FMO DATABASE

FMODB ID: R9268

Calculation Name: 5LSJ-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSJ

Chain ID: F

ChEMBL ID:

UniProt ID: Q03188

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-466704.867044
FMO2-HF: Nuclear repulsion	424700.891711
FMO2-HF: Total energy	-42003.975333
FMO2-MP2: Total energy	-42122.9418

3D Structure

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(F:203:SER)

Summations of interaction energy for fragment #1(F:203: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.
-14.138	-7.828	1.193	-3.121	-4.383	0.014

Interaction energy analysis for fragmet #1(F:203:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : -0.002

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	F	205	GLU	-1	-0.902	-0.960	3.185	-5.687	-1.735	0.209	-1.850	-2.311	0.001
4	F	206	ALA	0	0.034	0.021	2.459	-6.215	-4.189	0.982	-1.177	-1.831	0.013
5	F	207	SER	0	0.022	0.022	4.270	-1.922	-1.590	0.002	-0.094	-0.241	0.000
6	F	208	VAL	0	0.000	-0.014	6.369	-0.451	-0.451	0.000	0.000	0.000	0.000
7	F	209	ALA	0	-0.002	0.006	7.122	-0.356	-0.356	0.000	0.000	0.000	0.000
8	F	210	GLU	-1	-0.900	-0.956	6.712	1.510	1.510	0.000	0.000	0.000	0.000
9	F	211	MET	0	-0.025	-0.007	10.067	-0.248	-0.248	0.000	0.000	0.000	0.000
10	F	212	LYS	1	0.894	0.926	11.577	-0.520	-0.520	0.000	0.000	0.000	0.000
11	F	213	GLU	-1	-0.899	-0.935	12.875	0.364	0.364	0.000	0.000	0.000	0.000
12	F	214	TYR	0	-0.030	-0.028	13.966	-0.086	-0.086	0.000	0.000	0.000	0.000
13	F	215	ILE	0	-0.030	0.005	16.100	-0.066	-0.066	0.000	0.000	0.000	0.000
14	F	216	THR	0	0.054	0.029	17.890	-0.038	-0.038	0.000	0.000	0.000	0.000
15	F	217	LYS	1	0.938	0.985	17.357	-0.406	-0.406	0.000	0.000	0.000	0.000
16	F	218	PHE	0	0.048	0.004	18.137	-0.021	-0.021	0.000	0.000	0.000	0.000
17	F	219	SER	0	-0.090	-0.043	21.888	-0.031	-0.031	0.000	0.000	0.000	0.000
18	F	220	LEU	0	0.012	0.006	23.046	-0.019	-0.019	0.000	0.000	0.000	0.000
19	F	221	GLU	-1	-0.866	-0.922	24.301	0.189	0.189	0.000	0.000	0.000	0.000
20	F	222	ARG	1	0.960	0.981	25.848	-0.174	-0.174	0.000	0.000	0.000	0.000
21	F	223	GLN	0	-0.020	-0.007	27.891	-0.012	-0.012	0.000	0.000	0.000	0.000
22	F	224	THR	0	-0.004	-0.023	28.791	-0.011	-0.011	0.000	0.000	0.000	0.000
23	F	225	TRP	0	-0.060	-0.027	28.115	-0.017	-0.017	0.000	0.000	0.000	0.000
24	F	226	ASP	-1	-0.925	-0.956	32.141	0.108	0.108	0.000	0.000	0.000	0.000
25	F	227	GLN	0	-0.030	-0.017	33.811	-0.003	-0.003	0.000	0.000	0.000	0.000
26	F	228	LEU	0	0.029	0.001	33.991	-0.007	-0.007	0.000	0.000	0.000	0.000
27	F	229	LEU	0	-0.012	0.006	36.242	-0.007	-0.007	0.000	0.000	0.000	0.000
28	F	230	LEU	0	-0.005	-0.015	38.017	-0.006	-0.006	0.000	0.000	0.000	0.000
