FMO DATABASE

FMODB ID: ZG65N

Calculation Name: 3KF8-B-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KF8

Chain ID: B

ChEMBL ID:

UniProt ID: C5M4J8

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-962468.200023
FMO2-HF: Nuclear repulsion	915517.130102
FMO2-HF: Total energy	-46951.06992
FMO2-MP2: Total energy	-47087.489584

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(B:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
-295.309	-287.887	0.508	-3.935	-3.994	-0.034

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.898

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	B	4	ILE	0	-0.021	-0.005	3.871	1.749	3.099	-0.018	-0.624	-0.708	-0.001
14	B	15	PHE	0	-0.048	-0.039	3.104	-7.551	-6.983	0.028	-0.248	-0.347	-0.002
23	B	24	GLU	-1	-0.898	-0.951	2.843	-84.770	-81.320	0.313	-2.107	-1.657	-0.022
24	B	25	ARG	1	0.751	0.854	4.055	40.583	40.793	-0.001	-0.030	-0.179	0.000
25	B	26	LEU	0	-0.001	0.004	2.959	-18.341	-16.540	0.187	-0.925	-1.062	-0.009
26	B	27	ARG	1	0.876	0.945	5.237	32.700	32.743	-0.001	-0.001	-0.041	0.000
4	B	5	ILE	0	-0.002	0.004	6.150	1.777	1.777	0.000	0.000	0.000	0.000
5	B	6	LEU	0	0.044	0.011	9.436	1.958	1.958	0.000	0.000	0.000	0.000
6	B	7	ILE	0	0.007	0.002	12.896	1.925	1.925	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.001	-0.006	13.082	-1.145	-1.145	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.017	0.007	13.541	-0.515	-0.515	0.000	0.000	0.000	0.000
9	B	10	ASN	0	0.010	0.010	12.742	1.182	1.182	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.001	0.015	8.832	-1.525	-1.525	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.014	-0.002	9.629	-2.155	-2.155	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.021	-0.018	12.161	-0.245	-0.245	0.000	0.000	0.000	0.000
13	B	14	GLU	-1	-0.894	-0.934	7.312	-34.892	-34.892	0.000	0.000	0.000	0.000
15	B	16	PRO	0	0.030	0.022	8.121	1.220	1.220	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.920	-0.967	10.367	-21.977	-21.977	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.052	-0.001	8.264	-0.095	-0.095	0.000	0.000	0.000	0.000
18	B	19	SER	0	0.015	-0.006	9.886	2.993	2.993	0.000	0.000	0.000	0.000
19	B	20	ILE	0	0.020	-0.001	12.079	-1.150	-1.150	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.070	-0.035	14.257	0.158	0.158	0.000	0.000	0.000	0.000
21	B	22	ASN	0	-0.073	-0.032	10.018	0.085	0.085	0.000	0.000	0.000	0.000
22	B	23	PRO	0	0.020	0.033	9.296	-1.569	-1.569	0.000	0.000	0.000	0.000
27	B	28	ILE	0	0.005	0.014	7.142	-1.217	-1.217	0.000	0.000	0.000	0.000
28	B	29	LEU	0	-0.006	0.000	10.313	1.881	1.881	0.000	0.000	0.000	0.000
29	B	30	ALA	0	0.011	0.007	13.287	0.081	0.081	0.000	0.000	0.000	0.000
30	B	31	GLN	0	-0.029	-0.014	16.330	0.759	0.759	0.000	0.000	0.000	0.000
31	B	32	VAL	0	0.029	0.018	20.110	-0.247	-0.247	0.000	0.000	0.000	0.000
32	B	33	LYS	1	0.803	0.904	21.816	13.849	13.849	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.871	-0.942	24.368	-10.388	-10.388	0.000	0.000	0.000	0.000
34	B	35	PHE	0	-0.024	-0.024	24.557	-0.569	-0.569	0.000	0.000	0.000	0.000
35	B	36	ILE	0	0.047	0.034	26.007	0.523	0.523	0.000	0.000	0.000	0.000
36	B	37	PRO	0	-0.014	-0.005	27.507	-0.210	-0.210	0.000	0.000	0.000	0.000
