FMO DATABASE

FMODB ID: V5N51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1317239.567453
FMO2-HF: Nuclear repulsion	1261275.648496
FMO2-HF: Total energy	-55963.918957
FMO2-MP2: Total energy	-56127.426196

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.
-3.166	-0.937	0.002	-1.194	-1.038	0.001

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 : 0.016 / 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	-0.012	0.009	3.420	-2.479	-0.326	0.003	-1.173	-0.983	0.001
4	A	57	PRO	0	0.006	0.002	4.288	-0.788	-0.712	-0.001	-0.021	-0.055	0.000
5	A	58	LEU	0	0.016	0.007	7.182	0.166	0.166	0.000	0.000	0.000	0.000
6	A	59	GLN	0	0.038	0.013	8.188	-0.100	-0.100	0.000	0.000	0.000	0.000
7	A	60	ILE	0	0.021	0.016	11.896	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	61	TRP	0	0.057	0.036	14.764	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	62	GLN	0	0.007	0.006	18.268	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	63	THR	0	-0.019	-0.012	21.391	0.009	0.009	0.000	0.000	0.000	0.000
11	A	64	ASN	0	0.009	0.013	24.747	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	65	PHE	0	0.032	0.003	28.400	0.006	0.006	0.000	0.000	0.000	0.000
13	A	66	THR	0	0.028	0.029	31.864	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	67	LEU	0	-0.031	-0.017	33.978	0.003	0.003	0.000	0.000	0.000	0.000
15	A	68	GLU	-1	-0.820	-0.920	36.931	0.001	0.001	0.000	0.000	0.000	0.000
16	A	69	PRO	0	0.035	-0.002	38.917	0.002	0.002	0.000	0.000	0.000	0.000
17	A	70	ARG	1	0.855	0.930	40.905	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	71	MET	0	-0.004	0.009	36.785	0.002	0.002	0.000	0.000	0.000	0.000
19	A	72	ALA	0	0.023	0.033	40.990	0.001	0.001	0.000	0.000	0.000	0.000
20	A	73	PRO	0	0.025	0.008	43.656	0.001	0.001	0.000	0.000	0.000	0.000
21	A	74	ARG	1	0.871	0.934	37.329	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	75	SER	0	0.067	0.032	39.058	0.002	0.002	0.000	0.000	0.000	0.000
23	A	76	TRP	0	0.027	0.035	36.028	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	77	LEU	0	0.021	0.009	32.617	0.003	0.003	0.000	0.000	0.000	0.000
25	A	78	ALA	0	0.000	0.014	29.437	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	79	VAL	0	-0.005	-0.019	26.242	0.006	0.006	0.000	0.000	0.000	0.000
27	A	80	THR	0	0.040	-0.008	21.473	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	81	VAL	0	-0.006	0.001	19.869	0.008	0.008	0.000	0.000	0.000	0.000
29	A	82	ASP	-1	-0.774	-0.864	15.215	0.067	0.067	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.092	-0.077	15.215	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	84	ALA	0	0.001	0.021	11.739	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	85	SER	0	-0.037	-0.062	13.591	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	86	SER	0	-0.041	-0.029	15.668	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	87	ALA	0	-0.001	0.020	18.512	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	88	ILE	0	-0.035	-0.033	20.488	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	89	VAL	0	0.053	0.014	22.726	0.009	0.009	0.000	0.000	0.000	0.000
37	A	90	VAL	0	-0.011	-0.011	25.300	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	91	THR	0	-0.021	-0.015	28.857	0.005	0.005	0.000	0.000	0.000	0.000
39	A	92	GLN	0	0.024	0.005	31.609	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	93	HIS	0	0.005	0.017	32.280	0.003	0.003	0.000	0.000	0.000	0.000
41	A	94	GLY	0	0.008	0.000	36.774	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	95	ARG	1	0.955	0.970	38.642	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	96	VAL	0	0.040	0.036	35.110	0.002	0.002	0.000	0.000	0.000	0.000
44	A	97	THR	0	-0.009	-0.007	35.617	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	98	SER	0	0.044	-0.001	32.949	0.000	0.000	0.000	0.000	0.000	0.000
46	A	99	VAL	0	0.019	0.013	32.243	0.002	0.002	0.000	0.000	0.000	0.000
