FMO DATABASE

FMODB ID: G6LV1

Calculation Name: 3VZ9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZ9

Chain ID: B

ChEMBL ID:

UniProt ID: E1C4Y2

Base Structure: X-ray

Registration Date: 2023-06-21

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-804679.110156
FMO2-HF: Nuclear repulsion	761676.707323
FMO2-HF: Total energy	-43002.402833
FMO2-MP2: Total energy	-43127.393926

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(B:131:THR)

Summations of interaction energy for fragment #1(B:131:THR)

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.
-10.433	-4.355	2.28	-3.36	-4.997	-0.028

Interaction energy analysis for fragmet #1(B:131:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.012

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	B	133	GLU	-1	-0.822	-0.916	2.240	-12.176	-8.298	1.935	-2.565	-3.248	-0.029
4	B	134	ARG	1	0.972	0.981	3.004	-1.096	0.024	0.168	-0.428	-0.860	0.002
5	B	135	VAL	0	0.030	0.006	2.491	0.371	1.336	0.178	-0.361	-0.781	-0.001
6	B	136	GLU	-1	-0.795	-0.863	5.061	-0.398	-0.283	-0.001	-0.006	-0.108	0.000
7	B	137	ARG	1	0.768	0.855	7.587	1.508	1.508	0.000	0.000	0.000	0.000
8	B	138	LEU	0	-0.021	-0.007	6.129	0.302	0.302	0.000	0.000	0.000	0.000
9	B	139	CYS	0	0.022	0.021	9.370	0.168	0.168	0.000	0.000	0.000	0.000
10	B	140	LYS	1	0.981	0.988	11.384	0.611	0.611	0.000	0.000	0.000	0.000
11	B	141	SER	0	-0.035	-0.018	12.640	0.088	0.088	0.000	0.000	0.000	0.000
12	B	142	LYS	1	0.829	0.905	13.666	0.237	0.237	0.000	0.000	0.000	0.000
13	B	143	GLU	-1	-0.799	-0.900	15.500	-0.215	-0.215	0.000	0.000	0.000	0.000
14	B	144	LEU	0	-0.039	-0.023	16.991	0.027	0.027	0.000	0.000	0.000	0.000
15	B	145	PHE	0	-0.041	-0.027	16.741	0.030	0.030	0.000	0.000	0.000	0.000
16	B	146	GLU	-1	-0.850	-0.909	19.624	-0.115	-0.115	0.000	0.000	0.000	0.000
17	B	147	GLU	-1	-0.933	-0.965	21.544	-0.184	-0.184	0.000	0.000	0.000	0.000
18	B	148	ARG	1	0.881	0.928	21.156	0.210	0.210	0.000	0.000	0.000	0.000
19	B	149	LEU	0	-0.055	-0.028	22.360	0.012	0.012	0.000	0.000	0.000	0.000
20	B	150	GLY	0	0.014	0.028	25.356	0.011	0.011	0.000	0.000	0.000	0.000
21	B	151	LEU	0	-0.063	-0.032	23.624	0.013	0.013	0.000	0.000	0.000	0.000
22	B	152	GLU	-1	-0.744	-0.823	22.287	-0.080	-0.080	0.000	0.000	0.000	0.000
23	B	153	ILE	0	-0.009	-0.014	20.133	0.015	0.015	0.000	0.000	0.000	0.000
24	B	154	ARG	1	0.832	0.911	20.502	0.036	0.036	0.000	0.000	0.000	0.000
25	B	155	ARG	1	0.949	0.976	16.852	-0.050	-0.050	0.000	0.000	0.000	0.000
26	B	156	ILE	0	-0.042	-0.017	22.034	-0.009	-0.009	0.000	0.000	0.000	0.000
27	B	157	HIS	0	0.022	0.008	24.964	0.008	0.008	0.000	0.000	0.000	0.000
28	B	158	ASN	0	0.013	-0.008	27.220	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	159	GLU	-1	-0.903	-0.943	23.311	0.073	0.073	0.000	0.000	0.000	0.000
