FMO DATABASE

FMODB ID: 89NKY

Calculation Name: 3TV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TV0

Chain ID: A

ChEMBL ID:

UniProt ID: O00399

Base Structure: X-ray

Registration Date: 2023-09-22

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1256201.450231
FMO2-HF: Nuclear repulsion	1200985.450419
FMO2-HF: Total energy	-55215.999812
FMO2-MP2: Total energy	-55372.306581

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:8:SER)

Summations of interaction energy for fragment #1(A:8:SER)

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.
0.597	3.577	0.148	-1.191	-1.934	0.003

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.014

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

Sort

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	10	LYS	1	0.797	0.890	3.740	4.570	6.284	0.003	-0.708	-1.009	0.002
4	A	11	ILE	0	0.038	0.019	6.028	0.483	0.483	0.000	0.000	0.000	0.000
5	A	12	ALA	0	0.013	0.017	9.503	0.051	0.051	0.000	0.000	0.000	0.000
6	A	13	PRO	0	-0.006	-0.010	12.442	0.081	0.081	0.000	0.000	0.000	0.000
7	A	14	GLY	0	0.007	-0.010	14.945	0.018	0.018	0.000	0.000	0.000	0.000
8	A	15	ALA	0	-0.027	0.008	13.831	0.028	0.028	0.000	0.000	0.000	0.000
9	A	16	VAL	0	-0.045	-0.026	15.981	0.020	0.020	0.000	0.000	0.000	0.000
10	A	17	VAL	0	0.025	0.004	11.371	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.033	0.007	14.706	0.018	0.018	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.023	0.015	14.147	0.013	0.013	0.000	0.000	0.000	0.000
13	A	20	GLU	-1	-0.891	-0.951	14.795	0.140	0.140	0.000	0.000	0.000	0.000
14	A	21	SER	0	-0.081	-0.031	13.539	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	22	GLU	-1	-0.837	-0.903	11.804	0.514	0.514	0.000	0.000	0.000	0.000
16	A	23	ILE	0	0.014	-0.003	7.153	-0.094	-0.094	0.000	0.000	0.000	0.000
17	A	24	ARG	1	0.833	0.892	6.465	-0.559	-0.559	0.000	0.000	0.000	0.000
18	A	25	GLY	0	0.045	0.028	4.625	-0.873	-0.785	0.000	-0.022	-0.065	0.000
19	A	26	ASP	-1	-0.886	-0.938	2.992	-2.755	-1.810	0.136	-0.429	-0.651	0.001
20	A	27	VAL	0	0.040	0.022	3.835	-0.785	-0.552	0.009	-0.032	-0.209	0.000
21	A	28	THR	0	-0.023	-0.018	6.222	-1.245	-1.245	0.000	0.000	0.000	0.000
22	A	29	ILE	0	0.022	0.015	8.612	0.310	0.310	0.000	0.000	0.000	0.000
23	A	30	GLY	0	0.038	0.015	11.627	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	31	PRO	0	-0.004	-0.011	14.641	0.035	0.035	0.000	0.000	0.000	0.000
25	A	32	ARG	1	0.948	0.962	16.902	0.242	0.242	0.000	0.000	0.000	0.000
26	A	33	THR	0	-0.021	0.014	15.609	0.053	0.053	0.000	0.000	0.000	0.000
27	A	34	VAL	0	-0.023	-0.008	17.146	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	35	ILE	0	0.004	0.001	12.658	0.009	0.009	0.000	0.000	0.000	0.000
29	A	36	HIS	0	0.035	0.002	16.621	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	37	PRO	0	0.018	-0.006	17.550	0.021	0.021	0.000	0.000	0.000	0.000
31	A	38	LYS	1	0.784	0.860	18.081	-0.086	-0.086	0.000	0.000	0.000	0.000
32	A	39	ALA	0	-0.024	0.028	16.366	0.015	0.015	0.000	0.000	0.000	0.000
33	A	40	ARG	1	0.879	0.927	13.945	-0.148	-0.148	0.000	0.000	0.000	0.000
34	A	41	ILE	0	0.016	0.008	10.793	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	42	ILE	0	0.012	-0.001	9.967	0.155	0.155	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.006	-0.004	6.894	-0.174	-0.174	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.923	-0.958	8.416	0.957	0.957	0.000	0.000	0.000	0.000
38	A	45	ALA	0	0.005	0.018	11.002	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	46	GLY	0	-0.050	-0.032	9.681	-0.125	-0.125	0.000	0.000	0.000	0.000
40	A	47	PRO	0	-0.013	0.006	7.040	0.205	0.205	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.021	0.023	7.997	0.090	0.090	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.061	-0.021	9.032	-0.257	-0.257	0.000	0.000	0.000	0.000
43	A	50	ILE	0	0.034	0.022	11.526	0.122	0.122	0.000	0.000	0.000	0.000
