FMO DATABASE

FMODB ID: YYGN2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-966157.755006
FMO2-HF: Nuclear repulsion	919378.024176
FMO2-HF: Total energy	-46779.73083
FMO2-MP2: Total energy	-46914.995569

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.
-26.145	-22.347	8.474	-4.093	-8.178	0.015

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 : 0.059 / q_NPA : 0.010

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	0.097	0.021	3.840	-2.983	-1.610	-0.003	-0.588	-0.781	0.002
4	A	732	HIS	0	-0.046	-0.006	2.285	-2.146	-1.523	3.743	-1.802	-2.565	0.001
5	A	733	MET	0	0.068	0.030	2.436	-4.547	-3.705	4.721	-1.469	-4.094	0.012
6	A	734	LYS	1	0.876	0.938	4.422	-3.975	-3.807	0.000	-0.045	-0.123	0.000
7	A	735	ARG	1	0.880	0.935	5.865	-6.014	-6.014	0.000	0.000	0.000	0.000
8	A	736	LYS	1	0.950	0.987	7.243	-2.501	-2.501	0.000	0.000	0.000	0.000
9	A	737	HIS	0	0.007	0.011	7.143	-0.254	-0.254	0.000	0.000	0.000	0.000
10	A	738	ILE	0	0.041	0.021	10.443	-0.085	-0.085	0.000	0.000	0.000	0.000
11	A	739	LYS	1	0.891	0.937	12.971	-0.571	-0.571	0.000	0.000	0.000	0.000
12	A	740	SER	0	0.029	0.010	12.055	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	741	LEU	0	-0.002	0.000	8.164	-0.130	-0.130	0.000	0.000	0.000	0.000
14	A	742	ILE	0	-0.031	-0.013	12.450	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	743	GLU	-1	-0.868	-0.933	15.759	0.261	0.261	0.000	0.000	0.000	0.000
16	A	744	LYS	1	0.830	0.939	13.345	0.294	0.294	0.000	0.000	0.000	0.000
17	A	745	ILE	0	-0.047	-0.015	14.706	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	746	PRO	0	0.033	0.029	18.013	0.040	0.040	0.000	0.000	0.000	0.000
19	A	747	THR	0	-0.021	-0.026	21.778	0.007	0.007	0.000	0.000	0.000	0.000
20	A	748	ALA	0	0.046	0.042	24.369	0.010	0.010	0.000	0.000	0.000	0.000
21	A	749	LYS	1	0.961	0.984	25.794	0.008	0.008	0.000	0.000	0.000	0.000
22	A	750	PRO	0	0.001	0.006	26.281	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	751	GLU	-1	-0.839	-0.936	24.887	-0.053	-0.053	0.000	0.000	0.000	0.000
24	A	752	LEU	0	-0.085	-0.049	20.328	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	753	PHE	0	-0.020	-0.043	21.923	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	754	ALA	0	-0.009	0.011	24.100	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	755	TYR	0	-0.050	-0.034	14.774	0.000	0.000	0.000	0.000	0.000	0.000
28	A	756	PRO	0	0.006	0.006	18.606	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	757	LEU	0	-0.024	-0.010	15.234	-0.069	-0.069	0.000	0.000	0.000	0.000
30	A	758	ASP	-1	-0.868	-0.949	13.181	-1.301	-1.301	0.000	0.000	0.000	0.000
31	A	759	TRP	0	0.050	0.000	14.122	-0.105	-0.105	0.000	0.000	0.000	0.000
32	A	760	SER	0	-0.015	0.003	13.594	0.055	0.055	0.000	0.000	0.000	0.000
33	A	761	ILE	0	-0.050	-0.012	8.534	-0.205	-0.205	0.000	0.000	0.000	0.000
34	A	762	VAL	0	-0.067	-0.022	11.056	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	763	ASP	-1	-0.843	-0.917	10.423	-1.670	-1.670	0.000	0.000	0.000	0.000
