FMO DATABASE

FMODB ID: 3J1JL

Calculation Name: 4WY4-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WY4

Chain ID: C

ChEMBL ID:

UniProt ID: O95721

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	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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-342571.088676
FMO2-HF: Nuclear repulsion	311000.204981
FMO2-HF: Total energy	-31570.883694
FMO2-MP2: Total energy	-31661.89035

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:39:ALA)

Summations of interaction energy for fragment #1(C:39:ALA)

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.
-0.26	4.45	2.482	-3.089	-4.104	-0.003

Interaction energy analysis for fragmet #1(C:39:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.034

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	C	41	ARG	1	0.949	0.973	3.282	-0.911	1.276	0.002	-1.107	-1.082	0.005
4	C	42	GLN	0	0.004	-0.006	2.179	-4.699	-2.806	2.477	-1.809	-2.562	-0.008
5	C	43	GLN	0	0.029	0.008	3.366	1.141	1.771	0.003	-0.173	-0.460	0.000
6	C	44	TYR	0	0.021	0.017	5.511	0.962	0.962	0.000	0.000	0.000	0.000
7	C	45	LEU	0	-0.002	-0.013	7.424	0.405	0.405	0.000	0.000	0.000	0.000
8	C	46	ARG	1	0.954	0.978	6.358	1.402	1.402	0.000	0.000	0.000	0.000
9	C	47	GLN	0	0.009	0.010	9.472	0.380	0.380	0.000	0.000	0.000	0.000
10	C	48	GLU	-1	-0.911	-0.954	11.424	-0.357	-0.357	0.000	0.000	0.000	0.000
11	C	49	VAL	0	0.031	0.012	12.786	0.122	0.122	0.000	0.000	0.000	0.000
12	C	50	LEU	0	-0.007	-0.005	12.587	0.089	0.089	0.000	0.000	0.000	0.000
13	C	51	ARG	1	0.982	1.001	15.414	0.594	0.594	0.000	0.000	0.000	0.000
14	C	52	ARG	1	0.892	0.951	16.203	0.441	0.441	0.000	0.000	0.000	0.000
15	C	53	ALA	0	0.000	0.005	18.483	0.048	0.048	0.000	0.000	0.000	0.000
16	C	54	GLU	-1	-0.922	-0.960	19.748	-0.236	-0.236	0.000	0.000	0.000	0.000
17	C	55	ALA	0	0.061	0.028	21.426	0.031	0.031	0.000	0.000	0.000	0.000
18	C	56	THR	0	-0.063	-0.045	22.759	0.032	0.032	0.000	0.000	0.000	0.000
19	C	57	ALA	0	0.017	0.024	24.244	0.023	0.023	0.000	0.000	0.000	0.000
20	C	58	ALA	0	0.036	0.020	25.722	0.021	0.021	0.000	0.000	0.000	0.000
21	C	59	SER	0	-0.064	-0.043	27.304	0.021	0.021	0.000	0.000	0.000	0.000
22	C	60	THR	0	-0.012	-0.027	28.316	0.016	0.016	0.000	0.000	0.000	0.000
23	C	61	SER	0	0.031	0.018	29.941	0.015	0.015	0.000	0.000	0.000	0.000
24	C	62	ARG	1	0.924	0.968	28.575	0.180	0.180	0.000	0.000	0.000	0.000
25	C	63	SER	0	-0.023	-0.010	33.233	0.010	0.010	0.000	0.000	0.000	0.000
26	C	64	LEU	0	0.014	0.013	34.595	0.007	0.007	0.000	0.000	0.000	0.000
27	C	65	ALA	0	0.007	0.003	36.178	0.007	0.007	0.000	0.000	0.000	0.000
28	C	66	LEU	0	-0.026	-0.013	36.903	0.006	0.006	0.000	0.000	0.000	0.000
29	C	67	MET	0	-0.013	0.001	39.207	0.005	0.005	0.000	0.000	0.000	0.000
30	C	68	TYR	0	0.040	0.007	38.366	0.005	0.005	0.000	0.000	0.000	0.000
31	C	69	GLU	-1	-0.928	-0.959	42.323	-0.066	-0.066	0.000	0.000	0.000	0.000
32	C	70	SER	0	-0.026	-0.023	43.782	0.004	0.004	0.000	0.000	0.000	0.000
33	C	71	GLU	-1	-0.944	-0.959	44.936	-0.059	-0.059	0.000	0.000	0.000	0.000
34	C	72	LYS	1	0.946	0.982	46.738	0.064	0.064	0.000	0.000	0.000	0.000
35	C	73	VAL	0	-0.013	-0.011	48.427	0.004	0.004	0.000	0.000	0.000	0.000
