FMO DATABASE

FMODB ID: 39YML

Calculation Name: 1VLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VLA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X021

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1281643.13753
FMO2-HF: Nuclear repulsion	1221005.012587
FMO2-HF: Total energy	-60638.124943
FMO2-MP2: Total energy	-60809.005931

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:-5:HIS)

Summations of interaction energy for fragment #1(A:-5:HIS)

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.
-0.414	0.818	-0.01	-0.487	-0.735	0.002

Interaction energy analysis for fragmet #1(A:-5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.017

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	HIS	0	0.032	0.017	3.859	-0.770	0.462	-0.010	-0.487	-0.735	0.002
4	A	-2	HIS	0	-0.044	-0.024	5.416	0.354	0.354	0.000	0.000	0.000	0.000
5	A	-1	HIS	0	0.007	0.009	8.474	-0.030	-0.030	0.000	0.000	0.000	0.000
6	A	0	HIS	0	0.000	-0.010	11.877	0.055	0.055	0.000	0.000	0.000	0.000
7	A	1	MET	0	-0.016	-0.010	15.063	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	2	GLN	0	0.010	0.017	18.781	0.023	0.023	0.000	0.000	0.000	0.000
9	A	3	ALA	0	0.009	0.004	21.989	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	4	ARG	1	0.868	0.929	25.698	-0.080	-0.080	0.000	0.000	0.000	0.000
11	A	5	TRP	0	-0.003	0.002	28.716	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	6	ILE	0	-0.061	-0.044	32.133	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	7	GLY	0	0.055	0.041	34.942	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	8	ASN	0	-0.041	-0.028	37.726	0.000	0.000	0.000	0.000	0.000	0.000
15	A	9	MET	0	0.020	0.024	36.751	0.004	0.004	0.000	0.000	0.000	0.000
16	A	10	MET	0	-0.007	0.013	34.949	0.003	0.003	0.000	0.000	0.000	0.000
17	A	11	PHE	0	-0.034	-0.032	29.624	0.003	0.003	0.000	0.000	0.000	0.000
18	A	12	HIS	0	-0.002	-0.003	27.995	0.000	0.000	0.000	0.000	0.000	0.000
19	A	13	VAL	0	0.006	0.002	23.617	0.008	0.008	0.000	0.000	0.000	0.000
20	A	14	ARG	1	0.833	0.912	23.650	-0.075	-0.075	0.000	0.000	0.000	0.000
21	A	15	THR	0	-0.011	-0.026	21.189	0.009	0.009	0.000	0.000	0.000	0.000
22	A	16	ASP	-1	-0.853	-0.921	15.658	0.115	0.115	0.000	0.000	0.000	0.000
23	A	17	SER	0	-0.017	-0.002	18.453	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	18	ASN	0	-0.003	0.005	20.548	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	19	HIS	0	-0.016	-0.008	22.950	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	20	ASP	-1	-0.838	-0.898	25.421	0.076	0.076	0.000	0.000	0.000	0.000
27	A	21	VAL	0	-0.011	-0.007	26.338	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	22	LEU	0	0.004	-0.005	28.815	0.002	0.002	0.000	0.000	0.000	0.000
29	A	23	MET	0	-0.020	-0.003	27.514	0.005	0.005	0.000	0.000	0.000	0.000
30	A	24	ASP	-1	-0.761	-0.872	32.902	0.069	0.069	0.000	0.000	0.000	0.000
