FMO DATABASE

FMODB ID: 5JNGZ

Calculation Name: 3L7W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7W

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DSR7

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-828166.343533
FMO2-HF: Nuclear repulsion	785201.20203
FMO2-HF: Total energy	-42965.141503
FMO2-MP2: Total energy	-43092.701197

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:MET)

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

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.
-27.941	-27.254	27.344	-9.864	-18.171	-0.07

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.018

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	TYR	0	0.035	0.009	3.240	-1.863	-0.181	0.031	-0.665	-1.049	0.002
4	A	4	PRO	0	0.006	0.006	2.082	-5.723	-5.776	3.816	-1.727	-2.037	-0.025
5	A	5	VAL	0	0.019	0.003	3.861	-0.202	-0.020	0.000	-0.029	-0.153	0.000
6	A	6	SER	0	0.027	0.013	6.267	0.225	0.225	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.054	0.006	9.966	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.042	0.020	12.800	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.039	0.024	8.535	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.019	-0.003	7.792	-0.087	-0.087	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.816	-0.903	11.141	-0.070	-0.070	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.011	0.013	12.129	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.027	0.009	7.896	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.019	-0.016	12.201	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.013	-0.011	13.925	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.046	0.028	14.293	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.040	-0.003	10.441	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.054	-0.033	15.077	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.065	-0.039	18.227	0.024	0.024	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.949	0.994	17.247	0.323	0.323	0.000	0.000	0.000	0.000
21	A	21	HIS	1	0.853	0.903	16.891	0.313	0.313	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.695	-0.789	19.435	-0.164	-0.164	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.011	0.005	16.565	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.007	-0.008	16.672	0.015	0.015	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.036	0.003	15.298	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.010	-0.003	12.760	-0.045	-0.045	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.857	-0.927	12.168	-0.513	-0.513	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.033	0.025	11.776	-0.113	-0.113	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.039	-0.053	9.376	-0.158	-0.158	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.017	-0.018	7.551	-0.241	-0.241	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.003	-0.007	7.198	-0.354	-0.354	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.011	-0.009	6.114	-0.243	-0.243	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.798	0.878	3.367	-0.281	0.165	0.030	-0.098	-0.378	0.000
34	A	34	LEU	0	-0.015	0.013	2.512	-3.712	-3.311	2.464	-1.107	-1.759	-0.015
35	A	35	ILE	0	-0.024	-0.012	2.537	-2.106	-0.386	0.632	-0.607	-1.745	-0.004
36	A	36	ALA	0	0.014	0.002	2.112	-6.180	-4.892	6.463	-2.547	-5.205	-0.037
37	A	37	SER	0	0.046	0.000	2.203	-5.690	-10.204	13.850	-3.809	-5.527	0.008
38	A	38	ILE	0	-0.044	-0.007	3.287	-0.399	-0.864	0.058	0.725	-0.318	0.001
39	A	39	LYS	1	1.005	1.005	6.314	-0.799	-0.799	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.681	-0.822	9.072	-0.301	-0.301	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.015	-0.014	11.939	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.050	-0.026	10.925	0.055	0.055	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.041	0.025	9.597	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.026	0.007	11.921	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.037	-0.017	14.830	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.032	0.026	12.461	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.012	0.010	14.681	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.967	0.986	17.276	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.796	0.881	18.824	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.028	0.009	16.456	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.810	-0.863	20.682	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.902	0.953	23.137	0.013	0.013	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.035	-0.014	23.376	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.031	0.027	25.375	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.010	0.009	21.754	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.011	-0.003	18.316	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.028	0.020	23.018	0.009	0.009	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.068	-0.067	22.702	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.010	-0.014	25.077	0.009	0.009	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.019	-0.014	25.245	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.016	0.005	25.070	0.014	0.014	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.814	-0.899	26.010	-0.106	-0.106	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.003	0.006	21.214	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.023	-0.031	20.611	0.004	0.004	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.056	0.041	25.584	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.921	0.963	21.221	0.145	0.145	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.909	0.949	25.330	0.079	0.079	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.871	0.957	17.179	0.239	0.239	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.844	0.899	21.225	0.097	0.097	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.013	-0.010	20.622	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.009	-0.009	18.874	0.027	0.027	0.000	0.000	0.000	0.000
72	A	72	HIS	1	0.896	0.925	21.342	0.100	0.100	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.017	0.021	20.364	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.035	-0.037	23.038	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.783	-0.893	25.873	-0.070	-0.070	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.048	-0.025	27.178	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.051	0.006	23.328	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.933	-0.960	22.754	-0.101	-0.101	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.948	0.979	24.167	0.035	0.035	0.000	0.000	0.000	0.000
80	A	80	HIS	0	0.006	-0.005	20.406	0.006	0.006	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.019	0.013	17.954	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.002	0.016	20.077	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.015	-0.005	21.009	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.012	-0.002	16.795	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.035	-0.032	17.236	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.811	0.904	18.295	0.016	0.016	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.780	-0.888	18.205	0.015	0.015	0.000	0.000	0.000	0.000
88	A	88	TRP	0	0.000	-0.006	9.084	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.031	-0.033	15.196	0.024	0.024	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.035	0.017	17.742	0.016	0.016	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.019	-0.001	9.702	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.916	0.976	12.524	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.020	0.020	14.784	0.008	0.008	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.028	-0.019	17.736	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.002	-0.002	11.985	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.872	-0.946	14.618	0.186	0.186	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.016	-0.014	16.894	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.017	-0.002	18.155	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.011	-0.003	14.865	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.862	-0.907	18.324	0.100	0.100	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.040	-0.018	21.155	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.802	0.873	20.779	-0.088	-0.088	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.030	0.014	21.185	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.837	0.899	21.910	-0.081	-0.081	0.000	0.000	0.000	0.000
105	A	105	HIS	0	0.034	0.023	25.682	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.971	-0.980	27.607	0.038	0.038	0.000	0.000	0.000	0.000

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