FMO DATABASE

FMODB ID: R5ZM8

Calculation Name: 4R8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R8O

Chain ID: A

ChEMBL ID:

UniProt ID: A6KZN2

Base Structure: X-ray

Registration Date: 2023-06-20

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-744257.196936
FMO2-HF: Nuclear repulsion	701532.086798
FMO2-HF: Total energy	-42725.110138
FMO2-MP2: Total energy	-42845.419946

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(A:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-27.335	-23.2	0.321	-1.694	-2.764	0.01

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.944 / q_NPA : -0.974

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	32	LEU	0	-0.074	-0.039	2.721	-13.707	-9.895	0.323	-1.659	-2.477	0.010
4	A	33	ILE	0	0.026	0.015	4.173	0.144	0.297	-0.001	-0.014	-0.139	0.000
5	A	34	TYR	0	0.027	0.007	4.261	-0.704	-0.534	-0.001	-0.021	-0.148	0.000
6	A	35	ASN	0	-0.041	-0.023	9.321	-1.133	-1.133	0.000	0.000	0.000	0.000
7	A	36	ALA	0	0.036	0.023	13.103	-0.238	-0.238	0.000	0.000	0.000	0.000
8	A	37	GLU	-1	-0.928	-0.954	15.368	12.328	12.328	0.000	0.000	0.000	0.000
9	A	38	GLU	-1	-0.941	-0.985	19.007	13.331	13.331	0.000	0.000	0.000	0.000
10	A	39	VAL	0	0.004	-0.012	21.290	-0.408	-0.408	0.000	0.000	0.000	0.000
11	A	40	ASN	0	-0.049	-0.035	24.899	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	41	GLY	0	0.023	0.026	24.280	-0.206	-0.206	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.010	0.005	21.785	0.433	0.433	0.000	0.000	0.000	0.000
14	A	43	VAL	0	0.030	0.011	16.512	-0.183	-0.183	0.000	0.000	0.000	0.000
15	A	44	VAL	0	0.027	0.019	19.376	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	45	SER	0	-0.032	-0.028	17.714	0.034	0.034	0.000	0.000	0.000	0.000
17	A	46	GLU	-1	-0.903	-0.948	10.905	21.560	21.560	0.000	0.000	0.000	0.000
18	A	47	THR	0	-0.047	-0.015	12.928	-0.488	-0.488	0.000	0.000	0.000	0.000
19	A	48	ILE	0	0.020	0.010	6.623	0.965	0.965	0.000	0.000	0.000	0.000
20	A	49	PHE	0	-0.013	-0.020	8.668	-1.817	-1.817	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.958	0.983	7.582	-24.484	-24.484	0.000	0.000	0.000	0.000
22	A	51	MET	0	-0.008	-0.012	9.039	-3.242	-3.242	0.000	0.000	0.000	0.000
23	A	52	GLU	-1	-0.908	-0.923	10.670	25.256	25.256	0.000	0.000	0.000	0.000
24	A	53	GLY	0	0.010	-0.005	12.175	-1.985	-1.985	0.000	0.000	0.000	0.000
25	A	54	THR	0	0.001	-0.017	13.489	0.530	0.530	0.000	0.000	0.000	0.000
26	A	55	MET	0	-0.042	-0.008	15.861	-0.683	-0.683	0.000	0.000	0.000	0.000
27	A	56	LEU	0	0.019	0.014	11.545	1.282	1.282	0.000	0.000	0.000	0.000
28	A	57	THR	0	-0.042	-0.023	12.394	-1.734	-1.734	0.000	0.000	0.000	0.000
29	A	58	ASN	0	0.036	0.013	12.159	1.932	1.932	0.000	0.000	0.000	0.000
30	A	59	TYR	0	-0.026	-0.017	7.788	-0.561	-0.561	0.000	0.000	0.000	0.000
31	A	60	MET	0	-0.044	-0.031	10.231	-0.441	-0.441	0.000	0.000	0.000	0.000
32	A	61	LYS	1	0.958	0.994	12.143	-13.435	-13.435	0.000	0.000	0.000	0.000
33	A	62	HIS	1	0.873	0.918	10.938	-19.065	-19.065	0.000	0.000	0.000	0.000
34	A	63	ASN	0	-0.020	-0.015	15.291	0.070	0.070	0.000	0.000	0.000	0.000
35	A	64	TYR	0	-0.006	0.007	13.768	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	65	LYS	1	0.917	0.968	20.252	-11.413	-11.413	0.000	0.000	0.000	0.000
37	A	66	TYR	0	0.026	0.017	19.770	0.555	0.555	0.000	0.000	0.000	0.000
38	A	67	ASP	-1	-0.816	-0.906	25.784	9.654	9.654	0.000	0.000	0.000	0.000
39	A	68	ALA	0	0.010	-0.012	29.304	0.064	0.064	0.000	0.000	0.000	0.000
40	A	69	ASN	0	-0.034	-0.022	31.009	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	70	ASN	0	0.000	0.012	26.943	0.025	0.025	0.000	0.000	0.000	0.000
42	A	71	GLN	0	-0.041	-0.002	25.004	0.569	0.569	0.000	0.000	0.000	0.000
43	A	72	ARG	1	0.899	0.949	16.145	-15.002	-15.002	0.000	0.000	0.000	0.000
44	A	73	THR	0	0.021	0.005	23.112	-0.168	-0.168	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.947	-0.986	22.156	11.096	11.096	0.000	0.000	0.000	0.000
46	A	75	ASP	-1	-0.844	-0.918	15.713	16.589	16.589	0.000	0.000	0.000	0.000