31	A	25	THR	0	-0.053	-0.040	36.242	0.003	0.003	0.000	0.000	0.000	0.000
32	A	26	LYS	1	0.865	0.911	38.804	-0.063	-0.063	0.000	0.000	0.000	0.000
33	A	27	GLU	-1	-0.844	-0.915	42.602	0.054	0.054	0.000	0.000	0.000	0.000
34	A	28	GLU	-1	-0.849	-0.918	45.170	0.058	0.058	0.000	0.000	0.000	0.000
35	A	29	VAL	0	-0.062	-0.029	40.732	0.001	0.001	0.000	0.000	0.000	0.000
36	A	30	GLY	0	0.014	0.012	41.320	0.003	0.003	0.000	0.000	0.000	0.000
37	A	31	GLY	0	-0.041	-0.018	40.194	0.001	0.001	0.000	0.000	0.000	0.000
38	A	32	LYS	1	0.825	0.889	40.745	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	33	ASP	-1	-0.819	-0.893	41.323	0.061	0.061	0.000	0.000	0.000	0.000
40	A	34	ALA	0	0.009	0.016	40.195	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	35	ALA	0	-0.046	-0.026	34.955	0.000	0.000	0.000	0.000	0.000	0.000
42	A	36	PRO	0	0.037	0.017	33.808	0.000	0.000	0.000	0.000	0.000	0.000
43	A	37	ARG	1	0.814	0.895	34.542	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	38	PRO	0	0.038	-0.003	29.569	0.003	0.003	0.000	0.000	0.000	0.000
45	A	39	LEU	0	-0.013	-0.005	30.027	0.006	0.006	0.000	0.000	0.000	0.000
46	A	40	GLU	-1	-0.761	-0.871	31.792	0.084	0.084	0.000	0.000	0.000	0.000
47	A	41	LEU	0	0.013	0.020	28.822	0.001	0.001	0.000	0.000	0.000	0.000
48	A	42	VAL	0	-0.019	-0.004	26.336	0.004	0.004	0.000	0.000	0.000	0.000
49	A	43	LEU	0	-0.006	-0.005	27.972	0.005	0.005	0.000	0.000	0.000	0.000
50	A	44	THR	0	-0.003	-0.018	30.381	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	45	GLY	0	0.011	0.007	26.224	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	46	LEU	0	-0.010	0.000	24.617	0.005	0.005	0.000	0.000	0.000	0.000
53	A	47	MET	0	0.013	0.009	26.844	0.000	0.000	0.000	0.000	0.000	0.000
54	A	48	GLY	0	0.012	0.010	27.485	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	49	CYS	0	-0.064	-0.035	23.112	0.001	0.001	0.000	0.000	0.000	0.000
56	A	50	THR	0	0.022	0.011	24.811	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	51	GLY	0	0.062	0.020	27.119	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	52	MET	0	-0.021	-0.019	24.724	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	53	ASP	-1	-0.784	-0.839	23.246	0.157	0.157	0.000	0.000	0.000	0.000
60	A	54	VAL	0	0.008	0.006	25.750	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	55	VAL	0	0.019	0.014	28.912	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	56	SER	0	-0.061	-0.033	23.825	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	57	ILE	0	-0.019	-0.017	25.846	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	58	LEU	0	0.067	0.023	28.294	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	59	ARG	1	0.961	0.992	28.265	-0.063	-0.063	0.000	0.000	0.000	0.000
66	A	60	LYS	1	0.924	0.964	24.493	-0.079	-0.079	0.000	0.000	0.000	0.000
