FMO DATABASE

FMODB ID: Z6Z4N

Calculation Name: 5VGL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VGL

Chain ID: A

ChEMBL ID:

UniProt ID: P59082

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1534888.466818
FMO2-HF: Nuclear repulsion	1472625.411806
FMO2-HF: Total energy	-62263.055013
FMO2-MP2: Total energy	-62439.99805

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:15:PRO)

Summations of interaction energy for fragment #1(A:15:PRO)

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.
-6.636	-1.063	2.423	-3.086	-4.908	-0.017

Interaction energy analysis for fragmet #1(A:15:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.039

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	17	ILE	0	-0.017	0.012	3.777	-0.343	2.032	-0.038	-1.247	-1.089	0.001
4	A	18	SER	0	-0.021	-0.024	7.131	-0.085	-0.085	0.000	0.000	0.000	0.000
5	A	19	GLY	0	-0.002	-0.001	9.527	0.108	0.108	0.000	0.000	0.000	0.000
6	A	20	GLY	0	-0.048	-0.013	12.483	0.032	0.032	0.000	0.000	0.000	0.000
7	A	21	GLY	0	0.028	0.007	11.421	0.065	0.065	0.000	0.000	0.000	0.000
8	A	22	GLY	0	-0.045	-0.034	12.473	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.013	0.018	13.265	0.039	0.039	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.896	0.941	14.839	0.017	0.017	0.000	0.000	0.000	0.000
11	A	25	VAL	0	0.004	0.020	15.961	0.018	0.018	0.000	0.000	0.000	0.000
12	A	26	HIS	0	0.021	0.006	18.850	0.002	0.002	0.000	0.000	0.000	0.000
13	A	27	ALA	0	0.013	0.024	22.115	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	28	LEU	0	-0.029	-0.023	24.631	0.006	0.006	0.000	0.000	0.000	0.000
15	A	29	LEU	0	0.004	0.015	27.739	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	30	PRO	0	-0.011	-0.004	31.064	0.005	0.005	0.000	0.000	0.000	0.000
17	A	31	ASN	0	-0.060	-0.049	34.106	0.010	0.010	0.000	0.000	0.000	0.000
18	A	32	THR	0	0.031	-0.001	33.715	0.000	0.000	0.000	0.000	0.000	0.000
19	A	33	LYS	1	0.878	0.971	35.318	0.055	0.055	0.000	0.000	0.000	0.000
20	A	34	PRO	0	0.090	0.035	34.130	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	35	GLU	-1	-0.825	-0.936	34.697	-0.064	-0.064	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.024	-0.003	36.690	0.000	0.000	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.078	0.035	31.204	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	38	TRP	0	0.014	0.013	29.467	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	39	THR	0	-0.079	-0.048	33.065	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	40	LEU	0	-0.018	-0.007	31.830	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	41	LEU	0	0.020	0.008	25.713	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	42	LYS	1	0.859	0.934	28.975	0.080	0.080	0.000	0.000	0.000	0.000
29	A	43	ASP	-1	-0.820	-0.888	31.356	-0.128	-0.128	0.000	0.000	0.000	0.000
30	A	44	PHE	0	0.026	0.011	24.519	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	45	ILE	0	-0.006	-0.014	27.224	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	46	ASN	0	-0.082	-0.066	29.208	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	47	LEU	0	0.092	0.046	22.329	0.007	0.007	0.000	0.000	0.000	0.000
34	A	48	HIS	0	0.066	0.027	25.736	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	49	LYS	1	0.804	0.919	26.687	0.131	0.131	0.000	0.000	0.000	0.000
36	A	50	VAL	0	-0.044	-0.033	26.626	0.011	0.011	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.009	0.017	18.920	0.004	0.004	0.000	0.000	0.000	0.000
38	A	52	PRO	0	0.009	-0.008	24.596	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	53	SER	0	-0.016	-0.015	19.550	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	54	LEU	0	-0.058	-0.025	20.072	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	55	SER	0	-0.033	-0.021	22.281	0.018	0.018	0.000	0.000	0.000	0.000
42	A	56	VAL	0	-0.024	-0.012	23.231	0.018	0.018	0.000	0.000	0.000	0.000
43	A	57	CYS	0	-0.043	-0.023	23.489	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	58	GLU	-1	-0.932	-0.943	25.782	-0.193	-0.193	0.000	0.000	0.000	0.000
45	A	59	LEU	0	-0.027	-0.017	27.250	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	60	VAL	0	-0.010	-0.012	25.723	0.001	0.001	0.000	0.000	0.000	0.000
