FMO DATABASE

FMODB ID: QY5NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-960791.475184
FMO2-HF: Nuclear repulsion	915152.146168
FMO2-HF: Total energy	-45639.329016
FMO2-MP2: Total energy	-45774.28864

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.
8.003	13.866	25.35	-15.531	-15.682	0.067

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 : -0.887 / q_NPA : -0.955

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	0.051	0.036	3.781	-1.922	1.117	-0.038	-1.542	-1.459	0.009
4	A	4	THR	0	-0.065	-0.049	7.140	-1.905	-1.905	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.006	-0.004	9.984	0.486	0.486	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.004	-0.021	13.540	-0.222	-0.222	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.016	0.012	16.047	-0.483	-0.483	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.014	0.007	19.136	0.389	0.389	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.837	-0.924	20.860	13.806	13.806	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.091	-0.056	22.956	-0.719	-0.719	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.014	0.006	26.234	0.252	0.252	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.010	-0.001	28.805	-0.127	-0.127	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.058	0.038	31.020	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.038	0.017	33.100	0.269	0.269	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.066	-0.034	33.466	-0.224	-0.224	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.034	-0.036	31.107	-0.091	-0.091	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.909	-0.953	27.692	10.746	10.746	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.033	-0.015	23.568	0.028	0.028	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.027	0.013	20.811	0.217	0.217	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.036	-0.016	18.087	0.067	0.067	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.015	-0.016	16.134	0.533	0.533	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.040	-0.010	11.221	0.812	0.812	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.024	0.001	10.257	-0.384	-0.384	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.006	-0.030	6.334	0.749	0.749	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.981	-0.982	3.760	48.282	49.059	0.008	-0.303	-0.482	0.000
26	A	26	THR	0	0.056	0.031	2.002	-5.332	-3.775	15.952	-10.508	-7.001	0.040
27	A	27	VAL	0	-0.032	-0.028	3.091	-19.111	-19.184	0.055	1.018	-1.001	0.011
28	A	28	TYR	0	-0.039	-0.015	2.927	-19.392	-16.993	0.226	-1.271	-1.354	0.014
29	A	29	SER	0	-0.032	-0.022	6.467	-2.209	-2.209	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.030	0.024	10.058	0.838	0.838	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.007	0.027	7.666	-0.611	-0.611	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.815	-0.886	9.818	20.326	20.326	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.026	-0.024	9.142	2.895	2.895	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.018	-0.020	11.472	-2.290	-2.290	0.000	0.000	0.000	0.000
35	A	35	TRP	0	-0.022	-0.017	12.887	0.746	0.746	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.006	0.010	14.073	-1.354	-1.354	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.826	0.909	17.217	-11.634	-11.634	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.009	0.017	19.937	-0.231	-0.231	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.925	0.962	21.709	-11.173	-11.173	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.034	-0.011	25.384	0.161	0.161	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.846	-0.899	27.583	10.463	10.463	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.034	-0.020	24.496	-0.132	-0.132	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.075	-0.029	23.842	0.456	0.456	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.046	0.010	16.880	0.078	0.078	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.011	-0.006	21.139	-0.291	-0.291	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.055	0.020	17.699	0.456	0.456	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.066	-0.029	18.859	-0.714	-0.714	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.025	0.000	18.126	-0.666	-0.666	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.047	-0.029	14.795	0.299	0.299	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.006	-0.008	15.250	-1.258	-1.258	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.772	-0.860	14.085	19.374	19.374	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.995	-1.029	14.250	19.253	19.253	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.067	-0.027	15.948	-1.184	-1.184	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.900	0.957	18.966	-16.326	-16.326	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.037	-0.032	18.551	0.826	0.826	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.947	-0.971	19.908	12.381	12.381	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.036	0.011	20.596	0.744	0.744	0.000	0.000	0.000	0.000
