FMO DATABASE

FMODB ID: YZGV2

Calculation Name: 1XTE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XTE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ERE3

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1014708.086589
FMO2-HF: Nuclear repulsion	966725.263056
FMO2-HF: Total energy	-47982.823533
FMO2-MP2: Total energy	-48124.702921

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:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
67.091	68.401	9.159	-5.376	-5.092	-0.062

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.945

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	6	SER	0	-0.079	-0.041	1.849	-42.676	-41.691	9.159	-5.354	-4.790	-0.062
4	A	7	CYS	0	0.000	0.009	3.590	7.995	8.291	0.001	-0.022	-0.275	0.000
5	A	8	PRO	0	-0.017	-0.008	5.220	1.501	1.530	-0.001	0.000	-0.027	0.000
6	A	9	SER	0	0.012	0.025	8.769	0.584	0.584	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.031	0.011	10.803	1.149	1.149	0.000	0.000	0.000	0.000
8	A	11	SER	0	0.028	0.022	14.523	0.540	0.540	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.024	0.002	17.819	0.274	0.274	0.000	0.000	0.000	0.000
10	A	13	PRO	0	0.010	0.009	20.692	0.678	0.678	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.009	-0.012	23.388	0.375	0.375	0.000	0.000	0.000	0.000
12	A	15	SER	0	-0.010	-0.018	26.333	-0.342	-0.342	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.932	-0.943	29.061	-10.420	-10.420	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.885	-0.940	32.121	-8.280	-8.280	0.000	0.000	0.000	0.000
15	A	18	HIS	0	0.007	0.008	32.245	0.167	0.167	0.000	0.000	0.000	0.000
16	A	19	ARG	1	0.966	0.964	36.784	7.452	7.452	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.907	-0.940	38.826	-8.181	-8.181	0.000	0.000	0.000	0.000
18	A	21	LYS	1	1.027	0.998	42.434	6.750	6.750	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.902	0.950	45.275	6.424	6.424	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.937	0.973	39.679	7.860	7.860	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.959	0.983	39.322	7.866	7.866	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.056	-0.034	33.919	-0.068	-0.068	0.000	0.000	0.000	0.000
23	A	26	THR	0	0.075	0.045	30.886	0.106	0.106	0.000	0.000	0.000	0.000
24	A	27	VAL	0	-0.054	-0.023	28.254	-0.209	-0.209	0.000	0.000	0.000	0.000
25	A	28	TYR	0	-0.001	-0.018	25.187	0.151	0.151	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.961	0.992	23.200	12.187	12.187	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.014	-0.026	18.342	-0.103	-0.103	0.000	0.000	0.000	0.000
28	A	31	LEU	0	0.002	0.001	17.292	0.411	0.411	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.026	-0.012	13.657	-0.721	-0.721	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.054	0.027	11.250	0.793	0.793	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.014	-0.001	7.806	-2.157	-2.157	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.010	0.001	6.502	0.254	0.254	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.919	0.947	7.256	29.263	29.263	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.003	0.014	10.273	2.995	2.995	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.843	-0.920	12.132	-21.186	-21.186	0.000	0.000	0.000	0.000
36	A	39	TRP	0	-0.064	-0.038	12.892	1.295	1.295	0.000	0.000	0.000	0.000
37	A	40	PHE	0	0.035	0.011	18.083	-0.270	-0.270	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.063	-0.026	19.322	0.271	0.271	0.000	0.000	0.000	0.000
39	A	42	PHE	0	0.008	0.002	22.025	0.098	0.098	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.851	0.945	22.180	13.644	13.644	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.996	0.987	26.175	10.186	10.186	0.000	0.000	0.000	0.000
42	A	45	TYR	0	0.037	-0.001	27.971	-0.149	-0.149	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.029	-0.025	28.658	-0.180	-0.180	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.843	-0.905	26.300	-11.625	-11.625	0.000	0.000	0.000	0.000
45	A	48	PHE	0	0.039	0.017	21.745	-0.289	-0.289	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.889	-0.959	25.365	-10.547	-10.547	0.000	0.000	0.000	0.000
47	A	50	LYS	1	0.947	0.981	27.673	11.221	11.221	0.000	0.000	0.000	0.000
48	A	51	LEU	0	0.019	0.012	19.939	0.079	0.079	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.016	0.005	24.189	-0.228	-0.228	0.000	0.000	0.000	0.000
50	A	53	ASN	0	-0.035	-0.033	25.125	0.079	0.079	0.000	0.000	0.000	0.000
51	A	54	SER	0	-0.054	-0.009	25.126	0.346	0.346	0.000	0.000	0.000	0.000
52	A	55	LEU	0	0.052	0.009	19.725	0.094	0.094	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.917	0.974	23.618	11.124	11.124	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.907	0.949	25.864	10.010	10.010	0.000	0.000	0.000	0.000
55	A	58	GLN	0	0.040	0.040	23.248	-0.311	-0.311	0.000	0.000	0.000	0.000