30	B	160	GLN	0	-0.021	0.009	25.001	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	161	LEU	0	-0.031	-0.023	20.742	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	162	GLN	0	0.050	0.027	24.543	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	163	PHE	0	0.006	0.001	23.484	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	164	ILE	0	-0.010	-0.022	26.022	0.004	0.004	0.000	0.000	0.000	0.000
35	B	165	PHE	0	-0.004	-0.014	27.080	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	166	ARG	1	0.888	0.929	26.433	0.074	0.074	0.000	0.000	0.000	0.000
37	B	167	HIS	0	-0.017	-0.019	27.350	0.007	0.007	0.000	0.000	0.000	0.000
38	B	168	ILE	0	-0.065	-0.016	32.219	0.002	0.002	0.000	0.000	0.000	0.000
39	B	169	ASP	-1	-0.793	-0.896	34.738	-0.035	-0.035	0.000	0.000	0.000	0.000
40	B	170	HIS	0	-0.019	-0.023	37.239	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	171	LYS	1	0.854	0.928	38.565	0.041	0.041	0.000	0.000	0.000	0.000
42	B	172	ASP	-1	-0.874	-0.939	37.218	-0.046	-0.046	0.000	0.000	0.000	0.000
43	B	173	PRO	0	-0.002	0.001	33.550	0.001	0.001	0.000	0.000	0.000	0.000
44	B	174	ASP	-1	-0.844	-0.922	30.991	-0.079	-0.079	0.000	0.000	0.000	0.000
45	B	175	LYS	1	0.807	0.914	32.826	0.034	0.034	0.000	0.000	0.000	0.000
46	B	176	PRO	0	-0.056	-0.026	31.497	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	177	TYR	0	-0.028	-0.034	32.279	0.006	0.006	0.000	0.000	0.000	0.000
48	B	178	MET	0	-0.001	-0.005	30.215	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	179	PHE	0	0.015	-0.001	28.485	0.003	0.003	0.000	0.000	0.000	0.000
50	B	180	THR	0	-0.038	-0.012	28.431	-0.004	-0.004	0.000	0.000	0.000	0.000
51	B	181	LEU	0	-0.035	-0.011	25.600	0.001	0.001	0.000	0.000	0.000	0.000
52	B	182	SER	0	0.044	0.015	27.148	0.002	0.002	0.000	0.000	0.000	0.000
53	B	183	ILE	0	-0.011	-0.002	25.035	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	184	ASN	0	0.017	0.005	28.240	0.007	0.007	0.000	0.000	0.000	0.000
55	B	185	GLU	-1	-0.876	-0.952	30.206	0.081	0.081	0.000	0.000	0.000	0.000
56	B	186	GLN	0	-0.094	-0.044	31.962	0.002	0.002	0.000	0.000	0.000	0.000
57	B	187	GLY	0	-0.024	-0.010	28.606	0.003	0.003	0.000	0.000	0.000	0.000
58	B	188	ASP	-1	-0.834	-0.916	28.999	0.050	0.050	0.000	0.000	0.000	0.000
59	B	189	TYR	0	-0.020	-0.011	25.644	0.000	0.000	0.000	0.000	0.000	0.000
60	B	190	GLU	-1	-0.839	-0.904	30.339	0.036	0.036	0.000	0.000	0.000	0.000
61	B	191	VAL	0	-0.008	-0.006	31.360	0.000	0.000	0.000	0.000	0.000	0.000
62	B	192	THR	0	-0.010	-0.011	31.566	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	193	SER	0	-0.010	-0.010	32.956	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	194	CYS	0	-0.048	-0.030	33.771	0.000	0.000	0.000	0.000	0.000	0.000
65	B	195	THR	0	-0.066	0.009	34.923	0.001	0.001	0.000	0.000	0.000	0.000
66	B	196	PRO	0	0.044	0.006	35.328	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	197	PRO	0	0.064	0.015	37.877	0.000	0.000	0.000	0.000	0.000	0.000
