FMO DATABASE

FMODB ID: YYKR2

Calculation Name: 4WXM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WXM

Chain ID: A

ChEMBL ID:

UniProt ID: G3XCV0

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptHSide
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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1113349.612884
FMO2-HF: Nuclear repulsion	1063277.650597
FMO2-HF: Total energy	-50071.962287
FMO2-MP2: Total energy	-50217.941122

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:4:GLU)

Summations of interaction energy for fragment #1(A:4:GLU)

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.
150.776	153.238	-0.036	-1.098	-1.327	0.002

Interaction energy analysis for fragmet #1(A:4:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -1.016 / q_NPA : -1.016

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	6	LYS	1	0.891	0.950	3.825	-51.614	-49.351	-0.035	-1.076	-1.152	0.002
4	A	7	LEU	0	-0.029	-0.021	6.786	-2.422	-2.422	0.000	0.000	0.000	0.000
5	A	8	LEU	0	0.012	0.004	10.323	0.205	0.205	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.022	-0.002	13.097	-1.095	-1.095	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.014	0.000	15.967	-0.281	-0.281	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.735	-0.863	19.100	11.971	11.971	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.718	-0.811	22.227	12.072	12.072	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.040	0.001	25.356	-0.256	-0.256	0.000	0.000	0.000	0.000
11	A	14	LEU	0	0.060	0.006	23.477	0.402	0.402	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.957	-0.968	24.231	11.069	11.069	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.748	0.824	23.496	-11.410	-11.410	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.025	0.020	20.266	0.714	0.714	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.974	0.985	20.046	-11.436	-11.436	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.920	-0.964	20.847	12.513	12.513	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.038	-0.025	18.087	0.354	0.354	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.044	0.020	16.160	0.742	0.742	0.000	0.000	0.000	0.000
19	A	22	VAL	0	-0.052	-0.018	16.333	0.819	0.819	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.028	-0.016	17.707	0.294	0.294	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.017	0.006	13.088	0.255	0.255	0.000	0.000	0.000	0.000
22	A	25	ASN	0	0.019	0.021	13.017	2.267	2.267	0.000	0.000	0.000	0.000
23	A	26	PHE	0	-0.088	-0.030	13.909	0.337	0.337	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.069	-0.054	13.509	-0.327	-0.327	0.000	0.000	0.000	0.000
25	A	28	GLY	0	-0.058	-0.015	11.285	0.539	0.539	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.949	-0.980	8.440	28.543	28.543	0.000	0.000	0.000	0.000
27	A	30	ASP	-1	-0.873	-0.942	5.672	37.870	37.870	0.000	0.000	0.000	0.000
28	A	31	GLN	0	-0.044	-0.026	8.269	-2.052	-2.052	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.007	0.018	9.472	0.135	0.135	0.000	0.000	0.000	0.000
30	A	33	THR	0	-0.014	-0.021	11.934	-1.158	-1.158	0.000	0.000	0.000	0.000
31	A	34	CYS	0	-0.050	-0.013	15.671	0.094	0.094	0.000	0.000	0.000	0.000
32	A	35	ASN	0	0.000	-0.005	18.167	-0.531	-0.531	0.000	0.000	0.000	0.000
33	A	36	SER	0	-0.046	-0.075	21.147	0.285	0.285	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-1.003	-0.997	23.567	10.794	10.794	0.000	0.000	0.000	0.000
35	A	38	ASP	-1	-0.782	-0.885	20.374	14.469	14.469	0.000	0.000	0.000	0.000
