FMO DATABASE

FMODB ID: 858QY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-805701.127884
FMO2-HF: Nuclear repulsion	762698.379181
FMO2-HF: Total energy	-43002.748703
FMO2-MP2: Total energy	-43127.761227

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.
-9.559	-7.12	6.571	-3.911	-5.098	-0.035

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 : 0.057 / 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

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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	-0.773	-0.877	1.943	-11.785	-11.408	6.446	-3.223	-3.600	-0.037
4	B	134	ARG	1	0.985	0.991	2.983	-1.028	0.276	0.102	-0.488	-0.918	0.003
5	B	135	VAL	0	0.029	0.014	2.992	0.632	1.274	0.024	-0.195	-0.470	-0.001
6	B	136	GLU	-1	-0.747	-0.836	5.391	-0.330	-0.214	-0.001	-0.005	-0.110	0.000
7	B	137	ARG	1	0.756	0.849	7.720	1.494	1.494	0.000	0.000	0.000	0.000
8	B	138	LEU	0	0.003	-0.002	6.111	0.285	0.285	0.000	0.000	0.000	0.000
9	B	139	CYS	0	0.019	0.009	9.366	0.169	0.169	0.000	0.000	0.000	0.000
10	B	140	LYS	1	0.907	0.945	11.387	0.754	0.754	0.000	0.000	0.000	0.000
11	B	141	SER	0	-0.031	-0.016	12.569	0.090	0.090	0.000	0.000	0.000	0.000
12	B	142	LYS	1	0.823	0.900	13.769	0.252	0.252	0.000	0.000	0.000	0.000
13	B	143	GLU	-1	-0.804	-0.894	15.730	-0.229	-0.229	0.000	0.000	0.000	0.000
14	B	144	LEU	0	-0.052	-0.024	17.103	0.030	0.030	0.000	0.000	0.000	0.000
15	B	145	PHE	0	-0.023	-0.022	16.727	0.032	0.032	0.000	0.000	0.000	0.000
16	B	146	GLU	-1	-0.838	-0.904	19.822	-0.127	-0.127	0.000	0.000	0.000	0.000
17	B	147	GLU	-1	-0.806	-0.911	21.653	-0.196	-0.196	0.000	0.000	0.000	0.000
18	B	148	ARG	1	0.773	0.885	21.982	0.215	0.215	0.000	0.000	0.000	0.000
19	B	149	LEU	0	-0.032	-0.013	22.415	0.013	0.013	0.000	0.000	0.000	0.000
20	B	150	GLY	0	0.007	0.023	25.709	0.011	0.011	0.000	0.000	0.000	0.000
21	B	151	LEU	0	-0.063	-0.043	23.785	0.013	0.013	0.000	0.000	0.000	0.000
22	B	152	GLU	-1	-0.737	-0.814	22.738	-0.089	-0.089	0.000	0.000	0.000	0.000
23	B	153	ILE	0	-0.031	-0.024	20.398	0.016	0.016	0.000	0.000	0.000	0.000
24	B	154	ARG	1	0.826	0.898	21.021	0.043	0.043	0.000	0.000	0.000	0.000
25	B	155	ARG	1	0.900	0.951	17.923	-0.022	-0.022	0.000	0.000	0.000	0.000
26	B	156	ILE	0	-0.047	-0.015	22.527	-0.009	-0.009	0.000	0.000	0.000	0.000
27	B	157	HIS	0	0.047	0.022	25.460	0.006	0.006	0.000	0.000	0.000	0.000
28	B	158	ASN	0	-0.004	-0.016	27.705	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	159	GLU	-1	-0.855	-0.922	22.984	0.049	0.049	0.000	0.000	0.000	0.000
30	B	160	GLN	0	-0.008	0.028	25.189	0.000	0.000	0.000	0.000	0.000	0.000
31	B	161	LEU	0	-0.018	-0.023	20.768	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	162	GLN	0	0.060	0.034	24.803	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	163	PHE	0	-0.004	-0.010	23.352	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	164	ILE	0	-0.006	-0.020	26.284	0.005	0.005	0.000	0.000	0.000	0.000
35	B	165	PHE	0	-0.005	-0.015	27.482	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	166	ARG	1	0.851	0.920	27.154	0.082	0.082	0.000	0.000	0.000	0.000
37	B	167	HIS	0	-0.017	-0.028	27.502	0.008	0.008	0.000	0.000	0.000	0.000
38	B	168	ILE	0	-0.059	-0.008	32.363	0.003	0.003	0.000	0.000	0.000	0.000
39	B	169	ASP	-1	-0.764	-0.874	34.835	-0.037	-0.037	0.000	0.000	0.000	0.000
40	B	170	HIS	0	0.001	-0.007	37.148	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	171	LYS	1	0.788	0.878	39.103	0.046	0.046	0.000	0.000	0.000	0.000
42	B	172	ASP	-1	-0.851	-0.921	36.821	-0.053	-0.053	0.000	0.000	0.000	0.000
43	B	173	PRO	0	0.001	-0.009	33.435	0.001	0.001	0.000	0.000	0.000	0.000
44	B	174	ASP	-1	-0.828	-0.922	30.751	-0.085	-0.085	0.000	0.000	0.000	0.000
45	B	175	LYS	1	0.821	0.926	32.818	0.037	0.037	0.000	0.000	0.000	0.000
46	B	176	PRO	0	-0.035	-0.003	31.761	0.000	0.000	0.000	0.000	0.000	0.000
47	B	177	TYR	0	-0.026	-0.038	32.631	0.007	0.007	0.000	0.000	0.000	0.000
48	B	178	MET	0	-0.013	-0.014	30.645	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	179	PHE	0	0.004	-0.006	28.606	0.004	0.004	0.000	0.000	0.000	0.000