47	A	100	ALA	0	-0.038	0.000	33.137	0.003	0.003	0.000	0.000	0.000	0.000
48	A	101	ALA	0	0.067	0.025	29.142	0.003	0.003	0.000	0.000	0.000	0.000
49	A	102	GLN	0	0.036	0.023	28.485	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	103	HIS	0	0.018	0.008	28.697	0.006	0.006	0.000	0.000	0.000	0.000
51	A	104	HIS	0	-0.013	0.020	26.421	0.003	0.003	0.000	0.000	0.000	0.000
52	A	105	TRP	0	0.014	-0.015	23.945	0.005	0.005	0.000	0.000	0.000	0.000
53	A	106	ALA	0	-0.016	-0.001	24.482	0.008	0.008	0.000	0.000	0.000	0.000
54	A	107	THR	0	-0.012	-0.012	25.943	0.008	0.008	0.000	0.000	0.000	0.000
55	A	108	ALA	0	0.003	0.003	22.571	0.008	0.008	0.000	0.000	0.000	0.000
56	A	109	ILE	0	-0.032	-0.006	20.565	0.012	0.012	0.000	0.000	0.000	0.000
57	A	110	ALA	0	-0.047	-0.016	21.253	0.018	0.018	0.000	0.000	0.000	0.000
58	A	111	VAL	0	-0.029	-0.005	22.487	0.007	0.007	0.000	0.000	0.000	0.000
59	A	112	LEU	0	-0.019	-0.017	18.090	0.012	0.012	0.000	0.000	0.000	0.000
60	A	113	GLY	0	0.024	0.033	17.087	0.033	0.033	0.000	0.000	0.000	0.000
61	A	114	ARG	1	0.879	0.909	16.984	-0.133	-0.133	0.000	0.000	0.000	0.000
62	A	115	PRO	0	-0.014	0.018	14.696	0.028	0.028	0.000	0.000	0.000	0.000
63	A	116	LYS	1	0.902	0.936	10.764	-0.113	-0.113	0.000	0.000	0.000	0.000
64	A	117	ALA	0	0.019	-0.001	14.170	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	118	ILE	0	0.000	0.000	16.814	0.006	0.006	0.000	0.000	0.000	0.000
66	A	119	LYS	1	0.824	0.943	17.990	0.113	0.113	0.000	0.000	0.000	0.000
67	A	120	THR	0	0.032	0.005	21.392	0.008	0.008	0.000	0.000	0.000	0.000
68	A	121	ASP	-1	-0.861	-0.944	25.128	-0.036	-0.036	0.000	0.000	0.000	0.000
69	A	122	ASN	0	-0.008	-0.018	28.210	0.000	0.000	0.000	0.000	0.000	0.000
70	A	123	GLY	0	0.084	0.058	30.783	0.002	0.002	0.000	0.000	0.000	0.000
71	A	124	SER	0	0.034	0.001	32.023	0.000	0.000	0.000	0.000	0.000	0.000
72	A	125	CYS	0	-0.055	-0.017	31.289	0.001	0.001	0.000	0.000	0.000	0.000
73	A	126	PHE	0	0.026	0.008	27.846	0.005	0.005	0.000	0.000	0.000	0.000
74	A	127	THR	0	0.003	0.002	28.665	0.000	0.000	0.000	0.000	0.000	0.000
75	A	128	SER	0	-0.004	0.023	30.786	0.001	0.001	0.000	0.000	0.000	0.000
76	A	129	LYS	1	0.945	0.952	31.715	0.000	0.000	0.000	0.000	0.000	0.000
77	A	130	SER	0	-0.021	-0.030	32.155	0.002	0.002	0.000	0.000	0.000	0.000
78	A	131	THR	0	0.008	-0.006	27.832	0.004	0.004	0.000	0.000	0.000	0.000
79	A	132	ARG	1	0.926	0.980	27.448	0.029	0.029	0.000	0.000	0.000	0.000
80	A	133	GLU	-1	-0.881	-0.921	27.139	0.010	0.010	0.000	0.000	0.000	0.000
81	A	134	TRP	0	-0.009	-0.011	24.351	0.003	0.003	0.000	0.000	0.000	0.000
82	A	135	LEU	0	0.018	-0.006	22.679	0.007	0.007	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.001	0.011	23.138	0.003	0.003	0.000	0.000	0.000	0.000
84	A	137	ARG	1	0.934	0.971	24.206	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	138	TRP	0	0.016	0.010	21.612	0.013	0.013	0.000	0.000	0.000	0.000
86	A	139	GLY	0	-0.027	0.007	20.180	0.013	0.013	0.000	0.000	0.000	0.000
87	A	140	ILE	0	-0.082	-0.032	18.324	0.002	0.002	0.000	0.000	0.000	0.000
88	A	141	ALA	0	0.014	0.013	17.153	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	142	HIS	0	0.004	-0.011	19.123	0.003	0.003	0.000	0.000	0.000	0.000
90	A	143	THR	0	-0.003	0.003	18.877	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	144	THR	0	-0.039	-0.027	22.080	0.004	0.004	0.000	0.000	0.000	0.000
92	A	145	GLY	0	0.066	0.030	24.622	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	146	ILE	0	0.028	0.014	27.123	0.007	0.007	0.000	0.000	0.000	0.000
94	A	147	PRO	0	0.076	0.024	28.996	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	148	GLY	0	0.041	0.029	28.981	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	149	ASN	0	-0.057	-0.028	24.851	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	150	SER	0	0.091	0.023	25.104	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	151	GLN	0	0.021	0.010	20.769	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	152	GLY	0	-0.005	-0.015	20.993	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	153	GLN	0	-0.050	-0.043	21.979	0.017	0.017	0.000	0.000	0.000	0.000
