FMO DATABASE

FMODB ID: KG8Y3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-866580.113647
FMO2-HF: Nuclear repulsion	820796.330909
FMO2-HF: Total energy	-45783.782739
FMO2-MP2: Total energy	-45918.98273

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.
-37.8	-36.147	20.584	-9.942	-12.298	0.117

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 : -0.806 / q_NPA : -0.905

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	0.014	0.010	2.021	-20.114	-18.556	7.456	-4.152	-4.862	0.046
4	A	8	LYS	1	0.823	0.893	1.843	-76.235	-78.026	13.092	-4.991	-6.311	0.068
5	A	9	THR	0	0.032	-0.004	3.073	-15.971	-14.435	0.034	-0.732	-0.839	0.003
6	A	10	LEU	0	-0.029	-0.001	5.404	-6.525	-6.525	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.835	0.890	6.530	-35.292	-35.292	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.044	-0.014	7.641	-2.389	-2.389	0.000	0.000	0.000	0.000
9	A	13	ASN	0	-0.035	-0.038	8.931	-5.006	-5.006	0.000	0.000	0.000	0.000
10	A	14	TYR	0	-0.037	-0.012	9.919	-0.772	-0.772	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.029	-0.017	11.244	-1.873	-1.873	0.000	0.000	0.000	0.000
12	A	16	PHE	0	0.009	0.015	13.403	-1.082	-1.082	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.871	-0.949	14.913	15.968	15.968	0.000	0.000	0.000	0.000
14	A	18	PHE	0	-0.028	-0.010	17.176	-1.011	-1.011	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.014	-0.051	15.699	-0.982	-0.982	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.047	-0.011	16.953	-0.417	-0.417	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.007	-0.001	18.128	-0.130	-0.130	0.000	0.000	0.000	0.000
18	A	22	LEU	0	-0.046	-0.010	19.489	-0.704	-0.704	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.004	0.008	15.189	0.592	0.592	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.014	-0.029	19.380	-0.787	-0.787	0.000	0.000	0.000	0.000
21	A	25	ASN	0	0.060	0.011	19.282	0.818	0.818	0.000	0.000	0.000	0.000
22	A	26	LYS	1	0.911	0.985	17.716	-14.075	-14.075	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.029	0.028	15.407	-0.653	-0.653	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.808	0.885	14.482	-13.903	-13.903	0.000	0.000	0.000	0.000
25	A	29	ASN	0	0.036	0.010	15.118	0.483	0.483	0.000	0.000	0.000	0.000
26	A	30	TYR	0	-0.046	-0.033	12.731	0.064	0.064	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.001	-0.003	9.622	1.396	1.396	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.743	-0.848	10.703	17.377	17.377	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.032	0.013	12.338	0.708	0.708	0.000	0.000	0.000	0.000
30	A	34	PHE	0	-0.055	-0.033	4.315	0.715	0.794	-0.001	-0.004	-0.074	0.000
31	A	35	TYR	0	-0.028	-0.028	3.440	0.620	0.891	0.003	-0.063	-0.212	0.000
32	A	36	LEU	0	0.004	0.011	8.240	0.639	0.639	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.906	-0.930	11.579	15.197	15.197	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.944	-0.956	8.887	24.793	24.793	0.000	0.000	0.000	0.000
35	A	39	TYR	0	-0.074	-0.044	9.997	-0.574	-0.574	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.042	-0.073	9.769	1.700	1.700	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.005	-0.029	8.333	-1.311	-1.311	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.049	-0.044	11.393	-0.868	-0.868	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.746	-0.814	13.862	17.362	17.362	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.006	0.031	11.084	-0.903	-0.903	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.057	-0.042	15.103	-0.687	-0.687	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.932	-0.954	17.151	12.246	12.246	0.000	0.000	0.000	0.000
43	A	47	THR	0	0.006	-0.007	17.928	-0.721	-0.721	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.040	-0.028	16.599	-0.462	-0.462	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.063	-0.025	20.741	-0.736	-0.736	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.064	-0.021	18.237	-0.272	-0.272	0.000	0.000	0.000	0.000
47	A	51	SER	0	0.004	-0.009	19.419	0.521	0.521	0.000	0.000	0.000	0.000
48	A	52	ARG	1	1.035	1.004	13.023	-19.794	-19.794	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.089	-0.035	13.836	1.285	1.285	0.000	0.000	0.000	0.000
50	A	54	ALA	0	0.015	-0.002	14.657	0.909	0.909	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.011	0.010	12.098	0.439	0.439	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.062	0.038	7.592	2.571	2.571	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.804	-0.899	10.556	22.411	22.411	0.000	0.000	0.000	0.000