56	A	59	PHE	0	0.029	0.018	19.607	-0.079	-0.079	0.000	0.000	0.000	0.000
57	A	60	PRO	0	0.001	0.003	23.597	-0.171	-0.171	0.000	0.000	0.000	0.000
58	A	61	ALA	0	0.011	-0.005	23.738	0.181	0.181	0.000	0.000	0.000	0.000
59	A	62	MET	0	-0.013	0.006	19.270	-0.403	-0.403	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.039	0.006	22.417	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	64	LEU	0	0.030	0.015	20.115	-0.067	-0.067	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.929	0.950	23.449	13.303	13.303	0.000	0.000	0.000	0.000
63	A	66	ILE	0	0.033	0.025	24.286	-0.545	-0.545	0.000	0.000	0.000	0.000
64	A	67	PRO	0	-0.002	0.008	26.311	0.412	0.412	0.000	0.000	0.000	0.000
65	A	68	ALA	0	0.040	0.038	29.238	0.029	0.029	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.994	0.996	32.750	9.118	9.118	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.854	0.940	33.973	7.762	7.762	0.000	0.000	0.000	0.000
68	A	71	ILE	0	0.026	0.027	36.143	-0.116	-0.116	0.000	0.000	0.000	0.000
69	A	72	PHE	0	-0.003	-0.008	38.902	0.093	0.093	0.000	0.000	0.000	0.000
70	A	73	GLY	0	0.079	0.025	42.564	0.056	0.056	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.831	-0.908	41.563	-7.794	-7.794	0.000	0.000	0.000	0.000
72	A	75	ASN	0	-0.039	-0.028	37.032	0.021	0.021	0.000	0.000	0.000	0.000
73	A	76	PHE	0	-0.102	-0.081	36.576	-0.293	-0.293	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.807	-0.881	38.419	-8.127	-8.127	0.000	0.000	0.000	0.000
75	A	78	PRO	0	0.025	-0.006	35.749	-0.319	-0.319	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.859	-0.919	34.433	-8.973	-8.973	0.000	0.000	0.000	0.000
77	A	80	PHE	0	-0.019	-0.013	33.944	-0.381	-0.381	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.034	-0.017	31.293	-0.432	-0.432	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.947	0.975	29.351	10.061	10.061	0.000	0.000	0.000	0.000
80	A	83	GLN	0	0.023	0.010	28.877	-0.418	-0.418	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.876	0.950	28.633	9.535	9.535	0.000	0.000	0.000	0.000
82	A	85	ARG	1	0.898	0.945	24.838	11.681	11.681	0.000	0.000	0.000	0.000
83	A	86	ALA	0	0.005	0.003	24.451	-0.658	-0.658	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.016	0.004	23.715	-0.524	-0.524	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.052	-0.032	23.794	-0.294	-0.294	0.000	0.000	0.000	0.000
86	A	89	ASN	0	0.033	0.003	19.085	-1.016	-1.016	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.845	-0.913	19.117	-16.882	-16.882	0.000	0.000	0.000	0.000
88	A	91	PHE	0	-0.048	-0.029	19.218	-0.711	-0.711	0.000	0.000	0.000	0.000
89	A	92	ILE	0	0.012	-0.009	17.410	-0.463	-0.463	0.000	0.000	0.000	0.000
90	A	93	GLN	0	-0.024	-0.021	14.794	-0.882	-0.882	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.010	-0.014	14.150	-1.768	-1.768	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.009	-0.006	14.952	-0.755	-0.755	0.000	0.000	0.000	0.000
93	A	96	VAL	0	-0.026	-0.008	11.008	-0.583	-0.583	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.846	0.931	10.013	16.547	16.547	0.000	0.000	0.000	0.000
95	A	98	TYR	0	0.012	0.010	10.297	-1.748	-1.748	0.000	0.000	0.000	0.000
96	A	99	PRO	0	0.070	0.041	9.036	1.040	1.040	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.903	-0.950	10.827	-17.696	-17.696	0.000	0.000	0.000	0.000
98	A	101	LEU	0	-0.031	-0.017	13.795	1.552	1.552	0.000	0.000	0.000	0.000
99	A	102	TYR	0	-0.014	-0.019	6.604	-0.288	-0.288	0.000	0.000	0.000	0.000
100	A	103	ASN	0	-0.020	-0.020	10.000	0.101	0.101	0.000	0.000	0.000	0.000
101	A	104	HIS	0	-0.032	-0.011	13.509	0.930	0.930	0.000	0.000	0.000	0.000
102	A	105	PRO	0	0.057	0.010	17.136	-0.364	-0.364	0.000	0.000	0.000	0.000
103	A	106	ASP	-1	-0.886	-0.940	19.244	-13.329	-13.329	0.000	0.000	0.000	0.000
104	A	107	VAL	0	-0.040	-0.020	15.435	0.346	0.346	0.000	0.000	0.000	0.000
105	A	108	ARG	1	0.863	0.897	10.986	23.688	23.688	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.004	0.015	16.636	0.120	0.120	0.000	0.000	0.000	0.000
107	A	110	PHE	0	-0.027	-0.027	19.407	0.505	0.505	0.000	0.000	0.000	0.000
108	A	111	LEU	0	0.036	0.003	14.524	0.593	0.593	0.000	0.000	0.000	0.000
109	A	112	GLN	0	-0.091	-0.048	17.164	-0.158	-0.158	0.000	0.000	0.000	0.000
110	A	113	MET	0	-0.026	-0.019	10.853	0.181	0.181	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.774	-0.830	14.420	-21.398	-21.398	0.000	0.000	0.000	0.000
112	A	115	SER	0	-0.031	-0.011	16.796	1.214	1.214	0.000	0.000	0.000	0.000
113	A	116	PRO	0	0.066	0.016	18.557	-0.569	-0.569	0.000	0.000	0.000	0.000
114	A	117	ARG	1	0.929	0.957	20.365	13.135	13.135	0.000	0.000	0.000	0.000
115	A	118	HIS	1	0.809	0.920	16.703	17.363	17.363	0.000	0.000	0.000	0.000
116	A	119	GLN	0	0.081	0.063	15.924	-0.500	-0.500	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)