FMO DATABASE

FMODB ID: YZ1Z2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1317346.487514
FMO2-HF: Nuclear repulsion	1261383.62033
FMO2-HF: Total energy	-55962.867184
FMO2-MP2: Total energy	-56126.492943

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.
-3.187	-0.994	0.001	-1.18	-1.015	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 : 0.013 / q_NPA : -0.004

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	0.012	3.498	-2.525	-0.400	0.002	-1.162	-0.965	0.002
4	A	57	PRO	0	0.005	0.004	4.331	-0.729	-0.661	-0.001	-0.018	-0.050	0.000
5	A	58	LEU	0	0.023	0.005	7.224	0.157	0.157	0.000	0.000	0.000	0.000
6	A	59	GLN	0	0.034	0.015	8.759	-0.090	-0.090	0.000	0.000	0.000	0.000
7	A	60	ILE	0	0.012	0.012	11.910	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	61	TRP	0	0.065	0.032	14.774	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	62	GLN	0	-0.008	0.007	18.283	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	63	THR	0	-0.016	-0.001	21.406	0.009	0.009	0.000	0.000	0.000	0.000
11	A	64	ASN	0	-0.009	-0.010	24.762	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	65	PHE	0	0.034	0.009	28.415	0.006	0.006	0.000	0.000	0.000	0.000
13	A	66	THR	0	0.006	0.012	31.881	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	67	LEU	0	-0.021	-0.013	34.000	0.003	0.003	0.000	0.000	0.000	0.000
15	A	68	GLU	-1	-0.849	-0.950	36.954	0.005	0.005	0.000	0.000	0.000	0.000
16	A	69	PRO	0	0.039	0.000	38.946	0.002	0.002	0.000	0.000	0.000	0.000
17	A	70	ARG	1	0.919	0.979	40.571	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	71	MET	0	0.019	0.017	37.097	0.002	0.002	0.000	0.000	0.000	0.000
19	A	72	ALA	0	0.017	0.028	41.021	0.001	0.001	0.000	0.000	0.000	0.000
20	A	73	PRO	0	0.014	-0.009	43.684	0.001	0.001	0.000	0.000	0.000	0.000
21	A	74	ARG	1	0.911	0.961	37.604	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	75	SER	0	0.079	0.043	39.083	0.002	0.002	0.000	0.000	0.000	0.000
23	A	76	TRP	0	0.022	0.037	35.816	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	77	LEU	0	0.018	0.006	32.628	0.003	0.003	0.000	0.000	0.000	0.000
25	A	78	ALA	0	-0.004	0.012	29.371	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	79	VAL	0	0.005	-0.014	26.169	0.006	0.006	0.000	0.000	0.000	0.000
27	A	80	THR	0	0.031	-0.010	21.443	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	81	VAL	0	-0.001	0.005	19.859	0.008	0.008	0.000	0.000	0.000	0.000
29	A	82	ASP	-1	-0.804	-0.903	15.262	0.097	0.097	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.088	-0.068	15.159	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	84	ALA	0	0.007	0.022	11.814	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	85	SER	0	-0.028	-0.035	13.630	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	86	SER	0	0.001	-0.018	15.715	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	87	ALA	0	-0.026	0.019	18.555	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	88	ILE	0	-0.016	-0.022	20.531	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	89	VAL	0	0.043	0.016	22.790	0.008	0.008	0.000	0.000	0.000	0.000
37	A	90	VAL	0	-0.009	-0.010	25.333	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	91	THR	0	-0.032	-0.032	28.887	0.005	0.005	0.000	0.000	0.000	0.000
39	A	92	GLN	0	-0.017	-0.024	31.635	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	93	HIS	0	0.014	0.041	32.531	0.003	0.003	0.000	0.000	0.000	0.000
41	A	94	GLY	0	0.001	-0.009	36.793	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	95	ARG	1	0.958	0.972	38.659	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	96	VAL	0	0.048	0.039	35.041	0.002	0.002	0.000	0.000	0.000	0.000
44	A	97	THR	0	-0.021	-0.014	35.590	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	98	SER	0	0.040	-0.011	32.941	0.000	0.000	0.000	0.000	0.000	0.000
46	A	99	VAL	0	0.024	0.016	32.244	0.002	0.002	0.000	0.000	0.000	0.000
