FMO DATABASE

FMODB ID: 14L6Z

Calculation Name: 3V53-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V53

Chain ID: A

ChEMBL ID:

UniProt ID: P49756

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-970164.731539
FMO2-HF: Nuclear repulsion	923383.83618
FMO2-HF: Total energy	-46780.89536
FMO2-MP2: Total energy	-46916.156842

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:729:HIS)

Summations of interaction energy for fragment #1(A:729:HIS)

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.
-29.988	-23.582	4.39	-3.963	-6.835	0.019

Interaction energy analysis for fragmet #1(A:729:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : 0.022

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	731	HIS	0	0.139	0.074	3.907	-3.575	-2.137	-0.006	-0.635	-0.797	0.001
4	A	732	HIS	0	-0.042	0.001	2.164	-2.309	-0.810	2.140	-1.716	-1.924	0.006
5	A	733	MET	0	0.072	0.036	2.366	-5.789	-3.640	2.243	-1.268	-3.124	0.013
6	A	734	LYS	1	0.828	0.894	4.711	-3.151	-3.025	-0.001	-0.025	-0.101	0.000
7	A	735	ARG	1	0.883	0.952	6.082	-5.797	-5.797	0.000	0.000	0.000	0.000
8	A	736	LYS	1	0.895	0.935	6.746	-2.766	-2.766	0.000	0.000	0.000	0.000
9	A	737	HIS	0	0.060	0.037	6.931	-0.208	-0.208	0.000	0.000	0.000	0.000
10	A	738	ILE	0	0.024	0.020	9.660	-0.345	-0.345	0.000	0.000	0.000	0.000
11	A	739	LYS	1	0.820	0.889	12.178	-0.410	-0.410	0.000	0.000	0.000	0.000
12	A	740	SER	0	0.031	0.003	10.981	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	741	LEU	0	0.002	0.005	7.255	-0.159	-0.159	0.000	0.000	0.000	0.000
14	A	742	ILE	0	-0.026	-0.015	11.793	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	743	GLU	-1	-0.795	-0.881	15.187	0.083	0.083	0.000	0.000	0.000	0.000
16	A	744	LYS	1	0.786	0.901	12.873	0.659	0.659	0.000	0.000	0.000	0.000
17	A	745	ILE	0	-0.043	-0.012	13.971	-0.050	-0.050	0.000	0.000	0.000	0.000
18	A	746	PRO	0	0.001	0.008	17.761	0.064	0.064	0.000	0.000	0.000	0.000
19	A	747	THR	0	-0.018	-0.022	21.602	0.001	0.001	0.000	0.000	0.000	0.000
20	A	748	ALA	0	0.018	0.030	23.898	0.015	0.015	0.000	0.000	0.000	0.000
21	A	749	LYS	1	0.854	0.912	25.411	0.103	0.103	0.000	0.000	0.000	0.000
22	A	750	PRO	0	0.001	0.005	26.053	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	751	GLU	-1	-0.837	-0.938	24.475	-0.179	-0.179	0.000	0.000	0.000	0.000
24	A	752	LEU	0	-0.066	-0.025	19.918	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	753	PHE	0	0.006	-0.036	21.747	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	754	ALA	0	-0.011	0.010	24.083	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	755	TYR	0	-0.021	-0.011	14.573	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	756	PRO	0	-0.009	0.003	18.273	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	757	LEU	0	-0.041	-0.018	14.901	-0.121	-0.121	0.000	0.000	0.000	0.000
30	A	758	ASP	-1	-0.775	-0.874	12.701	-1.582	-1.582	0.000	0.000	0.000	0.000
31	A	759	TRP	0	0.063	0.006	13.770	-0.192	-0.192	0.000	0.000	0.000	0.000
32	A	760	SER	0	-0.047	-0.029	13.200	0.086	0.086	0.000	0.000	0.000	0.000
33	A	761	ILE	0	-0.076	-0.023	8.428	-0.267	-0.267	0.000	0.000	0.000	0.000
