FMO DATABASE

FMODB ID: QYMZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-552759.885094
FMO2-HF: Nuclear repulsion	516257.365643
FMO2-HF: Total energy	-36502.519451
FMO2-MP2: Total energy	-36598.646564

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.
-5.505	-0.403	1.028	-2.613	-3.514	-0.011

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 : -0.002 / q_NPA : 0.001

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	0.865	0.918	3.768	1.040	3.060	-0.014	-0.856	-1.150	0.004
4	C	19	CYS	0	-0.015	-0.017	5.189	-0.031	0.018	-0.002	-0.003	-0.044	0.000
5	C	20	LYS	1	0.827	0.910	8.800	0.633	0.633	0.000	0.000	0.000	0.000
6	C	21	CYS	0	0.053	0.051	12.190	-0.069	-0.069	0.000	0.000	0.000	0.000
7	C	22	HIS	0	-0.041	-0.008	14.415	0.029	0.029	0.000	0.000	0.000	0.000
8	C	23	HIS	0	-0.017	-0.011	18.032	0.041	0.041	0.000	0.000	0.000	0.000
9	C	24	HIS	0	-0.022	-0.020	18.073	-0.026	-0.026	0.000	0.000	0.000	0.000
10	C	26	PRO	0	0.030	0.029	11.828	0.032	0.032	0.000	0.000	0.000	0.000
11	C	27	GLU	-1	-0.860	-0.947	13.797	-0.164	-0.164	0.000	0.000	0.000	0.000
12	C	28	ASP	-1	-0.960	-0.976	10.741	-0.044	-0.044	0.000	0.000	0.000	0.000
13	C	29	SER	0	-0.069	-0.053	9.898	-0.022	-0.022	0.000	0.000	0.000	0.000
14	C	30	VAL	0	0.054	0.038	11.273	-0.053	-0.053	0.000	0.000	0.000	0.000
15	C	31	ASN	0	-0.097	-0.054	12.349	-0.019	-0.019	0.000	0.000	0.000	0.000
16	C	32	ASN	0	-0.039	-0.030	13.811	-0.023	-0.023	0.000	0.000	0.000	0.000
17	C	33	ILE	0	-0.037	-0.011	7.366	-0.079	-0.079	0.000	0.000	0.000	0.000
18	C	34	CYS	0	0.031	0.067	8.187	-0.132	-0.132	0.000	0.000	0.000	0.000
19	C	35	SER	0	-0.029	-0.045	2.791	-0.773	-0.393	0.250	-0.134	-0.495	0.001
20	C	36	THR	0	-0.042	-0.031	3.835	0.242	0.614	0.003	-0.092	-0.282	0.000
21	C	37	ASP	-1	-0.839	-0.931	2.682	-3.898	-1.669	0.792	-1.522	-1.498	-0.016
22	C	38	GLY	0	-0.023	0.001	4.382	-0.074	-0.022	-0.001	-0.006	-0.045	0.000
23	C	39	TYR	0	-0.011	-0.016	7.284	-0.365	-0.365	0.000	0.000	0.000	0.000
24	C	41	PHE	0	0.032	0.009	10.483	0.087	0.087	0.000	0.000	0.000	0.000
25	C	42	THR	0	0.021	-0.006	14.197	-0.032	-0.032	0.000	0.000	0.000	0.000
26	C	43	MET	0	-0.024	0.007	17.603	0.015	0.015	0.000	0.000	0.000	0.000
27	C	44	ILE	0	-0.028	-0.004	20.766	0.003	0.003	0.000	0.000	0.000	0.000
28	C	45	GLU	-1	-0.787	-0.895	24.480	-0.140	-0.140	0.000	0.000	0.000	0.000
29	C	46	GLU	-1	-0.848	-0.908	26.951	-0.114	-0.114	0.000	0.000	0.000	0.000
30	C	47	ASP	-1	-0.813	-0.893	29.847	-0.102	-0.102	0.000	0.000	0.000	0.000
31	C	48	ASP	-1	-0.910	-0.959	31.144	-0.078	-0.078	0.000	0.000	0.000	0.000
32	C	49	SER	0	-0.118	-0.078	33.978	0.007	0.007	0.000	0.000	0.000	0.000
33	C	50	GLY	0	-0.049	-0.013	34.408	0.003	0.003	0.000	0.000	0.000	0.000
34	C	51	MET	0	-0.053	-0.030	31.910	0.000	0.000	0.000	0.000	0.000	0.000
35	C	52	PRO	0	0.002	-0.008	28.699	-0.003	-0.003	0.000	0.000	0.000	0.000
36	C	53	VAL	0	0.002	0.010	24.735	-0.010	-0.010	0.000	0.000	0.000	0.000
37	C	54	VAL	0	0.017	0.015	21.196	-0.007	-0.007	0.000	0.000	0.000	0.000
38	C	55	THR	0	-0.040	-0.030	19.647	-0.003	-0.003	0.000	0.000	0.000	0.000
