FMO DATABASE

FMODB ID: 17Y7Z

Calculation Name: 1VSK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VSK

Chain ID: A

ChEMBL ID:

UniProt ID: O92956

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1319319.146625
FMO2-HF: Nuclear repulsion	1263354.694965
FMO2-HF: Total energy	-55964.45166
FMO2-MP2: Total energy	-56127.969163

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:54:GLY)

Summations of interaction energy for fragment #1(A:54:GLY)

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.
-3.33	-0.71	0.026	-1.459	-1.186	0.002

Interaction energy analysis for fragmet #1(A:54:GLY)

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 : -0.009

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	56	GLY	0	-0.010	0.017	3.109	-2.454	0.150	0.027	-1.454	-1.177	0.002
4	A	57	PRO	0	0.009	0.006	4.725	-0.953	-0.937	-0.001	-0.005	-0.009	0.000
5	A	58	LEU	0	0.017	-0.002	6.958	0.214	0.214	0.000	0.000	0.000	0.000
6	A	59	GLN	0	0.048	0.022	7.779	-0.093	-0.093	0.000	0.000	0.000	0.000
7	A	60	ILE	0	0.023	0.019	11.840	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	61	TRP	0	0.029	0.028	14.649	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	62	GLN	0	0.027	0.011	18.233	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	63	THR	0	0.003	-0.007	21.531	0.011	0.011	0.000	0.000	0.000	0.000
11	A	64	ASN	0	0.029	0.016	24.825	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	65	PHE	0	0.013	-0.006	28.554	0.007	0.007	0.000	0.000	0.000	0.000
13	A	66	THR	0	0.012	0.011	32.058	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	67	LEU	0	-0.012	0.005	34.400	0.004	0.004	0.000	0.000	0.000	0.000
15	A	68	GLU	-1	-0.824	-0.918	37.104	0.007	0.007	0.000	0.000	0.000	0.000
16	A	69	PRO	0	0.037	-0.001	39.109	0.002	0.002	0.000	0.000	0.000	0.000
17	A	70	ARG	1	0.854	0.922	41.089	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	71	MET	0	-0.006	0.008	36.886	0.002	0.002	0.000	0.000	0.000	0.000
19	A	72	ALA	0	0.041	0.039	40.927	0.001	0.001	0.000	0.000	0.000	0.000
20	A	73	PRO	0	0.035	0.013	43.620	0.001	0.001	0.000	0.000	0.000	0.000
21	A	74	ARG	1	0.867	0.931	37.249	-0.032	-0.032	0.000	0.000	0.000	0.000
22	A	75	SER	0	0.068	0.035	38.828	0.002	0.002	0.000	0.000	0.000	0.000
23	A	76	TRP	0	-0.012	-0.001	36.307	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	77	LEU	0	0.023	0.008	32.982	0.003	0.003	0.000	0.000	0.000	0.000
25	A	78	ALA	0	0.007	0.016	29.797	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	79	VAL	0	-0.017	-0.019	26.687	0.006	0.006	0.000	0.000	0.000	0.000
27	A	80	THR	0	0.045	-0.005	21.598	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	81	VAL	0	-0.014	-0.001	20.026	0.007	0.007	0.000	0.000	0.000	0.000
29	A	82	ASP	-1	-0.781	-0.869	15.106	0.118	0.118	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.087	-0.087	15.178	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	84	ALA	0	-0.015	0.014	11.618	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	85	SER	0	-0.020	-0.051	13.389	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	86	SER	0	-0.049	-0.031	15.756	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	87	ALA	0	0.018	0.032	18.515	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	88	ILE	0	-0.028	-0.026	20.438	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	89	VAL	0	0.042	0.015	22.874	0.009	0.009	0.000	0.000	0.000	0.000
37	A	90	VAL	0	-0.009	-0.013	25.424	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	91	THR	0	0.004	-0.002	29.044	0.006	0.006	0.000	0.000	0.000	0.000
39	A	92	GLN	0	0.019	0.006	31.861	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	93	HIS	0	0.015	0.024	32.541	0.003	0.003	0.000	0.000	0.000	0.000
41	A	94	GLY	0	0.015	0.011	37.111	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	95	ARG	1	0.948	0.965	38.925	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	96	VAL	0	0.030	0.037	35.403	0.003	0.003	0.000	0.000	0.000	0.000