34	A	762	VAL	0	-0.025	-0.006	10.673	-0.138	-0.138	0.000	0.000	0.000	0.000
35	A	763	ASP	-1	-0.749	-0.871	10.037	-2.216	-2.216	0.000	0.000	0.000	0.000
36	A	764	SER	0	0.049	0.006	13.428	0.053	0.053	0.000	0.000	0.000	0.000
37	A	765	ILE	0	0.037	0.024	9.326	0.141	0.141	0.000	0.000	0.000	0.000
38	A	766	LEU	0	-0.050	-0.032	9.213	0.220	0.220	0.000	0.000	0.000	0.000
39	A	767	MET	0	0.019	0.010	11.582	0.278	0.278	0.000	0.000	0.000	0.000
40	A	768	GLU	-1	-0.916	-0.945	14.872	-0.190	-0.190	0.000	0.000	0.000	0.000
41	A	769	ARG	1	0.820	0.901	6.873	-0.157	-0.157	0.000	0.000	0.000	0.000
42	A	770	ARG	1	0.811	0.894	12.124	-0.089	-0.089	0.000	0.000	0.000	0.000
43	A	771	ILE	0	0.006	0.005	13.977	0.091	0.091	0.000	0.000	0.000	0.000
44	A	772	ARG	1	0.926	0.912	16.515	0.214	0.214	0.000	0.000	0.000	0.000
45	A	773	PRO	0	-0.020	-0.004	16.462	0.048	0.048	0.000	0.000	0.000	0.000
46	A	774	TRP	0	-0.051	-0.019	17.430	0.045	0.045	0.000	0.000	0.000	0.000
47	A	775	ILE	0	0.021	0.001	19.453	0.027	0.027	0.000	0.000	0.000	0.000
48	A	776	ASN	0	0.018	0.011	22.347	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	777	LYS	1	0.816	0.891	21.560	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	778	LYS	1	0.793	0.872	22.449	-0.120	-0.120	0.000	0.000	0.000	0.000
51	A	779	ILE	0	0.047	0.034	24.928	0.002	0.002	0.000	0.000	0.000	0.000
52	A	780	ILE	0	0.056	0.042	27.797	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	781	GLU	-1	-0.833	-0.900	26.509	0.193	0.193	0.000	0.000	0.000	0.000
54	A	782	TYR	0	-0.151	-0.095	27.568	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	783	ILE	0	0.019	0.004	31.953	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	784	GLY	0	0.037	0.037	33.116	0.000	0.000	0.000	0.000	0.000	0.000
57	A	785	GLU	-1	-0.998	-1.032	33.409	0.100	0.100	0.000	0.000	0.000	0.000
58	A	786	GLU	-1	-0.955	-0.951	34.570	0.008	0.008	0.000	0.000	0.000	0.000
59	A	787	GLU	-1	-0.780	-0.879	31.674	-0.072	-0.072	0.000	0.000	0.000	0.000
60	A	788	ALA	0	-0.045	-0.036	29.885	0.013	0.013	0.000	0.000	0.000	0.000
61	A	789	THR	0	-0.087	-0.050	29.207	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	790	LEU	0	0.024	0.011	29.580	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	791	VAL	0	0.009	0.007	24.411	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	792	ASP	-1	-0.750	-0.843	24.645	-0.219	-0.219	0.000	0.000	0.000	0.000
65	A	793	PHE	0	0.015	0.034	25.634	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	794	VAL	0	0.047	0.034	23.584	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	795	CYS	0	-0.073	-0.052	21.373	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	796	SER	0	-0.043	-0.034	21.826	-0.067	-0.067	0.000	0.000	0.000	0.000
69	A	797	LYS	1	0.883	0.933	24.027	0.217	0.217	0.000	0.000	0.000	0.000
70	A	798	VAL	0	0.003	0.002	18.407	-0.041	-0.041	0.000	0.000	0.000	0.000
71	A	799	MET	0	-0.065	-0.031	16.452	-0.099	-0.099	0.000	0.000	0.000	0.000
72	A	800	ALA	0	-0.019	-0.002	20.395	-0.049	-0.049	0.000	0.000	0.000	0.000
73	A	801	HIS	1	0.786	0.889	17.200	0.829	0.829	0.000	0.000	0.000	0.000