47	A	61	GLU	-1	-0.862	-0.939	28.578	-0.162	-0.162	0.000	0.000	0.000	0.000
48	A	62	GLY	0	0.004	0.005	30.728	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.905	-0.956	33.290	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.031	-0.001	33.251	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	65	ASN	0	-0.026	-0.028	31.659	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	66	VAL	0	0.007	0.019	32.834	0.007	0.007	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.001	-0.005	30.448	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.008	0.004	29.928	0.008	0.008	0.000	0.000	0.000	0.000
55	A	69	CYS	0	-0.108	-0.027	29.817	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	70	VAL	0	0.023	0.003	24.414	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.773	0.879	21.842	0.250	0.250	0.000	0.000	0.000	0.000
58	A	72	TYR	0	-0.009	-0.003	20.329	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	73	VAL	0	0.014	-0.005	19.251	0.022	0.022	0.000	0.000	0.000	0.000
60	A	74	LYS	1	0.831	0.900	18.898	0.354	0.354	0.000	0.000	0.000	0.000
61	A	75	GLY	0	0.050	0.013	17.966	0.048	0.048	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.054	0.006	16.248	-0.051	-0.051	0.000	0.000	0.000	0.000
63	A	77	MET	0	-0.008	0.020	9.783	0.031	0.031	0.000	0.000	0.000	0.000
64	A	78	HIS	1	0.798	0.883	14.158	0.320	0.320	0.000	0.000	0.000	0.000
65	A	79	PRO	0	-0.025	-0.026	12.723	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.007	-0.017	8.864	0.052	0.052	0.000	0.000	0.000	0.000
67	A	81	GLU	-1	-0.850	-0.898	12.157	-0.358	-0.358	0.000	0.000	0.000	0.000
68	A	82	GLU	-1	-0.909	-0.946	9.213	-1.178	-1.178	0.000	0.000	0.000	0.000
69	A	83	GLU	-1	-0.840	-0.918	13.302	-0.420	-0.420	0.000	0.000	0.000	0.000
70	A	84	PHE	0	0.000	0.006	12.348	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	85	TRP	0	0.002	-0.013	14.297	0.088	0.088	0.000	0.000	0.000	0.000
72	A	86	ALA	0	0.023	0.009	15.595	-0.064	-0.064	0.000	0.000	0.000	0.000
73	A	87	LYS	1	0.833	0.917	17.884	0.333	0.333	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.741	-0.878	18.757	-0.350	-0.350	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.816	0.917	21.825	0.191	0.191	0.000	0.000	0.000	0.000
76	A	90	LEU	0	0.004	0.012	24.544	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	91	VAL	0	-0.017	-0.017	25.006	0.011	0.011	0.000	0.000	0.000	0.000
78	A	92	ALA	0	-0.008	-0.010	27.685	0.014	0.014	0.000	0.000	0.000	0.000
79	A	93	LEU	0	0.014	0.003	28.719	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	94	ASP	-1	-0.820	-0.883	31.263	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	95	ASN	0	0.042	-0.010	33.169	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.931	0.985	35.566	0.047	0.047	0.000	0.000	0.000	0.000
83	A	97	ASN	0	-0.092	-0.075	32.205	0.007	0.007	0.000	0.000	0.000	0.000
84	A	98	MET	0	-0.035	0.007	31.788	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	99	SER	0	0.050	0.023	27.709	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	100	TYR	0	0.021	0.007	24.388	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	101	SER	0	-0.002	-0.013	24.015	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	102	TYR	0	-0.035	-0.022	18.744	0.022	0.022	0.000	0.000	0.000	0.000
89	A	103	ILE	0	0.013	0.014	20.094	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	104	PHE	0	0.001	0.005	12.974	0.010	0.010	0.000	0.000	0.000	0.000
91	A	105	THR	0	-0.033	-0.025	18.691	0.014	0.014	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.877	-0.929	18.425	-0.320	-0.320	0.000	0.000	0.000	0.000
93	A	107	CYS	0	-0.061	-0.007	12.735	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	108	PHE	0	0.045	0.022	9.480	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	109	THR	0	0.001	-0.011	7.527	-0.042	-0.042	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.060	0.030	9.979	0.203	0.203	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.037	-0.040	10.216	-0.150	-0.150	0.000	0.000	0.000	0.000
98	A	112	GLU	-1	-0.840	-0.904	12.534	-0.128	-0.128	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.893	-0.959	15.068	-0.196	-0.196	0.000	0.000	0.000	0.000