47	A	100	ALA	0	-0.038	-0.002	33.142	0.003	0.003	0.000	0.000	0.000	0.000
48	A	101	ALA	0	0.059	0.025	29.128	0.003	0.003	0.000	0.000	0.000	0.000
49	A	102	GLN	0	0.034	0.006	28.492	0.000	0.000	0.000	0.000	0.000	0.000
50	A	103	HIS	0	0.015	0.007	28.702	0.006	0.006	0.000	0.000	0.000	0.000
51	A	104	HIS	0	-0.026	0.007	26.348	0.005	0.005	0.000	0.000	0.000	0.000
52	A	105	TRP	0	0.024	-0.011	23.908	0.005	0.005	0.000	0.000	0.000	0.000
53	A	106	ALA	0	-0.015	-0.002	24.493	0.009	0.009	0.000	0.000	0.000	0.000
54	A	107	THR	0	-0.012	-0.005	25.957	0.008	0.008	0.000	0.000	0.000	0.000
55	A	108	ALA	0	-0.001	-0.002	22.559	0.008	0.008	0.000	0.000	0.000	0.000
56	A	109	ILE	0	-0.035	-0.003	20.623	0.013	0.013	0.000	0.000	0.000	0.000
57	A	110	ALA	0	-0.043	-0.017	21.271	0.018	0.018	0.000	0.000	0.000	0.000
58	A	111	VAL	0	-0.036	-0.003	22.452	0.007	0.007	0.000	0.000	0.000	0.000
59	A	112	LEU	0	-0.022	-0.024	18.121	0.012	0.012	0.000	0.000	0.000	0.000
60	A	113	GLY	0	0.028	0.036	17.108	0.034	0.034	0.000	0.000	0.000	0.000
61	A	114	ARG	1	0.879	0.917	16.830	-0.138	-0.138	0.000	0.000	0.000	0.000
62	A	115	PRO	0	-0.003	0.018	14.706	0.031	0.031	0.000	0.000	0.000	0.000
63	A	116	LYS	1	0.884	0.925	10.716	-0.131	-0.131	0.000	0.000	0.000	0.000
64	A	117	ALA	0	0.028	0.004	14.159	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	118	ILE	0	0.008	0.008	16.806	0.008	0.008	0.000	0.000	0.000	0.000
66	A	119	LYS	1	0.890	0.983	17.573	0.102	0.102	0.000	0.000	0.000	0.000
67	A	120	THR	0	0.001	0.008	21.393	0.007	0.007	0.000	0.000	0.000	0.000
68	A	121	ASP	-1	-0.828	-0.915	25.130	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	122	ASN	0	0.023	-0.018	28.210	0.000	0.000	0.000	0.000	0.000	0.000
70	A	123	GLY	0	0.029	0.032	30.778	0.002	0.002	0.000	0.000	0.000	0.000
71	A	124	SER	0	0.038	-0.001	32.018	0.000	0.000	0.000	0.000	0.000	0.000
72	A	125	CYS	0	-0.068	-0.023	31.288	0.001	0.001	0.000	0.000	0.000	0.000
73	A	126	PHE	0	0.027	0.003	27.817	0.005	0.005	0.000	0.000	0.000	0.000
74	A	127	THR	0	0.007	0.004	28.655	0.000	0.000	0.000	0.000	0.000	0.000
75	A	128	SER	0	0.022	0.040	30.773	0.000	0.000	0.000	0.000	0.000	0.000
76	A	129	LYS	1	1.009	0.984	31.699	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	130	SER	0	-0.035	-0.025	32.137	0.001	0.001	0.000	0.000	0.000	0.000
78	A	131	THR	0	0.008	0.003	27.862	0.004	0.004	0.000	0.000	0.000	0.000
79	A	132	ARG	1	0.946	0.993	27.441	0.022	0.022	0.000	0.000	0.000	0.000
80	A	133	GLU	-1	-0.915	-0.956	27.118	0.012	0.012	0.000	0.000	0.000	0.000
81	A	134	TRP	0	-0.035	-0.013	24.320	0.003	0.003	0.000	0.000	0.000	0.000
82	A	135	LEU	0	0.020	-0.009	22.686	0.007	0.007	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.009	0.014	23.120	0.003	0.003	0.000	0.000	0.000	0.000
84	A	137	ARG	1	0.934	0.979	24.181	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	138	TRP	0	0.009	0.005	21.466	0.012	0.012	0.000	0.000	0.000	0.000
86	A	139	GLY	0	-0.019	0.009	20.156	0.013	0.013	0.000	0.000	0.000	0.000
87	A	140	ILE	0	-0.080	-0.030	18.116	0.003	0.003	0.000	0.000	0.000	0.000
88	A	141	ALA	0	0.008	0.011	17.101	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	142	HIS	0	-0.018	-0.038	19.102	0.005	0.005	0.000	0.000	0.000	0.000
90	A	143	THR	0	-0.023	0.004	19.306	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	144	THR	0	-0.010	-0.015	22.066	0.005	0.005	0.000	0.000	0.000	0.000
92	A	145	GLY	0	0.060	0.021	24.613	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	146	ILE	0	0.028	0.015	27.118	0.007	0.007	0.000	0.000	0.000	0.000
94	A	147	PRO	0	0.077	0.034	29.000	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	148	GLY	0	0.045	0.029	28.998	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	149	ASN	0	-0.048	-0.036	24.849	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	150	SER	0	0.111	0.032	25.022	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	151	GLN	0	-0.037	-0.021	21.070	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	152	GLY	0	-0.055	-0.046	21.004	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	153	GLN	0	-0.019	-0.035	21.988	0.017	0.017	0.000	0.000	0.000	0.000