37	B	38	HIS	0	-0.036	-0.026	29.402	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.881	-0.944	26.712	-10.876	-10.876	0.000	0.000	0.000	0.000
39	B	40	SER	0	-0.029	-0.003	25.057	-0.512	-0.512	0.000	0.000	0.000	0.000
40	B	41	THR	0	0.002	-0.012	22.068	-0.836	-0.836	0.000	0.000	0.000	0.000
41	B	42	ILE	0	-0.024	0.007	17.939	0.588	0.588	0.000	0.000	0.000	0.000
42	B	43	VAL	0	0.016	0.017	20.953	-0.564	-0.564	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.013	-0.014	15.212	0.197	0.197	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.797	-0.889	18.798	-15.287	-15.287	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.889	0.938	17.029	14.337	14.337	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.014	-0.001	17.134	1.024	1.024	0.000	0.000	0.000	0.000
47	B	48	PRO	0	-0.031	-0.025	19.517	-0.059	-0.059	0.000	0.000	0.000	0.000
48	B	49	THR	0	-0.031	-0.028	22.751	-0.083	-0.083	0.000	0.000	0.000	0.000
49	B	50	ILE	0	0.002	0.028	16.248	0.228	0.228	0.000	0.000	0.000	0.000
50	B	51	THR	0	0.062	0.031	18.396	0.238	0.238	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.033	-0.012	21.171	0.147	0.147	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.894	-0.943	17.011	-18.323	-18.323	0.000	0.000	0.000	0.000
53	B	54	GLN	0	-0.031	-0.020	21.294	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	55	SER	0	0.009	-0.019	18.754	-1.234	-1.234	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.038	-0.020	19.100	1.160	1.160	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.016	-0.015	19.185	-0.675	-0.675	0.000	0.000	0.000	0.000
57	B	58	ILE	0	0.012	0.013	14.680	0.175	0.175	0.000	0.000	0.000	0.000
58	B	59	ASN	0	0.007	-0.003	19.074	0.200	0.200	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.025	0.010	14.528	-0.543	-0.543	0.000	0.000	0.000	0.000
60	B	61	CYS	0	-0.021	0.006	18.678	0.668	0.668	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.023	-0.003	18.089	-0.766	-0.766	0.000	0.000	0.000	0.000
62	B	63	PHE	0	0.025	0.002	20.441	0.274	0.274	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.026	-0.023	20.240	0.864	0.864	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.016	0.012	16.274	-0.179	-0.179	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.045	-0.020	20.920	0.235	0.235	0.000	0.000	0.000	0.000
66	B	67	GLU	-1	-0.977	-0.977	24.335	-10.902	-10.902	0.000	0.000	0.000	0.000
67	B	68	ALA	0	-0.011	-0.005	21.310	0.237	0.237	0.000	0.000	0.000	0.000
68	B	69	CYS	0	-0.051	-0.014	21.076	-0.413	-0.413	0.000	0.000	0.000	0.000
69	B	70	SER	0	0.036	0.025	22.580	0.762	0.762	0.000	0.000	0.000	0.000
70	B	71	SER	0	0.053	-0.001	24.210	-0.368	-0.368	0.000	0.000	0.000	0.000
71	B	72	ARG	1	0.799	0.890	24.858	11.709	11.709	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.003	-0.004	19.566	0.024	0.024	0.000	0.000	0.000	0.000
73	B	74	LEU	0	0.011	0.014	21.979	-0.467	-0.467	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.055	-0.010	24.532	0.403	0.403	0.000	0.000	0.000	0.000
75	B	76	PRO	0	0.054	0.038	25.181	-0.462	-0.462	0.000	0.000	0.000	0.000
76	B	77	GLY	0	-0.037	-0.022	25.291	0.409	0.409	0.000	0.000	0.000	0.000
77	B	78	THR	0	-0.067	-0.047	21.760	-0.068	-0.068	0.000	0.000	0.000	0.000
78	B	79	LEU	0	-0.011	0.002	19.592	-0.376	-0.376	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.016	-0.006	16.489	0.368	0.368	0.000	0.000	0.000	0.000