100	A	114	TYR	0	-0.004	0.005	13.148	0.009	0.009	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.002	-0.015	16.498	0.025	0.025	0.000	0.000	0.000	0.000
102	A	116	ALA	0	-0.011	0.003	17.692	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	117	THR	0	0.009	0.006	19.416	0.013	0.013	0.000	0.000	0.000	0.000
104	A	118	MET	0	-0.028	0.015	20.860	0.002	0.002	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.040	-0.043	23.975	0.007	0.007	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.033	0.005	26.878	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	121	VAL	0	-0.010	-0.008	28.893	0.006	0.006	0.000	0.000	0.000	0.000
108	A	122	GLU	-1	-0.842	-0.914	31.320	-0.039	-0.039	0.000	0.000	0.000	0.000
109	A	123	GLY	0	0.030	0.023	31.999	0.000	0.000	0.000	0.000	0.000	0.000
110	A	124	PRO	0	-0.001	-0.009	31.146	0.004	0.004	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.921	-0.972	33.744	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	126	HIS	1	0.778	0.872	36.543	0.030	0.030	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.881	0.960	36.378	0.043	0.043	0.000	0.000	0.000	0.000
114	A	128	GLY	0	-0.018	0.008	35.054	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	129	SER	0	-0.005	-0.032	31.829	0.002	0.002	0.000	0.000	0.000	0.000
116	A	130	ARG	1	0.730	0.833	24.011	0.066	0.066	0.000	0.000	0.000	0.000
117	A	131	PHE	0	-0.017	0.001	22.459	0.002	0.002	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.762	-0.856	23.211	-0.080	-0.080	0.000	0.000	0.000	0.000
119	A	133	TRP	0	0.031	0.007	18.088	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.023	-0.018	17.990	0.008	0.008	0.000	0.000	0.000	0.000
121	A	135	PHE	0	0.002	0.007	10.818	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	136	GLN	0	0.008	0.011	15.561	0.048	0.048	0.000	0.000	0.000	0.000
123	A	137	CYS	0	-0.068	-0.017	12.152	-0.064	-0.064	0.000	0.000	0.000	0.000
124	A	138	LYS	1	0.872	0.931	14.218	0.200	0.200	0.000	0.000	0.000	0.000
125	A	139	TYR	0	-0.056	-0.059	7.889	0.049	0.049	0.000	0.000	0.000	0.000
126	A	140	ILE	0	0.003	0.002	7.245	0.101	0.101	0.000	0.000	0.000	0.000
127	A	141	GLU	-1	-0.879	-0.918	6.322	-1.805	-1.805	0.000	0.000	0.000	0.000
128	A	142	GLY	0	0.043	0.011	2.896	-0.156	0.459	0.138	-0.213	-0.540	-0.001
129	A	143	MET	0	-0.011	-0.003	2.726	-1.916	-0.061	0.954	-1.098	-1.712	-0.015
130	A	144	THR	0	0.000	0.007	2.223	-0.613	-0.001	1.368	-0.502	-1.477	-0.002
131	A	145	GLU	-1	-0.802	-0.902	4.211	-0.181	-0.065	0.001	-0.026	-0.090	0.000
132	A	146	SER	0	-0.022	-0.010	7.539	-0.054	-0.054	0.000	0.000	0.000	0.000
133	A	147	ALA	0	0.015	0.009	5.145	-0.027	-0.027	0.000	0.000	0.000	0.000
134	A	148	PHE	0	0.052	0.010	7.108	-0.032	-0.032	0.000	0.000	0.000	0.000
135	A	149	THR	0	-0.001	-0.021	8.888	0.064	0.064	0.000	0.000	0.000	0.000
136	A	150	GLU	-1	-0.861	-0.924	10.438	-0.147	-0.147	0.000	0.000	0.000	0.000
137	A	151	ILE	0	-0.018	-0.006	8.807	0.016	0.016	0.000	0.000	0.000	0.000
138	A	152	LEU	0	-0.007	0.000	12.432	0.044	0.044	0.000	0.000	0.000	0.000
139	A	153	GLN	0	-0.029	-0.018	14.697	0.051	0.051	0.000	0.000	0.000	0.000
140	A	154	HIS	0	-0.064	-0.038	14.268	0.032	0.032	0.000	0.000	0.000	0.000
141	A	155	TRP	0	0.008	-0.010	14.437	0.016	0.016	0.000	0.000	0.000	0.000
142	A	156	ALA	0	0.013	0.005	18.735	0.022	0.022	0.000	0.000	0.000	0.000
143	A	157	THR	0	-0.034	-0.031	20.479	0.022	0.022	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.848	-0.885	21.656	-0.220	-0.220	0.000	0.000	0.000	0.000
145	A	159	ILE	0	0.036	0.005	21.705	0.012	0.012	0.000	0.000	0.000	0.000
146	A	160	GLY	0	-0.014	-0.009	24.747	0.013	0.013	0.000	0.000	0.000	0.000
147	A	161	GLN	0	-0.028	-0.020	25.772	0.009	0.009	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.825	0.914	27.478	0.134	0.134	0.000	0.000	0.000	0.000
149	A	163	ILE	0	0.017	0.001	28.022	0.008	0.008	0.000	0.000	0.000	0.000
150	A	164	GLU	-1	-0.776	-0.870	30.775	-0.065	-0.065	0.000	0.000	0.000	0.000
151	A	165	GLU	-1	-0.865	-0.901	32.040	-0.108	-0.108	0.000	0.000	0.000	0.000
152	A	166	VAL	0	0.002	0.000	32.761	0.005	0.005	0.000	0.000	0.000	0.000
153	A	167	CYS	0	-0.100	-0.046	34.206	0.005	0.005	0.000	0.000	0.000	0.000
154	A	168	SER	0	-0.118	-0.047	36.800	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:PRO)