47	A	76	GLU	-1	-0.845	-0.917	18.351	12.410	12.410	0.000	0.000	0.000	0.000
48	A	77	ALA	0	0.014	0.013	14.861	0.562	0.562	0.000	0.000	0.000	0.000
49	A	78	GLN	0	-0.031	-0.038	16.124	-0.186	-0.186	0.000	0.000	0.000	0.000
50	A	79	LYS	1	0.988	0.994	14.750	-14.093	-14.093	0.000	0.000	0.000	0.000
51	A	80	TRP	0	0.011	0.014	14.855	-1.220	-1.220	0.000	0.000	0.000	0.000
52	A	81	ASN	0	-0.111	-0.073	16.636	0.774	0.774	0.000	0.000	0.000	0.000
53	A	82	SER	0	0.100	0.033	18.017	-0.433	-0.433	0.000	0.000	0.000	0.000
54	A	83	ASN	0	-0.018	-0.009	19.816	0.006	0.006	0.000	0.000	0.000	0.000
55	A	84	LYS	1	0.918	0.975	22.758	-11.126	-11.126	0.000	0.000	0.000	0.000
56	A	85	ASN	0	-0.032	-0.019	21.693	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	86	ARG	1	0.923	0.973	21.454	-12.016	-12.016	0.000	0.000	0.000	0.000
58	A	87	TRP	0	0.066	0.038	14.086	0.359	0.359	0.000	0.000	0.000	0.000
59	A	88	GLU	-1	-0.941	-0.971	19.380	11.909	11.909	0.000	0.000	0.000	0.000
60	A	89	ASN	0	0.000	0.008	19.438	0.681	0.681	0.000	0.000	0.000	0.000
61	A	90	ASN	0	-0.010	-0.007	16.093	-0.683	-0.683	0.000	0.000	0.000	0.000
62	A	91	LEU	0	0.008	0.008	15.926	-0.492	-0.492	0.000	0.000	0.000	0.000
63	A	92	CYS	0	-0.013	0.003	19.211	0.057	0.057	0.000	0.000	0.000	0.000
64	A	93	ILE	0	0.020	0.033	16.594	-0.306	-0.306	0.000	0.000	0.000	0.000
65	A	94	ARG	1	0.940	0.964	20.946	-10.597	-10.597	0.000	0.000	0.000	0.000
66	A	95	TYR	0	0.000	0.000	17.793	0.115	0.115	0.000	0.000	0.000	0.000
67	A	96	THR	0	0.014	0.013	24.807	-0.329	-0.329	0.000	0.000	0.000	0.000
68	A	97	TYR	0	-0.028	-0.022	23.958	0.228	0.228	0.000	0.000	0.000	0.000
69	A	98	GLY	0	0.025	0.017	29.737	-0.298	-0.298	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.036	-0.047	32.358	0.221	0.221	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.912	0.941	33.173	-7.954	-7.954	0.000	0.000	0.000	0.000
72	A	101	SER	0	0.041	0.042	29.976	0.195	0.195	0.000	0.000	0.000	0.000
73	A	102	MET	0	0.040	0.044	21.924	-0.094	-0.094	0.000	0.000	0.000	0.000
74	A	103	THR	0	-0.015	-0.020	26.958	0.005	0.005	0.000	0.000	0.000	0.000
75	A	104	THR	0	-0.026	-0.023	21.904	0.226	0.226	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.905	-0.946	24.270	9.826	9.826	0.000	0.000	0.000	0.000
77	A	106	TYR	0	0.019	0.014	18.498	0.582	0.582	0.000	0.000	0.000	0.000
78	A	107	TYR	0	-0.012	-0.005	22.586	-0.519	-0.519	0.000	0.000	0.000	0.000
79	A	108	LYS	1	0.921	0.956	20.385	-12.527	-12.527	0.000	0.000	0.000	0.000
80	A	109	TRP	0	-0.017	0.004	22.948	-0.501	-0.501	0.000	0.000	0.000	0.000
81	A	110	ASN	0	0.012	-0.010	24.771	0.132	0.132	0.000	0.000	0.000	0.000
82	A	111	SER	0	0.031	0.013	26.841	-0.155	-0.155	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.928	0.951	28.748	-8.937	-8.937	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.957	0.981	31.436	-8.796	-8.796	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.900	0.969	29.628	-8.880	-8.880	0.000	0.000	0.000	0.000
86	A	115	GLU	-1	-0.884	-0.934	29.506	8.578	8.578	0.000	0.000	0.000	0.000
87	A	116	TYR	0	-0.048	-0.049	21.670	0.315	0.315	0.000	0.000	0.000	0.000
88	A	117	ILE	0	-0.029	-0.025	26.934	-0.288	-0.288	0.000	0.000	0.000	0.000
89	A	118	LEU	0	0.052	0.028	26.798	0.364	0.364	0.000	0.000	0.000	0.000
90	A	119	VAL	0	-0.004	0.002	24.445	-0.204	-0.204	0.000	0.000	0.000	0.000
91	A	120	PRO	0	-0.020	0.002	26.332	0.267	0.267	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.943	-0.983	26.841	10.405	10.405	0.000	0.000	0.000	0.000
93	A	122	MET	0	-0.019	-0.018	20.561	0.105	0.105	0.000	0.000	0.000	0.000
94	A	123	THR	0	-0.022	-0.005	23.867	0.449	0.449	0.000	0.000	0.000	0.000
95	A	124	VAL	0	-0.009	0.007	22.584	-0.122	-0.122	0.000	0.000	0.000	0.000
96	A	125	THR	0	-0.014	-0.012	25.652	-0.117	-0.117	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.034	-0.014	22.992	0.083	0.083	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.928	-0.951	27.219	9.641	9.641	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)