FMO DATABASE

FMODB ID: QVY3Y

Calculation Name: 3JTE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JTE

Chain ID: A

ChEMBL ID:

UniProt ID: A3DCZ0

Base Structure: X-ray

Registration Date: 2023-09-21

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1088621.978171
FMO2-HF: Nuclear repulsion	1039012.742842
FMO2-HF: Total energy	-49609.235329
FMO2-MP2: Total energy	-49751.122362

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-13.162	-6.03	1.303	-3.74	-4.696	-0.025

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.010

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	5	LYS	1	0.916	0.970	3.588	-0.179	2.226	0.009	-1.204	-1.210	0.005
4	A	6	ILE	0	-0.013	-0.014	6.070	0.687	0.687	0.000	0.000	0.000	0.000
5	A	7	LEU	0	-0.019	0.006	8.823	0.095	0.095	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.011	-0.016	11.910	0.073	0.073	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.032	-0.034	14.467	0.041	0.041	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.822	-0.941	18.232	-0.350	-0.350	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.896	-0.963	20.827	-0.279	-0.279	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.951	-0.956	23.043	-0.214	-0.214	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.006	-0.016	21.409	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.025	0.001	20.213	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.028	0.030	19.829	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.010	-0.004	16.392	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.058	-0.032	15.786	-0.071	-0.071	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.020	-0.011	15.194	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.006	0.001	13.465	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.831	0.906	10.364	0.592	0.592	0.000	0.000	0.000	0.000
19	A	21	PHE	0	0.010	0.006	10.252	-0.092	-0.092	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.018	-0.009	10.579	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.023	-0.003	8.489	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.797	-0.874	5.951	-1.053	-1.053	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.077	-0.030	5.790	0.005	0.005	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.901	-0.921	7.778	-0.736	-0.736	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.012	0.011	3.584	0.019	0.268	0.008	-0.061	-0.197	0.000
26	A	28	ASN	0	-0.114	-0.077	2.791	-7.192	-3.459	1.257	-2.347	-2.643	-0.030
27	A	29	GLU	-1	-0.895	-0.951	3.219	-2.653	-1.926	0.030	-0.122	-0.635	0.000
28	A	30	VAL	0	-0.034	-0.032	4.718	-0.021	-0.003	-0.001	-0.006	-0.011	0.000
29	A	31	LEU	0	-0.002	0.005	8.458	0.233	0.233	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.001	-0.007	11.365	0.007	0.007	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.031	-0.010	14.829	0.035	0.035	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.010	0.000	18.318	0.013	0.013	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.028	-0.003	21.604	0.038	0.038	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.077	0.016	22.114	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.010	-0.003	22.987	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.858	-0.914	19.657	-0.399	-0.399	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.054	0.014	18.500	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.016	0.000	18.505	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.860	0.959	20.562	0.367	0.367	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.053	0.023	14.642	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.031	-0.003	14.715	-0.068	-0.068	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.015	-0.029	16.471	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.951	-0.975	17.180	-0.442	-0.442	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.078	-0.039	12.042	-0.098	-0.098	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.031	-0.002	12.725	-0.153	-0.153	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.003	-0.011	13.175	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.057	-0.028	8.290	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.002	0.022	8.097	-0.528	-0.528	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.832	-0.908	6.278	-2.951	-2.951	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.022	-0.015	9.514	0.304	0.304	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.001	0.012	11.511	-0.099	-0.099	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.007	0.008	11.886	0.090	0.090	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.017	0.003	15.521	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.737	-0.841	18.974	-0.297	-0.297	0.000	0.000	0.000	0.000
55	A	57	MET	0	-0.024	-0.012	21.951	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.764	0.883	24.929	0.230	0.230	0.000	0.000	0.000	0.000
57	A	59	MET	0	0.038	0.042	23.077	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	60	PRO	0	0.028	0.018	26.670	0.018	0.018	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.885	0.947	28.508	0.185	0.185	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.019	-0.008	26.864	0.008	0.008	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.029	-0.001	26.798	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.061	0.014	23.725	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.010	0.000	24.218	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.844	-0.906	26.679	-0.242	-0.242	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.001	0.000	20.930	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.011	0.000	21.806	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.826	0.895	23.159	0.223	0.223	0.000	0.000	0.000	0.000
68	A	70	GLU	-1	-0.885	-0.960	24.574	-0.268	-0.268	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.010	0.009	18.304	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.784	0.911	19.760	0.412	0.412	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.884	0.954	22.871	0.267	0.267	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.029	0.005	19.913	0.016	0.016	0.000	0.000	0.000	0.000
73	A	75	THR	0	-0.016	-0.010	16.450	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.032	0.009	19.477	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	77	HIS	0	-0.040	-0.031	17.875	0.004	0.004	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.022	0.016	13.132	-0.053	-0.053	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.003	0.007	13.852	0.090	0.090	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.013	0.002	15.179	-0.079	-0.079	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.019	0.008	13.817	0.067	0.067	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.010	-0.011	17.620	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.024	0.025	17.317	0.028	0.028	0.000	0.000	0.000	0.000
82	A	84	THR	0	-0.020	-0.023	21.293	0.015	0.015	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.021	-0.001	25.073	0.004	0.004	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.008	-0.012	27.911	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	GLY	0	0.000	-0.006	31.707	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.757	-0.857	28.235	-0.225	-0.225	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.011	-0.002	29.733	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.863	-0.935	30.727	-0.154	-0.154	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.015	-0.007	29.394	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.020	0.010	26.426	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.005	-0.008	27.097	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.024	-0.015	29.372	0.000	0.000	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.085	0.021	24.990	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	MET	0	-0.048	-0.005	22.873	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.862	0.940	26.140	0.171	0.171	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.878	-0.917	27.061	-0.218	-0.218	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.012	0.004	24.368	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.031	-0.020	21.450	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.068	-0.031	16.373	0.011	0.011	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.886	-0.964	18.113	-0.338	-0.338	0.000	0.000	0.000	0.000
101	A	103	TYR	0	0.004	-0.003	20.188	-0.023	-0.023	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.001	0.006	17.074	0.020	0.020	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.927	0.966	21.540	0.174	0.174	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.862	0.933	23.067	0.289	0.289	0.000	0.000	0.000	0.000
105	A	107	PRO	0	-0.035	-0.037	23.964	0.018	0.018	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.026	0.010	18.177	0.009	0.009	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.036	-0.042	19.428	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.046	0.006	14.406	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.006	0.007	14.475	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.827	-0.898	15.749	-0.274	-0.274	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.000	-0.005	12.905	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.008	-0.019	10.231	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.025	-0.014	11.769	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.027	0.020	14.296	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	117	ILE	0	0.017	0.002	8.196	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.003	0.009	9.977	-0.044	-0.044	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.026	-0.022	11.032	0.076	0.076	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.020	-0.006	12.144	0.039	0.039	0.000	0.000	0.000	0.000
119	A	121	ILE	0	0.015	0.003	6.291	0.027	0.027	0.000	0.000	0.000	0.000
120	A	122	ASN	0	-0.025	-0.012	10.012	0.128	0.128	0.000	0.000	0.000	0.000
121	A	123	ARG	1	0.951	0.981	12.457	0.433	0.433	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.840	0.905	9.003	1.519	1.519	0.000	0.000	0.000	0.000
123	A	125	LYS	1	0.953	0.954	7.124	0.185	0.185	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.044	-0.014	12.623	0.069	0.069	0.000	0.000	0.000	0.000
125	A	127	LEU	0	-0.056	-0.022	15.665	0.033	0.033	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.068	0.004	8.942	0.067	0.067	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)