58	A	57	ALA	0	-0.007	-0.009	22.641	-0.326	-0.326	0.000	0.000	0.000	0.000
59	A	57	ASP	-1	-0.847	-0.916	24.191	10.603	10.603	0.000	0.000	0.000	0.000
60	A	57	PHE	0	-0.098	-0.049	23.781	-0.274	-0.274	0.000	0.000	0.000	0.000
61	A	57	THR	0	-0.075	-0.053	23.387	-0.097	-0.097	0.000	0.000	0.000	0.000
62	A	57	GLN	0	0.037	0.015	26.749	0.256	0.256	0.000	0.000	0.000	0.000
63	A	58	GLY	0	-0.011	-0.008	29.200	-0.355	-0.355	0.000	0.000	0.000	0.000
64	A	59	ARG	1	0.788	0.887	29.055	-10.329	-10.329	0.000	0.000	0.000	0.000
65	A	60	PHE	0	0.000	0.010	23.021	0.166	0.166	0.000	0.000	0.000	0.000
66	A	61	SER	0	-0.020	-0.003	23.570	-0.158	-0.158	0.000	0.000	0.000	0.000
67	A	62	VAL	0	0.050	0.027	18.053	0.257	0.257	0.000	0.000	0.000	0.000
68	A	63	LYS	1	0.918	0.958	19.264	-14.044	-14.044	0.000	0.000	0.000	0.000
69	A	64	HIS	0	0.037	0.031	13.921	1.958	1.958	0.000	0.000	0.000	0.000
70	A	65	ILE	0	-0.062	-0.024	15.950	-0.917	-0.917	0.000	0.000	0.000	0.000
71	A	66	LEU	0	0.080	0.034	14.172	1.128	1.128	0.000	0.000	0.000	0.000
72	A	67	THR	0	-0.037	-0.026	13.565	1.448	1.448	0.000	0.000	0.000	0.000
73	A	68	GLN	0	-0.033	-0.021	13.760	0.532	0.532	0.000	0.000	0.000	0.000
74	A	69	LYS	1	0.927	1.003	7.693	-34.278	-34.278	0.000	0.000	0.000	0.000
75	A	70	ALA	0	0.009	0.004	10.654	0.950	0.950	0.000	0.000	0.000	0.000
76	A	71	PHE	0	0.069	0.013	12.794	-0.535	-0.535	0.000	0.000	0.000	0.000
77	A	72	HIS	0	0.032	0.026	14.547	0.085	0.085	0.000	0.000	0.000	0.000
78	A	73	LEU	0	0.046	0.043	17.457	-0.443	-0.443	0.000	0.000	0.000	0.000
79	A	74	VAL	0	-0.025	-0.006	19.590	-0.178	-0.178	0.000	0.000	0.000	0.000
80	A	75	ILE	0	-0.027	-0.002	22.977	-0.108	-0.108	0.000	0.000	0.000	0.000
81	A	76	SER	0	-0.031	0.003	25.860	-0.320	-0.320	0.000	0.000	0.000	0.000
82	A	77	PRO	0	0.009	0.013	29.449	-0.062	-0.062	0.000	0.000	0.000	0.000
83	A	78	VAL	0	0.032	0.002	27.471	0.101	0.101	0.000	0.000	0.000	0.000
84	A	79	ARG	1	0.906	0.943	30.093	-9.233	-9.233	0.000	0.000	0.000	0.000
85	A	80	THR	0	0.047	0.009	30.587	0.285	0.285	0.000	0.000	0.000	0.000
86	A	81	GLU	-1	-0.893	-0.942	30.025	9.589	9.589	0.000	0.000	0.000	0.000
87	A	82	ASP	-1	-0.747	-0.868	26.462	10.951	10.951	0.000	0.000	0.000	0.000
88	A	83	SER	0	-0.021	0.013	25.766	0.468	0.468	0.000	0.000	0.000	0.000
89	A	84	ALA	0	-0.018	-0.003	22.914	-0.100	-0.100	0.000	0.000	0.000	0.000
90	A	85	THR	0	-0.026	-0.004	18.536	-0.164	-0.164	0.000	0.000	0.000	0.000
91	A	86	TYR	0	-0.018	-0.026	17.959	0.267	0.267	0.000	0.000	0.000	0.000
92	A	87	TYR	0	0.006	-0.004	13.383	-0.087	-0.087	0.000	0.000	0.000	0.000
93	A	89	ALA	0	0.018	-0.009	8.317	0.749	0.749	0.000	0.000	0.000	0.000
94	A	90	PHE	0	0.029	0.019	1.820	-1.861	-4.175	6.406	-1.707	-2.385	-0.007
95	A	91	THR	0	-0.016	-0.015	6.790	1.503	1.503	0.000	0.000	0.000	0.000
96	A	92	LEU	0	-0.042	-0.008	3.484	2.478	3.343	0.037	-0.402	-0.500	0.003
97	A	98	PRO	0	0.037	0.017	6.579	-4.385	-4.385	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.067	0.050	9.811	0.615	0.615	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.065	-0.048	11.908	0.933	0.933	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.046	-0.025	8.266	-1.728	-1.728	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.838	-0.913	10.787	21.692	21.692	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.846	0.914	9.523	-25.785	-25.785	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.021	0.010	8.084	2.917	2.917	0.000	0.000	0.000	0.000
104	A	105	ILE	0	0.006	0.024	2.346	-0.779	-1.166	2.704	-0.816	-1.500	-0.003
105	A	106	PHE	0	-0.002	-0.020	6.108	-0.954	-0.954	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.010	0.014	8.383	1.370	1.370	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.893	0.928	10.140	-17.910	-17.910	0.000	0.000	0.000	0.000
108	A	109	GLY	0	-0.002	0.016	13.222	-0.928	-0.928	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.019	-0.013	15.753	0.194	0.194	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.915	0.951	18.666	-11.547	-11.547	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.017	0.014	22.148	-0.098	-0.098	0.000	0.000	0.000	0.000
112	A	113	THR	0	-0.028	-0.007	24.663	0.055	0.055	0.000	0.000	0.000	0.000
113	A	114	VAL	0	-0.004	-0.006	28.171	-0.099	-0.099	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.896	-0.950	30.768	8.696	8.696	0.000	0.000	0.000	0.000
115	A	116	PRO	0	-0.030	-0.012	34.394	-0.031	-0.031	0.000	0.000	0.000	0.000

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