29	F	231	HIS	0	-0.014	0.004	39.459	-0.006	-0.006	0.000	0.000	0.000	0.000
30	F	232	TYR	0	0.017	-0.001	38.424	-0.005	-0.005	0.000	0.000	0.000	0.000
31	F	233	GLN	0	-0.028	0.000	41.515	-0.004	-0.004	0.000	0.000	0.000	0.000
32	F	234	GLN	0	-0.088	-0.054	43.623	-0.003	-0.003	0.000	0.000	0.000	0.000
33	F	235	GLU	-1	-0.901	-0.940	45.336	0.059	0.059	0.000	0.000	0.000	0.000
34	F	236	ALA	0	0.029	0.016	46.697	-0.003	-0.003	0.000	0.000	0.000	0.000
35	F	237	LYS	1	0.900	0.942	47.464	-0.057	-0.057	0.000	0.000	0.000	0.000
36	F	238	GLU	-1	-0.867	-0.948	49.948	0.046	0.046	0.000	0.000	0.000	0.000
37	F	239	ILE	0	-0.004	-0.006	50.718	-0.003	-0.003	0.000	0.000	0.000	0.000
38	F	240	LEU	0	-0.062	-0.028	52.711	-0.002	-0.002	0.000	0.000	0.000	0.000
39	F	241	SER	0	-0.043	-0.026	54.370	-0.002	-0.002	0.000	0.000	0.000	0.000
40	F	242	ARG	1	0.893	0.968	53.708	-0.045	-0.045	0.000	0.000	0.000	0.000
41	F	243	GLY	0	-0.034	-0.013	57.381	-0.001	-0.001	0.000	0.000	0.000	0.000
42	F	244	SER	0	-0.046	-0.012	60.096	-0.002	-0.002	0.000	0.000	0.000	0.000
43	F	245	THR	0	0.008	0.007	60.064	-0.001	-0.001	0.000	0.000	0.000	0.000
44	F	260	LEU	0	-0.006	-0.020	67.082	0.000	0.000	0.000	0.000	0.000	0.000
45	F	261	GLY	0	0.024	0.017	64.685	-0.001	-0.001	0.000	0.000	0.000	0.000
46	F	262	SER	0	-0.047	-0.022	64.962	0.001	0.001	0.000	0.000	0.000	0.000
47	F	263	SER	0	0.059	0.021	66.742	0.000	0.000	0.000	0.000	0.000	0.000
48	F	264	GLN	0	-0.012	0.002	67.685	0.000	0.000	0.000	0.000	0.000	0.000
49	F	265	ASN	0	0.070	0.046	67.749	-0.001	-0.001	0.000	0.000	0.000	0.000
50	F	266	GLU	-1	-0.904	-0.965	70.995	0.020	0.020	0.000	0.000	0.000	0.000
51	F	267	VAL	0	-0.021	-0.032	74.003	-0.001	-0.001	0.000	0.000	0.000	0.000
52	F	268	LEU	0	-0.032	-0.007	71.646	0.000	0.000	0.000	0.000	0.000	0.000
53	F	269	ASN	0	-0.018	-0.013	71.738	0.000	0.000	0.000	0.000	0.000	0.000
54	F	270	THR	0	-0.049	0.001	75.953	-0.001	-0.001	0.000	0.000	0.000	0.000
55	F	271	LYS	1	0.959	0.977	79.182	-0.019	-0.019	0.000	0.000	0.000	0.000
56	F	272	PRO	0	-0.023	-0.006	81.162	0.000	0.000	0.000	0.000	0.000	0.000
57	F	273	ASP	-1	-0.851	-0.923	84.856	0.016	0.016	0.000	0.000	0.000	0.000
58	F	274	TYR	0	0.049	-0.001	84.297	0.000	0.000	0.000	0.000	0.000	0.000
59	F	275	GLN	0	0.024	0.024	87.958	-0.001	-0.001	0.000	0.000	0.000	0.000
60	F	276	LYS	1	0.988	0.982	89.846	-0.015	-0.015	0.000	0.000	0.000	0.000
61	F	277	ILE	0	-0.032	-0.007	89.882	0.000	0.000	0.000	0.000	0.000	0.000
62	F	278	LEU	0	0.038	0.004	91.939	0.000	0.000	0.000	0.000	0.000	0.000
63	F	279	GLN	0	0.001	0.004	93.540	0.000	0.000	0.000	0.000	0.000	0.000
64	F	280	ASN	0	-0.041	-0.045	94.528	0.000	0.000	0.000	0.000	0.000	0.000
65	F	281	GLN	0	-0.008	0.000	96.983	0.000	0.000	0.000	0.000	0.000	0.000
