FMO DATABASE

FMODB ID: 1N58Z

Calculation Name: 3VBZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VBZ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG57

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptAll
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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-971537.885496
FMO2-HF: Nuclear repulsion	921032.857261
FMO2-HF: Total energy	-50505.028235
FMO2-MP2: Total energy	-50639.293187

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:1:ASN)

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

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.
-58.704	-52.662	37.784	-18.197	-25.63	-0.035

Interaction energy analysis for fragmet #1(A:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.024

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	3	VAL	0	-0.015	-0.002	1.932	-10.636	-10.676	8.546	-3.879	-4.627	0.042
4	A	4	GLN	0	-0.020	-0.010	2.272	-12.323	-8.575	3.543	-2.004	-5.286	0.021
5	A	5	PHE	0	0.050	0.034	3.761	-2.879	-2.387	0.000	-0.178	-0.315	0.000
6	A	6	GLY	0	0.043	0.020	5.545	-0.703	-0.703	0.000	0.000	0.000	0.000
7	A	7	PHE	0	-0.005	-0.016	5.740	-0.712	-0.712	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.030	0.009	6.180	-0.656	-0.656	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.019	0.013	8.915	-0.330	-0.330	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.825	-0.915	11.503	1.510	1.510	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.131	-0.035	11.991	-0.259	-0.259	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.011	-0.003	13.114	-0.141	-0.141	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.043	-0.003	14.921	-0.111	-0.111	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.890	0.920	15.803	-0.607	-0.607	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.049	-0.038	14.893	-0.151	-0.151	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.897	0.972	17.618	-0.449	-0.449	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.876	0.943	18.409	-0.707	-0.707	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.033	0.029	15.100	0.075	0.075	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.042	0.003	10.595	-0.086	-0.086	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.015	-0.010	12.631	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.880	-0.944	14.146	0.692	0.692	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.018	-0.015	13.913	-0.173	-0.173	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.029	-0.010	10.708	0.012	0.012	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.020	-0.023	14.450	-0.083	-0.083	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.035	-0.041	18.190	-0.041	-0.041	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.033	0.007	19.259	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.115	-0.007	21.250	0.019	0.019	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.021	-0.036	16.636	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.043	0.023	13.928	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.032	0.008	13.928	0.104	0.104	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.090	-0.044	14.864	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.074	-0.055	18.260	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.037	17.616	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.843	0.916	18.243	-0.200	-0.200	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.022	0.016	21.967	0.030	0.030	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.010	-0.002	24.105	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.006	0.011	21.582	0.023	0.023	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.078	-0.031	23.441	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.785	-0.857	22.808	0.245	0.245	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.768	-0.877	22.655	0.041	0.041	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.045	0.036	18.205	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.718	-0.886	18.208	0.256	0.256	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.824	0.885	18.424	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.042	0.008	14.681	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	46	GLN	0	-0.025	-0.015	14.343	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.028	0.008	15.040	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	48	HIS	0	-0.078	-0.041	7.231	0.149	0.149	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.847	-0.928	11.218	-0.233	-0.233	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.891	-0.935	12.884	-0.338	-0.338	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.067	-0.011	7.981	0.167	0.167	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.009	-0.061	4.777	-0.373	-0.289	-0.001	-0.005	-0.077	0.000