101	A	154	ALA	0	0.053	0.049	23.962	0.007	0.007	0.000	0.000	0.000	0.000
102	A	155	MET	0	-0.040	-0.006	18.194	0.002	0.002	0.000	0.000	0.000	0.000
103	A	156	VAL	0	0.022	0.014	23.357	0.009	0.009	0.000	0.000	0.000	0.000
104	A	157	GLU	-1	-0.897	-0.940	25.262	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	158	ARG	1	0.940	0.973	24.606	0.034	0.034	0.000	0.000	0.000	0.000
106	A	159	ALA	0	0.004	0.000	25.045	0.005	0.005	0.000	0.000	0.000	0.000
107	A	160	ASN	0	-0.023	-0.020	27.132	0.004	0.004	0.000	0.000	0.000	0.000
108	A	161	ARG	1	0.932	0.966	30.403	0.021	0.021	0.000	0.000	0.000	0.000
109	A	162	LEU	0	0.029	0.013	26.984	0.002	0.002	0.000	0.000	0.000	0.000
110	A	163	LEU	0	0.001	0.011	29.854	0.004	0.004	0.000	0.000	0.000	0.000
111	A	164	LYS	1	0.849	0.912	31.617	0.008	0.008	0.000	0.000	0.000	0.000
112	A	165	ASP	-1	-0.822	-0.894	34.122	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	166	LYS	1	0.945	0.970	31.887	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	167	ILE	0	-0.002	-0.004	34.386	0.002	0.002	0.000	0.000	0.000	0.000
115	A	168	ARG	1	0.831	0.920	37.074	0.001	0.001	0.000	0.000	0.000	0.000
116	A	169	VAL	0	0.003	0.001	37.928	0.001	0.001	0.000	0.000	0.000	0.000
117	A	170	LEU	0	-0.034	-0.022	35.188	0.001	0.001	0.000	0.000	0.000	0.000
118	A	171	ALA	0	0.009	0.008	39.713	0.001	0.001	0.000	0.000	0.000	0.000
119	A	172	GLU	-1	-0.840	-0.928	42.314	0.003	0.003	0.000	0.000	0.000	0.000
120	A	173	GLY	0	-0.015	-0.001	43.075	0.000	0.000	0.000	0.000	0.000	0.000
121	A	174	ASP	-1	-0.926	-0.962	42.529	0.021	0.021	0.000	0.000	0.000	0.000
122	A	175	GLY	0	0.014	0.013	45.691	0.000	0.000	0.000	0.000	0.000	0.000
123	A	176	PHE	0	-0.049	-0.036	44.422	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	177	MET	0	0.057	0.030	45.840	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	178	LYS	1	0.928	0.954	47.080	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	179	ARG	1	0.817	0.893	45.413	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	180	ILE	0	0.030	0.022	40.593	0.000	0.000	0.000	0.000	0.000	0.000
128	A	181	PRO	0	0.027	0.016	44.750	0.000	0.000	0.000	0.000	0.000	0.000
129	A	182	THR	0	0.076	0.022	44.355	0.001	0.001	0.000	0.000	0.000	0.000
130	A	183	SER	0	-0.009	0.009	43.377	0.001	0.001	0.000	0.000	0.000	0.000
131	A	184	LYS	1	0.873	0.929	43.009	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	185	GLN	0	-0.016	-0.008	39.840	0.002	0.002	0.000	0.000	0.000	0.000
133	A	186	GLY	0	0.008	0.013	37.269	0.001	0.001	0.000	0.000	0.000	0.000
134	A	187	GLU	-1	-0.807	-0.899	36.234	0.033	0.033	0.000	0.000	0.000	0.000
135	A	188	LEU	0	-0.035	-0.002	36.646	0.001	0.001	0.000	0.000	0.000	0.000
136	A	189	LEU	0	-0.003	-0.021	32.848	0.000	0.000	0.000	0.000	0.000	0.000
137	A	190	ALA	0	0.015	0.001	32.032	0.001	0.001	0.000	0.000	0.000	0.000
138	A	191	LYS	1	0.940	0.979	31.768	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	192	ALA	0	-0.004	-0.009	32.638	0.000	0.000	0.000	0.000	0.000	0.000
140	A	193	MET	0	-0.011	0.010	25.291	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	194	TYR	0	0.024	0.016	27.588	0.004	0.004	0.000	0.000	0.000	0.000
142	A	195	ALA	0	-0.018	-0.008	28.323	0.001	0.001	0.000	0.000	0.000	0.000
143	A	196	LEU	0	-0.058	-0.033	26.898	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	197	ASN	0	-0.033	-0.003	23.219	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	198	HIS	0	0.014	0.021	23.673	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	199	PHE	0	-0.064	-0.024	22.249	-0.010	-0.010	0.000	0.000	0.000	0.000

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