FMO DATABASE

FMODB ID: Z6LKN

Calculation Name: 3EVS-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EVS

Chain ID: C

ChEMBL ID:

UniProt ID: P36898

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-553036.435747
FMO2-HF: Nuclear repulsion	516535.040998
FMO2-HF: Total energy	-36501.394749
FMO2-MP2: Total energy	-36597.583895

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(C:16:ILE)

Summations of interaction energy for fragment #1(C:16:ILE)

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.
-1.113	3.401	1.731	-2.595	-3.65	-0.015

Interaction energy analysis for fragmet #1(C:16:ILE)

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 : -0.031

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	C	18	ARG	1	0.925	0.962	3.786	-0.233	1.375	-0.021	-0.537	-1.050	0.003
4	C	19	CYS	0	-0.024	-0.007	5.590	0.082	0.082	0.000	0.000	0.000	0.000
5	C	20	LYS	1	0.910	0.962	9.004	0.146	0.146	0.000	0.000	0.000	0.000
6	C	21	CYS	0	-0.016	-0.005	12.353	0.019	0.019	0.000	0.000	0.000	0.000
7	C	22	HIS	0	-0.080	-0.044	14.531	-0.023	-0.023	0.000	0.000	0.000	0.000
8	C	23	HIS	0	-0.002	0.013	18.113	-0.001	-0.001	0.000	0.000	0.000	0.000
9	C	24	HIS	0	0.005	-0.008	18.104	0.001	0.001	0.000	0.000	0.000	0.000
10	C	26	PRO	0	0.002	0.024	11.559	0.008	0.008	0.000	0.000	0.000	0.000
11	C	27	GLU	-1	-0.820	-0.922	13.995	-0.160	-0.160	0.000	0.000	0.000	0.000
12	C	28	ASP	-1	-1.010	-1.016	11.637	-0.118	-0.118	0.000	0.000	0.000	0.000
13	C	29	SER	0	-0.090	-0.094	9.662	-0.048	-0.048	0.000	0.000	0.000	0.000
14	C	30	VAL	0	0.087	0.111	11.426	0.017	0.017	0.000	0.000	0.000	0.000
15	C	31	ASN	0	-0.086	-0.069	12.330	-0.035	-0.035	0.000	0.000	0.000	0.000
16	C	32	ASN	0	-0.066	-0.017	14.077	-0.014	-0.014	0.000	0.000	0.000	0.000
17	C	33	ILE	0	0.002	-0.009	7.741	-0.016	-0.016	0.000	0.000	0.000	0.000
18	C	34	CYS	0	-0.013	0.033	8.066	-0.007	-0.007	0.000	0.000	0.000	0.000
19	C	35	SER	0	-0.006	-0.027	2.621	-0.567	-0.149	0.202	-0.126	-0.493	0.001
20	C	36	THR	0	-0.011	-0.005	3.794	-0.074	0.288	0.001	-0.091	-0.272	0.000
21	C	37	ASP	-1	-0.871	-0.941	2.516	-1.028	1.043	1.550	-1.826	-1.795	-0.019
22	C	38	GLY	0	-0.017	-0.005	4.236	0.186	0.241	-0.001	-0.015	-0.040	0.000
23	C	39	TYR	0	-0.018	-0.015	7.209	0.334	0.334	0.000	0.000	0.000	0.000
24	C	41	PHE	0	0.048	0.016	10.550	0.043	0.043	0.000	0.000	0.000	0.000
25	C	42	THR	0	0.018	-0.011	14.173	-0.052	-0.052	0.000	0.000	0.000	0.000
26	C	43	MET	0	-0.016	0.001	17.518	0.027	0.027	0.000	0.000	0.000	0.000
27	C	44	ILE	0	-0.046	-0.015	20.541	-0.018	-0.018	0.000	0.000	0.000	0.000
28	C	45	GLU	-1	-0.868	-0.955	24.206	0.058	0.058	0.000	0.000	0.000	0.000
29	C	46	GLU	-1	-0.928	-0.971	26.627	0.021	0.021	0.000	0.000	0.000	0.000
30	C	47	ASP	-1	-0.846	-0.919	29.600	0.014	0.014	0.000	0.000	0.000	0.000
31	C	48	ASP	-1	-0.892	-0.966	31.021	0.020	0.020	0.000	0.000	0.000	0.000
32	C	49	SER	0	-0.122	-0.048	33.633	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	50	GLY	0	0.007	0.012	33.653	0.000	0.000	0.000	0.000	0.000	0.000
34	C	51	MET	0	-0.094	-0.054	31.481	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	52	PRO	0	-0.011	0.001	28.316	0.002	0.002	0.000	0.000	0.000	0.000
36	C	53	VAL	0	0.016	0.014	24.958	-0.007	-0.007	0.000	0.000	0.000	0.000