44	A	51	GLY	0	0.027	0.017	14.239	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.945	-0.993	16.766	-0.258	-0.258	0.000	0.000	0.000	0.000
46	A	53	GLY	0	0.068	0.022	19.196	0.024	0.024	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.041	-0.014	17.766	0.057	0.057	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.019	0.011	19.745	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	56	ILE	0	-0.023	-0.012	16.172	0.011	0.011	0.000	0.000	0.000	0.000
50	A	57	GLU	-1	-0.787	-0.900	19.084	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.739	-0.876	20.444	0.048	0.048	0.000	0.000	0.000	0.000
52	A	59	GLN	0	-0.056	-0.034	20.564	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	60	ALA	0	0.006	0.045	19.529	0.017	0.017	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.059	-0.034	16.048	0.029	0.029	0.000	0.000	0.000	0.000
55	A	62	ILE	0	0.033	0.020	14.496	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	63	ILE	0	0.003	-0.005	13.579	0.055	0.055	0.000	0.000	0.000	0.000
57	A	64	ASN	0	-0.024	-0.010	11.545	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	65	ALA	0	0.042	0.025	13.331	0.071	0.071	0.000	0.000	0.000	0.000
59	A	66	TYR	0	0.004	-0.015	12.481	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	67	PRO	0	-0.019	-0.005	17.594	0.003	0.003	0.000	0.000	0.000	0.000
61	A	68	ASP	-1	-0.884	-0.934	20.997	0.059	0.059	0.000	0.000	0.000	0.000
62	A	69	ASN	0	-0.096	-0.062	23.439	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	70	ILE	0	0.020	0.020	22.750	0.003	0.003	0.000	0.000	0.000	0.000
64	A	80	LYS	1	0.930	0.948	10.677	0.107	0.107	0.000	0.000	0.000	0.000
65	A	81	PRO	0	-0.027	-0.022	11.089	0.052	0.052	0.000	0.000	0.000	0.000
66	A	82	MET	0	-0.013	0.013	12.110	0.037	0.037	0.000	0.000	0.000	0.000
67	A	83	ILE	0	-0.075	-0.043	13.075	-0.087	-0.087	0.000	0.000	0.000	0.000
68	A	84	ILE	0	0.020	0.003	15.113	0.053	0.053	0.000	0.000	0.000	0.000
69	A	85	GLY	0	0.018	0.023	16.875	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	86	THR	0	-0.071	-0.060	18.912	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	87	ASN	0	-0.037	-0.032	21.516	0.026	0.026	0.000	0.000	0.000	0.000
72	A	88	ASN	0	0.000	0.004	20.632	0.037	0.037	0.000	0.000	0.000	0.000
73	A	89	VAL	0	0.008	-0.001	21.962	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	90	PHE	0	0.003	-0.024	18.984	0.009	0.009	0.000	0.000	0.000	0.000
75	A	91	GLU	-1	-0.746	-0.864	22.333	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	92	VAL	0	0.019	0.005	23.965	0.013	0.013	0.000	0.000	0.000	0.000
77	A	93	GLY	0	-0.064	-0.040	23.298	0.001	0.001	0.000	0.000	0.000	0.000
78	A	94	CYS	0	-0.122	-0.012	23.019	0.006	0.006	0.000	0.000	0.000	0.000
79	A	95	TYR	0	0.002	-0.009	19.304	0.020	0.020	0.000	0.000	0.000	0.000
80	A	96	SER	0	0.014	0.003	18.843	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	97	GLN	0	0.004	-0.017	18.049	0.017	0.017	0.000	0.000	0.000	0.000
82	A	98	ALA	0	0.021	0.037	18.828	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	99	MET	0	-0.030	-0.011	14.952	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	100	LYS	1	0.927	0.958	17.417	0.148	0.148	0.000	0.000	0.000	0.000
85	A	101	MET	0	-0.015	0.009	19.587	0.025	0.025	0.000	0.000	0.000	0.000
86	A	102	GLY	0	0.013	0.021	20.455	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	103	ASP	-1	-0.816	-0.886	22.088	-0.231	-0.231	0.000	0.000	0.000	0.000
88	A	104	ASN	0	-0.001	-0.007	24.580	0.014	0.014	0.000	0.000	0.000	0.000
89	A	105	ASN	0	-0.051	-0.028	24.094	0.024	0.024	0.000	0.000	0.000	0.000
90	A	106	VAL	0	0.025	0.007	25.766	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	107	ILE	0	-0.031	-0.012	22.502	0.005	0.005	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.805	-0.905	26.034	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	109	SER	0	-0.018	-0.047	27.494	0.009	0.009	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.858	0.916	26.603	-0.049	-0.049	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.018	0.030	27.514	0.006	0.006	0.000	0.000	0.000	0.000