44	A	97	THR	0	-0.014	-0.014	35.146	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	98	SER	0	0.042	-0.001	32.558	0.001	0.001	0.000	0.000	0.000	0.000
46	A	99	VAL	0	0.002	0.013	31.994	0.002	0.002	0.000	0.000	0.000	0.000
47	A	100	ALA	0	-0.015	0.004	32.853	0.004	0.004	0.000	0.000	0.000	0.000
48	A	101	ALA	0	0.060	0.029	28.921	0.004	0.004	0.000	0.000	0.000	0.000
49	A	102	GLN	0	0.042	0.034	28.241	0.000	0.000	0.000	0.000	0.000	0.000
50	A	103	HIS	0	0.032	0.011	28.356	0.008	0.008	0.000	0.000	0.000	0.000
51	A	104	HIS	0	-0.031	0.021	26.653	0.005	0.005	0.000	0.000	0.000	0.000
52	A	105	TRP	0	0.024	-0.015	23.947	0.005	0.005	0.000	0.000	0.000	0.000
53	A	106	ALA	0	-0.018	-0.004	24.257	0.011	0.011	0.000	0.000	0.000	0.000
54	A	107	THR	0	-0.023	-0.017	25.721	0.010	0.010	0.000	0.000	0.000	0.000
55	A	108	ALA	0	0.008	0.004	22.469	0.009	0.009	0.000	0.000	0.000	0.000
56	A	109	ILE	0	-0.033	-0.021	20.271	0.015	0.015	0.000	0.000	0.000	0.000
57	A	110	ALA	0	-0.057	-0.021	21.268	0.021	0.021	0.000	0.000	0.000	0.000
58	A	111	VAL	0	-0.032	-0.009	22.668	0.005	0.005	0.000	0.000	0.000	0.000
59	A	112	LEU	0	-0.021	-0.008	18.049	0.011	0.011	0.000	0.000	0.000	0.000
60	A	113	GLY	0	0.034	0.038	16.897	0.037	0.037	0.000	0.000	0.000	0.000
61	A	114	ARG	1	0.894	0.925	16.673	-0.156	-0.156	0.000	0.000	0.000	0.000
62	A	115	PRO	0	0.010	0.026	14.528	0.032	0.032	0.000	0.000	0.000	0.000
63	A	116	LYS	1	0.841	0.908	10.771	-0.160	-0.160	0.000	0.000	0.000	0.000
64	A	117	ALA	0	0.016	0.005	14.172	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	118	ILE	0	0.013	0.007	16.795	0.012	0.012	0.000	0.000	0.000	0.000
66	A	119	LYS	1	0.802	0.934	18.710	0.104	0.104	0.000	0.000	0.000	0.000
67	A	120	THR	0	-0.016	-0.020	21.511	0.011	0.011	0.000	0.000	0.000	0.000
68	A	121	ASP	-1	-0.794	-0.901	25.321	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	122	ASN	0	0.025	0.000	28.036	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	123	GLY	0	0.044	0.028	30.622	0.002	0.002	0.000	0.000	0.000	0.000
71	A	124	SER	0	0.032	0.011	32.182	0.001	0.001	0.000	0.000	0.000	0.000
72	A	125	CYS	0	-0.043	-0.011	31.469	0.001	0.001	0.000	0.000	0.000	0.000
73	A	126	PHE	0	0.039	0.014	27.925	0.005	0.005	0.000	0.000	0.000	0.000
74	A	127	THR	0	-0.013	-0.005	28.571	0.000	0.000	0.000	0.000	0.000	0.000
75	A	128	SER	0	-0.004	0.015	30.839	0.000	0.000	0.000	0.000	0.000	0.000
76	A	129	LYS	1	0.960	0.961	31.597	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	130	SER	0	-0.026	-0.030	32.019	0.002	0.002	0.000	0.000	0.000	0.000
78	A	131	THR	0	0.017	0.005	27.773	0.004	0.004	0.000	0.000	0.000	0.000
79	A	132	ARG	1	0.866	0.931	27.181	0.028	0.028	0.000	0.000	0.000	0.000
80	A	133	GLU	-1	-0.840	-0.882	27.104	0.016	0.016	0.000	0.000	0.000	0.000
81	A	134	TRP	0	-0.011	-0.015	24.093	0.003	0.003	0.000	0.000	0.000	0.000
82	A	135	LEU	0	0.012	-0.002	22.422	0.008	0.008	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.004	0.009	22.910	0.004	0.004	0.000	0.000	0.000	0.000
84	A	137	ARG	1	0.895	0.933	23.851	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	138	TRP	0	0.023	0.007	21.260	0.015	0.015	0.000	0.000	0.000	0.000
86	A	139	GLY	0	-0.026	0.008	19.946	0.017	0.017	0.000	0.000	0.000	0.000
87	A	140	ILE	0	-0.075	-0.031	18.171	0.007	0.007	0.000	0.000	0.000	0.000
88	A	141	ALA	0	0.020	0.013	17.477	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	142	HIS	0	0.020	0.002	19.345	0.004	0.004	0.000	0.000	0.000	0.000
90	A	143	THR	0	0.000	-0.001	19.120	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	144	THR	0	-0.026	-0.010	22.403	0.005	0.005	0.000	0.000	0.000	0.000
92	A	145	GLY	0	0.061	0.025	24.811	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	146	ILE	0	0.031	0.019	27.402	0.007	0.007	0.000	0.000	0.000	0.000
94	A	147	PRO	0	0.043	0.002	29.408	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	148	GLY	0	0.056	0.032	29.523	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	149	ASN	0	-0.042	-0.014	25.359	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	150	SER	0	0.079	0.015	25.030	0.001	0.001	0.000	0.000	0.000	0.000