67	A	61	MET	0	-0.071	-0.035	29.204	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	62	LYS	1	0.880	0.946	32.243	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	63	VAL	0	0.086	0.038	34.567	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	64	ILE	0	-0.037	-0.008	32.254	0.000	0.000	0.000	0.000	0.000	0.000
71	A	65	ASP	-1	-0.909	-0.951	35.713	0.034	0.034	0.000	0.000	0.000	0.000
72	A	66	GLN	0	0.003	0.006	38.537	0.000	0.000	0.000	0.000	0.000	0.000
73	A	67	MET	0	-0.068	-0.026	34.281	0.002	0.002	0.000	0.000	0.000	0.000
74	A	68	LYS	1	0.849	0.913	39.041	-0.032	-0.032	0.000	0.000	0.000	0.000
75	A	69	ASP	-1	-0.830	-0.908	39.855	0.045	0.045	0.000	0.000	0.000	0.000
76	A	70	PHE	0	-0.071	-0.052	31.679	0.002	0.002	0.000	0.000	0.000	0.000
77	A	71	ARG	1	0.758	0.864	36.043	-0.059	-0.059	0.000	0.000	0.000	0.000
78	A	72	ILE	0	-0.011	0.002	31.330	0.002	0.002	0.000	0.000	0.000	0.000
79	A	73	GLU	-1	-0.802	-0.881	35.524	0.063	0.063	0.000	0.000	0.000	0.000
80	A	74	ILE	0	-0.015	-0.021	31.950	0.004	0.004	0.000	0.000	0.000	0.000
81	A	75	GLU	-1	-0.842	-0.908	36.036	0.071	0.071	0.000	0.000	0.000	0.000
82	A	76	TYR	0	-0.021	-0.033	35.055	0.006	0.006	0.000	0.000	0.000	0.000
83	A	77	GLU	-1	-0.811	-0.877	36.589	0.078	0.078	0.000	0.000	0.000	0.000
84	A	78	ARG	1	0.874	0.916	32.392	-0.110	-0.110	0.000	0.000	0.000	0.000
85	A	79	THR	0	0.011	0.020	36.596	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	80	GLU	-1	-0.800	-0.884	38.061	0.084	0.084	0.000	0.000	0.000	0.000
87	A	81	GLU	-1	-0.862	-0.916	40.172	0.087	0.087	0.000	0.000	0.000	0.000
88	A	82	HIS	0	-0.056	-0.038	36.115	0.010	0.010	0.000	0.000	0.000	0.000
89	A	83	PRO	0	-0.006	-0.008	32.364	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	84	ARG	1	0.810	0.888	34.340	-0.092	-0.092	0.000	0.000	0.000	0.000
91	A	85	ILE	0	-0.009	0.006	30.971	0.007	0.007	0.000	0.000	0.000	0.000
92	A	86	PHE	0	0.040	0.009	30.697	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	87	THR	0	0.007	-0.003	33.082	0.004	0.004	0.000	0.000	0.000	0.000
94	A	88	LYS	1	0.866	0.932	35.295	-0.088	-0.088	0.000	0.000	0.000	0.000
95	A	89	VAL	0	0.018	-0.001	31.172	0.000	0.000	0.000	0.000	0.000	0.000
96	A	90	HIS	0	-0.037	0.012	34.041	0.008	0.008	0.000	0.000	0.000	0.000
97	A	91	LEU	0	0.003	-0.011	30.336	0.000	0.000	0.000	0.000	0.000	0.000
98	A	92	LYS	1	0.862	0.938	34.785	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	93	TYR	0	-0.014	-0.032	29.640	0.000	0.000	0.000	0.000	0.000	0.000
100	A	94	ILE	0	-0.015	0.000	36.343	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	95	PHE	0	0.011	-0.010	34.521	0.001	0.001	0.000	0.000	0.000	0.000
102	A	96	LYS	1	0.810	0.918	39.988	-0.047	-0.047	0.000	0.000	0.000	0.000
103	A	97	PHE	0	0.025	-0.007	37.423	0.001	0.001	0.000	0.000	0.000	0.000
104	A	98	ASP	-1	-0.871	-0.909	43.076	0.028	0.028	0.000	0.000	0.000	0.000
105	A	99	GLY	0	0.012	0.002	44.987	0.000	0.000	0.000	0.000	0.000	0.000
106	A	100	GLU	-1	-0.797	-0.890	45.128	0.043	0.043	0.000	0.000	0.000	0.000
