FMO DATABASE

FMODB ID: YV9J2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-968658.498635
FMO2-HF: Nuclear repulsion	918154.857699
FMO2-HF: Total energy	-50503.640936
FMO2-MP2: Total energy	-50638.087825

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.
-52.463	-56.014	49.514	-21.944	-24.017	-0.038

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 : -0.009 / q_NPA : -0.014

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	-0.013	0.012	2.365	-6.559	-3.736	3.384	-2.516	-3.691	0.028
4	A	4	GLN	0	-0.039	-0.031	1.932	-19.643	-23.736	17.597	-5.554	-7.949	0.017
5	A	5	PHE	0	0.046	0.035	3.947	-3.612	-3.016	0.014	-0.256	-0.353	0.001
6	A	6	GLY	0	0.050	0.023	5.892	-1.359	-1.359	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.014	-0.013	5.720	-0.715	-0.715	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.060	-0.014	6.148	-1.030	-1.030	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.017	0.019	9.378	-0.545	-0.545	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.898	-0.950	11.352	1.819	1.819	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.147	-0.063	12.121	-0.260	-0.260	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.017	-0.026	13.445	-0.218	-0.218	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.042	0.004	15.346	-0.171	-0.171	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.888	0.931	16.336	-0.859	-0.859	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.029	-0.025	15.313	0.037	0.037	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.954	0.993	17.394	-0.740	-0.740	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.838	0.907	17.924	-0.853	-0.853	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.023	0.037	15.176	0.114	0.114	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.089	0.030	10.713	-0.086	-0.086	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.011	-0.012	12.725	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.852	-0.917	14.257	0.730	0.730	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.026	-0.027	13.885	-0.164	-0.164	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.035	-0.010	10.881	0.119	0.119	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.016	-0.012	14.829	-0.110	-0.110	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.033	-0.050	18.167	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.021	0.004	19.315	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.113	-0.021	21.150	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.034	-0.050	16.612	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.059	0.015	13.942	0.131	0.131	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.051	0.020	13.727	0.035	0.035	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.087	-0.048	14.633	-0.054	-0.054	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.068	-0.051	16.950	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.062	0.059	17.191	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.888	0.940	17.893	-0.281	-0.281	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.037	0.025	21.489	0.020	0.020	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.042	-0.006	23.701	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.015	0.007	21.609	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.063	-0.041	23.301	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.792	-0.865	23.321	0.453	0.453	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.831	-0.921	23.181	0.349	0.349	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.001	0.017	18.497	0.044	0.044	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.705	-0.866	18.667	0.562	0.562	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.928	0.967	18.427	-0.298	-0.298	0.000	0.000	0.000	0.000
44	A	44	CYS	0	0.008	0.037	15.447	-0.097	-0.097	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.033	0.034	14.292	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.012	-0.006	15.539	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	48	HIS	0	-0.069	-0.047	7.715	-0.240	-0.240	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.864	-0.927	11.306	0.527	0.527	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.970	-0.991	12.733	0.146	0.146	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.106	-0.037	8.463	-0.146	-0.146	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.004	-0.080	4.913	-0.491	-0.415	-0.001	-0.003	-0.072	0.000