37	C	54	VAL	0	-0.008	-0.010	20.928	0.005	0.005	0.000	0.000	0.000	0.000
38	C	55	THR	0	-0.028	-0.024	19.117	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	56	SER	0	-0.009	-0.014	15.219	0.001	0.001	0.000	0.000	0.000	0.000
40	C	57	GLY	0	0.063	0.032	12.395	-0.032	-0.032	0.000	0.000	0.000	0.000
41	C	59	LEU	0	0.017	0.010	9.910	-0.036	-0.036	0.000	0.000	0.000	0.000
42	C	60	GLY	0	0.061	0.031	8.540	0.150	0.150	0.000	0.000	0.000	0.000
43	C	61	LEU	0	0.014	0.006	8.404	-0.058	-0.058	0.000	0.000	0.000	0.000
44	C	62	GLU	-1	-0.934	-0.950	10.280	0.183	0.183	0.000	0.000	0.000	0.000
45	C	63	GLY	0	0.012	0.003	13.737	-0.026	-0.026	0.000	0.000	0.000	0.000
46	C	64	SER	0	-0.004	-0.027	12.536	-0.033	-0.033	0.000	0.000	0.000	0.000
47	C	65	ASP	-1	-0.905	-0.945	14.659	0.354	0.354	0.000	0.000	0.000	0.000
48	C	66	PHE	0	-0.077	-0.060	17.553	-0.037	-0.037	0.000	0.000	0.000	0.000
49	C	67	GLN	0	-0.012	-0.004	15.714	0.004	0.004	0.000	0.000	0.000	0.000
50	C	68	CYS	0	-0.070	-0.043	13.257	-0.015	-0.015	0.000	0.000	0.000	0.000
51	C	69	ARG	1	0.901	0.957	17.410	-0.223	-0.223	0.000	0.000	0.000	0.000
52	C	70	ASP	-1	-0.755	-0.865	21.154	0.110	0.110	0.000	0.000	0.000	0.000
53	C	71	THR	0	-0.060	-0.040	24.204	0.002	0.002	0.000	0.000	0.000	0.000
54	C	72	PRO	0	-0.028	-0.013	26.661	-0.005	-0.005	0.000	0.000	0.000	0.000
55	C	73	ILE	0	0.015	0.007	27.094	0.001	0.001	0.000	0.000	0.000	0.000
56	C	74	PRO	0	-0.006	-0.012	30.767	-0.003	-0.003	0.000	0.000	0.000	0.000
57	C	75	HIS	0	-0.035	-0.024	33.596	-0.001	-0.001	0.000	0.000	0.000	0.000
58	C	76	GLN	0	0.014	0.024	27.689	0.000	0.000	0.000	0.000	0.000	0.000
59	C	77	ARG	1	0.828	0.938	30.351	-0.032	-0.032	0.000	0.000	0.000	0.000
60	C	78	ARG	1	0.983	0.971	23.255	-0.087	-0.087	0.000	0.000	0.000	0.000
61	C	79	SER	0	-0.099	-0.035	24.216	0.003	0.003	0.000	0.000	0.000	0.000
62	C	80	ILE	0	-0.012	-0.005	16.807	-0.012	-0.012	0.000	0.000	0.000	0.000
63	C	81	GLU	-1	-0.887	-0.939	18.316	0.117	0.117	0.000	0.000	0.000	0.000
64	C	83	CYS	0	-0.093	-0.015	11.067	0.020	0.020	0.000	0.000	0.000	0.000
65	C	84	THR	0	0.036	-0.002	8.193	0.016	0.016	0.000	0.000	0.000	0.000
66	C	85	GLU	-1	-0.878	-0.925	8.589	0.318	0.318	0.000	0.000	0.000	0.000
67	C	86	ARG	1	0.859	0.927	9.136	-0.063	-0.063	0.000	0.000	0.000	0.000
68	C	87	ASN	0	0.050	0.009	5.431	-0.164	-0.164	0.000	0.000	0.000	0.000
69	C	88	GLU	-1	-0.902	-0.980	8.495	-0.226	-0.226	0.000	0.000	0.000	0.000
70	C	90	ASN	0	0.066	0.015	12.439	-0.023	-0.023	0.000	0.000	0.000	0.000
71	C	91	LYS	1	0.861	0.937	14.517	0.165	0.165	0.000	0.000	0.000	0.000
72	C	92	ASP	-1	-0.950	-0.961	16.691	-0.045	-0.045	0.000	0.000	0.000	0.000
73	C	93	LEU	0	-0.042	-0.001	15.055	0.016	0.016	0.000	0.000	0.000	0.000
74	C	94	HIS	0	-0.032	-0.029	19.039	-0.014	-0.014	0.000	0.000	0.000	0.000
75	C	95	PRO	0	0.044	0.050	20.534	0.000	0.000	0.000	0.000	0.000	0.000
76	C	96	THR	0	-0.051	-0.034	23.309	-0.013	-0.013	0.000	0.000	0.000	0.000
77	C	97	LEU	0	0.010	-0.003	27.029	0.006	0.006	0.000	0.000	0.000	0.000
78	C	98	PRO	0	0.017	0.025	28.246	-0.001	-0.001	0.000	0.000	0.000	0.000
79	C	99	PRO	0	0.002	-0.009	30.889	-0.005	-0.005	0.000	0.000	0.000	0.000
80	C	100	LEU	0	-0.003	0.005	34.510	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:16:ILE)