107	A	101	PRO	0	-0.016	-0.002	42.012	0.001	0.001	0.000	0.000	0.000	0.000
108	A	102	PRO	0	0.004	0.020	38.298	0.000	0.000	0.000	0.000	0.000	0.000
109	A	103	LYS	1	0.849	0.896	38.348	-0.042	-0.042	0.000	0.000	0.000	0.000
110	A	104	ASP	-1	-0.846	-0.912	37.935	0.059	0.059	0.000	0.000	0.000	0.000
111	A	105	LYS	1	0.815	0.896	34.476	-0.041	-0.041	0.000	0.000	0.000	0.000
112	A	106	VAL	0	0.012	0.014	33.516	0.007	0.007	0.000	0.000	0.000	0.000
113	A	107	GLU	-1	-0.815	-0.897	33.948	0.074	0.074	0.000	0.000	0.000	0.000
114	A	108	LYS	1	0.928	0.970	29.470	-0.098	-0.098	0.000	0.000	0.000	0.000
115	A	109	ALA	0	-0.010	-0.015	29.558	0.010	0.010	0.000	0.000	0.000	0.000
116	A	110	VAL	0	0.023	0.016	29.061	0.010	0.010	0.000	0.000	0.000	0.000
117	A	111	GLN	0	0.001	0.001	29.587	0.013	0.013	0.000	0.000	0.000	0.000
118	A	112	LEU	0	-0.080	-0.034	25.355	0.011	0.011	0.000	0.000	0.000	0.000
119	A	113	SER	0	0.006	-0.006	25.095	0.016	0.016	0.000	0.000	0.000	0.000
120	A	114	GLN	0	0.015	-0.001	25.053	0.021	0.021	0.000	0.000	0.000	0.000
121	A	115	GLU	-1	-0.786	-0.868	26.161	0.159	0.159	0.000	0.000	0.000	0.000
122	A	116	LYS	1	0.850	0.933	21.319	-0.191	-0.191	0.000	0.000	0.000	0.000
123	A	117	TYR	0	-0.070	-0.041	20.527	0.023	0.023	0.000	0.000	0.000	0.000
124	A	118	CYS	0	-0.034	-0.004	20.642	0.021	0.021	0.000	0.000	0.000	0.000
125	A	119	SER	0	-0.016	-0.033	21.953	0.012	0.012	0.000	0.000	0.000	0.000
126	A	120	VAL	0	-0.002	0.007	23.010	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	121	SER	0	0.042	0.006	24.739	0.003	0.003	0.000	0.000	0.000	0.000
128	A	122	ALA	0	-0.036	0.000	19.419	0.005	0.005	0.000	0.000	0.000	0.000
129	A	123	ILE	0	-0.056	-0.022	20.072	0.020	0.020	0.000	0.000	0.000	0.000
130	A	124	LEU	0	-0.031	-0.017	22.126	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	125	LYS	1	0.947	0.970	22.622	-0.227	-0.227	0.000	0.000	0.000	0.000
132	A	126	CYS	0	-0.025	0.001	26.709	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	127	SER	0	-0.036	-0.017	30.168	0.004	0.004	0.000	0.000	0.000	0.000
134	A	128	SER	0	-0.038	-0.045	32.371	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	129	LYS	1	0.820	0.889	28.813	-0.139	-0.139	0.000	0.000	0.000	0.000
136	A	130	VAL	0	0.016	0.011	28.535	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	131	THR	0	-0.017	-0.017	31.452	0.002	0.002	0.000	0.000	0.000	0.000
138	A	132	TYR	0	-0.034	-0.051	31.190	0.004	0.004	0.000	0.000	0.000	0.000
139	A	133	GLU	-1	-0.860	-0.913	35.327	0.070	0.070	0.000	0.000	0.000	0.000
140	A	134	ILE	0	-0.015	-0.011	35.264	0.003	0.003	0.000	0.000	0.000	0.000
141	A	135	VAL	0	0.006	0.016	38.839	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	136	TYR	0	-0.031	-0.050	39.719	0.001	0.001	0.000	0.000	0.000	0.000
143	A	137	GLU	-1	-0.800	-0.882	43.663	0.050	0.050	0.000	0.000	0.000	0.000
144	A	138	ASN	0	-0.001	-0.009	45.844	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:HIS)