68	B	198	LEU	0	0.010	0.001	35.943	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	199	ASP	-1	-0.892	-0.944	40.006	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	200	CYS	0	-0.044	-0.021	38.350	0.001	0.001	0.000	0.000	0.000	0.000
71	B	201	ILE	0	0.012	0.012	33.474	0.002	0.002	0.000	0.000	0.000	0.000
72	B	202	SER	0	0.041	0.009	36.889	0.002	0.002	0.000	0.000	0.000	0.000
73	B	203	GLU	-1	-0.915	-0.951	38.852	0.010	0.010	0.000	0.000	0.000	0.000
74	B	204	PHE	0	-0.015	-0.023	34.877	0.001	0.001	0.000	0.000	0.000	0.000
75	B	205	GLN	0	0.047	0.033	33.847	0.001	0.001	0.000	0.000	0.000	0.000
76	B	206	LEU	0	0.024	0.024	35.231	0.004	0.004	0.000	0.000	0.000	0.000
77	B	207	LYS	1	0.869	0.919	36.256	-0.014	-0.014	0.000	0.000	0.000	0.000
78	B	208	VAL	0	-0.055	-0.012	29.870	0.002	0.002	0.000	0.000	0.000	0.000
79	B	209	ARG	1	0.757	0.861	32.295	-0.036	-0.036	0.000	0.000	0.000	0.000
80	B	210	GLU	-1	-0.863	-0.902	34.142	0.026	0.026	0.000	0.000	0.000	0.000
81	B	211	THR	0	-0.083	-0.072	33.593	0.001	0.001	0.000	0.000	0.000	0.000
82	B	212	ASN	0	0.004	0.007	27.224	0.001	0.001	0.000	0.000	0.000	0.000
83	B	213	ASN	0	0.004	0.013	28.617	0.003	0.003	0.000	0.000	0.000	0.000
84	B	214	PHE	0	0.060	0.021	23.348	-0.007	-0.007	0.000	0.000	0.000	0.000
85	B	215	SER	0	0.003	0.000	25.764	-0.009	-0.009	0.000	0.000	0.000	0.000
86	B	216	ALA	0	0.030	0.005	27.064	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	217	PHE	0	0.024	0.026	28.694	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	218	ILE	0	0.020	0.016	25.749	-0.005	-0.005	0.000	0.000	0.000	0.000
89	B	219	ALA	0	-0.007	-0.006	29.090	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	220	ASN	0	-0.077	-0.060	30.747	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	221	ILE	0	0.032	0.031	30.984	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	222	ARG	1	0.906	0.971	30.027	0.046	0.046	0.000	0.000	0.000	0.000
93	B	223	LYS	1	0.955	0.974	32.628	0.013	0.013	0.000	0.000	0.000	0.000
94	B	224	ALA	0	0.016	0.007	35.787	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	225	PHE	0	0.040	0.013	32.419	0.000	0.000	0.000	0.000	0.000	0.000
96	B	226	THR	0	-0.043	-0.021	35.463	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	227	ALA	0	-0.043	-0.018	37.745	0.000	0.000	0.000	0.000	0.000	0.000
98	B	228	LEU	0	0.032	0.013	39.547	0.000	0.000	0.000	0.000	0.000	0.000
99	B	229	SER	0	0.048	0.032	38.839	0.000	0.000	0.000	0.000	0.000	0.000
100	B	230	PHE	0	-0.004	-0.004	40.968	0.000	0.000	0.000	0.000	0.000	0.000
101	B	231	LYS	1	0.869	0.934	43.521	0.019	0.019	0.000	0.000	0.000	0.000
102	B	232	GLN	0	-0.001	0.003	40.519	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	233	SER	0	-0.048	0.002	43.937	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:131:THR)