FMO DATABASE

FMODB ID: 248NR

Calculation Name: 1K5J-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K5J

Chain ID: B

ChEMBL ID:

UniProt ID: P05221

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-743214.461335
FMO2-HF: Nuclear repulsion	702403.868412
FMO2-HF: Total energy	-40810.592924
FMO2-MP2: Total energy	-40927.796722

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:16:SER)

Summations of interaction energy for fragment #1(A:16: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.
-226.56	-217.644	6.757	-7.958	-7.714	-0.05

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.908

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	18	ILE	0	0.003	0.002	3.842	4.199	5.432	-0.018	-0.476	-0.739	0.000
101	A	116	GLN	0	-0.059	-0.016	2.476	0.188	1.885	0.459	-0.860	-1.295	0.007
102	A	117	HIS	0	0.055	0.041	4.635	1.741	1.992	-0.001	-0.067	-0.183	0.000
103	A	118	VAL	0	-0.098	-0.062	2.061	-26.694	-24.281	5.899	-4.917	-3.395	-0.030
104	A	119	ALA	-1	-0.804	-0.882	2.667	-75.935	-72.613	0.418	-1.638	-2.102	-0.027
4	A	19	TRP	0	0.039	0.009	6.482	0.112	0.112	0.000	0.000	0.000	0.000
5	A	20	GLY	0	0.034	0.003	8.830	1.081	1.081	0.000	0.000	0.000	0.000
6	A	21	CYS	0	-0.092	-0.012	12.515	0.021	0.021	0.000	0.000	0.000	0.000
7	A	22	GLU	-1	-0.822	-0.911	15.885	-12.942	-12.942	0.000	0.000	0.000	0.000
8	A	23	LEU	0	-0.003	0.013	19.603	0.068	0.068	0.000	0.000	0.000	0.000
9	A	24	ASN	0	0.025	-0.019	22.225	0.476	0.476	0.000	0.000	0.000	0.000
10	A	25	GLU	-1	-0.940	-0.968	25.892	-9.342	-9.342	0.000	0.000	0.000	0.000
11	A	26	GLN	0	-0.025	-0.003	28.337	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	27	ASN	0	-0.031	-0.011	23.633	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	28	LYS	1	0.925	0.954	24.086	9.713	9.713	0.000	0.000	0.000	0.000
14	A	29	THR	0	-0.035	-0.036	22.152	0.089	0.089	0.000	0.000	0.000	0.000
15	A	30	PHE	0	0.035	0.022	14.208	0.154	0.154	0.000	0.000	0.000	0.000
16	A	31	GLU	-1	-0.859	-0.909	17.542	-14.714	-14.714	0.000	0.000	0.000	0.000
17	A	32	PHE	0	-0.023	-0.013	8.316	-0.179	-0.179	0.000	0.000	0.000	0.000
18	A	33	LYS	1	0.848	0.883	13.778	19.535	19.535	0.000	0.000	0.000	0.000
19	A	34	VAL	0	-0.015	0.006	8.995	-0.196	-0.196	0.000	0.000	0.000	0.000
20	A	35	GLU	-1	-0.859	-0.921	11.933	-18.158	-18.158	0.000	0.000	0.000	0.000
21	A	36	ASP	-1	-0.842	-0.906	9.456	-31.174	-31.174	0.000	0.000	0.000	0.000
22	A	37	ASP	-1	-0.940	-0.962	12.373	-16.006	-16.006	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.845	-0.917	13.264	-19.794	-19.794	0.000	0.000	0.000	0.000
24	A	39	GLU	-1	-0.862	-0.918	13.411	-18.381	-18.381	0.000	0.000	0.000	0.000
25	A	40	LYS	1	0.734	0.830	13.410	16.356	16.356	0.000	0.000	0.000	0.000
26	A	41	CYS	0	-0.061	-0.028	9.429	-0.920	-0.920	0.000	0.000	0.000	0.000