80	B	81	ASN	0	-0.043	-0.023	11.524	-2.119	-2.119	0.000	0.000	0.000	0.000
81	B	82	ILE	0	0.012	-0.002	12.269	1.333	1.333	0.000	0.000	0.000	0.000
82	B	83	ASP	-1	-0.791	-0.866	8.813	-31.457	-31.457	0.000	0.000	0.000	0.000
83	B	84	ALA	0	0.037	0.007	8.373	2.653	2.653	0.000	0.000	0.000	0.000
84	B	85	PHE	0	0.001	-0.004	7.675	-5.004	-5.004	0.000	0.000	0.000	0.000
85	B	86	TYR	0	-0.028	-0.012	7.716	2.637	2.637	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.761	-0.847	9.063	-22.988	-22.988	0.000	0.000	0.000	0.000
87	B	88	GLY	0	0.050	0.041	11.391	1.161	1.161	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-1.021	-1.001	12.832	-14.809	-14.809	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.031	-0.054	15.110	0.809	0.809	0.000	0.000	0.000	0.000
90	B	91	ILE	0	-0.032	-0.026	11.461	-1.979	-1.979	0.000	0.000	0.000	0.000
91	B	92	ASN	0	-0.059	-0.038	12.399	2.850	2.850	0.000	0.000	0.000	0.000
92	B	93	PRO	0	-0.019	-0.011	12.419	-1.967	-1.967	0.000	0.000	0.000	0.000
93	B	94	VAL	0	-0.040	-0.041	11.123	0.936	0.936	0.000	0.000	0.000	0.000
94	B	95	ASP	-1	-0.872	-0.940	13.345	-17.585	-17.585	0.000	0.000	0.000	0.000
95	B	96	ILE	0	-0.033	-0.020	13.812	-1.158	-1.158	0.000	0.000	0.000	0.000
96	B	97	TYR	0	-0.003	0.016	13.264	0.875	0.875	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.797	-0.882	17.558	-13.053	-13.053	0.000	0.000	0.000	0.000
98	B	99	VAL	0	-0.028	-0.014	15.872	-0.176	-0.176	0.000	0.000	0.000	0.000
99	B	100	ASN	0	-0.006	-0.005	19.295	0.468	0.468	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.085	0.032	20.940	-0.564	-0.564	0.000	0.000	0.000	0.000
101	B	102	ALA	0	-0.019	-0.017	22.486	-0.215	-0.215	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.032	-0.020	17.608	-0.106	-0.106	0.000	0.000	0.000	0.000
103	B	104	PHE	0	0.001	0.009	15.618	-0.604	-0.604	0.000	0.000	0.000	0.000
104	B	105	THR	0	-0.024	-0.020	19.834	0.322	0.322	0.000	0.000	0.000	0.000
105	B	106	MET	0	0.030	0.010	19.673	-0.946	-0.946	0.000	0.000	0.000	0.000
106	B	107	GLU	-1	-0.841	-0.920	19.471	-14.287	-14.287	0.000	0.000	0.000	0.000
107	B	108	ASN	0	-0.016	-0.011	16.498	-0.872	-0.872	0.000	0.000	0.000	0.000
108	B	109	ILE	0	-0.039	-0.016	15.000	-1.477	-1.477	0.000	0.000	0.000	0.000
109	B	110	GLN	0	-0.018	-0.009	14.927	-0.976	-0.976	0.000	0.000	0.000	0.000
110	B	111	LEU	0	0.053	0.025	12.699	-1.018	-1.018	0.000	0.000	0.000	0.000
111	B	112	ILE	0	-0.041	-0.032	9.943	-1.869	-1.869	0.000	0.000	0.000	0.000
112	B	113	ASP	-1	-0.978	-0.969	10.194	-25.624	-25.624	0.000	0.000	0.000	0.000
113	B	114	GLU	-1	-0.876	-0.943	11.000	-20.928	-20.928	0.000	0.000	0.000	0.000
114	B	115	MET	0	-0.086	-0.030	7.778	-1.146	-1.146	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.020	-0.003	6.510	-11.455	-11.455	0.000	0.000	0.000	0.000
116	B	117	ASN	0	-0.010	-0.013	7.473	-2.536	-2.536	0.000	0.000	0.000	0.000
117	B	118	SER	0	-0.076	-0.039	9.266	1.125	1.125	0.000	0.000	0.000	0.000
118	B	119	ILE	0	-0.049	-0.029	7.306	1.741	1.741	0.000	0.000	0.000	0.000
119	B	120	GLY	0	0.009	-0.005	8.852	-2.142	-2.142	0.000	0.000	0.000	0.000
120	B	121	LYS	0	-0.013	0.012	11.484	0.744	0.744	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)