FMO DATABASE

FMODB ID: 172VZ

Calculation Name: 4A9A-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A9A

Chain ID: C

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2023-06-21

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-595206.538989
FMO2-HF: Nuclear repulsion	553604.195612
FMO2-HF: Total energy	-41602.343377
FMO2-MP2: Total energy	-41725.776204

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(C:214:LEU)

Summations of interaction energy for fragment #1(C:214:LEU)

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.
0.013	2.15	0.051	-0.819	-1.369	0.001

Interaction energy analysis for fragmet #1(C:214:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.026

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	C	216	LYS	1	0.827	0.903	3.716	1.667	2.902	-0.006	-0.615	-0.613	0.002
4	C	217	GLN	0	0.080	0.038	3.015	-1.268	-0.366	0.057	-0.204	-0.756	-0.001
5	C	218	PRO	0	-0.042	0.003	6.029	0.330	0.330	0.000	0.000	0.000	0.000
6	C	219	LYS	1	0.953	0.956	9.222	0.243	0.243	0.000	0.000	0.000	0.000
7	C	220	ILE	0	0.022	0.025	10.387	-0.024	-0.024	0.000	0.000	0.000	0.000
8	C	221	THR	0	-0.023	-0.032	13.108	0.037	0.037	0.000	0.000	0.000	0.000
9	C	222	LEU	0	-0.010	-0.018	15.409	0.025	0.025	0.000	0.000	0.000	0.000
10	C	223	GLU	-1	-0.812	-0.919	17.304	0.036	0.036	0.000	0.000	0.000	0.000
11	C	224	GLU	-1	-0.763	-0.849	14.658	-0.108	-0.108	0.000	0.000	0.000	0.000
12	C	225	PHE	0	-0.055	-0.036	12.125	0.022	0.022	0.000	0.000	0.000	0.000
13	C	226	ILE	0	-0.054	-0.033	14.556	0.028	0.028	0.000	0.000	0.000	0.000
14	C	227	GLU	-1	-0.957	-0.977	17.795	0.009	0.009	0.000	0.000	0.000	0.000
15	C	228	THR	0	-0.058	-0.030	15.732	-0.018	-0.018	0.000	0.000	0.000	0.000
16	C	229	GLU	-1	-0.931	-0.970	10.322	-0.052	-0.052	0.000	0.000	0.000	0.000
17	C	230	ARG	1	0.914	0.963	11.665	-0.171	-0.171	0.000	0.000	0.000	0.000
18	C	231	GLY	0	-0.025	-0.017	13.402	0.030	0.030	0.000	0.000	0.000	0.000
19	C	232	LYS	1	0.920	0.972	10.606	0.138	0.138	0.000	0.000	0.000	0.000
20	C	233	LEU	0	-0.061	-0.015	8.023	0.022	0.022	0.000	0.000	0.000	0.000
21	C	234	ASP	-1	-0.793	-0.892	11.487	0.172	0.172	0.000	0.000	0.000	0.000
22	C	235	LYS	1	1.000	0.965	13.188	-0.111	-0.111	0.000	0.000	0.000	0.000
23	C	236	SER	0	-0.082	-0.033	15.581	0.017	0.017	0.000	0.000	0.000	0.000
24	C	237	LYS	1	0.935	0.966	11.757	-0.253	-0.253	0.000	0.000	0.000	0.000
25	C	238	LEU	0	-0.044	0.000	11.095	0.077	0.077	0.000	0.000	0.000	0.000
26	C	239	THR	0	-0.003	0.000	11.533	0.007	0.007	0.000	0.000	0.000	0.000
27	C	240	PRO	0	0.014	0.013	13.411	0.006	0.006	0.000	0.000	0.000	0.000
28	C	241	ILE	0	0.047	0.030	14.611	0.040	0.040	0.000	0.000	0.000	0.000
29	C	242	THR	0	0.021	0.011	16.898	-0.028	-0.028	0.000	0.000	0.000	0.000
30	C	243	ILE	0	0.084	0.022	18.761	0.033	0.033	0.000	0.000	0.000	0.000
