FMO DATABASE

FMODB ID: QV5JY

Calculation Name: 4YEW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YEW

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACF0

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-324263.679784
FMO2-HF: Nuclear repulsion	299121.361316
FMO2-HF: Total energy	-25142.318467
FMO2-MP2: Total energy	-25216.4544

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.
-21.45	-23.09	20.405	-9.332	-9.43	0.027

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 : 0.051 / q_NPA : 0.046

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	LYS	1	0.892	0.908	3.473	-1.017	1.708	0.007	-1.573	-1.159	0.005
4	A	4	SER	0	0.018	-0.006	5.865	0.914	0.914	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.045	0.020	2.344	-4.252	-2.196	3.084	-1.961	-3.179	-0.019
6	A	6	LEU	0	-0.014	0.003	2.922	1.459	2.770	0.087	-0.310	-1.087	-0.001
7	A	7	ILE	0	0.020	0.010	4.206	0.573	0.776	0.001	-0.033	-0.170	0.000
8	A	8	ASP	-1	-0.818	-0.899	7.005	0.889	0.889	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.907	0.935	2.150	-18.166	-26.101	17.226	-5.455	-3.835	0.042
10	A	10	ILE	0	-0.010	0.003	7.364	-0.268	-0.268	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.033	-0.024	9.758	-0.231	-0.231	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.002	-0.005	10.611	-0.128	-0.128	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.019	-0.009	10.877	-0.109	-0.109	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.037	-0.019	11.958	-0.120	-0.120	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.908	-0.930	15.061	0.706	0.706	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.042	-0.007	14.249	-0.158	-0.158	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.017	-0.005	15.549	0.054	0.054	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.898	0.913	10.761	-0.505	-0.505	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.025	0.019	13.613	-0.074	-0.074	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.033	0.000	16.375	-0.074	-0.074	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.065	0.033	11.088	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.000	-0.009	11.433	-0.042	-0.042	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.922	0.945	12.450	-0.145	-0.145	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.024	0.022	13.603	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.006	0.001	7.332	-0.061	-0.061	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.783	-0.880	11.484	-0.799	-0.799	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.005	0.012	13.798	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.000	0.022	12.490	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.008	-0.005	9.698	-0.071	-0.071	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.013	0.007	14.013	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.009	-0.023	17.628	0.013	0.013	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.001	-0.001	15.230	0.013	0.013	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.051	-0.042	16.694	-0.038	-0.038	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.836	-0.907	19.024	-0.230	-0.230	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.024	-0.032	21.385	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.010	-0.012	18.307	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.747	0.867	22.633	0.233	0.233	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.991	-0.995	24.903	-0.118	-0.118	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.067	-0.021	25.998	0.015	0.015	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.882	-0.913	24.876	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.865	-0.948	22.872	-0.182	-0.182	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.018	0.015	18.401	0.039	0.039	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.020	-0.018	19.068	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.016	-0.004	14.797	0.042	0.042	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.042	0.005	17.221	0.023	0.023	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.011	0.003	17.363	0.063	0.063	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.018	0.003	9.223	0.020	0.020	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.028	-0.006	14.199	-0.071	-0.071	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.025	-0.005	16.392	0.047	0.047	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.047	-0.019	12.091	-0.066	-0.066	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.019	0.010	18.146	0.039	0.039	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.035	0.018	21.138	-0.062	-0.062	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.854	0.928	21.023	0.350	0.350	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.810	-0.889	25.721	-0.210	-0.210	0.000	0.000	0.000	0.000
55	A	74	ALA	0	0.053	0.028	27.994	0.002	0.002	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.795	0.884	26.950	0.205	0.205	0.000	0.000	0.000	0.000
57	A	76	VAL	0	-0.013	-0.006	21.343	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.055	0.027	18.554	0.030	0.030	0.000	0.000	0.000	0.000
59	A	78	SER	0	-0.018	-0.011	18.781	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.025	0.020	12.719	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	80	ARG	1	0.925	0.963	17.043	0.142	0.142	0.000	0.000	0.000	0.000
62	A	81	ALA	0	0.055	0.046	14.053	0.048	0.048	0.000	0.000	0.000	0.000
63	A	82	GLY	0	0.002	-0.009	15.467	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.936	0.962	16.108	-0.179	-0.179	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.079	0.045	14.332	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	85	LEU	0	-0.017	0.003	9.072	0.075	0.075	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.875	0.933	11.924	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	87	ASP	-1	-0.894	-0.966	14.603	0.267	0.267	0.000	0.000	0.000	0.000
69	A	88	ALA	0	-0.046	-0.014	10.175	0.021	0.021	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.067	-0.028	9.353	0.051	0.051	0.000	0.000	0.000	0.000
71	A	90	ASN	0	-0.037	-0.003	11.971	-0.065	-0.065	0.000	0.000	0.000	0.000

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