52	A	53	ALA	0	0.038	0.024	10.079	-0.098	-0.098	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.040	-0.023	13.382	0.058	0.058	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.003	-0.008	9.385	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.911	-0.969	11.251	-0.710	-0.710	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.760	0.881	12.386	0.642	0.642	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.027	-0.001	12.654	0.119	0.119	0.000	0.000	0.000	0.000
58	A	59	GLY	0	-0.019	0.002	14.206	0.011	0.011	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.050	-0.017	8.273	0.010	0.010	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.064	0.021	7.952	0.269	0.269	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.010	0.027	5.435	-0.847	-0.847	0.000	0.000	0.000	0.000
62	A	63	SER	0	0.060	0.022	3.133	-3.880	-2.398	0.095	-0.643	-0.935	-0.005
63	A	64	LEU	0	-0.008	-0.009	2.528	-1.843	0.384	1.676	-1.771	-2.133	-0.021
64	A	65	THR	0	-0.060	-0.035	3.233	-2.529	-0.926	0.207	-0.728	-1.082	-0.006
65	A	66	THR	0	-0.002	0.019	1.884	-19.773	-23.423	19.777	-8.304	-7.822	-0.058
66	A	67	TYR	0	-0.032	-0.057	2.264	2.011	1.651	3.939	-0.485	-3.095	-0.007
67	A	68	GLN	0	-0.076	-0.036	4.927	1.004	1.042	-0.001	-0.001	-0.036	0.000
68	A	69	TRP	0	0.028	-0.001	6.222	-0.366	-0.366	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.852	-0.906	9.155	0.150	0.150	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.828	0.880	13.451	0.059	0.059	0.000	0.000	0.000	0.000
71	A	73	GLN	0	-0.022	-0.020	17.129	0.021	0.021	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.031	-0.015	19.752	0.015	0.015	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.010	0.018	16.753	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	76	ASN	0	0.008	-0.014	10.398	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.825	-0.877	12.179	-0.305	-0.305	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.023	0.014	5.475	0.278	0.278	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.030	-0.036	10.538	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	80	SER	0	-0.004	0.002	8.120	-0.179	-0.179	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.935	0.973	10.215	1.142	1.142	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.052	-0.060	9.767	0.132	0.132	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.021	-0.002	10.606	-0.147	-0.147	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.777	-0.862	5.911	-2.415	-2.415	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.005	-0.004	6.884	-0.131	-0.131	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.004	0.003	9.673	0.117	0.117	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.041	0.018	4.080	0.158	0.280	0.000	-0.022	-0.100	0.000
86	A	90	ALA	0	0.000	-0.004	6.351	0.519	0.519	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.704	-0.797	3.643	-4.164	-3.868	0.003	-0.177	-0.122	-0.001
88	A	93	LEU	0	-0.010	-0.017	7.213	0.536	0.536	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.043	-0.020	9.709	0.212	0.212	0.000	0.000	0.000	0.000
90	A	95	ALA	0	0.051	0.029	10.194	0.132	0.132	0.000	0.000	0.000	0.000
91	A	96	ALA	0	-0.010	-0.005	9.612	0.156	0.156	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.920	0.957	11.622	0.127	0.127	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.018	-0.011	12.378	0.041	0.041	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.047	-0.025	15.610	0.057	0.057	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.091	-0.052	17.314	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.924	-0.958	19.652	0.092	0.092	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.919	-0.956	21.546	0.265	0.265	0.000	0.000	0.000	0.000
98	A	104	TYR	0	-0.060	-0.042	19.295	0.006	0.006	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.047	0.021	23.442	0.007	0.007	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.029	-0.003	25.373	0.023	0.023	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.046	-0.016	26.194	0.019	0.019	0.000	0.000	0.000	0.000
102	A	108	HIS	0	-0.077	-0.059	24.254	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	109	PHE	0	0.047	0.034	18.925	0.009	0.009	0.000	0.000	0.000	0.000
104	A	110	ASN	0	-0.057	-0.016	22.044	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	111	ILE	0	-0.009	0.014	23.652	-0.044	-0.044	0.000	0.000	0.000	0.000
106	A	112	ASN	0	0.007	-0.022	25.764	0.013	0.013	0.000	0.000	0.000	0.000
107	A	113	THR	0	0.062	0.012	22.453	-0.037	-0.037	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.003	0.014	25.733	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.951	-0.974	28.676	0.124	0.124	0.000	0.000	0.000	0.000
110	A	116	ARG	1	0.954	0.959	27.387	-0.209	-0.209	0.000	0.000	0.000	0.000
111	A	118	LYS	1	0.875	0.951	25.775	-0.127	-0.127	0.000	0.000	0.000	0.000

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