54	A	58	ASN	0	-0.095	-0.036	12.919	0.670	0.670	0.000	0.000	0.000	0.000
55	A	59	ILE	0	0.070	0.055	7.534	-0.210	-0.210	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.916	0.966	6.579	-36.458	-36.458	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.884	0.913	9.098	-18.632	-18.632	0.000	0.000	0.000	0.000
58	A	62	THR	0	0.010	0.004	11.900	-1.234	-1.234	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.094	0.039	8.285	-0.624	-0.624	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.928	-0.966	7.558	39.505	39.505	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.031	-0.007	9.872	-1.086	-1.086	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.026	0.007	11.587	-1.223	-1.223	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.786	-0.864	8.367	33.923	33.923	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.884	-0.914	11.722	16.808	16.808	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.019	-0.031	14.717	-1.409	-1.409	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.724	-0.831	14.196	17.882	17.882	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.880	0.940	14.704	-19.489	-19.489	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.775	0.856	16.586	-17.727	-17.727	0.000	0.000	0.000	0.000
69	A	73	LEU	0	-0.022	0.004	19.411	-0.978	-0.978	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.847	-0.898	18.441	13.966	13.966	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.014	0.013	19.519	-0.520	-0.520	0.000	0.000	0.000	0.000
72	A	76	TYR	0	-0.064	-0.042	14.350	0.124	0.124	0.000	0.000	0.000	0.000
73	A	77	GLN	0	-0.081	-0.056	17.394	0.174	0.174	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.922	0.942	18.773	-14.409	-14.409	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.058	-0.009	20.955	-0.841	-0.841	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.765	-0.859	18.216	15.526	15.526	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.016	-0.012	21.625	-0.369	-0.369	0.000	0.000	0.000	0.000
78	A	82	ARG	1	0.846	0.893	23.794	-12.776	-12.776	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.735	0.850	21.396	-14.210	-14.210	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.825	-0.903	23.521	12.665	12.665	0.000	0.000	0.000	0.000
81	A	85	ILE	0	0.047	0.034	26.339	-0.501	-0.501	0.000	0.000	0.000	0.000
82	A	86	TYR	0	-0.018	-0.019	28.552	-0.386	-0.386	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.847	-0.911	27.145	10.940	10.940	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.837	-0.890	29.710	9.931	9.931	0.000	0.000	0.000	0.000
85	A	89	MET	0	-0.045	-0.011	32.059	-0.341	-0.341	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.818	0.894	30.549	-10.608	-10.608	0.000	0.000	0.000	0.000
87	A	91	GLN	0	-0.071	-0.030	32.773	-0.433	-0.433	0.000	0.000	0.000	0.000
88	A	92	HIS	0	-0.054	-0.035	35.041	-0.399	-0.399	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.010	0.006	38.056	-0.184	-0.184	0.000	0.000	0.000	0.000
90	A	94	SER	0	-0.045	-0.019	40.861	-0.118	-0.118	0.000	0.000	0.000	0.000
91	A	95	ASN	0	-0.031	-0.014	41.459	-0.225	-0.225	0.000	0.000	0.000	0.000
92	A	96	PRO	0	0.046	0.021	42.003	0.188	0.188	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.864	-0.939	42.567	7.205	7.205	0.000	0.000	0.000	0.000
94	A	98	GLN	0	-0.035	-0.006	36.093	-0.096	-0.096	0.000	0.000	0.000	0.000
95	A	99	ILE	0	-0.007	0.002	37.796	0.250	0.250	0.000	0.000	0.000	0.000
96	A	100	GLN	0	0.030	0.006	38.173	0.214	0.214	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.864	0.932	37.303	-8.002	-8.002	0.000	0.000	0.000	0.000
98	A	102	TYR	0	-0.020	-0.044	32.643	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	103	ILE	0	-0.002	-0.008	33.826	0.264	0.264	0.000	0.000	0.000	0.000
100	A	104	GLN	0	-0.084	-0.036	35.165	-0.100	-0.100	0.000	0.000	0.000	0.000
101	A	105	GLN	0	0.018	0.001	30.959	0.222	0.222	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.053	-0.025	29.779	0.413	0.413	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.930	-0.960	31.131	8.808	8.808	0.000	0.000	0.000	0.000
104	A	108	ASP	-1	-0.913	-0.962	31.671	9.615	9.615	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.063	-0.017	25.320	0.371	0.371	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.986	-0.966	27.440	11.574	11.574	0.000	0.000	0.000	0.000

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