FMO DATABASE

FMODB ID: 1729Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-804091.979378
FMO2-HF: Nuclear repulsion	761090.040847
FMO2-HF: Total energy	-43001.938532
FMO2-MP2: Total energy	-43126.865486

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.
-5.119	0.258	0.613	-2.228	-3.76	-0.007

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 : 0.069 / q_NPA : 0.015

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	-0.820	-0.907	2.944	-7.227	-3.963	0.119	-1.414	-1.968	-0.006
4	B	134	ARG	1	0.956	0.978	2.892	-0.742	0.258	0.197	-0.378	-0.819	0.001
5	B	135	VAL	0	0.030	0.002	2.372	0.544	1.536	0.298	-0.428	-0.861	-0.002
6	B	136	GLU	-1	-0.914	-0.942	4.953	-0.345	-0.224	-0.001	-0.008	-0.112	0.000
7	B	137	ARG	1	0.897	0.939	7.606	1.374	1.374	0.000	0.000	0.000	0.000
8	B	138	LEU	0	-0.031	-0.011	6.429	0.292	0.292	0.000	0.000	0.000	0.000
9	B	139	CYS	0	0.011	0.019	9.281	0.175	0.175	0.000	0.000	0.000	0.000
10	B	140	LYS	1	0.992	0.990	11.284	0.547	0.547	0.000	0.000	0.000	0.000
11	B	141	SER	0	-0.038	-0.022	12.591	0.081	0.081	0.000	0.000	0.000	0.000
12	B	142	LYS	1	0.839	0.915	13.643	0.185	0.185	0.000	0.000	0.000	0.000
13	B	143	GLU	-1	-0.808	-0.910	15.426	-0.166	-0.166	0.000	0.000	0.000	0.000
14	B	144	LEU	0	-0.021	-0.014	16.853	0.021	0.021	0.000	0.000	0.000	0.000
15	B	145	PHE	0	-0.057	-0.033	16.885	0.026	0.026	0.000	0.000	0.000	0.000
16	B	146	GLU	-1	-0.854	-0.909	19.595	-0.085	-0.085	0.000	0.000	0.000	0.000
17	B	147	GLU	-1	-0.935	-0.968	21.481	-0.158	-0.158	0.000	0.000	0.000	0.000
18	B	148	ARG	1	0.867	0.920	20.694	0.188	0.188	0.000	0.000	0.000	0.000
19	B	149	LEU	0	-0.058	-0.032	22.559	0.010	0.010	0.000	0.000	0.000	0.000
20	B	150	GLY	0	0.017	0.036	25.323	0.010	0.010	0.000	0.000	0.000	0.000
21	B	151	LEU	0	-0.057	-0.030	23.673	0.012	0.012	0.000	0.000	0.000	0.000
22	B	152	GLU	-1	-0.829	-0.900	22.154	-0.057	-0.057	0.000	0.000	0.000	0.000
23	B	153	ILE	0	-0.012	-0.012	20.058	0.012	0.012	0.000	0.000	0.000	0.000
24	B	154	ARG	1	0.870	0.938	20.515	0.013	0.013	0.000	0.000	0.000	0.000
25	B	155	ARG	1	0.959	0.980	16.381	-0.108	-0.108	0.000	0.000	0.000	0.000
26	B	156	ILE	0	-0.037	-0.009	22.072	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	157	HIS	0	0.009	0.000	25.024	0.009	0.009	0.000	0.000	0.000	0.000
28	B	158	ASN	0	0.010	-0.013	27.270	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	159	GLU	-1	-0.897	-0.940	23.568	0.100	0.100	0.000	0.000	0.000	0.000
30	B	160	GLN	0	-0.006	0.024	25.116	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	161	LEU	0	-0.031	-0.024	20.739	0.001	0.001	0.000	0.000	0.000	0.000
32	B	162	GLN	0	0.046	0.030	24.627	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	163	PHE	0	0.005	0.002	23.605	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	164	ILE	0	-0.018	-0.022	26.045	0.002	0.002	0.000	0.000	0.000	0.000
35	B	165	PHE	0	0.001	-0.014	27.082	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	166	ARG	1	0.918	0.952	26.095	0.052	0.052	0.000	0.000	0.000	0.000
37	B	167	HIS	0	-0.011	-0.014	27.670	0.006	0.006	0.000	0.000	0.000	0.000
38	B	168	ILE	0	-0.094	-0.034	32.121	0.001	0.001	0.000	0.000	0.000	0.000
39	B	169	ASP	-1	-0.824	-0.910	34.734	-0.027	-0.027	0.000	0.000	0.000	0.000
40	B	170	HIS	0	-0.029	-0.031	36.966	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	171	LYS	1	0.848	0.922	38.524	0.032	0.032	0.000	0.000	0.000	0.000
42	B	172	ASP	-1	-0.894	-0.946	37.228	-0.034	-0.034	0.000	0.000	0.000	0.000
43	B	173	PRO	0	-0.001	0.003	33.510	0.001	0.001	0.000	0.000	0.000	0.000
44	B	174	ASP	-1	-0.838	-0.915	31.257	-0.061	-0.061	0.000	0.000	0.000	0.000
45	B	175	LYS	1	0.895	0.963	32.758	0.023	0.023	0.000	0.000	0.000	0.000
46	B	176	PRO	0	-0.064	-0.029	31.487	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	177	TYR	0	-0.026	-0.023	32.274	0.003	0.003	0.000	0.000	0.000	0.000
48	B	178	MET	0	-0.012	-0.008	29.903	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	179	PHE	0	0.014	-0.003	28.548	0.001	0.001	0.000	0.000	0.000	0.000
