FMO DATABASE

FMODB ID: R8MZ8

Calculation Name: 1XSV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XSV

Chain ID: A

ChEMBL ID:

UniProt ID: P67248

Base Structure: X-ray

Registration Date: 2023-09-23

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864608.901879
FMO2-HF: Nuclear repulsion	818826.118459
FMO2-HF: Total energy	-45782.783419
FMO2-MP2: Total energy	-45918.05051

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
-29.813	-27.828	18.87	-10.134	-10.721	0.103

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.876 / q_NPA : -0.936

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	A	7	VAL	0	0.029	0.017	2.661	-11.281	-7.095	1.066	-2.325	-2.928	0.020
4	A	8	LYS	1	0.878	0.945	1.741	-78.073	-81.725	17.747	-7.263	-6.831	0.077
5	A	9	THR	0	0.027	0.004	3.647	-16.401	-15.165	0.057	-0.508	-0.785	0.006
6	A	10	LEU	0	-0.041	-0.012	5.662	-6.555	-6.555	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.835	0.895	6.572	-35.851	-35.851	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.038	-0.010	7.701	-2.583	-2.583	0.000	0.000	0.000	0.000
9	A	13	ASN	0	-0.031	-0.024	9.439	-5.226	-5.226	0.000	0.000	0.000	0.000
10	A	14	TYR	0	-0.016	0.003	9.882	-0.793	-0.793	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.037	-0.029	10.748	-1.902	-1.902	0.000	0.000	0.000	0.000
12	A	16	PHE	0	-0.014	0.009	13.646	-1.284	-1.284	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.863	-0.948	15.113	16.290	16.290	0.000	0.000	0.000	0.000
14	A	18	PHE	0	-0.057	-0.017	16.934	-1.052	-1.052	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.005	-0.040	15.302	-1.136	-1.136	0.000	0.000	0.000	0.000
16	A	20	GLN	0	0.009	0.014	17.495	-0.307	-0.307	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.045	-0.025	18.474	-0.116	-0.116	0.000	0.000	0.000	0.000
18	A	22	LEU	0	-0.019	-0.006	19.392	-0.629	-0.629	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.056	-0.003	15.126	0.082	0.082	0.000	0.000	0.000	0.000
20	A	24	THR	0	0.007	-0.010	19.319	-0.883	-0.883	0.000	0.000	0.000	0.000
21	A	25	ASN	0	0.048	0.003	19.682	0.701	0.701	0.000	0.000	0.000	0.000
22	A	26	LYS	1	0.944	0.986	18.022	-14.192	-14.192	0.000	0.000	0.000	0.000
23	A	27	GLN	0	-0.011	0.006	15.692	-0.457	-0.457	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.955	0.989	14.878	-13.652	-13.652	0.000	0.000	0.000	0.000
25	A	29	ASN	0	0.011	0.007	15.771	0.453	0.453	0.000	0.000	0.000	0.000
26	A	30	TYR	0	-0.037	-0.027	13.249	0.139	0.139	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.004	0.000	9.597	1.507	1.507	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.826	-0.946	11.392	18.483	18.483	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.056	0.018	13.278	0.665	0.665	0.000	0.000	0.000	0.000
30	A	34	PHE	0	-0.072	-0.028	5.080	0.599	0.599	0.000	0.000	0.000	0.000
31	A	35	TYR	0	-0.014	-0.035	3.906	-0.365	-0.150	0.000	-0.038	-0.177	0.000
32	A	36	LEU	0	-0.030	0.014	8.886	0.803	0.803	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.959	-0.978	12.255	16.309	16.309	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.955	-0.954	10.094	24.702	24.702	0.000	0.000	0.000	0.000
35	A	39	TYR	0	-0.011	0.002	11.169	-1.201	-1.201	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.057	-0.050	10.704	2.011	2.011	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.019	-0.024	8.956	-1.186	-1.186	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.045	-0.043	12.302	-0.809	-0.809	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.785	-0.854	14.765	17.489	17.489	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.010	0.020	12.234	-0.851	-0.851	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.063	-0.051	16.240	-0.707	-0.707	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.934	-0.961	18.037	12.308	12.308	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.004	0.013	19.129	-0.620	-0.620	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.065	-0.043	17.982	-0.556	-0.556	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.022	0.009	21.886	-0.262	-0.262	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.077	-0.036	18.828	-0.261	-0.261	0.000	0.000	0.000	0.000
47	A	51	SER	0	0.008	-0.001	19.401	0.473	0.473	0.000	0.000	0.000	0.000
48	A	52	ARG	1	1.068	1.014	11.920	-19.928	-19.928	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.075	-0.023	14.035	0.964	0.964	0.000	0.000	0.000	0.000