36	A	39	TRP	0	-0.001	-0.016	17.236	0.855	0.855	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.872	0.935	17.152	-12.706	-12.706	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.919	-0.960	17.417	14.431	14.431	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.009	0.009	13.939	1.033	1.033	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.002	-0.004	13.035	1.630	1.630	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.081	-0.033	13.003	1.093	1.093	0.000	0.000	0.000	0.000
42	A	45	GLY	0	-0.031	-0.009	12.195	0.249	0.249	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.075	-0.026	7.535	2.293	2.293	0.000	0.000	0.000	0.000
44	A	47	SER	0	-0.047	-0.037	7.083	-2.616	-2.616	0.000	0.000	0.000	0.000
45	A	48	ASN	0	-0.034	-0.037	9.055	-1.478	-1.478	0.000	0.000	0.000	0.000
46	A	49	SER	0	0.028	-0.004	9.921	1.480	1.480	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.784	0.860	6.176	-26.027	-26.027	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.776	-0.858	4.787	43.270	43.469	-0.001	-0.022	-0.175	0.000
49	A	52	ALA	0	0.016	0.010	6.498	1.959	1.959	0.000	0.000	0.000	0.000
50	A	53	LEU	0	-0.006	0.008	7.360	-1.866	-1.866	0.000	0.000	0.000	0.000
51	A	54	CYS	0	-0.043	-0.045	9.075	-2.124	-2.124	0.000	0.000	0.000	0.000
52	A	55	VAL	0	0.005	0.011	12.646	0.652	0.652	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.033	-0.019	14.146	-0.843	-0.843	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.006	-0.005	17.039	-0.081	-0.081	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.032	0.030	20.565	-0.318	-0.318	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.026	-0.025	23.562	-0.302	-0.302	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.060	-0.031	24.511	0.223	0.223	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.947	-0.974	26.954	9.332	9.332	0.000	0.000	0.000	0.000
59	A	62	SER	0	0.037	0.010	27.259	-0.309	-0.309	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.893	0.928	29.729	-8.998	-8.998	0.000	0.000	0.000	0.000
61	A	64	GLY	0	0.014	0.000	31.009	0.150	0.150	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.021	0.016	29.991	0.002	0.002	0.000	0.000	0.000	0.000
63	A	66	ALA	0	0.065	0.017	26.187	0.250	0.250	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.018	0.010	25.991	0.328	0.328	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.870	-0.917	27.374	10.575	10.575	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.031	0.022	21.389	0.146	0.146	0.000	0.000	0.000	0.000
67	A	70	LEU	0	0.015	-0.001	21.685	0.445	0.445	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.856	0.924	22.745	-9.992	-9.992	0.000	0.000	0.000	0.000
69	A	72	GLN	0	-0.051	-0.024	23.236	0.582	0.582	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.046	0.033	18.111	0.322	0.322	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.012	0.006	18.618	0.584	0.584	0.000	0.000	0.000	0.000
72	A	75	SER	0	-0.119	-0.067	20.525	-0.146	-0.146	0.000	0.000	0.000	0.000
73	A	76	TRP	0	-0.054	-0.031	12.761	0.011	0.011	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.740	-0.843	12.903	19.847	19.847	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.846	-0.881	16.542	12.746	12.746	0.000	0.000	0.000	0.000
76	A	79	TYR	0	-0.061	-0.036	14.568	-0.431	-0.431	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.012	0.009	12.776	0.723	0.723	0.000	0.000	0.000	0.000
78	A	81	PRO	0	-0.033	0.004	13.162	-1.079	-1.079	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.009	-0.026	15.721	0.613	0.613	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.004	-0.007	16.049	-0.502	-0.502	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.010	0.009	18.785	0.091	0.091	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.001	-0.007	18.169	-0.122	-0.122	0.000	0.000	0.000	0.000