50	B	180	THR	0	-0.033	-0.014	28.639	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	181	LEU	0	-0.045	-0.015	25.966	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	182	SER	0	0.041	0.021	27.270	0.005	0.005	0.000	0.000	0.000	0.000
53	B	183	ILE	0	-0.011	-0.007	25.246	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	184	ASN	0	0.067	0.047	28.426	0.007	0.007	0.000	0.000	0.000	0.000
55	B	185	GLU	-1	-0.876	-0.960	30.417	0.090	0.090	0.000	0.000	0.000	0.000
56	B	186	GLN	0	-0.101	-0.049	32.112	0.001	0.001	0.000	0.000	0.000	0.000
57	B	187	GLY	0	-0.016	-0.003	28.814	0.002	0.002	0.000	0.000	0.000	0.000
58	B	188	ASP	-1	-0.900	-0.956	29.233	0.054	0.054	0.000	0.000	0.000	0.000
59	B	189	TYR	0	-0.026	-0.020	24.940	0.000	0.000	0.000	0.000	0.000	0.000
60	B	190	GLU	-1	-0.911	-0.959	30.531	0.041	0.041	0.000	0.000	0.000	0.000
61	B	191	VAL	0	-0.020	-0.019	31.505	0.001	0.001	0.000	0.000	0.000	0.000
62	B	192	THR	0	-0.009	-0.012	31.564	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	193	SER	0	-0.029	-0.007	33.424	-0.002	-0.002	0.000	0.000	0.000	0.000
64	B	194	CYS	0	-0.014	-0.018	33.854	0.000	0.000	0.000	0.000	0.000	0.000
65	B	195	THR	0	-0.065	0.009	34.970	0.001	0.001	0.000	0.000	0.000	0.000
66	B	196	PRO	0	0.025	-0.002	35.350	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	197	PRO	0	0.065	0.012	37.928	0.000	0.000	0.000	0.000	0.000	0.000
68	B	198	LEU	0	0.006	0.000	36.046	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	199	ASP	-1	-0.882	-0.939	40.091	0.003	0.003	0.000	0.000	0.000	0.000
70	B	200	CYS	0	-0.040	-0.016	38.520	0.000	0.000	0.000	0.000	0.000	0.000
71	B	201	ILE	0	0.007	0.008	33.527	0.001	0.001	0.000	0.000	0.000	0.000
72	B	202	SER	0	0.040	0.006	37.034	0.003	0.003	0.000	0.000	0.000	0.000
73	B	203	GLU	-1	-0.915	-0.944	39.018	0.012	0.012	0.000	0.000	0.000	0.000
74	B	204	PHE	0	-0.021	-0.029	34.991	0.001	0.001	0.000	0.000	0.000	0.000
75	B	205	GLN	0	0.048	0.030	34.386	0.002	0.002	0.000	0.000	0.000	0.000
76	B	206	LEU	0	0.003	0.016	35.426	0.004	0.004	0.000	0.000	0.000	0.000
77	B	207	LYS	1	0.985	0.987	36.617	-0.013	-0.013	0.000	0.000	0.000	0.000
78	B	208	VAL	0	-0.059	-0.015	30.043	0.001	0.001	0.000	0.000	0.000	0.000
79	B	209	ARG	1	0.878	0.939	32.518	-0.040	-0.040	0.000	0.000	0.000	0.000
80	B	210	GLU	-1	-0.931	-0.954	34.366	0.026	0.026	0.000	0.000	0.000	0.000
81	B	211	THR	0	-0.103	-0.074	33.688	0.000	0.000	0.000	0.000	0.000	0.000
82	B	212	ASN	0	0.021	0.016	27.497	0.001	0.001	0.000	0.000	0.000	0.000
83	B	213	ASN	0	-0.005	0.007	28.854	0.003	0.003	0.000	0.000	0.000	0.000
84	B	214	PHE	0	0.058	0.018	23.292	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	215	SER	0	-0.002	0.000	25.884	-0.007	-0.007	0.000	0.000	0.000	0.000
86	B	216	ALA	0	0.031	0.004	27.236	-0.006	-0.006	0.000	0.000	0.000	0.000
87	B	217	PHE	0	0.018	0.024	28.870	-0.004	-0.004	0.000	0.000	0.000	0.000
88	B	218	ILE	0	0.027	0.018	25.936	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	219	ALA	0	-0.010	-0.009	29.219	-0.005	-0.005	0.000	0.000	0.000	0.000
90	B	220	ASN	0	-0.080	-0.059	30.866	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	221	ILE	0	0.028	0.030	31.094	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	222	ARG	1	0.972	1.003	30.123	0.036	0.036	0.000	0.000	0.000	0.000
93	B	223	LYS	1	0.942	0.967	32.703	0.011	0.011	0.000	0.000	0.000	0.000
94	B	224	ALA	0	0.017	0.005	35.869	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	225	PHE	0	0.036	0.009	32.571	0.000	0.000	0.000	0.000	0.000	0.000
96	B	226	THR	0	-0.020	-0.001	35.446	-0.002	-0.002	0.000	0.000	0.000	0.000
97	B	227	ALA	0	-0.059	-0.028	37.784	0.000	0.000	0.000	0.000	0.000	0.000
98	B	228	LEU	0	0.018	0.006	39.512	0.000	0.000	0.000	0.000	0.000	0.000
99	B	229	SER	0	-0.009	0.002	38.869	0.000	0.000	0.000	0.000	0.000	0.000
100	B	230	PHE	0	0.031	0.007	40.981	0.000	0.000	0.000	0.000	0.000	0.000
101	B	231	LYS	1	0.882	0.940	43.538	0.013	0.013	0.000	0.000	0.000	0.000
102	B	232	GLN	0	-0.012	-0.006	40.831	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	233	SER	0	-0.044	0.005	43.918	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)