FMO DATABASE

FMODB ID: ZV1ZN

Calculation Name: 3E0E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E0E

Chain ID: A

ChEMBL ID:

UniProt ID: Q6LYF9

Base Structure: X-ray

Registration Date: 2023-09-23

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-680517.483499
FMO2-HF: Nuclear repulsion	643265.111547
FMO2-HF: Total energy	-37252.371951
FMO2-MP2: Total energy	-37361.900037

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:0:MET)

Summations of interaction energy for fragment #1(A:0: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.
-21.761	-13.578	8.699	-5.811	-11.07	-0.036

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.004

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	2	TYR	0	-0.027	-0.019	2.456	-11.037	-5.416	7.226	-4.216	-8.630	-0.012
4	A	3	LYS	1	0.844	0.896	3.478	3.984	4.179	0.007	0.117	-0.320	0.000
5	A	4	ILE	0	-0.040	-0.041	5.891	0.088	0.088	0.000	0.000	0.000	0.000
6	A	5	SER	0	-0.054	-0.040	8.401	0.154	0.154	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.858	-0.921	2.702	-11.605	-9.238	1.466	-1.712	-2.120	-0.024
8	A	7	LEU	0	-0.051	-0.010	6.132	0.531	0.531	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.001	-0.005	8.125	0.398	0.398	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.019	-0.029	10.858	-0.105	-0.105	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.048	-0.014	13.555	0.085	0.085	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.009	0.040	5.776	0.147	0.147	0.000	0.000	0.000	0.000
13	A	12	SER	0	0.020	0.001	9.485	-0.096	-0.096	0.000	0.000	0.000	0.000
14	A	13	GLY	0	-0.003	0.002	6.089	-0.174	-0.174	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.014	0.011	5.620	1.079	1.079	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.022	0.036	5.844	-1.229	-1.229	0.000	0.000	0.000	0.000
17	A	16	ASN	0	-0.011	-0.020	8.364	-0.111	-0.111	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.003	0.005	10.917	0.024	0.024	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.790	-0.878	13.227	-0.551	-0.551	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.018	-0.001	16.910	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.001	0.016	18.213	0.087	0.087	0.000	0.000	0.000	0.000
22	A	21	THR	0	-0.058	-0.047	20.821	0.089	0.089	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.054	0.032	21.988	-0.052	-0.052	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.029	-0.011	22.720	0.033	0.033	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.008	-0.004	26.814	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.807	0.894	28.075	0.282	0.282	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.871	0.941	28.842	0.342	0.342	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.821	-0.910	30.006	-0.250	-0.250	0.000	0.000	0.000	0.000
29	A	28	PHE	0	-0.016	-0.003	27.797	0.012	0.012	0.000	0.000	0.000	0.000
30	A	29	SER	0	0.036	0.015	33.460	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.793	0.893	28.219	0.205	0.205	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.918	0.955	29.123	0.197	0.197	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.800	-0.909	29.731	-0.192	-0.192	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.064	0.049	33.075	0.013	0.013	0.000	0.000	0.000	0.000
35	A	34	THR	0	0.025	-0.011	32.439	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	35	DLY	1	0.824	0.919	32.834	0.211	0.211	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.018	0.013	29.397	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	37	GLN	0	-0.048	-0.028	27.751	0.031	0.031	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.015	0.005	23.573	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	39	LYS	1	0.852	0.930	23.383	0.498	0.498	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.004	0.002	22.079	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.022	0.015	18.204	0.039	0.039	0.000	0.000	0.000	0.000
43	A	42	PHE	0	-0.020	-0.014	18.795	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	43	LEU	0	0.016	0.016	14.158	0.038	0.038	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.850	0.896	14.412	0.733	0.733	0.000	0.000	0.000	0.000
