FMO DATABASE

FMODB ID: VRGK1

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-966544.54371
FMO2-HF: Nuclear repulsion	919764.169602
FMO2-HF: Total energy	-46780.374108
FMO2-MP2: Total energy	-46915.658626

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.
-26.83	-22.518	7.905	-4.261	-7.956	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 : 0.059 / q_NPA : 0.005

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	0.114	0.033	3.840	-2.866	-1.483	-0.004	-0.582	-0.797	0.002
4	A	732	HIS	0	-0.045	0.000	2.167	-1.995	-1.346	3.739	-1.943	-2.445	0.004
5	A	733	MET	0	0.067	0.024	2.559	-5.056	-3.723	4.158	-1.480	-4.011	0.013
6	A	734	LYS	1	0.834	0.910	4.423	-3.929	-3.742	0.001	-0.056	-0.132	0.000
7	A	735	ARG	1	0.883	0.942	5.872	-6.134	-6.134	0.000	0.000	0.000	0.000
8	A	736	LYS	1	0.915	0.959	6.864	-3.151	-3.151	0.000	0.000	0.000	0.000
9	A	737	HIS	0	0.039	0.040	7.452	-0.230	-0.230	0.000	0.000	0.000	0.000
10	A	738	ILE	0	0.045	0.022	10.281	-0.118	-0.118	0.000	0.000	0.000	0.000
11	A	739	LYS	1	0.838	0.890	12.863	-0.612	-0.612	0.000	0.000	0.000	0.000
12	A	740	SER	0	0.025	0.007	11.890	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	741	LEU	0	0.007	0.003	7.684	-0.135	-0.135	0.000	0.000	0.000	0.000
14	A	742	ILE	0	-0.037	-0.016	12.313	-0.125	-0.125	0.000	0.000	0.000	0.000
15	A	743	GLU	-1	-0.811	-0.889	15.616	0.285	0.285	0.000	0.000	0.000	0.000
16	A	744	LYS	1	0.800	0.912	13.307	0.301	0.301	0.000	0.000	0.000	0.000
17	A	745	ILE	0	-0.046	-0.016	14.541	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	746	PRO	0	0.030	0.022	17.903	0.045	0.045	0.000	0.000	0.000	0.000
19	A	747	THR	0	-0.022	-0.025	21.673	0.002	0.002	0.000	0.000	0.000	0.000
20	A	748	ALA	0	0.031	0.037	24.254	0.010	0.010	0.000	0.000	0.000	0.000
21	A	749	LYS	1	0.850	0.918	25.703	0.032	0.032	0.000	0.000	0.000	0.000
22	A	750	PRO	0	0.009	0.008	26.207	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	751	GLU	-1	-0.838	-0.936	24.863	-0.071	-0.071	0.000	0.000	0.000	0.000
24	A	752	LEU	0	-0.100	-0.047	20.084	-0.035	-0.035	0.000	0.000	0.000	0.000
25	A	753	PHE	0	-0.014	-0.046	21.859	-0.036	-0.036	0.000	0.000	0.000	0.000
26	A	754	ALA	0	-0.006	0.014	24.059	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	755	TYR	0	-0.042	-0.027	14.766	0.003	0.003	0.000	0.000	0.000	0.000
28	A	756	PRO	0	0.004	0.005	18.584	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	757	LEU	0	-0.034	-0.011	15.079	-0.074	-0.074	0.000	0.000	0.000	0.000
30	A	758	ASP	-1	-0.807	-0.880	13.190	-1.364	-1.364	0.000	0.000	0.000	0.000
31	A	759	TRP	0	0.059	0.001	14.147	-0.138	-0.138	0.000	0.000	0.000	0.000
32	A	760	SER	0	-0.027	-0.026	13.281	0.040	0.040	0.000	0.000	0.000	0.000
33	A	761	ILE	0	-0.071	-0.018	8.445	-0.235	-0.235	0.000	0.000	0.000	0.000
34	A	762	VAL	0	-0.040	-0.018	10.817	-0.095	-0.095	0.000	0.000	0.000	0.000
35	A	763	ASP	-1	-0.798	-0.897	9.933	-2.112	-2.112	0.000	0.000	0.000	0.000