52	A	53	ALA	0	0.058	0.039	10.186	-0.164	-0.164	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.104	-0.052	13.452	-0.093	-0.093	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.010	0.002	9.540	-0.075	-0.075	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.946	-0.976	10.597	-0.426	-0.426	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.879	0.946	12.354	0.056	0.056	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.044	-0.013	13.483	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	59	GLY	0	-0.024	0.002	14.186	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.033	-0.019	8.391	0.017	0.017	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.068	0.022	7.839	0.210	0.210	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.010	0.026	5.369	-0.935	-0.935	0.000	0.000	0.000	0.000
62	A	63	SER	0	0.022	0.006	3.035	-2.086	-0.503	0.152	-0.695	-1.040	-0.006
63	A	64	LEU	0	-0.009	-0.017	2.722	-3.060	-0.739	1.317	-1.728	-1.910	-0.017
64	A	65	THR	0	-0.039	-0.001	3.328	-2.713	-1.103	0.051	-0.748	-0.913	-0.002
65	A	66	THR	0	0.006	0.007	1.648	-13.494	-23.633	26.163	-9.901	-6.123	-0.060
66	A	67	TYR	0	-0.015	-0.043	3.228	-0.059	1.389	0.839	-0.512	-1.776	0.001
67	A	68	GLN	0	-0.124	-0.060	5.150	-0.093	-0.068	-0.001	0.000	-0.023	0.000
68	A	69	TRP	0	0.083	0.023	6.155	0.228	0.228	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.920	-0.944	9.238	0.132	0.132	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.950	0.980	13.528	-0.437	-0.437	0.000	0.000	0.000	0.000
71	A	73	GLN	0	-0.031	-0.022	17.105	0.040	0.040	0.000	0.000	0.000	0.000
72	A	74	VAL	0	0.001	-0.029	20.303	0.020	0.020	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.007	0.013	17.320	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	76	ASN	0	0.015	0.012	11.098	-0.165	-0.165	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.942	-0.974	12.760	0.063	0.063	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.032	0.024	6.248	0.837	0.837	0.000	0.000	0.000	0.000
77	A	79	ASN	0	0.040	0.017	10.771	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	80	SER	0	0.012	0.007	8.411	-0.267	-0.267	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.962	0.982	10.316	1.070	1.070	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.011	0.004	9.479	0.235	0.235	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.037	0.013	11.057	0.082	0.082	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.859	-0.932	6.163	-2.274	-2.274	0.000	0.000	0.000	0.000
83	A	86	VAL	0	-0.030	-0.026	7.302	0.419	0.419	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.022	-0.004	9.954	0.247	0.247	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.059	0.022	4.333	-0.003	0.112	0.000	-0.019	-0.096	0.000
86	A	90	ALA	0	-0.002	-0.007	7.045	0.247	0.247	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.703	-0.777	4.580	4.469	4.553	-0.001	-0.012	-0.071	0.000
88	A	93	LEU	0	-0.025	-0.034	8.090	-0.069	-0.069	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.061	-0.034	10.466	-0.073	-0.073	0.000	0.000	0.000	0.000
90	A	95	ALA	0	0.062	0.045	10.766	-0.080	-0.080	0.000	0.000	0.000	0.000
91	A	96	ALA	0	-0.003	-0.005	10.421	-0.044	-0.044	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.917	0.952	12.413	-0.627	-0.627	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.019	-0.016	13.059	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.099	-0.052	16.373	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.120	-0.059	17.958	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.897	-0.934	20.390	0.401	0.401	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.915	-0.945	22.284	0.415	0.415	0.000	0.000	0.000	0.000
98	A	104	TYR	0	-0.080	-0.065	19.278	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.032	0.005	23.708	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.055	0.020	25.256	0.019	0.019	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.042	-0.014	26.327	0.003	0.003	0.000	0.000	0.000	0.000
102	A	108	HIS	0	-0.099	-0.079	24.304	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	109	PHE	0	0.027	0.026	19.474	0.019	0.019	0.000	0.000	0.000	0.000
104	A	110	ASN	0	-0.037	-0.001	22.401	-0.028	-0.028	0.000	0.000	0.000	0.000
105	A	111	ILE	0	-0.026	0.001	23.844	-0.053	-0.053	0.000	0.000	0.000	0.000
106	A	112	ASN	0	0.029	0.019	25.692	0.003	0.003	0.000	0.000	0.000	0.000
107	A	113	THR	0	0.093	0.016	22.246	-0.028	-0.028	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.006	0.014	25.622	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.998	-1.021	28.286	0.177	0.177	0.000	0.000	0.000	0.000
110	A	116	ARG	1	0.905	0.952	27.269	-0.321	-0.321	0.000	0.000	0.000	0.000
111	A	118	LYS	1	0.896	0.947	25.549	-0.188	-0.188	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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