FMO DATABASE

FMODB ID: R5NM8

Calculation Name: 3V53-A-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-972939.042354
FMO2-HF: Nuclear repulsion	925988.161563
FMO2-HF: Total energy	-46950.880791
FMO2-MP2: Total energy	-47086.663395

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:728:ACE )

Summations of interaction energy for fragment #1(A:728:ACE )

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.
0.861	3.212	0.524	-1.258	-1.617	-0.004

Interaction energy analysis for fragmet #1(A:728:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.006

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	730	HIS	0	0.058	0.046	3.256	-0.573	1.053	0.068	-0.874	-0.821	-0.002
4	A	731	HIS	0	0.082	0.027	5.395	0.029	0.029	0.000	0.000	0.000	0.000
5	A	732	HIS	0	-0.034	-0.009	2.855	0.275	0.892	0.456	-0.368	-0.704	-0.002
6	A	733	MET	0	0.059	0.028	4.837	0.232	0.340	0.000	-0.016	-0.092	0.000
7	A	734	LYS	1	0.873	0.935	7.449	0.494	0.494	0.000	0.000	0.000	0.000
8	A	735	ARG	1	0.893	0.944	5.837	-0.099	-0.099	0.000	0.000	0.000	0.000
9	A	736	LYS	1	0.947	0.987	7.823	0.577	0.577	0.000	0.000	0.000	0.000
10	A	737	HIS	0	0.003	0.009	9.810	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	738	ILE	0	0.042	0.021	12.780	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	739	LYS	1	0.890	0.937	14.840	0.102	0.102	0.000	0.000	0.000	0.000
13	A	740	SER	0	0.028	0.010	16.218	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	741	LEU	0	-0.002	0.000	12.903	0.004	0.004	0.000	0.000	0.000	0.000
15	A	742	ILE	0	-0.030	-0.013	17.367	0.011	0.011	0.000	0.000	0.000	0.000
16	A	743	GLU	-1	-0.867	-0.932	19.865	-0.104	-0.104	0.000	0.000	0.000	0.000
17	A	744	LYS	1	0.828	0.939	19.895	0.190	0.190	0.000	0.000	0.000	0.000
18	A	745	ILE	0	-0.045	-0.014	20.002	0.005	0.005	0.000	0.000	0.000	0.000
19	A	746	PRO	0	0.030	0.027	23.745	0.008	0.008	0.000	0.000	0.000	0.000
20	A	747	THR	0	-0.018	-0.025	27.556	0.000	0.000	0.000	0.000	0.000	0.000
21	A	748	ALA	0	0.044	0.041	29.368	0.005	0.005	0.000	0.000	0.000	0.000
22	A	749	LYS	1	0.961	0.984	31.844	0.043	0.043	0.000	0.000	0.000	0.000
23	A	750	PRO	0	0.001	0.006	32.721	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	751	GLU	-1	-0.839	-0.936	31.471	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	752	LEU	0	-0.086	-0.049	26.153	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	753	PHE	0	-0.022	-0.043	28.881	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	754	ALA	0	-0.007	0.012	31.403	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	755	TYR	0	-0.050	-0.034	22.378	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	756	PRO	0	0.008	0.006	26.723	0.000	0.000	0.000	0.000	0.000	0.000
30	A	757	LEU	0	-0.030	-0.012	22.795	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	758	ASP	-1	-0.865	-0.949	21.697	-0.188	-0.188	0.000	0.000	0.000	0.000
32	A	759	TRP	0	0.049	-0.001	22.413	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	760	SER	0	-0.015	0.004	22.426	0.008	0.008	0.000	0.000	0.000	0.000
34	A	761	ILE	0	-0.047	-0.011	16.847	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	762	VAL	0	-0.070	-0.023	18.881	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	763	ASP	-1	-0.840	-0.916	18.012	-0.222	-0.222	0.000	0.000	0.000	0.000
37	A	764	SER	0	0.007	-0.015	21.208	0.001	0.001	0.000	0.000	0.000	0.000
38	A	765	ILE	0	0.035	0.020	15.007	0.007	0.007	0.000	0.000	0.000	0.000
39	A	766	LEU	0	-0.065	-0.038	15.418	0.001	0.001	0.000	0.000	0.000	0.000
40	A	767	MET	0	0.048	0.011	17.741	0.014	0.014	0.000	0.000	0.000	0.000
41	A	768	GLU	-1	-0.891	-0.929	19.292	-0.059	-0.059	0.000	0.000	0.000	0.000
42	A	769	ARG	1	0.853	0.935	10.321	0.365	0.365	0.000	0.000	0.000	0.000
43	A	770	ARG	1	0.834	0.916	14.874	0.127	0.127	0.000	0.000	0.000	0.000
44	A	771	ILE	0	-0.012	-0.002	17.289	0.016	0.016	0.000	0.000	0.000	0.000
45	A	772	ARG	1	0.958	0.958	20.765	0.059	0.059	0.000	0.000	0.000	0.000
46	A	773	PRO	0	0.009	0.012	19.383	0.010	0.010	0.000	0.000	0.000	0.000
47	A	774	TRP	0	-0.054	-0.016	20.327	0.007	0.007	0.000	0.000	0.000	0.000
48	A	775	ILE	0	0.007	-0.012	22.181	0.006	0.006	0.000	0.000	0.000	0.000
49	A	776	ASN	0	-0.006	-0.014	25.457	0.005	0.005	0.000	0.000	0.000	0.000
50	A	777	LYS	1	0.823	0.911	23.457	0.015	0.015	0.000	0.000	0.000	0.000
51	A	778	LYS	1	0.718	0.832	24.812	0.032	0.032	0.000	0.000	0.000	0.000
52	A	779	ILE	0	0.072	0.044	27.362	0.001	0.001	0.000	0.000	0.000	0.000
53	A	780	ILE	0	0.011	0.018	29.078	0.002	0.002	0.000	0.000	0.000	0.000
54	A	781	GLU	-1	-0.808	-0.891	28.009	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	782	TYR	0	-0.018	0.005	30.512	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	783	ILE	0	0.010	0.019	34.479	0.001	0.001	0.000	0.000	0.000	0.000
