	-0.818	-0.901	20.103	-13.007	-13.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)