50	B	180	THR	0	-0.028	-0.006	28.624	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	181	LEU	0	-0.019	-0.003	26.053	0.002	0.002	0.000	0.000	0.000	0.000
52	B	182	SER	0	0.017	0.003	27.444	0.000	0.000	0.000	0.000	0.000	0.000
53	B	183	ILE	0	-0.010	-0.005	25.002	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	184	ASN	0	0.034	0.017	28.173	0.007	0.007	0.000	0.000	0.000	0.000
55	B	185	GLU	-1	-0.880	-0.953	30.389	0.066	0.066	0.000	0.000	0.000	0.000
56	B	186	GLN	0	-0.105	-0.052	32.468	0.000	0.000	0.000	0.000	0.000	0.000
57	B	187	GLY	0	-0.034	-0.008	28.506	0.003	0.003	0.000	0.000	0.000	0.000
58	B	188	ASP	-1	-0.836	-0.919	28.822	0.042	0.042	0.000	0.000	0.000	0.000
59	B	189	TYR	0	-0.024	-0.022	26.000	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	190	GLU	-1	-0.835	-0.888	30.528	0.028	0.028	0.000	0.000	0.000	0.000
61	B	191	VAL	0	-0.014	-0.012	31.526	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	192	THR	0	-0.019	-0.023	31.747	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	193	SER	0	-0.002	-0.004	33.382	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	194	CYS	0	-0.063	-0.035	33.853	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	195	THR	0	-0.071	-0.008	35.242	0.001	0.001	0.000	0.000	0.000	0.000
66	B	196	PRO	0	0.069	0.030	35.448	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	197	PRO	0	0.053	0.009	37.827	0.000	0.000	0.000	0.000	0.000	0.000
68	B	198	LEU	0	0.028	0.005	36.006	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	199	ASP	-1	-0.910	-0.944	40.035	-0.006	-0.006	0.000	0.000	0.000	0.000
70	B	200	CYS	0	-0.020	-0.005	38.618	0.001	0.001	0.000	0.000	0.000	0.000
71	B	201	ILE	0	0.008	0.006	33.615	0.002	0.002	0.000	0.000	0.000	0.000
72	B	202	SER	0	0.034	0.008	36.858	0.002	0.002	0.000	0.000	0.000	0.000
73	B	203	GLU	-1	-0.894	-0.944	39.024	0.008	0.008	0.000	0.000	0.000	0.000
74	B	204	PHE	0	-0.027	-0.027	34.845	0.001	0.001	0.000	0.000	0.000	0.000
75	B	205	GLN	0	0.050	0.032	33.894	0.001	0.001	0.000	0.000	0.000	0.000
76	B	206	LEU	0	0.009	0.019	35.190	0.004	0.004	0.000	0.000	0.000	0.000
77	B	207	LYS	1	0.850	0.907	35.853	-0.010	-0.010	0.000	0.000	0.000	0.000
78	B	208	VAL	0	-0.049	-0.005	29.763	0.002	0.002	0.000	0.000	0.000	0.000
79	B	209	ARG	1	0.763	0.846	32.095	-0.027	-0.027	0.000	0.000	0.000	0.000
80	B	210	GLU	-1	-0.856	-0.912	34.168	0.022	0.022	0.000	0.000	0.000	0.000
81	B	211	THR	0	-0.059	-0.054	33.387	0.001	0.001	0.000	0.000	0.000	0.000
82	B	212	ASN	0	0.021	0.025	26.529	0.001	0.001	0.000	0.000	0.000	0.000
83	B	213	ASN	0	0.014	0.016	28.205	0.001	0.001	0.000	0.000	0.000	0.000
84	B	214	PHE	0	0.054	0.008	23.701	-0.007	-0.007	0.000	0.000	0.000	0.000
85	B	215	SER	0	-0.013	0.002	25.874	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	216	ALA	0	0.029	0.003	27.137	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	217	PHE	0	0.010	0.021	28.735	-0.004	-0.004	0.000	0.000	0.000	0.000
88	B	218	ILE	0	0.031	0.020	25.663	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	219	ALA	0	-0.002	0.002	28.966	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	220	ASN	0	-0.042	-0.049	30.698	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	221	ILE	0	0.039	0.041	31.050	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	222	ARG	1	0.874	0.961	29.821	0.053	0.053	0.000	0.000	0.000	0.000
93	B	223	LYS	1	0.912	0.962	32.459	0.013	0.013	0.000	0.000	0.000	0.000
94	B	224	ALA	0	0.009	0.008	35.576	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	225	PHE	0	0.037	0.010	32.444	0.000	0.000	0.000	0.000	0.000	0.000
96	B	226	THR	0	-0.025	-0.017	35.172	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	227	ALA	0	-0.040	-0.024	37.606	0.000	0.000	0.000	0.000	0.000	0.000
98	B	228	LEU	0	0.029	0.016	39.675	0.001	0.001	0.000	0.000	0.000	0.000
99	B	229	SER	0	0.057	0.033	38.883	0.000	0.000	0.000	0.000	0.000	0.000
100	B	230	PHE	0	-0.039	-0.024	41.010	0.000	0.000	0.000	0.000	0.000	0.000
101	B	231	LYS	1	0.828	0.915	43.778	0.022	0.022	0.000	0.000	0.000	0.000
102	B	232	GLN	0	0.010	0.014	40.403	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	233	SER	0	-0.027	0.011	44.142	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)