31	C	244	ALA	0	0.004	0.010	19.899	0.018	0.018	0.000	0.000	0.000	0.000
32	C	245	ASN	0	0.007	-0.015	15.035	0.046	0.046	0.000	0.000	0.000	0.000
33	C	246	PHE	0	0.012	0.010	14.752	0.076	0.076	0.000	0.000	0.000	0.000
34	C	247	ALA	0	0.021	0.008	15.534	0.042	0.042	0.000	0.000	0.000	0.000
35	C	248	GLN	0	-0.008	-0.001	11.880	-0.080	-0.080	0.000	0.000	0.000	0.000
36	C	249	TRP	0	0.023	0.016	8.624	-0.027	-0.027	0.000	0.000	0.000	0.000
37	C	250	LYS	1	0.944	0.969	11.973	-0.338	-0.338	0.000	0.000	0.000	0.000
38	C	251	LYS	1	0.943	0.977	14.648	-0.606	-0.606	0.000	0.000	0.000	0.000
39	C	252	ASP	-1	-0.829	-0.928	9.664	0.989	0.989	0.000	0.000	0.000	0.000
40	C	253	HIS	0	-0.073	-0.030	10.004	-0.107	-0.107	0.000	0.000	0.000	0.000
41	C	254	VAL	0	-0.017	-0.026	11.821	-0.052	-0.052	0.000	0.000	0.000	0.000
42	C	255	ILE	0	0.035	0.020	12.993	-0.065	-0.065	0.000	0.000	0.000	0.000
43	C	256	ALA	0	0.028	0.019	9.779	-0.057	-0.057	0.000	0.000	0.000	0.000
44	C	257	LYS	1	0.915	0.968	11.670	-0.517	-0.517	0.000	0.000	0.000	0.000
45	C	258	ILE	0	0.040	0.023	14.287	-0.073	-0.073	0.000	0.000	0.000	0.000
46	C	259	ASN	0	-0.005	-0.006	12.317	-0.134	-0.134	0.000	0.000	0.000	0.000
47	C	260	ALA	0	-0.025	-0.018	12.351	-0.077	-0.077	0.000	0.000	0.000	0.000
48	C	261	GLU	-1	-0.818	-0.909	14.069	0.032	0.032	0.000	0.000	0.000	0.000
49	C	262	LYS	1	0.950	0.996	17.630	-0.257	-0.257	0.000	0.000	0.000	0.000
50	C	263	LYS	1	0.915	0.961	12.312	0.065	0.065	0.000	0.000	0.000	0.000
51	C	264	LEU	0	0.036	0.012	16.836	-0.040	-0.040	0.000	0.000	0.000	0.000
52	C	265	SER	0	0.014	-0.024	19.559	-0.013	-0.013	0.000	0.000	0.000	0.000
53	C	266	SER	0	-0.064	-0.027	21.414	-0.006	-0.006	0.000	0.000	0.000	0.000
54	C	267	LYS	1	0.876	0.944	17.576	0.088	0.088	0.000	0.000	0.000	0.000
55	C	268	ARG	1	0.842	0.952	22.679	-0.062	-0.062	0.000	0.000	0.000	0.000
56	C	269	LYS	1	0.971	0.981	25.396	0.030	0.030	0.000	0.000	0.000	0.000
57	C	270	PRO	0	0.010	0.006	28.868	0.006	0.006	0.000	0.000	0.000	0.000
58	C	271	THR	0	0.035	0.010	29.496	-0.003	-0.003	0.000	0.000	0.000	0.000
59	C	272	GLY	0	0.066	0.021	32.120	0.000	0.000	0.000	0.000	0.000	0.000
60	C	273	ARG	1	1.003	1.003	30.934	-0.067	-0.067	0.000	0.000	0.000	0.000
61	C	274	GLU	-1	-0.868	-0.956	28.340	0.043	0.043	0.000	0.000	0.000	0.000
62	C	275	ILE	0	-0.059	-0.027	33.055	0.000	0.000	0.000	0.000	0.000	0.000
63	C	276	ILE	0	0.073	0.032	35.826	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	277	LEU	0	-0.021	-0.014	33.123	0.001	0.001	0.000	0.000	0.000	0.000
65	C	278	LYS	1	0.903	0.971	31.120	-0.018	-0.018	0.000	0.000	0.000	0.000
66	C	279	MET	0	-0.001	-0.012	36.654	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	280	SER	0	-0.060	-0.014	39.476	0.000	0.000	0.000	0.000	0.000	0.000
68	C	281	ALA	0	-0.026	-0.007	37.384	0.000	0.000	0.000	0.000	0.000	0.000