98	A	151	GLN	0	0.037	0.032	21.444	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	152	GLY	0	-0.025	-0.039	21.037	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	153	GLN	0	-0.048	-0.030	22.664	0.016	0.016	0.000	0.000	0.000	0.000
101	A	154	ALA	0	0.049	0.035	24.698	0.007	0.007	0.000	0.000	0.000	0.000
102	A	155	MET	0	-0.028	0.010	18.259	0.000	0.000	0.000	0.000	0.000	0.000
103	A	156	VAL	0	0.000	0.010	23.498	0.010	0.010	0.000	0.000	0.000	0.000
104	A	157	GLU	-1	-0.891	-0.952	25.366	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	158	ARG	1	0.937	0.968	24.797	0.022	0.022	0.000	0.000	0.000	0.000
106	A	159	ALA	0	0.013	0.005	25.295	0.005	0.005	0.000	0.000	0.000	0.000
107	A	160	ASN	0	-0.018	-0.013	27.363	0.005	0.005	0.000	0.000	0.000	0.000
108	A	161	ARG	1	0.928	0.958	30.612	0.012	0.012	0.000	0.000	0.000	0.000
109	A	162	LEU	0	0.004	0.003	27.562	0.002	0.002	0.000	0.000	0.000	0.000
110	A	163	LEU	0	0.013	0.014	30.067	0.004	0.004	0.000	0.000	0.000	0.000
111	A	164	LYS	1	0.836	0.909	31.795	0.000	0.000	0.000	0.000	0.000	0.000
112	A	165	ASP	-1	-0.782	-0.872	34.557	0.002	0.002	0.000	0.000	0.000	0.000
113	A	166	LYS	1	0.900	0.961	31.422	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	167	ILE	0	0.007	-0.009	34.461	0.001	0.001	0.000	0.000	0.000	0.000
115	A	168	ARG	1	0.800	0.888	37.181	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	169	VAL	0	0.019	0.007	38.095	0.000	0.000	0.000	0.000	0.000	0.000
117	A	170	LEU	0	-0.021	-0.011	35.417	0.001	0.001	0.000	0.000	0.000	0.000
118	A	171	ALA	0	-0.015	-0.002	39.876	0.001	0.001	0.000	0.000	0.000	0.000
119	A	172	GLU	-1	-0.799	-0.904	42.552	0.009	0.009	0.000	0.000	0.000	0.000
120	A	173	GLY	0	-0.029	-0.006	43.088	0.000	0.000	0.000	0.000	0.000	0.000
121	A	174	ASP	-1	-0.850	-0.920	42.217	0.030	0.030	0.000	0.000	0.000	0.000
122	A	175	GLY	0	0.034	0.024	45.295	0.000	0.000	0.000	0.000	0.000	0.000
123	A	176	PHE	0	-0.020	-0.022	44.095	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	177	MET	0	0.014	0.007	45.789	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	178	LYS	1	0.925	0.945	46.982	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	179	ARG	1	0.818	0.902	45.437	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	180	ILE	0	0.024	0.031	40.624	0.000	0.000	0.000	0.000	0.000	0.000
128	A	181	PRO	0	0.024	0.015	44.794	0.000	0.000	0.000	0.000	0.000	0.000
129	A	182	THR	0	0.074	0.021	44.142	0.001	0.001	0.000	0.000	0.000	0.000
130	A	183	SER	0	-0.024	0.006	43.457	0.002	0.002	0.000	0.000	0.000	0.000
131	A	184	LYS	1	0.869	0.912	42.783	-0.032	-0.032	0.000	0.000	0.000	0.000
132	A	185	GLN	0	-0.042	-0.015	40.082	0.003	0.003	0.000	0.000	0.000	0.000
133	A	186	GLY	0	0.023	0.016	37.338	0.001	0.001	0.000	0.000	0.000	0.000
134	A	187	GLU	-1	-0.785	-0.879	36.388	0.041	0.041	0.000	0.000	0.000	0.000
135	A	188	LEU	0	-0.023	-0.002	36.819	0.002	0.002	0.000	0.000	0.000	0.000
136	A	189	LEU	0	0.013	-0.001	32.921	0.000	0.000	0.000	0.000	0.000	0.000
137	A	190	ALA	0	0.018	0.012	32.267	0.002	0.002	0.000	0.000	0.000	0.000
138	A	191	LYS	1	0.845	0.922	32.146	-0.030	-0.030	0.000	0.000	0.000	0.000
139	A	192	ALA	0	-0.011	-0.014	33.115	0.001	0.001	0.000	0.000	0.000	0.000
140	A	193	MET	0	0.001	0.002	25.632	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	194	TYR	0	0.031	0.025	27.950	0.006	0.006	0.000	0.000	0.000	0.000
142	A	195	ALA	0	-0.013	-0.009	28.575	0.002	0.002	0.000	0.000	0.000	0.000
143	A	196	LEU	0	-0.074	-0.030	26.884	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	197	ASN	0	-0.032	-0.029	23.244	0.004	0.004	0.000	0.000	0.000	0.000
145	A	198	HIS	0	0.033	0.021	23.895	0.000	0.000	0.000	0.000	0.000	0.000
146	A	199	PHE	0	-0.070	-0.023	22.351	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:54:GLY)