101	A	154	ALA	0	0.066	0.050	24.006	0.006	0.006	0.000	0.000	0.000	0.000
102	A	155	MET	0	-0.036	-0.002	18.150	0.000	0.000	0.000	0.000	0.000	0.000
103	A	156	VAL	0	0.010	0.006	23.385	0.008	0.008	0.000	0.000	0.000	0.000
104	A	157	GLU	-1	-0.903	-0.943	25.288	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	158	ARG	1	0.925	0.970	24.786	0.022	0.022	0.000	0.000	0.000	0.000
106	A	159	ALA	0	0.015	0.001	25.092	0.005	0.005	0.000	0.000	0.000	0.000
107	A	160	ASN	0	-0.023	-0.014	27.168	0.000	0.000	0.000	0.000	0.000	0.000
108	A	161	ARG	1	0.988	1.000	30.436	0.017	0.017	0.000	0.000	0.000	0.000
109	A	162	LEU	0	0.011	0.007	26.899	0.001	0.001	0.000	0.000	0.000	0.000
110	A	163	LEU	0	0.006	0.014	29.936	0.003	0.003	0.000	0.000	0.000	0.000
111	A	164	LYS	1	0.895	0.945	31.657	0.003	0.003	0.000	0.000	0.000	0.000
112	A	165	ASP	-1	-0.882	-0.938	34.130	0.001	0.001	0.000	0.000	0.000	0.000
113	A	166	LYS	1	0.941	0.968	32.118	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	167	ILE	0	-0.005	-0.001	34.581	0.002	0.002	0.000	0.000	0.000	0.000
115	A	168	ARG	1	0.896	0.953	37.116	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	169	VAL	0	-0.008	-0.004	37.974	0.000	0.000	0.000	0.000	0.000	0.000
117	A	170	LEU	0	-0.035	-0.023	35.311	0.001	0.001	0.000	0.000	0.000	0.000
118	A	171	ALA	0	0.003	0.005	39.761	0.001	0.001	0.000	0.000	0.000	0.000
119	A	172	GLU	-1	-0.950	-0.991	42.358	0.007	0.007	0.000	0.000	0.000	0.000
120	A	173	GLY	0	-0.028	-0.006	43.123	0.000	0.000	0.000	0.000	0.000	0.000
121	A	174	ASP	-1	-0.938	-0.958	42.939	0.024	0.024	0.000	0.000	0.000	0.000
122	A	175	GLY	0	-0.006	-0.004	45.739	0.000	0.000	0.000	0.000	0.000	0.000
123	A	176	PHE	0	-0.040	-0.038	44.361	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	177	MET	0	0.086	0.053	45.883	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	178	LYS	1	0.914	0.946	47.158	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	179	ARG	1	0.844	0.926	45.449	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	180	ILE	0	0.034	0.028	40.563	0.000	0.000	0.000	0.000	0.000	0.000
128	A	181	PRO	0	-0.012	-0.005	44.788	0.000	0.000	0.000	0.000	0.000	0.000
129	A	182	THR	0	0.070	0.010	44.287	0.001	0.001	0.000	0.000	0.000	0.000
130	A	183	SER	0	-0.011	0.000	43.411	0.001	0.001	0.000	0.000	0.000	0.000
131	A	184	LYS	1	0.966	0.990	43.080	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	185	GLN	0	-0.029	-0.017	39.859	0.002	0.002	0.000	0.000	0.000	0.000
133	A	186	GLY	0	0.010	0.017	37.304	0.001	0.001	0.000	0.000	0.000	0.000
134	A	187	GLU	-1	-0.867	-0.937	36.272	0.040	0.040	0.000	0.000	0.000	0.000
135	A	188	LEU	0	-0.034	-0.002	36.689	0.001	0.001	0.000	0.000	0.000	0.000
136	A	189	LEU	0	-0.018	-0.024	32.953	0.000	0.000	0.000	0.000	0.000	0.000
137	A	190	ALA	0	0.019	0.001	32.072	0.001	0.001	0.000	0.000	0.000	0.000
138	A	191	LYS	1	0.989	0.996	31.812	-0.029	-0.029	0.000	0.000	0.000	0.000
139	A	192	ALA	0	-0.010	-0.012	32.684	0.000	0.000	0.000	0.000	0.000	0.000
140	A	193	MET	0	-0.026	-0.002	25.472	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	194	TYR	0	0.002	-0.006	27.635	0.004	0.004	0.000	0.000	0.000	0.000
142	A	195	ALA	0	-0.020	-0.008	28.375	0.002	0.002	0.000	0.000	0.000	0.000
143	A	196	LEU	0	-0.054	-0.035	26.950	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	197	ASN	0	0.008	0.014	23.565	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	198	HIS	0	-0.020	0.011	23.727	0.001	0.001	0.000	0.000	0.000	0.000
146	A	199	PHE	0	-0.027	-0.004	22.288	-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:54:GLY)