27	A	42	GLU	-1	-0.938	-0.950	8.379	-30.104	-30.104	0.000	0.000	0.000	0.000
28	A	43	HIS	0	-0.033	-0.017	6.967	-4.864	-4.864	0.000	0.000	0.000	0.000
29	A	44	GLN	0	-0.027	-0.014	6.849	6.131	6.131	0.000	0.000	0.000	0.000
30	A	45	LEU	0	-0.050	-0.041	6.702	-4.599	-4.599	0.000	0.000	0.000	0.000
31	A	46	ALA	0	0.018	0.017	6.819	2.810	2.810	0.000	0.000	0.000	0.000
32	A	47	LEU	0	-0.008	-0.007	8.395	-0.822	-0.822	0.000	0.000	0.000	0.000
33	A	48	ARG	1	0.852	0.919	6.246	27.956	27.956	0.000	0.000	0.000	0.000
34	A	49	THR	0	-0.018	0.012	11.571	0.964	0.964	0.000	0.000	0.000	0.000
35	A	50	VAL	0	0.051	0.035	14.916	-0.511	-0.511	0.000	0.000	0.000	0.000
36	A	51	CYS	0	-0.058	-0.030	17.925	0.343	0.343	0.000	0.000	0.000	0.000
37	A	52	LEU	0	0.027	0.024	20.399	-0.107	-0.107	0.000	0.000	0.000	0.000
38	A	53	GLY	0	0.037	0.027	23.549	-0.144	-0.144	0.000	0.000	0.000	0.000
39	A	54	ASP	-1	-0.865	-0.932	24.655	-10.389	-10.389	0.000	0.000	0.000	0.000
40	A	55	LYS	1	0.799	0.880	27.736	10.312	10.312	0.000	0.000	0.000	0.000
41	A	56	ALA	0	0.003	0.034	26.987	0.164	0.164	0.000	0.000	0.000	0.000
42	A	57	LYS	1	0.910	0.944	29.112	9.017	9.017	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.757	-0.857	31.429	-9.185	-9.185	0.000	0.000	0.000	0.000
44	A	59	GLU	-1	-0.858	-0.929	32.085	-8.778	-8.778	0.000	0.000	0.000	0.000
45	A	60	PHE	0	-0.003	-0.010	30.476	-0.228	-0.228	0.000	0.000	0.000	0.000
46	A	61	HIS	0	-0.001	0.012	26.033	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	62	ILE	0	-0.025	-0.012	26.087	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	63	VAL	0	0.016	0.012	20.130	0.038	0.038	0.000	0.000	0.000	0.000
49	A	64	GLU	-1	-0.762	-0.877	22.406	-11.226	-11.226	0.000	0.000	0.000	0.000
50	A	65	ILE	0	0.028	0.025	16.927	-0.299	-0.299	0.000	0.000	0.000	0.000
51	A	66	VAL	0	-0.034	-0.019	20.467	0.679	0.679	0.000	0.000	0.000	0.000
52	A	67	THR	0	-0.002	0.001	20.412	-0.631	-0.631	0.000	0.000	0.000	0.000
53	A	68	GLN	0	-0.009	-0.013	23.012	0.275	0.275	0.000	0.000	0.000	0.000
54	A	69	GLU	-1	-0.825	-0.911	25.544	-11.422	-11.422	0.000	0.000	0.000	0.000
55	A	70	GLU	-1	-0.946	-0.978	27.857	-9.116	-9.116	0.000	0.000	0.000	0.000
56	A	71	GLY	0	-0.008	0.006	29.831	0.321	0.321	0.000	0.000	0.000	0.000
57	A	72	ALA	0	-0.023	-0.001	31.213	0.142	0.142	0.000	0.000	0.000	0.000
58	A	73	GLU	-1	-0.815	-0.887	27.168	-11.330	-11.330	0.000	0.000	0.000	0.000
59	A	74	LYS	1	0.808	0.893	26.205	11.544	11.544	0.000	0.000	0.000	0.000
60	A	75	SER	0	-0.012	-0.001	24.834	-0.378	-0.378	0.000	0.000	0.000	0.000
61	A	76	VAL	0	0.006	-0.005	22.479	0.531	0.531	0.000	0.000	0.000	0.000
62	A	77	PRO	0	-0.038	-0.029	22.670	-0.545	-0.545	0.000	0.000	0.000	0.000
63	A	78	ILE	0	-0.001	0.006	17.735	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	79	ALA	0	0.006	0.003	20.652	-0.152	-0.152	0.000	0.000	0.000	0.000