50	A	54	ALA	0	0.018	0.004	14.983	0.848	0.848	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.025	0.016	12.621	0.627	0.627	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.032	0.026	7.810	2.976	2.976	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.868	-0.947	10.994	21.859	21.859	0.000	0.000	0.000	0.000
54	A	58	ASN	0	-0.087	-0.047	13.143	1.087	1.087	0.000	0.000	0.000	0.000
55	A	59	ILE	0	0.075	0.035	7.799	-0.151	-0.151	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.923	0.966	7.528	-32.131	-32.131	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.941	0.966	9.321	-18.562	-18.562	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.008	-0.007	11.833	-1.110	-1.110	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.078	0.028	7.870	-0.407	-0.407	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.970	-0.983	8.234	35.702	35.702	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.053	-0.021	10.010	-1.402	-1.402	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.025	0.007	11.188	-1.367	-1.367	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.812	-0.895	8.086	34.049	34.049	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.925	-0.959	11.385	17.933	17.933	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.004	-0.017	14.423	-1.867	-1.867	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.769	-0.856	13.388	18.561	18.561	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.917	0.963	14.455	-20.223	-20.223	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.863	0.926	16.053	-17.529	-17.529	0.000	0.000	0.000	0.000
69	A	73	LEU	0	-0.037	-0.020	18.899	-0.973	-0.973	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.933	-0.950	17.842	14.851	14.851	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.017	-0.014	18.908	-0.570	-0.570	0.000	0.000	0.000	0.000
72	A	76	TYR	0	-0.023	-0.001	13.737	-0.524	-0.524	0.000	0.000	0.000	0.000
73	A	77	GLN	0	-0.052	-0.030	16.927	0.204	0.204	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.981	0.980	18.258	-14.202	-14.202	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.075	-0.024	20.609	-0.920	-0.920	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.796	-0.907	18.059	15.231	15.231	0.000	0.000	0.000	0.000
77	A	81	GLN	0	0.023	0.021	21.292	0.002	0.002	0.000	0.000	0.000	0.000
78	A	82	ARG	1	0.962	0.989	23.516	-13.048	-13.048	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.824	0.903	20.748	-14.875	-14.875	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.887	-0.947	23.352	12.708	12.708	0.000	0.000	0.000	0.000
81	A	85	ILE	0	0.047	0.034	26.248	-0.525	-0.525	0.000	0.000	0.000	0.000
82	A	86	TYR	0	-0.045	-0.033	28.789	-0.384	-0.384	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.896	-0.954	27.578	10.888	10.888	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.930	-0.971	28.926	10.326	10.326	0.000	0.000	0.000	0.000
85	A	89	MET	0	-0.054	-0.027	32.029	-0.353	-0.353	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.845	0.924	31.154	-10.504	-10.504	0.000	0.000	0.000	0.000
87	A	91	GLN	0	-0.048	-0.012	33.811	-0.402	-0.402	0.000	0.000	0.000	0.000
88	A	92	HIS	0	-0.038	-0.021	35.405	-0.376	-0.376	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.018	0.012	38.308	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	94	SER	0	-0.034	-0.012	40.900	-0.141	-0.141	0.000	0.000	0.000	0.000
91	A	95	ASN	0	-0.034	-0.012	41.347	-0.243	-0.243	0.000	0.000	0.000	0.000
92	A	96	PRO	0	0.046	0.013	42.050	0.192	0.192	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.871	-0.942	42.811	7.118	7.118	0.000	0.000	0.000	0.000
94	A	98	GLN	0	-0.047	-0.032	36.408	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	99	ILE	0	-0.005	-0.002	38.091	0.249	0.249	0.000	0.000	0.000	0.000
96	A	100	GLN	0	0.025	0.005	38.228	0.257	0.257	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.895	0.965	37.014	-7.921	-7.921	0.000	0.000	0.000	0.000
98	A	102	TYR	0	0.013	0.002	32.907	0.020	0.020	0.000	0.000	0.000	0.000
99	A	103	ILE	0	0.014	0.009	33.722	0.275	0.275	0.000	0.000	0.000	0.000
100	A	104	GLN	0	-0.018	0.010	34.998	-0.097	-0.097	0.000	0.000	0.000	0.000
101	A	105	GLN	0	-0.013	-0.015	30.842	0.408	0.408	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.046	-0.029	29.487	0.373	0.373	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.911	-0.962	30.895	8.844	8.844	0.000	0.000	0.000	0.000
104	A	108	ASP	-1	-0.957	-0.976	31.275	9.614	9.614	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.106	-0.046	25.155	0.407	0.407	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-1.055	-1.014	27.286	10.710	10.710	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)