36	A	764	SER	0	0.009	-0.014	13.740	0.086	0.086	0.000	0.000	0.000	0.000
37	A	765	ILE	0	0.035	0.020	9.989	0.147	0.147	0.000	0.000	0.000	0.000
38	A	766	LEU	0	-0.063	-0.037	9.350	0.258	0.258	0.000	0.000	0.000	0.000
39	A	767	MET	0	0.048	0.012	12.084	0.260	0.260	0.000	0.000	0.000	0.000
40	A	768	GLU	-1	-0.895	-0.931	15.473	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	769	ARG	1	0.846	0.934	7.166	-0.803	-0.803	0.000	0.000	0.000	0.000
42	A	770	ARG	1	0.835	0.916	11.901	-0.414	-0.414	0.000	0.000	0.000	0.000
43	A	771	ILE	0	-0.009	0.001	13.931	0.081	0.081	0.000	0.000	0.000	0.000
44	A	772	ARG	1	0.954	0.957	16.341	0.122	0.122	0.000	0.000	0.000	0.000
45	A	773	PRO	0	-0.002	0.005	17.050	0.025	0.025	0.000	0.000	0.000	0.000
46	A	774	TRP	0	-0.050	-0.015	17.413	0.059	0.059	0.000	0.000	0.000	0.000
47	A	775	ILE	0	0.017	-0.004	19.438	0.013	0.013	0.000	0.000	0.000	0.000
48	A	776	ASN	0	0.030	0.009	22.160	0.002	0.002	0.000	0.000	0.000	0.000
49	A	777	LYS	1	0.820	0.906	21.957	-0.303	-0.303	0.000	0.000	0.000	0.000
50	A	778	LYS	1	0.778	0.858	22.388	-0.244	-0.244	0.000	0.000	0.000	0.000
51	A	779	ILE	0	0.052	0.030	25.011	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	780	ILE	0	0.018	0.019	27.359	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	781	GLU	-1	-0.797	-0.877	26.431	0.275	0.275	0.000	0.000	0.000	0.000
54	A	782	TYR	0	-0.025	0.001	27.220	0.008	0.008	0.000	0.000	0.000	0.000
55	A	783	ILE	0	0.011	0.017	32.154	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	784	GLY	0	0.011	0.026	32.828	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	785	GLU	-1	-0.996	-1.026	33.323	0.142	0.142	0.000	0.000	0.000	0.000
58	A	786	GLU	-1	-0.941	-0.948	34.964	0.043	0.043	0.000	0.000	0.000	0.000
59	A	787	GLU	-1	-0.834	-0.915	31.574	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	788	ALA	0	-0.058	-0.048	30.585	0.014	0.014	0.000	0.000	0.000	0.000
61	A	789	THR	0	-0.014	-0.008	29.894	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	790	LEU	0	0.023	0.024	29.871	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	791	VAL	0	0.030	0.007	24.824	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	792	ASP	-1	-0.836	-0.920	25.459	-0.101	-0.101	0.000	0.000	0.000	0.000
65	A	793	PHE	0	0.032	0.023	25.973	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	794	VAL	0	0.028	0.020	23.742	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	795	CYS	0	-0.084	-0.048	21.689	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	796	SER	0	-0.007	-0.014	22.044	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	797	LYS	1	0.957	0.988	24.225	0.134	0.134	0.000	0.000	0.000	0.000
70	A	798	VAL	0	-0.014	-0.004	18.503	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	799	MET	0	-0.039	-0.031	17.282	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	800	ALA	0	-0.044	-0.007	20.729	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	801	HIS	1	0.814	0.911	18.112	0.604	0.604	0.000	0.000	0.000	0.000
74	A	802	SER	0	0.029	0.026	22.193	0.019	0.019	0.000	0.000	0.000	0.000