74	A	802	SER	0	0.028	0.026	21.669	0.022	0.022	0.000	0.000	0.000	0.000
75	A	803	SER	0	0.009	-0.004	23.677	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	804	PRO	0	0.053	0.025	23.291	0.019	0.019	0.000	0.000	0.000	0.000
77	A	805	GLN	0	0.004	-0.014	25.128	0.026	0.026	0.000	0.000	0.000	0.000
78	A	806	SER	0	0.025	0.033	28.606	0.009	0.009	0.000	0.000	0.000	0.000
79	A	807	ILE	0	-0.021	-0.017	23.587	0.005	0.005	0.000	0.000	0.000	0.000
80	A	808	LEU	0	-0.046	-0.020	27.852	0.018	0.018	0.000	0.000	0.000	0.000
81	A	809	ASP	-1	-0.819	-0.910	29.462	-0.146	-0.146	0.000	0.000	0.000	0.000
82	A	810	ASP	-1	-0.838	-0.913	30.231	-0.196	-0.196	0.000	0.000	0.000	0.000
83	A	811	VAL	0	-0.039	-0.027	28.156	0.014	0.014	0.000	0.000	0.000	0.000
84	A	812	ALA	0	0.029	0.006	31.573	0.018	0.018	0.000	0.000	0.000	0.000
85	A	813	MET	0	-0.091	-0.029	34.283	0.013	0.013	0.000	0.000	0.000	0.000
86	A	814	VAL	0	-0.046	-0.024	33.889	0.004	0.004	0.000	0.000	0.000	0.000
87	A	815	LEU	0	-0.030	-0.019	30.634	0.012	0.012	0.000	0.000	0.000	0.000
88	A	816	ASP	-1	-0.845	-0.911	34.123	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	817	GLU	-1	-0.914	-0.975	34.286	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	818	GLU	-1	-0.830	-0.884	30.290	0.049	0.049	0.000	0.000	0.000	0.000
91	A	819	ALA	0	0.016	0.008	29.971	0.000	0.000	0.000	0.000	0.000	0.000
92	A	820	GLU	-1	-0.848	-0.926	28.847	-0.100	-0.100	0.000	0.000	0.000	0.000
93	A	821	VAL	0	0.068	0.028	27.433	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	822	PHE	0	-0.029	0.001	23.917	0.013	0.013	0.000	0.000	0.000	0.000
95	A	823	ILE	0	0.030	0.011	23.965	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	824	VAL	0	0.003	0.012	22.888	-0.029	-0.029	0.000	0.000	0.000	0.000
97	A	825	LYS	1	0.781	0.873	21.678	-0.052	-0.052	0.000	0.000	0.000	0.000
98	A	826	MET	0	-0.014	0.004	19.529	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	827	TRP	0	0.040	0.010	18.174	-0.061	-0.061	0.000	0.000	0.000	0.000
100	A	828	ARG	1	0.972	0.988	17.396	-0.131	-0.131	0.000	0.000	0.000	0.000
101	A	829	LEU	0	-0.045	-0.007	13.446	0.005	0.005	0.000	0.000	0.000	0.000
102	A	830	LEU	0	0.009	0.001	13.319	-0.100	-0.100	0.000	0.000	0.000	0.000
103	A	831	ILE	0	0.046	0.042	13.113	-0.225	-0.225	0.000	0.000	0.000	0.000
104	A	832	TYR	0	-0.029	-0.020	9.376	-0.250	-0.250	0.000	0.000	0.000	0.000
105	A	833	GLU	-1	-0.758	-0.874	8.627	0.132	0.132	0.000	0.000	0.000	0.000
106	A	834	THR	0	-0.033	-0.029	7.802	-0.716	-0.716	0.000	0.000	0.000	0.000
107	A	835	GLU	-1	-0.791	-0.885	8.626	-1.651	-1.651	0.000	0.000	0.000	0.000
108	A	836	ALA	0	-0.018	-0.026	5.391	-0.305	-0.305	0.000	0.000	0.000	0.000
109	A	837	LYS	1	0.745	0.868	3.851	0.482	0.999	0.002	-0.156	-0.363	-0.001
110	A	838	LYS	1	0.898	0.947	4.603	-0.441	-0.330	-0.001	-0.008	-0.102	0.000
111	A	839	ILE	0	-0.037	-0.009	4.361	0.316	0.456	-0.001	-0.009	-0.130	0.000
112	A	840	GLY	0	-0.079	-0.022	3.541	0.720	0.995	0.012	-0.117	-0.170	0.000
113	A	841	LEU	0	-0.002	0.004	4.258	0.212	0.363	0.002	-0.029	-0.124	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:729:HIS)