57	A	784	GLY	0	-0.001	0.013	34.688	0.002	0.002	0.000	0.000	0.000	0.000
58	A	785	GLU	-1	-0.985	-1.013	35.135	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	786	GLU	-1	-0.931	-0.949	29.850	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	787	GLU	-1	-0.848	-0.915	33.454	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	788	ALA	0	0.016	-0.006	32.678	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	789	THR	0	-0.027	-0.025	33.145	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	790	LEU	0	0.041	0.028	34.197	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	791	VAL	0	0.049	0.023	28.491	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	792	ASP	-1	-0.828	-0.917	29.935	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	793	PHE	0	0.023	0.017	31.093	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	794	VAL	0	0.026	0.019	29.188	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	795	CYS	0	-0.078	-0.045	26.957	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	796	SER	0	-0.008	-0.014	28.140	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	797	LYS	1	0.951	0.986	30.507	0.050	0.050	0.000	0.000	0.000	0.000
71	A	798	VAL	0	-0.008	-0.002	24.967	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	799	MET	0	-0.038	-0.030	24.605	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	800	ALA	0	-0.047	-0.008	27.814	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	801	HIS	1	0.814	0.912	25.969	0.113	0.113	0.000	0.000	0.000	0.000
75	A	802	SER	0	0.029	0.025	29.854	0.005	0.005	0.000	0.000	0.000	0.000
76	A	803	SER	0	0.020	0.003	31.256	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	804	PRO	0	0.062	0.027	30.220	0.004	0.004	0.000	0.000	0.000	0.000
78	A	805	GLN	0	-0.008	-0.021	31.979	0.002	0.002	0.000	0.000	0.000	0.000
79	A	806	SER	0	-0.015	0.005	35.437	0.003	0.003	0.000	0.000	0.000	0.000
80	A	807	ILE	0	-0.007	-0.006	30.442	0.002	0.002	0.000	0.000	0.000	0.000
81	A	808	LEU	0	-0.018	-0.008	33.890	0.003	0.003	0.000	0.000	0.000	0.000
82	A	809	ASP	-1	-0.853	-0.921	35.450	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	810	ASP	-1	-0.889	-0.955	36.847	-0.042	-0.042	0.000	0.000	0.000	0.000
84	A	811	VAL	0	-0.073	-0.047	33.376	0.002	0.002	0.000	0.000	0.000	0.000
85	A	812	ALA	0	0.018	0.013	36.741	0.003	0.003	0.000	0.000	0.000	0.000
86	A	813	MET	0	-0.073	-0.022	39.418	0.003	0.003	0.000	0.000	0.000	0.000
87	A	814	VAL	0	-0.053	-0.026	37.968	0.002	0.002	0.000	0.000	0.000	0.000
88	A	815	LEU	0	-0.037	-0.028	34.340	0.001	0.001	0.000	0.000	0.000	0.000
89	A	816	ASP	-1	-0.824	-0.901	38.236	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	817	GLU	-1	-0.953	-0.989	39.068	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	818	GLU	-1	-0.899	-0.952	35.403	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	819	ALA	0	-0.027	-0.016	34.148	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	820	GLU	-1	-0.958	-0.988	33.742	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	821	VAL	0	0.038	0.010	31.081	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	822	PHE	0	-0.039	-0.018	27.514	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	823	ILE	0	0.042	0.011	28.551	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	824	VAL	0	0.042	0.039	28.170	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	825	LYS	1	0.820	0.904	25.628	0.030	0.030	0.000	0.000	0.000	0.000
99	A	826	MET	0	0.005	0.012	24.140	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	827	TRP	0	0.047	0.016	23.683	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	828	ARG	1	0.950	0.974	22.436	0.068	0.068	0.000	0.000	0.000	0.000
102	A	829	LEU	0	-0.054	-0.011	18.226	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	830	LEU	0	0.033	0.007	19.183	-0.029	-0.029	0.000	0.000	0.000	0.000
104	A	831	ILE	0	0.035	0.045	19.924	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	832	TYR	0	-0.026	-0.014	13.522	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	833	GLU	-1	-0.829	-0.924	14.693	-0.312	-0.312	0.000	0.000	0.000	0.000
107	A	834	THR	0	-0.037	-0.046	15.398	-0.055	-0.055	0.000	0.000	0.000	0.000
108	A	835	GLU	-1	-0.829	-0.914	17.091	-0.250	-0.250	0.000	0.000	0.000	0.000
109	A	836	ALA	0	0.002	-0.009	11.949	-0.044	-0.044	0.000	0.000	0.000	0.000
110	A	837	LYS	1	0.884	0.934	11.977	0.274	0.274	0.000	0.000	0.000	0.000
111	A	838	LYS	1	0.940	0.987	13.125	0.208	0.208	0.000	0.000	0.000	0.000
112	A	839	ILE	0	-0.057	-0.014	11.323	0.004	0.004	0.000	0.000	0.000	0.000
113	A	840	GLY	0	-0.071	-0.026	10.429	-0.055	-0.055	0.000	0.000	0.000	0.000
114	A	841	LEU	0	0.029	0.010	11.136	0.086	0.086	0.000	0.000	0.000	0.000
115	A	842	NME	0	-0.006	0.012	12.495	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:728:ACE )