75	A	803	SER	0	0.019	0.003	23.784	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	804	PRO	0	0.062	0.027	23.353	0.013	0.013	0.000	0.000	0.000	0.000
77	A	805	GLN	0	-0.006	-0.021	25.044	0.027	0.027	0.000	0.000	0.000	0.000
78	A	806	SER	0	-0.017	0.004	28.354	0.004	0.004	0.000	0.000	0.000	0.000
79	A	807	ILE	0	-0.007	-0.006	23.932	0.004	0.004	0.000	0.000	0.000	0.000
80	A	808	LEU	0	-0.019	-0.009	28.021	0.014	0.014	0.000	0.000	0.000	0.000
81	A	809	ASP	-1	-0.851	-0.921	29.497	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	810	ASP	-1	-0.891	-0.955	30.831	-0.107	-0.107	0.000	0.000	0.000	0.000
83	A	811	VAL	0	-0.072	-0.046	28.037	0.009	0.009	0.000	0.000	0.000	0.000
84	A	812	ALA	0	0.017	0.011	31.499	0.015	0.015	0.000	0.000	0.000	0.000
85	A	813	MET	0	-0.073	-0.023	34.260	0.008	0.008	0.000	0.000	0.000	0.000
86	A	814	VAL	0	-0.048	-0.023	33.568	0.002	0.002	0.000	0.000	0.000	0.000
87	A	815	LEU	0	-0.038	-0.027	30.438	0.011	0.011	0.000	0.000	0.000	0.000
88	A	816	ASP	-1	-0.825	-0.901	34.197	0.047	0.047	0.000	0.000	0.000	0.000
89	A	817	GLU	-1	-0.953	-0.989	34.444	0.032	0.032	0.000	0.000	0.000	0.000
90	A	818	GLU	-1	-0.898	-0.952	32.084	0.114	0.114	0.000	0.000	0.000	0.000
91	A	819	ALA	0	-0.027	-0.016	29.944	0.010	0.010	0.000	0.000	0.000	0.000
92	A	820	GLU	-1	-0.958	-0.988	28.831	0.031	0.031	0.000	0.000	0.000	0.000
93	A	821	VAL	0	0.040	0.011	27.411	0.006	0.006	0.000	0.000	0.000	0.000
94	A	822	PHE	0	-0.039	-0.019	23.813	0.026	0.026	0.000	0.000	0.000	0.000
95	A	823	ILE	0	0.046	0.013	23.728	0.011	0.011	0.000	0.000	0.000	0.000
96	A	824	VAL	0	0.038	0.037	22.658	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	825	LYS	1	0.816	0.903	21.580	-0.175	-0.175	0.000	0.000	0.000	0.000
98	A	826	MET	0	0.008	0.013	19.324	0.025	0.025	0.000	0.000	0.000	0.000
99	A	827	TRP	0	0.046	0.015	18.080	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	828	ARG	1	0.947	0.973	17.398	-0.332	-0.332	0.000	0.000	0.000	0.000
101	A	829	LEU	0	-0.053	-0.010	14.375	0.068	0.068	0.000	0.000	0.000	0.000
102	A	830	LEU	0	0.033	0.008	13.444	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	831	ILE	0	0.034	0.043	12.909	-0.138	-0.138	0.000	0.000	0.000	0.000
104	A	832	TYR	0	-0.023	-0.013	10.163	-0.126	-0.126	0.000	0.000	0.000	0.000
105	A	833	GLU	-1	-0.826	-0.924	9.060	0.672	0.672	0.000	0.000	0.000	0.000
106	A	834	THR	0	-0.037	-0.046	8.012	-0.390	-0.390	0.000	0.000	0.000	0.000
107	A	835	GLU	-1	-0.829	-0.914	8.785	-1.127	-1.127	0.000	0.000	0.000	0.000
108	A	836	ALA	0	0.005	-0.007	5.800	-0.131	-0.131	0.000	0.000	0.000	0.000
109	A	837	LYS	1	0.878	0.931	3.552	1.391	1.821	0.004	-0.089	-0.344	0.000
110	A	838	LYS	1	0.941	0.987	4.637	-0.291	-0.211	-0.001	-0.001	-0.077	0.000
111	A	839	ILE	0	-0.054	-0.012	5.136	0.160	0.160	0.000	0.000	0.000	0.000
112	A	840	GLY	0	-0.066	-0.023	3.531	0.793	0.981	0.010	-0.084	-0.114	0.000
113	A	841	LEU	0	0.019	0.020	4.323	-0.437	-0.343	0.000	-0.015	-0.080	0.000

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