FMO DATABASE

FMODB ID: K9Q23

Calculation Name: 1TVD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TVD

Chain ID: A

ChEMBL ID:

UniProt ID: A0JD37

Base Structure: X-ray

Registration Date: 2023-06-26

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-961667.602716
FMO2-HF: Nuclear repulsion	916027.994846
FMO2-HF: Total energy	-45639.60787
FMO2-MP2: Total energy	-45774.598862

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:1:ASP)

Summations of interaction energy for fragment #1(A:1: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.
-7.572	-15.805	45.173	-20.652	-16.287	0.103

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.865 / q_NPA : -0.916

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	3	VAL	0	0.066	0.046	3.781	-1.022	1.791	-0.034	-1.399	-1.379	0.007
4	A	4	THR	0	-0.065	-0.046	7.160	-1.735	-1.735	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.016	-0.002	10.051	0.625	0.625	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.010	-0.010	13.585	-0.247	-0.247	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.011	0.013	16.116	-0.499	-0.499	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.007	0.017	19.140	0.382	0.382	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.837	-0.919	20.800	14.160	14.160	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.075	-0.050	22.956	-0.670	-0.670	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.022	0.013	26.261	0.271	0.271	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.004	0.003	28.933	-0.123	-0.123	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.057	0.041	31.071	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.040	0.009	33.170	0.274	0.274	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.060	-0.031	33.550	-0.230	-0.230	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.038	-0.028	31.243	-0.089	-0.089	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.869	-0.908	27.869	10.737	10.737	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.044	-0.022	23.721	0.026	0.026	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.030	0.013	20.867	0.228	0.228	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.033	-0.011	18.140	0.045	0.045	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.017	-0.018	16.197	0.543	0.543	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.030	-0.009	11.347	0.869	0.869	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.004	0.012	9.550	-1.327	-1.327	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.053	-0.046	6.429	0.784	0.784	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.973	-0.978	3.819	44.560	45.129	0.004	-0.255	-0.319	0.000
26	A	26	THR	0	0.043	-0.006	1.527	-9.012	-24.405	39.818	-16.806	-7.619	0.065
27	A	27	VAL	0	-0.031	-0.029	3.191	-19.565	-20.850	0.048	1.986	-0.749	0.009
28	A	28	TYR	0	-0.036	-0.011	2.658	-24.258	-21.203	0.879	-1.781	-2.153	0.021
29	A	29	SER	0	-0.018	-0.018	6.253	-2.064	-2.064	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.015	0.022	9.791	1.101	1.101	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.017	0.028	7.071	-0.556	-0.556	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.798	-0.876	9.221	20.338	20.338	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.043	-0.026	9.452	3.267	3.267	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.005	-0.019	11.601	-2.472	-2.472	0.000	0.000	0.000	0.000
35	A	35	TRP	0	-0.020	-0.023	12.992	0.785	0.785	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.001	0.006	13.840	-1.421	-1.421	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.828	0.904	17.277	-11.795	-11.795	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.008	0.015	19.955	-0.233	-0.233	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.887	0.926	21.718	-10.964	-10.964	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.030	-0.014	25.373	0.151	0.151	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.814	-0.849	27.568	10.597	10.597	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.020	-0.013	24.476	-0.164	-0.164	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.069	-0.047	23.822	0.431	0.431	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.034	0.006	16.784	0.097	0.097	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.015	-0.009	21.179	-0.394	-0.394	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.049	0.021	17.704	0.459	0.459	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.060	-0.028	18.946	-0.732	-0.732	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.017	0.002	18.289	-0.689	-0.689	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.044	-0.032	15.546	0.309	0.309	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.009	-0.006	15.405	-1.331	-1.331	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.732	-0.843	13.762	19.602	19.602	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.984	-1.028	13.805	19.864	19.864	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.089	-0.034	15.479	-1.217	-1.217	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.822	0.916	18.503	-17.014	-17.014	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.015	-0.026	18.437	1.024	1.024	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.938	-0.955	20.059	12.868	12.868	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.058	0.014	20.735	0.765	0.765	0.000	0.000	0.000	0.000