69	C	282	GLU	-1	-0.986	-0.979	39.343	0.019	0.019	0.000	0.000	0.000	0.000
70	C	302	ALA	0	-0.017	-0.025	54.310	0.000	0.000	0.000	0.000	0.000	0.000
71	C	303	TRP	0	-0.015	-0.008	52.975	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	304	ASP	-1	-0.857	-0.915	53.138	0.021	0.021	0.000	0.000	0.000	0.000
73	C	305	LEU	0	0.004	-0.008	48.887	0.000	0.000	0.000	0.000	0.000	0.000
74	C	306	THR	0	0.013	0.000	51.912	0.001	0.001	0.000	0.000	0.000	0.000
75	C	307	GLU	-1	-0.846	-0.910	52.620	0.024	0.024	0.000	0.000	0.000	0.000
76	C	308	PHE	0	-0.018	-0.014	52.233	0.001	0.001	0.000	0.000	0.000	0.000
77	C	309	THR	0	-0.083	-0.051	48.005	0.002	0.002	0.000	0.000	0.000	0.000
78	C	310	ASP	-1	-0.944	-0.971	49.034	0.033	0.033	0.000	0.000	0.000	0.000
79	C	311	ALA	0	-0.001	-0.008	50.521	0.002	0.002	0.000	0.000	0.000	0.000
80	C	312	LEU	0	-0.013	0.007	44.988	0.001	0.001	0.000	0.000	0.000	0.000
81	C	313	LYS	1	0.968	0.972	45.522	-0.034	-0.034	0.000	0.000	0.000	0.000
82	C	314	LYS	1	0.948	0.979	46.544	-0.030	-0.030	0.000	0.000	0.000	0.000
83	C	315	ALA	0	-0.013	-0.017	48.585	0.001	0.001	0.000	0.000	0.000	0.000
84	C	316	ASP	-1	-0.979	-0.992	42.214	0.048	0.048	0.000	0.000	0.000	0.000
85	C	317	HIS	1	0.844	0.908	40.830	-0.052	-0.052	0.000	0.000	0.000	0.000
86	C	318	GLN	0	-0.078	-0.019	45.142	0.001	0.001	0.000	0.000	0.000	0.000
87	C	319	ASP	-1	-0.897	-0.948	45.295	0.043	0.043	0.000	0.000	0.000	0.000
88	C	320	ASP	-1	-0.816	-0.907	42.250	0.061	0.061	0.000	0.000	0.000	0.000
89	C	321	GLY	0	-0.065	-0.019	42.310	0.004	0.004	0.000	0.000	0.000	0.000
90	C	322	GLY	0	-0.079	-0.039	42.879	0.003	0.003	0.000	0.000	0.000	0.000
91	C	323	ILE	0	0.002	0.003	37.987	0.002	0.002	0.000	0.000	0.000	0.000
92	C	324	LYS	1	0.784	0.880	31.090	-0.121	-0.121	0.000	0.000	0.000	0.000
93	C	325	ASP	-1	-0.809	-0.904	35.500	0.085	0.085	0.000	0.000	0.000	0.000
94	C	326	TYR	0	-0.056	-0.037	29.287	0.010	0.010	0.000	0.000	0.000	0.000
95	C	327	GLY	0	0.039	0.028	30.999	0.009	0.009	0.000	0.000	0.000	0.000
96	C	328	ASP	-1	-0.895	-0.916	29.550	0.130	0.130	0.000	0.000	0.000	0.000
97	C	329	GLY	0	-0.024	-0.008	27.293	0.005	0.005	0.000	0.000	0.000	0.000
98	C	330	SER	0	-0.128	-0.101	25.446	0.023	0.023	0.000	0.000	0.000	0.000
99	C	331	ASN	0	-0.084	-0.053	25.083	0.010	0.010	0.000	0.000	0.000	0.000
100	C	332	PRO	0	0.044	0.046	24.787	-0.009	-0.009	0.000	0.000	0.000	0.000
101	C	333	THR	0	0.037	0.021	27.222	0.011	0.011	0.000	0.000	0.000	0.000
102	C	334	PHE	0	-0.027	-0.033	25.641	-0.008	-0.008	0.000	0.000	0.000	0.000
103	C	335	ASP	-1	-0.878	-0.915	30.539	0.126	0.126	0.000	0.000	0.000	0.000
104	C	336	ILE	0	-0.028	-0.013	33.017	-0.004	-0.004	0.000	0.000	0.000	0.000
105	C	337	LYS	1	0.972	0.985	36.093	-0.085	-0.085	0.000	0.000	0.000	0.000
106	C	338	LYS	1	0.995	1.002	39.777	-0.060	-0.060	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:214:LEU)