36	A	764	SER	0	0.032	-0.003	13.524	0.067	0.067	0.000	0.000	0.000	0.000
37	A	765	ILE	0	0.033	0.022	9.842	0.132	0.132	0.000	0.000	0.000	0.000
38	A	766	LEU	0	-0.061	-0.042	9.262	0.234	0.234	0.000	0.000	0.000	0.000
39	A	767	MET	0	0.052	0.021	11.784	0.267	0.267	0.000	0.000	0.000	0.000
40	A	768	GLU	-1	-0.894	-0.927	15.194	-0.259	-0.259	0.000	0.000	0.000	0.000
41	A	769	ARG	1	0.849	0.933	7.028	-0.201	-0.201	0.000	0.000	0.000	0.000
42	A	770	ARG	1	0.828	0.910	11.824	-0.229	-0.229	0.000	0.000	0.000	0.000
43	A	771	ILE	0	-0.016	-0.009	13.928	0.101	0.101	0.000	0.000	0.000	0.000
44	A	772	ARG	1	0.927	0.922	16.326	0.242	0.242	0.000	0.000	0.000	0.000
45	A	773	PRO	0	-0.003	0.004	17.069	0.044	0.044	0.000	0.000	0.000	0.000
46	A	774	TRP	0	-0.050	-0.019	17.397	0.053	0.053	0.000	0.000	0.000	0.000
47	A	775	ILE	0	0.016	-0.004	19.393	0.025	0.025	0.000	0.000	0.000	0.000
48	A	776	ASN	0	0.029	0.015	22.126	0.004	0.004	0.000	0.000	0.000	0.000
49	A	777	LYS	1	0.829	0.900	21.894	-0.232	-0.232	0.000	0.000	0.000	0.000
50	A	778	LYS	1	0.784	0.864	22.417	-0.176	-0.176	0.000	0.000	0.000	0.000
51	A	779	ILE	0	0.037	0.024	24.950	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	780	ILE	0	0.023	0.015	27.737	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	781	GLU	-1	-0.812	-0.879	26.547	0.224	0.224	0.000	0.000	0.000	0.000
54	A	782	TYR	0	-0.041	-0.020	27.297	0.009	0.009	0.000	0.000	0.000	0.000
55	A	783	ILE	0	-0.004	0.013	32.100	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	784	GLY	0	0.045	0.040	32.776	0.000	0.000	0.000	0.000	0.000	0.000
57	A	785	GLU	-1	-0.996	-1.023	33.323	0.096	0.096	0.000	0.000	0.000	0.000
58	A	786	GLU	-1	-0.943	-0.949	35.008	0.008	0.008	0.000	0.000	0.000	0.000
59	A	787	GLU	-1	-0.806	-0.906	31.781	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	788	ALA	0	-0.059	-0.040	30.487	0.011	0.011	0.000	0.000	0.000	0.000
61	A	789	THR	0	-0.048	-0.018	29.678	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	790	LEU	0	0.015	0.008	29.846	-0.025	-0.025	0.000	0.000	0.000	0.000
63	A	791	VAL	0	0.021	0.006	24.803	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	792	ASP	-1	-0.792	-0.882	24.943	-0.207	-0.207	0.000	0.000	0.000	0.000
65	A	793	PHE	0	0.007	0.020	25.677	-0.042	-0.042	0.000	0.000	0.000	0.000
66	A	794	VAL	0	0.038	0.025	23.538	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	795	CYS	0	-0.064	-0.037	21.392	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	796	SER	0	-0.021	-0.020	21.754	-0.060	-0.060	0.000	0.000	0.000	0.000
69	A	797	LYS	1	0.924	0.968	23.960	0.182	0.182	0.000	0.000	0.000	0.000
70	A	798	VAL	0	-0.013	-0.009	18.528	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	799	MET	0	-0.065	-0.034	16.617	-0.078	-0.078	0.000	0.000	0.000	0.000
72	A	800	ALA	0	-0.029	0.001	20.473	-0.045	-0.045	0.000	0.000	0.000	0.000
73	A	801	HIS	1	0.789	0.898	17.629	0.710	0.710	0.000	0.000	0.000	0.000
74	A	802	SER	0	0.036	0.031	22.015	0.026	0.026	0.000	0.000	0.000	0.000