58	A	57	ALA	0	-0.011	-0.006	22.774	-0.338	-0.338	0.000	0.000	0.000	0.000
59	A	57	ASP	-1	-0.864	-0.922	24.303	10.942	10.942	0.000	0.000	0.000	0.000
60	A	57	PHE	0	-0.084	-0.043	23.711	-0.304	-0.304	0.000	0.000	0.000	0.000
61	A	57	THR	0	-0.069	-0.059	23.441	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	57	GLN	0	0.028	0.013	26.868	0.287	0.287	0.000	0.000	0.000	0.000
63	A	58	GLY	0	-0.005	-0.006	29.334	-0.365	-0.365	0.000	0.000	0.000	0.000
64	A	59	ARG	1	0.763	0.860	29.037	-10.435	-10.435	0.000	0.000	0.000	0.000
65	A	60	PHE	0	-0.005	0.006	23.227	0.187	0.187	0.000	0.000	0.000	0.000
66	A	61	SER	0	-0.013	0.005	23.731	-0.160	-0.160	0.000	0.000	0.000	0.000
67	A	62	VAL	0	0.044	0.019	18.227	0.256	0.256	0.000	0.000	0.000	0.000
68	A	63	LYS	1	0.918	0.960	19.398	-14.163	-14.163	0.000	0.000	0.000	0.000
69	A	64	HIS	0	0.047	0.032	13.513	2.038	2.038	0.000	0.000	0.000	0.000
70	A	65	ILE	0	-0.061	-0.022	15.960	-0.915	-0.915	0.000	0.000	0.000	0.000
71	A	66	LEU	0	0.075	0.035	13.973	1.166	1.166	0.000	0.000	0.000	0.000
72	A	67	THR	0	-0.030	-0.025	13.556	1.441	1.441	0.000	0.000	0.000	0.000
73	A	68	GLN	0	-0.039	-0.023	13.797	0.306	0.306	0.000	0.000	0.000	0.000
74	A	69	LYS	1	0.909	0.992	7.076	-37.491	-37.491	0.000	0.000	0.000	0.000
75	A	70	ALA	0	0.009	0.002	10.672	0.977	0.977	0.000	0.000	0.000	0.000
76	A	71	PHE	0	0.068	0.015	12.904	-0.521	-0.521	0.000	0.000	0.000	0.000
77	A	72	HIS	0	0.029	0.028	14.623	0.148	0.148	0.000	0.000	0.000	0.000
78	A	73	LEU	0	0.048	0.042	17.483	-0.441	-0.441	0.000	0.000	0.000	0.000
79	A	74	VAL	0	-0.041	-0.012	19.715	-0.202	-0.202	0.000	0.000	0.000	0.000
80	A	75	ILE	0	-0.031	-0.008	22.926	-0.105	-0.105	0.000	0.000	0.000	0.000
81	A	76	SER	0	-0.051	-0.026	25.970	-0.325	-0.325	0.000	0.000	0.000	0.000
82	A	77	PRO	0	0.018	0.013	29.565	-0.067	-0.067	0.000	0.000	0.000	0.000
83	A	78	VAL	0	0.015	-0.009	27.513	0.116	0.116	0.000	0.000	0.000	0.000
84	A	79	ARG	1	0.880	0.911	30.181	-9.377	-9.377	0.000	0.000	0.000	0.000
85	A	80	THR	0	0.053	0.009	30.652	0.282	0.282	0.000	0.000	0.000	0.000
86	A	81	GLU	-1	-0.842	-0.887	30.030	9.656	9.656	0.000	0.000	0.000	0.000
87	A	82	ASP	-1	-0.745	-0.843	26.536	11.073	11.073	0.000	0.000	0.000	0.000
88	A	83	SER	0	-0.016	0.009	25.819	0.465	0.465	0.000	0.000	0.000	0.000
89	A	84	ALA	0	-0.018	0.001	22.937	-0.102	-0.102	0.000	0.000	0.000	0.000
90	A	85	THR	0	-0.038	-0.010	18.559	-0.154	-0.154	0.000	0.000	0.000	0.000
91	A	86	TYR	0	-0.009	-0.021	18.055	0.286	0.286	0.000	0.000	0.000	0.000
92	A	87	TYR	0	0.013	0.002	13.359	-0.130	-0.130	0.000	0.000	0.000	0.000
93	A	89	ALA	0	0.011	-0.011	8.393	0.701	0.701	0.000	0.000	0.000	0.000
94	A	90	PHE	0	0.027	0.014	2.047	-5.499	-4.242	2.415	-1.447	-2.225	0.001
95	A	91	THR	0	-0.025	-0.020	6.873	1.422	1.422	0.000	0.000	0.000	0.000
96	A	92	LEU	0	-0.031	-0.001	3.457	3.109	3.987	0.047	-0.373	-0.551	0.002
97	A	98	PRO	0	0.043	0.016	6.562	-4.707	-4.707	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.063	0.049	9.734	0.471	0.471	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.076	-0.049	11.867	0.931	0.931	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.047	-0.021	8.185	-1.779	-1.779	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.856	-0.932	10.754	22.332	22.332	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.864	0.927	9.613	-25.535	-25.535	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.020	0.012	8.116	3.118	3.118	0.000	0.000	0.000	0.000
104	A	105	ILE	0	0.000	0.019	2.452	-1.167	-1.294	1.996	-0.577	-1.292	-0.002
105	A	106	PHE	0	-0.003	-0.020	6.085	-0.747	-0.747	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.016	0.020	8.344	1.257	1.257	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.835	0.912	10.141	-16.997	-16.997	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.023	0.020	13.186	-0.989	-0.989	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.048	-0.033	15.750	0.173	0.173	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.908	0.934	18.685	-11.537	-11.537	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.019	0.014	22.204	-0.100	-0.100	0.000	0.000	0.000	0.000
112	A	113	THR	0	-0.035	-0.012	24.699	0.052	0.052	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.002	0.001	28.198	-0.100	-0.100	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.874	-0.938	30.812	8.845	8.845	0.000	0.000	0.000	0.000
115	A	116	PRO	0	-0.032	-0.015	34.432	-0.030	-0.030	0.000	0.000	0.000	0.000

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