96	A	112	TYR	0	-0.064	-0.051	22.106	0.003	0.003	0.000	0.000	0.000	0.000
97	A	113	VAL	0	0.004	0.006	23.240	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	114	GLY	0	0.075	0.020	22.637	0.006	0.006	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.870	0.925	16.501	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	116	ASN	0	-0.069	-0.028	21.583	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	117	VAL	0	-0.006	0.023	24.010	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	118	ILE	0	-0.058	-0.031	22.354	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	119	LEU	0	0.032	0.011	23.434	0.008	0.008	0.000	0.000	0.000	0.000
104	A	120	THR	0	-0.034	-0.038	24.247	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	121	SER	0	0.091	0.044	25.445	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	122	GLY	0	-0.014	0.011	27.782	0.010	0.010	0.000	0.000	0.000	0.000
107	A	123	CYS	0	-0.081	-0.020	28.232	0.010	0.010	0.000	0.000	0.000	0.000
108	A	124	ILE	0	0.008	-0.003	29.031	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	125	ILE	0	-0.029	-0.017	27.383	0.005	0.005	0.000	0.000	0.000	0.000
110	A	126	GLY	0	0.053	0.019	29.821	0.002	0.002	0.000	0.000	0.000	0.000
111	A	127	ALA	0	0.039	0.000	31.024	0.005	0.005	0.000	0.000	0.000	0.000
112	A	128	CYS	0	-0.123	-0.061	30.622	0.004	0.004	0.000	0.000	0.000	0.000
113	A	129	CYS	0	-0.081	0.006	31.141	0.002	0.002	0.000	0.000	0.000	0.000
114	A	130	ASN	0	0.010	0.007	29.189	0.006	0.006	0.000	0.000	0.000	0.000
115	A	131	LEU	0	0.047	0.015	27.996	0.000	0.000	0.000	0.000	0.000	0.000
116	A	132	ASN	0	-0.046	-0.029	26.308	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	133	THR	0	-0.030	-0.042	28.217	0.003	0.003	0.000	0.000	0.000	0.000
118	A	134	PHE	0	0.000	-0.019	27.613	0.000	0.000	0.000	0.000	0.000	0.000
119	A	135	GLU	-1	-0.775	-0.823	28.242	-0.037	-0.037	0.000	0.000	0.000	0.000
120	A	136	VAL	0	0.000	-0.003	27.064	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	137	ILE	0	0.014	0.012	27.872	0.003	0.003	0.000	0.000	0.000	0.000
122	A	138	PRO	0	0.014	0.020	29.585	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	139	GLU	-1	-0.860	-0.919	29.965	-0.110	-0.110	0.000	0.000	0.000	0.000
124	A	140	ASN	0	-0.074	-0.042	31.794	0.003	0.003	0.000	0.000	0.000	0.000
125	A	141	THR	0	-0.004	-0.014	32.480	0.008	0.008	0.000	0.000	0.000	0.000
126	A	142	VAL	0	-0.011	-0.001	32.437	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	143	ILE	0	-0.009	-0.016	30.972	0.003	0.003	0.000	0.000	0.000	0.000
128	A	144	TYR	0	0.026	0.000	33.268	0.003	0.003	0.000	0.000	0.000	0.000
129	A	145	GLY	0	0.023	0.020	35.671	0.001	0.001	0.000	0.000	0.000	0.000
130	A	146	ALA	0	0.036	0.008	34.389	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	147	ASP	-1	-0.872	-0.954	34.223	0.000	0.000	0.000	0.000	0.000	0.000
132	A	149	LEU	0	-0.016	-0.009	35.174	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	150	ARG	1	0.890	0.966	38.399	0.006	0.006	0.000	0.000	0.000	0.000
134	A	151	ARG	1	0.841	0.880	32.885	0.031	0.031	0.000	0.000	0.000	0.000
135	A	152	VAL	0	-0.023	-0.003	37.706	0.002	0.002	0.000	0.000	0.000	0.000
136	A	153	GLN	0	0.031	0.023	35.652	0.000	0.000	0.000	0.000	0.000	0.000
137	A	154	THR	0	0.013	-0.001	34.363	0.003	0.003	0.000	0.000	0.000	0.000
138	A	155	GLU	-1	-0.954	-0.971	37.600	-0.045	-0.045	0.000	0.000	0.000	0.000
139	A	156	ARG	1	0.877	0.939	35.978	0.060	0.060	0.000	0.000	0.000	0.000
140	A	157	PRO	0	-0.027	-0.010	36.411	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	158	GLN	0	0.091	0.036	29.980	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	159	PRO	0	-0.027	0.006	31.048	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)