75	A	803	SER	0	0.019	0.001	23.784	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	804	PRO	0	0.058	0.028	23.255	0.012	0.012	0.000	0.000	0.000	0.000
77	A	805	GLN	0	0.008	-0.027	25.014	0.027	0.027	0.000	0.000	0.000	0.000
78	A	806	SER	0	-0.009	0.009	28.350	0.004	0.004	0.000	0.000	0.000	0.000
79	A	807	ILE	0	-0.007	-0.007	23.947	0.004	0.004	0.000	0.000	0.000	0.000
80	A	808	LEU	0	-0.036	-0.019	28.126	0.015	0.015	0.000	0.000	0.000	0.000
81	A	809	ASP	-1	-0.830	-0.904	29.460	-0.094	-0.094	0.000	0.000	0.000	0.000
82	A	810	ASP	-1	-0.844	-0.924	30.779	-0.155	-0.155	0.000	0.000	0.000	0.000
83	A	811	VAL	0	-0.069	-0.049	28.004	0.009	0.009	0.000	0.000	0.000	0.000
84	A	812	ALA	0	0.018	0.013	31.470	0.016	0.016	0.000	0.000	0.000	0.000
85	A	813	MET	0	-0.067	-0.016	34.218	0.011	0.011	0.000	0.000	0.000	0.000
86	A	814	VAL	0	-0.050	-0.029	33.566	0.003	0.003	0.000	0.000	0.000	0.000
87	A	815	LEU	0	-0.033	-0.024	30.431	0.011	0.011	0.000	0.000	0.000	0.000
88	A	816	ASP	-1	-0.835	-0.906	34.136	0.019	0.019	0.000	0.000	0.000	0.000
89	A	817	GLU	-1	-0.943	-0.982	34.384	0.005	0.005	0.000	0.000	0.000	0.000
90	A	818	GLU	-1	-0.907	-0.958	31.692	0.088	0.088	0.000	0.000	0.000	0.000
91	A	819	ALA	0	-0.016	-0.005	29.906	0.006	0.006	0.000	0.000	0.000	0.000
92	A	820	GLU	-1	-0.843	-0.926	28.772	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	821	VAL	0	0.060	0.027	27.354	0.003	0.003	0.000	0.000	0.000	0.000
94	A	822	PHE	0	-0.043	-0.002	23.602	0.021	0.021	0.000	0.000	0.000	0.000
95	A	823	ILE	0	0.048	0.016	23.698	0.005	0.005	0.000	0.000	0.000	0.000
96	A	824	VAL	0	0.042	0.037	22.593	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	825	LYS	1	0.802	0.878	21.484	-0.117	-0.117	0.000	0.000	0.000	0.000
98	A	826	MET	0	0.004	0.015	19.239	0.012	0.012	0.000	0.000	0.000	0.000
99	A	827	TRP	0	0.035	0.012	18.019	-0.047	-0.047	0.000	0.000	0.000	0.000
100	A	828	ARG	1	0.945	0.972	17.328	-0.285	-0.285	0.000	0.000	0.000	0.000
101	A	829	LEU	0	-0.052	-0.009	13.673	0.063	0.063	0.000	0.000	0.000	0.000
102	A	830	LEU	0	0.029	0.006	13.372	-0.049	-0.049	0.000	0.000	0.000	0.000
103	A	831	ILE	0	0.029	0.038	12.863	-0.163	-0.163	0.000	0.000	0.000	0.000
104	A	832	TYR	0	-0.016	-0.013	9.591	-0.166	-0.166	0.000	0.000	0.000	0.000
105	A	833	GLU	-1	-0.794	-0.899	8.964	0.442	0.442	0.000	0.000	0.000	0.000
106	A	834	THR	0	-0.038	-0.042	7.966	-0.465	-0.465	0.000	0.000	0.000	0.000
107	A	835	GLU	-1	-0.796	-0.888	8.770	-1.086	-1.086	0.000	0.000	0.000	0.000
108	A	836	ALA	0	-0.007	-0.009	5.653	-0.097	-0.097	0.000	0.000	0.000	0.000
109	A	837	LYS	1	0.793	0.898	3.574	1.791	2.195	0.003	-0.100	-0.307	0.000
110	A	838	LYS	1	0.920	0.956	4.642	-0.044	0.034	-0.001	-0.001	-0.076	0.000
111	A	839	ILE	0	-0.052	-0.009	5.080	0.245	0.245	0.000	0.000	0.000	0.000
112	A	840	GLY	0	-0.072	-0.028	3.574	0.943	1.128	0.009	-0.084	-0.110	0.000
113	A	841	LEU	0	0.022	0.023	4.335	-0.502	-0.409	0.000	-0.015	-0.078	0.000

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