66	F	282	SER	0	0.016	0.006	99.092	0.000	0.000	0.000	0.000	0.000	0.000
67	F	283	LYS	1	0.951	0.997	97.753	-0.012	-0.012	0.000	0.000	0.000	0.000
68	F	284	VAL	0	-0.045	-0.015	101.075	0.000	0.000	0.000	0.000	0.000	0.000
69	F	285	PHE	0	-0.012	-0.021	102.831	0.000	0.000	0.000	0.000	0.000	0.000
70	F	286	ASP	-1	-0.847	-0.905	105.141	0.011	0.011	0.000	0.000	0.000	0.000
71	F	287	CYS	0	-0.096	-0.055	105.989	0.000	0.000	0.000	0.000	0.000	0.000
72	F	288	MET	0	0.015	-0.022	107.653	0.000	0.000	0.000	0.000	0.000	0.000
73	F	289	GLU	-1	-0.921	-0.935	109.605	0.010	0.010	0.000	0.000	0.000	0.000
74	F	290	LEU	0	0.012	0.004	109.562	0.000	0.000	0.000	0.000	0.000	0.000
75	F	291	VAL	0	-0.032	-0.004	110.897	0.000	0.000	0.000	0.000	0.000	0.000
76	F	292	MET	0	-0.012	-0.024	113.578	0.000	0.000	0.000	0.000	0.000	0.000
77	F	293	ASP	-1	-0.910	-0.935	115.536	0.009	0.009	0.000	0.000	0.000	0.000
78	F	294	GLU	-1	-0.963	-0.989	116.121	0.009	0.009	0.000	0.000	0.000	0.000
79	F	295	LEU	0	-0.037	-0.013	117.700	0.000	0.000	0.000	0.000	0.000	0.000
80	F	296	GLN	0	-0.006	-0.017	119.719	0.000	0.000	0.000	0.000	0.000	0.000
81	F	297	GLY	0	0.005	0.006	121.352	0.000	0.000	0.000	0.000	0.000	0.000
82	F	298	SER	0	-0.013	-0.018	121.765	0.000	0.000	0.000	0.000	0.000	0.000
83	F	299	VAL	0	-0.039	-0.009	123.480	0.000	0.000	0.000	0.000	0.000	0.000
84	F	300	LYS	1	0.953	0.978	126.107	-0.008	-0.008	0.000	0.000	0.000	0.000
85	F	301	GLN	0	-0.023	-0.005	126.962	0.000	0.000	0.000	0.000	0.000	0.000
86	F	302	LEU	0	-0.003	0.006	128.336	0.000	0.000	0.000	0.000	0.000	0.000
87	F	303	GLN	0	-0.026	-0.026	130.043	0.000	0.000	0.000	0.000	0.000	0.000
88	F	304	ALA	0	0.024	0.018	132.009	0.000	0.000	0.000	0.000	0.000	0.000
89	F	305	PHE	0	0.038	0.026	133.234	0.000	0.000	0.000	0.000	0.000	0.000
90	F	306	MET	0	-0.003	0.032	132.503	0.000	0.000	0.000	0.000	0.000	0.000
91	F	307	ASP	-1	-0.875	-0.937	136.062	0.006	0.006	0.000	0.000	0.000	0.000
92	F	308	GLU	-1	-0.981	-1.016	137.673	0.006	0.006	0.000	0.000	0.000	0.000
93	F	309	SER	0	-0.013	-0.049	137.760	0.000	0.000	0.000	0.000	0.000	0.000
94	F	310	THR	0	-0.024	-0.011	140.301	0.000	0.000	0.000	0.000	0.000	0.000
95	F	311	GLN	0	-0.048	-0.008	141.931	0.000	0.000	0.000	0.000	0.000	0.000
96	F	312	CYS	0	-0.009	-0.021	143.414	0.000	0.000	0.000	0.000	0.000	0.000
97	F	313	PHE	0	-0.020	-0.015	142.686	0.000	0.000	0.000	0.000	0.000	0.000
98	F	314	GLN	0	-0.018	0.010	146.097	0.000	0.000	0.000	0.000	0.000	0.000
99	F	315	LYS	1	0.874	0.929	147.455	-0.006	-0.006	0.000	0.000	0.000	0.000
100	F	316	VAL	0	-0.027	0.003	149.305	0.000	0.000	0.000	0.000	0.000	0.000
101	F	317	SER	0	-0.053	-0.007	151.903	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:203:SER)