65	A	80	THR	0	-0.051	-0.034	22.673	0.431	0.431	0.000	0.000	0.000	0.000
66	A	81	LEU	0	-0.013	0.013	21.655	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	82	LYS	1	0.849	0.914	26.272	9.062	9.062	0.000	0.000	0.000	0.000
68	A	83	PRO	0	0.005	0.019	28.579	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	84	SER	0	-0.080	-0.072	29.608	-0.050	-0.050	0.000	0.000	0.000	0.000
70	A	85	ILE	0	-0.084	-0.037	30.787	0.229	0.229	0.000	0.000	0.000	0.000
71	A	86	LEU	0	-0.003	-0.005	24.462	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	87	PRO	0	0.048	0.030	24.926	-0.196	-0.196	0.000	0.000	0.000	0.000
73	A	88	MET	0	0.004	-0.015	18.097	-0.375	-0.375	0.000	0.000	0.000	0.000
74	A	89	ALA	0	0.018	0.013	19.973	0.494	0.494	0.000	0.000	0.000	0.000
75	A	90	THR	0	-0.002	-0.008	14.948	-0.565	-0.565	0.000	0.000	0.000	0.000
76	A	91	MET	0	-0.054	-0.009	13.808	0.679	0.679	0.000	0.000	0.000	0.000
77	A	92	VAL	0	0.013	-0.017	13.522	-1.069	-1.069	0.000	0.000	0.000	0.000
78	A	93	GLY	0	0.013	0.006	13.186	0.809	0.809	0.000	0.000	0.000	0.000
79	A	94	ILE	0	-0.019	-0.001	14.010	0.245	0.245	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.937	-0.968	9.500	-27.484	-27.484	0.000	0.000	0.000	0.000
81	A	96	LEU	0	-0.048	-0.022	11.011	1.837	1.837	0.000	0.000	0.000	0.000
82	A	97	THR	0	0.070	0.015	11.097	-1.618	-1.618	0.000	0.000	0.000	0.000
83	A	98	PRO	0	-0.076	0.008	11.011	1.465	1.465	0.000	0.000	0.000	0.000
84	A	99	PRO	0	-0.027	-0.030	13.820	0.337	0.337	0.000	0.000	0.000	0.000
85	A	100	VAL	0	0.012	0.002	13.716	0.676	0.676	0.000	0.000	0.000	0.000
86	A	101	THR	0	-0.024	-0.020	16.219	-0.845	-0.845	0.000	0.000	0.000	0.000
87	A	102	PHE	0	-0.011	-0.004	13.690	0.536	0.536	0.000	0.000	0.000	0.000
88	A	103	ARG	1	0.777	0.849	19.319	11.645	11.645	0.000	0.000	0.000	0.000
89	A	104	LEU	0	-0.036	-0.014	22.992	-0.093	-0.093	0.000	0.000	0.000	0.000
90	A	105	LYS	1	0.824	0.899	25.024	10.975	10.975	0.000	0.000	0.000	0.000
91	A	106	ALA	0	-0.016	-0.014	27.953	0.477	0.477	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.037	0.018	28.219	-0.380	-0.380	0.000	0.000	0.000	0.000
93	A	108	SER	0	-0.013	-0.019	29.263	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	109	GLY	0	0.023	0.023	26.250	-0.228	-0.228	0.000	0.000	0.000	0.000
95	A	110	PRO	0	-0.016	0.000	23.557	0.518	0.518	0.000	0.000	0.000	0.000
96	A	111	LEU	0	-0.013	-0.019	20.284	0.227	0.227	0.000	0.000	0.000	0.000
97	A	112	TYR	0	-0.029	-0.024	17.395	-0.151	-0.151	0.000	0.000	0.000	0.000
98	A	113	ILE	0	-0.006	-0.002	14.226	0.400	0.400	0.000	0.000	0.000	0.000
99	A	114	SER	0	0.002	-0.018	11.588	-1.071	-1.071	0.000	0.000	0.000	0.000
100	A	115	GLY	0	0.054	0.004	9.003	1.205	1.205	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)