36	C	74	GLY	0	0.012	0.004	49.600	0.003	0.003	0.000	0.000	0.000	0.000
37	C	75	VAL	0	0.016	0.011	50.601	0.003	0.003	0.000	0.000	0.000	0.000
38	C	76	ALA	0	0.017	0.012	52.834	0.003	0.003	0.000	0.000	0.000	0.000
39	C	77	SER	0	-0.016	-0.005	54.266	0.002	0.002	0.000	0.000	0.000	0.000
40	C	78	SER	0	-0.002	-0.012	54.600	0.002	0.002	0.000	0.000	0.000	0.000
41	C	79	GLU	-1	-0.957	-0.980	56.630	-0.040	-0.040	0.000	0.000	0.000	0.000
42	C	80	GLU	-1	-1.012	-1.008	58.805	-0.040	-0.040	0.000	0.000	0.000	0.000
43	C	81	LEU	0	0.036	0.009	58.700	0.002	0.002	0.000	0.000	0.000	0.000
44	C	82	ALA	0	-0.041	-0.012	61.337	0.002	0.002	0.000	0.000	0.000	0.000
45	C	83	ARG	1	0.942	0.966	60.106	0.040	0.040	0.000	0.000	0.000	0.000
46	C	84	GLN	0	-0.003	0.000	63.210	0.002	0.002	0.000	0.000	0.000	0.000
47	C	85	ARG	1	0.934	0.977	63.733	0.032	0.032	0.000	0.000	0.000	0.000
48	C	86	GLY	0	0.040	0.031	67.629	0.001	0.001	0.000	0.000	0.000	0.000
49	C	87	VAL	0	-0.057	-0.034	69.474	0.001	0.001	0.000	0.000	0.000	0.000
50	C	88	LEU	0	0.018	0.017	68.664	0.001	0.001	0.000	0.000	0.000	0.000
51	C	89	GLU	-1	-0.825	-0.919	70.020	-0.027	-0.027	0.000	0.000	0.000	0.000
52	C	90	ARG	1	0.887	0.942	72.710	0.027	0.027	0.000	0.000	0.000	0.000
53	C	91	THR	0	-0.036	-0.039	74.669	0.001	0.001	0.000	0.000	0.000	0.000
54	C	92	GLU	-1	-0.902	-0.946	75.732	-0.023	-0.023	0.000	0.000	0.000	0.000
55	C	93	LYS	1	0.966	0.985	76.276	0.024	0.024	0.000	0.000	0.000	0.000
56	C	94	MET	0	-0.068	-0.032	79.786	0.001	0.001	0.000	0.000	0.000	0.000
57	C	95	VAL	0	0.004	-0.005	80.005	0.001	0.001	0.000	0.000	0.000	0.000
58	C	96	ASP	-1	-0.853	-0.918	81.302	-0.020	-0.020	0.000	0.000	0.000	0.000
59	C	97	LYS	1	0.827	0.910	83.913	0.019	0.019	0.000	0.000	0.000	0.000
60	C	98	MET	0	-0.028	-0.017	83.710	0.001	0.001	0.000	0.000	0.000	0.000
61	C	99	ASP	-1	-0.864	-0.921	86.728	-0.017	-0.017	0.000	0.000	0.000	0.000
62	C	100	GLN	0	-0.021	-0.016	88.277	0.001	0.001	0.000	0.000	0.000	0.000
63	C	101	ASP	-1	-0.847	-0.934	90.095	-0.017	-0.017	0.000	0.000	0.000	0.000
64	C	102	LEU	0	0.010	0.005	90.628	0.001	0.001	0.000	0.000	0.000	0.000
65	C	103	LYS	1	0.911	0.960	89.720	0.017	0.017	0.000	0.000	0.000	0.000
66	C	104	ILE	0	-0.061	-0.025	93.614	0.001	0.001	0.000	0.000	0.000	0.000
67	C	105	SER	0	0.014	0.001	95.590	0.000	0.000	0.000	0.000	0.000	0.000
68	C	106	GLN	0	-0.022	-0.001	97.325	0.000	0.000	0.000	0.000	0.000	0.000
69	C	107	LYS	1	0.929	0.964	97.172	0.015	0.015	0.000	0.000	0.000	0.000
70	C	108	HIS	0	0.055	0.025	99.107	0.001	0.001	0.000	0.000	0.000	0.000
71	C	109	ILE	0	0.020	0.016	99.822	0.000	0.000	0.000	0.000	0.000	0.000
72	C	110	ASN	0	-0.032	-0.030	102.560	0.000	0.000	0.000	0.000	0.000	0.000
73	C	111	SER	0	-0.011	0.002	105.023	0.000	0.000	0.000	0.000	0.000	0.000
74	C	112	ILE	0	-0.015	0.003	104.570	0.000	0.000	0.000	0.000	0.000	0.000
75	C	113	LYS	1	0.900	0.942	106.401	0.013	0.013	0.000	0.000	0.000	0.000
76	C	114	SER	0	-0.066	-0.029	109.147	0.000	0.000	0.000	0.000	0.000	0.000
77	C	115	VAL	0	-0.003	0.010	111.543	0.000	0.000	0.000	0.000	0.000	0.000
78	C	116	PHE	0	-0.008	0.001	114.625	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:39:ALA)