39	C	56	SER	0	0.025	-0.002	15.262	-0.024	-0.024	0.000	0.000	0.000	0.000
40	C	57	GLY	0	0.043	0.015	12.579	0.047	0.047	0.000	0.000	0.000	0.000
41	C	59	LEU	0	0.033	0.018	9.915	0.138	0.138	0.000	0.000	0.000	0.000
42	C	60	GLY	0	0.060	0.051	8.589	-0.173	-0.173	0.000	0.000	0.000	0.000
43	C	61	LEU	0	0.018	0.001	8.219	-0.088	-0.088	0.000	0.000	0.000	0.000
44	C	62	GLU	-1	-0.940	-0.956	9.937	0.118	0.118	0.000	0.000	0.000	0.000
45	C	63	GLY	0	0.003	0.001	13.422	-0.041	-0.041	0.000	0.000	0.000	0.000
46	C	64	SER	0	0.021	-0.008	12.346	-0.024	-0.024	0.000	0.000	0.000	0.000
47	C	65	ASP	-1	-0.917	-0.947	14.500	-0.130	-0.130	0.000	0.000	0.000	0.000
48	C	66	PHE	0	-0.082	-0.052	17.498	0.002	0.002	0.000	0.000	0.000	0.000
49	C	67	GLN	0	-0.013	0.000	15.520	-0.007	-0.007	0.000	0.000	0.000	0.000
50	C	68	CYS	0	-0.051	-0.045	13.381	-0.050	-0.050	0.000	0.000	0.000	0.000
51	C	69	ARG	1	0.861	0.919	17.276	0.153	0.153	0.000	0.000	0.000	0.000
52	C	70	ASP	-1	-0.729	-0.826	21.117	-0.184	-0.184	0.000	0.000	0.000	0.000
53	C	71	THR	0	-0.057	-0.051	24.327	0.016	0.016	0.000	0.000	0.000	0.000
54	C	72	PRO	0	-0.036	-0.015	26.907	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	73	ILE	0	0.029	0.017	26.863	0.007	0.007	0.000	0.000	0.000	0.000
56	C	74	PRO	0	-0.029	-0.025	31.226	-0.002	-0.002	0.000	0.000	0.000	0.000
57	C	75	HIS	0	-0.026	-0.023	33.934	-0.002	-0.002	0.000	0.000	0.000	0.000
58	C	76	GLN	0	0.012	0.022	28.090	0.002	0.002	0.000	0.000	0.000	0.000
59	C	77	ARG	1	0.749	0.866	30.767	0.115	0.115	0.000	0.000	0.000	0.000
60	C	78	ARG	1	0.866	0.906	23.383	0.135	0.135	0.000	0.000	0.000	0.000
61	C	79	SER	0	-0.070	-0.044	24.642	0.003	0.003	0.000	0.000	0.000	0.000
62	C	80	ILE	0	-0.032	-0.022	17.226	-0.014	-0.014	0.000	0.000	0.000	0.000
63	C	81	GLU	-1	-0.834	-0.914	18.415	-0.316	-0.316	0.000	0.000	0.000	0.000
64	C	83	CYS	0	-0.063	0.004	10.756	0.160	0.160	0.000	0.000	0.000	0.000
65	C	84	THR	0	0.053	0.005	7.732	-0.073	-0.073	0.000	0.000	0.000	0.000
66	C	85	GLU	-1	-0.827	-0.886	8.083	-1.159	-1.159	0.000	0.000	0.000	0.000
67	C	86	ARG	1	0.770	0.853	9.738	0.811	0.811	0.000	0.000	0.000	0.000
68	C	87	ASN	0	0.045	0.014	5.688	-0.624	-0.624	0.000	0.000	0.000	0.000
69	C	88	GLU	-1	-0.812	-0.904	8.516	-0.459	-0.459	0.000	0.000	0.000	0.000
70	C	90	ASN	0	0.025	-0.006	12.212	0.008	0.008	0.000	0.000	0.000	0.000
71	C	91	LYS	1	0.832	0.908	13.700	0.666	0.666	0.000	0.000	0.000	0.000
72	C	92	ASP	-1	-0.893	-0.930	16.549	-0.483	-0.483	0.000	0.000	0.000	0.000
73	C	93	LEU	0	-0.054	-0.005	15.171	0.011	0.011	0.000	0.000	0.000	0.000
74	C	94	HIS	0	-0.063	-0.034	19.110	0.029	0.029	0.000	0.000	0.000	0.000
75	C	95	PRO	0	0.014	0.039	20.839	0.024	0.024	0.000	0.000	0.000	0.000
76	C	96	THR	0	-0.034	-0.032	23.610	0.017	0.017	0.000	0.000	0.000	0.000
77	C	97	LEU	0	0.000	0.006	27.364	0.002	0.002	0.000	0.000	0.000	0.000
78	C	98	PRO	0	0.033	0.032	28.536	0.006	0.006	0.000	0.000	0.000	0.000
79	C	99	PRO	0	-0.016	-0.007	31.168	0.005	0.005	0.000	0.000	0.000	0.000
80	C	100	LEU	0	-0.004	0.002	34.958	0.004	0.004	0.000	0.000	0.000	0.000

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