46	A	45	ASP	-1	-0.704	-0.824	9.067	-2.033	-2.033	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.841	-0.905	10.845	-1.428	-1.428	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.089	-0.046	8.817	0.009	0.009	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.046	0.020	11.846	0.124	0.124	0.000	0.000	0.000	0.000
50	A	49	SER	0	-0.030	-0.022	13.314	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.008	0.009	12.283	0.067	0.067	0.000	0.000	0.000	0.000
52	A	51	ARG	1	0.847	0.916	15.240	0.497	0.497	0.000	0.000	0.000	0.000
53	A	52	GLY	0	0.064	0.037	16.554	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	53	THR	0	-0.082	-0.055	17.450	0.098	0.098	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.057	0.052	18.754	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	55	TRP	0	0.035	-0.010	19.682	0.090	0.090	0.000	0.000	0.000	0.000
57	A	56	ASN	0	0.024	-0.010	23.260	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.835	-0.911	23.391	-0.332	-0.332	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.034	0.022	18.502	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.055	-0.022	22.616	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.789	-0.892	25.072	-0.309	-0.309	0.000	0.000	0.000	0.000
62	A	61	PHE	0	0.010	0.023	19.807	0.012	0.012	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.848	-0.909	24.062	-0.407	-0.407	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.033	-0.011	19.732	0.001	0.001	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.804	0.891	23.137	0.490	0.490	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.857	0.914	22.836	0.460	0.460	0.000	0.000	0.000	0.000
67	A	66	GLY	0	-0.005	-0.008	21.853	0.037	0.037	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.791	-0.896	20.390	-0.554	-0.554	0.000	0.000	0.000	0.000
69	A	68	ILE	0	-0.011	0.001	14.980	-0.063	-0.063	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.011	-0.003	16.160	0.017	0.017	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.878	-0.928	9.295	-2.018	-2.018	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.035	-0.035	11.485	0.261	0.261	0.000	0.000	0.000	0.000
73	A	72	SER	0	0.029	0.003	9.296	-0.254	-0.254	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.004	-0.017	10.415	0.323	0.323	0.000	0.000	0.000	0.000
75	A	74	TYR	0	0.017	0.019	10.711	-0.214	-0.214	0.000	0.000	0.000	0.000
76	A	75	VAL	0	-0.007	-0.006	9.919	0.095	0.095	0.000	0.000	0.000	0.000
77	A	76	LYS	1	0.851	0.920	12.788	0.620	0.620	0.000	0.000	0.000	0.000
78	A	77	GLN	0	0.052	0.014	16.204	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	78	GLY	0	-0.049	-0.034	18.742	0.010	0.010	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.045	-0.016	21.517	0.005	0.005	0.000	0.000	0.000	0.000
81	A	80	SER	0	-0.046	-0.030	20.613	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.054	0.023	19.109	0.021	0.021	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.003	0.012	12.574	0.047	0.047	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.758	-0.878	16.087	-0.486	-0.486	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.021	0.027	10.643	0.051	0.051	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.021	-0.006	14.568	0.084	0.084	0.000	0.000	0.000	0.000
87	A	86	VAL	0	-0.065	-0.027	14.995	-0.074	-0.074	0.000	0.000	0.000	0.000
88	A	87	ASP	-1	-0.868	-0.944	12.910	-0.819	-0.819	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.037	-0.039	12.048	0.243	0.243	0.000	0.000	0.000	0.000
90	A	89	ILE	0	-0.043	-0.015	14.129	-0.143	-0.143	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.025	0.027	15.415	0.118	0.118	0.000	0.000	0.000	0.000
92	A	91	ILE	0	-0.065	-0.041	16.468	-0.068	-0.068	0.000	0.000	0.000	0.000
93	A	92	ILE	0	-0.020	0.013	12.324	0.067	0.067	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.921	-0.964	16.163	-0.489	-0.489	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.924	0.956	19.341	0.419	0.419	0.000	0.000	0.000	0.000
96	A	95	SER	0	0.002	-0.001	22.608	0.014	0.014	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.034	0.004	24.540	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)