83	A	86	GLY	0	-0.039	-0.020	22.639	-0.069	-0.069	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.809	-0.896	26.077	10.283	10.283	0.000	0.000	0.000	0.000
85	A	88	PRO	0	-0.057	-0.024	27.913	0.035	0.035	0.000	0.000	0.000	0.000
86	A	89	ALA	0	0.031	0.023	28.647	0.253	0.253	0.000	0.000	0.000	0.000
87	A	90	PRO	0	-0.011	0.013	28.326	-0.406	-0.406	0.000	0.000	0.000	0.000
88	A	91	ALA	0	-0.030	-0.044	30.856	0.151	0.151	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.935	-0.978	32.902	8.692	8.692	0.000	0.000	0.000	0.000
90	A	93	TRP	0	0.021	0.017	24.990	0.042	0.042	0.000	0.000	0.000	0.000
91	A	94	PRO	0	0.056	0.022	29.979	-0.150	-0.150	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.828	-0.905	28.983	10.115	10.115	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.888	-0.945	27.317	10.161	10.161	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.039	-0.026	24.652	0.379	0.379	0.000	0.000	0.000	0.000
95	A	98	ARG	1	0.878	0.937	24.523	-9.202	-9.202	0.000	0.000	0.000	0.000
96	A	99	ARG	1	0.807	0.893	23.696	-10.142	-10.142	0.000	0.000	0.000	0.000
97	A	100	ARG	1	0.857	0.920	19.429	-12.658	-12.658	0.000	0.000	0.000	0.000
98	A	101	VAL	0	-0.035	0.005	19.582	0.716	0.716	0.000	0.000	0.000	0.000
99	A	102	LEU	0	-0.006	0.016	15.922	-0.456	-0.456	0.000	0.000	0.000	0.000
100	A	103	ALA	0	-0.021	-0.022	20.373	-0.428	-0.428	0.000	0.000	0.000	0.000
101	A	104	SER	0	0.005	0.004	21.827	0.303	0.303	0.000	0.000	0.000	0.000
102	A	105	LEU	0	-0.071	-0.036	19.526	-0.406	-0.406	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.818	-0.895	23.649	10.702	10.702	0.000	0.000	0.000	0.000
104	A	107	MET	0	0.031	0.047	22.745	0.596	0.596	0.000	0.000	0.000	0.000
105	A	108	PRO	0	-0.017	-0.033	23.692	-0.411	-0.411	0.000	0.000	0.000	0.000
106	A	109	PRO	0	0.041	0.038	19.977	-0.383	-0.383	0.000	0.000	0.000	0.000
107	A	110	SER	0	-0.046	-0.033	22.960	-0.053	-0.053	0.000	0.000	0.000	0.000
108	A	111	TYR	0	0.080	0.020	17.442	0.079	0.079	0.000	0.000	0.000	0.000
109	A	112	ASN	0	0.030	0.000	19.388	0.641	0.641	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.861	0.932	19.741	-10.533	-10.533	0.000	0.000	0.000	0.000
111	A	114	LEU	0	0.053	0.049	16.023	0.191	0.191	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.058	0.024	14.644	0.563	0.563	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.906	-0.937	15.255	14.432	14.432	0.000	0.000	0.000	0.000
114	A	117	SER	0	-0.037	-0.044	16.894	0.039	0.039	0.000	0.000	0.000	0.000
115	A	118	LEU	0	0.008	0.008	11.764	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	119	HIS	0	0.009	0.005	12.326	1.685	1.685	0.000	0.000	0.000	0.000
117	A	120	ARG	1	0.828	0.900	13.501	-13.397	-13.397	0.000	0.000	0.000	0.000
118	A	121	ALA	0	0.034	-0.003	12.536	-0.320	-0.320	0.000	0.000	0.000	0.000
119	A	122	GLN	0	-0.022	0.003	6.505	0.936	0.936	0.000	0.000	0.000	0.000
120	A	123	VAL	0	0.036	0.008	10.656	-0.052	-0.052	0.000	0.000	0.000	0.000
121	A	124	TYR	0	-0.032	-0.010	13.359	-0.741	-0.741	0.000	0.000	0.000	0.000
122	A	125	ARG	1	0.806	0.869	9.601	-21.896	-21.896	0.000	0.000	0.000	0.000
123	A	126	GLU	-1	-0.919	-0.954	9.596	22.179	22.179	0.000	0.000	0.000	0.000
124	A	127	MET	0	-0.128	-0.069	11.689	-0.988	-0.988	0.000	0.000	0.000	0.000
125	A	128	TYR	0	-0.063	-0.023	14.416	-1.196	-1.196	0.000	0.000	0.000	0.000
126	A	129	ASP	-1	-0.890	-0.882	10.225	21.386	21.386	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLU)