FMO DATABASE

FMODB ID: KG423

Calculation Name: 4YTW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YTW

Chain ID: B

ChEMBL ID:

UniProt ID: O60200

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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1478469.891845
FMO2-HF: Nuclear repulsion	1410872.795746
FMO2-HF: Total energy	-67597.096099
FMO2-MP2: Total energy	-67793.961969

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-8.159	-5.397	9.125	-4.966	-6.921	-0.033

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.012

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	B	3	LEU	0	0.001	0.007	2.589	-1.503	1.028	0.660	-0.824	-2.367	0.002
4	B	4	LEU	0	-0.038	-0.019	5.005	0.025	0.077	-0.001	-0.002	-0.048	0.000
5	B	5	HIS	0	0.021	0.016	7.640	-0.042	-0.042	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.941	0.949	11.697	-0.118	-0.118	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.012	0.014	15.466	0.016	0.016	0.000	0.000	0.000	0.000
8	B	8	THR	0	0.015	-0.007	18.770	-0.002	-0.002	0.000	0.000	0.000	0.000
9	B	9	HIS	0	-0.047	-0.017	22.442	0.002	0.002	0.000	0.000	0.000	0.000
10	B	10	ILE	0	0.041	0.012	25.419	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	11	PHE	0	-0.004	0.005	26.387	0.001	0.001	0.000	0.000	0.000	0.000
12	B	12	PRO	0	0.056	0.048	31.312	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	13	THR	0	-0.049	-0.047	34.501	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	14	ASP	-1	-0.724	-0.817	34.802	0.031	0.031	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.071	0.033	30.857	0.001	0.001	0.000	0.000	0.000	0.000
16	B	16	ALA	0	0.003	0.029	34.029	0.001	0.001	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.060	-0.073	35.808	0.000	0.000	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.007	0.020	29.604	0.001	0.001	0.000	0.000	0.000	0.000
19	B	19	SER	0	-0.004	-0.028	30.695	0.001	0.001	0.000	0.000	0.000	0.000
20	B	20	ARG	1	0.914	0.950	31.661	-0.028	-0.028	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.034	0.014	31.241	0.000	0.000	0.000	0.000	0.000	0.000
22	B	22	PHE	0	-0.004	0.000	23.517	0.002	0.002	0.000	0.000	0.000	0.000
23	B	23	PHE	0	-0.005	-0.033	28.458	0.000	0.000	0.000	0.000	0.000	0.000
24	B	24	ASN	0	-0.057	-0.025	30.814	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	25	ARG	1	0.912	0.983	22.201	-0.057	-0.057	0.000	0.000	0.000	0.000
26	B	26	TYR	0	-0.019	0.002	23.339	0.006	0.006	0.000	0.000	0.000	0.000
27	B	27	PRO	0	0.066	0.036	29.965	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.011	-0.024	26.898	0.001	0.001	0.000	0.000	0.000	0.000
29	B	29	PRO	0	0.033	0.012	29.546	0.002	0.002	0.000	0.000	0.000	0.000
30	B	30	TYR	0	0.024	0.016	26.288	0.001	0.001	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.069	-0.033	24.817	0.009	0.009	0.000	0.000	0.000	0.000
32	B	32	PRO	0	0.042	0.024	25.824	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	HIS	0	-0.066	-0.035	22.550	0.000	0.000	0.000	0.000	0.000	0.000
34	B	34	VAL	0	-0.044	-0.013	23.683	0.000	0.000	0.000	0.000	0.000	0.000
35	B	35	LEU	0	-0.025	-0.014	25.740	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.023	-0.019	27.333	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.014	-0.021	26.432	0.004	0.004	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.850	-0.891	28.304	0.019	0.019	0.000	0.000	0.000	0.000
39	B	39	THR	0	-0.017	-0.036	28.918	0.001	0.001	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.001	0.006	26.986	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	41	SER	0	0.019	0.003	29.289	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.895	0.937	31.027	-0.024	-0.024	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.029	-0.002	32.190	0.000	0.000	0.000	0.000	0.000	0.000
44	B	44	VAL	0	0.033	0.017	34.658	0.001	0.001	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.726	-0.832	33.037	0.029	0.029	0.000	0.000	0.000	0.000
46	B	46	GLN	0	0.007	-0.013	35.916	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.982	-0.986	32.994	0.034	0.034	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.004	0.017	37.260	0.000	0.000	0.000	0.000	0.000	0.000
49	B	49	ASN	0	-0.057	-0.042	32.348	0.001	0.001	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.017	-0.003	33.128	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.863	0.921	27.919	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	52	THR	0	-0.009	-0.009	29.077	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	53	THR	0	-0.012	0.002	25.049	0.002	0.002	0.000	0.000	0.000	0.000
54	B	54	ARG	1	0.761	0.846	25.729	-0.035	-0.035	0.000	0.000	0.000	0.000
55	B	55	LEU	0	-0.001	0.008	22.997	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.040	0.022	22.592	0.001	0.001	0.000	0.000	0.000	0.000
57	B	57	LYS	1	0.848	0.941	23.024	-0.017	-0.017	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.905	0.945	18.435	-0.108	-0.108	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.077	0.037	21.265	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	GLY	0	-0.018	-0.029	18.966	0.016	0.016	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.968	0.975	18.438	-0.073	-0.073	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.021	0.031	13.807	0.029	0.029	0.000	0.000	0.000	0.000
63	B	63	PRO	0	0.039	0.012	12.404	-0.031	-0.031	0.000	0.000	0.000	0.000
64	B	64	THR	0	0.009	-0.007	15.293	-0.015	-0.015	0.000	0.000	0.000	0.000
65	B	65	TRP	0	0.073	0.033	7.554	-0.034	-0.034	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.011	0.001	10.267	-0.031	-0.031	0.000	0.000	0.000	0.000
67	B	67	LYS	1	0.950	0.978	12.654	-0.058	-0.058	0.000	0.000	0.000	0.000
68	B	68	PRO	0	0.031	0.029	14.631	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	69	PHE	0	-0.080	-0.049	11.146	-0.043	-0.043	0.000	0.000	0.000	0.000
70	B	70	LEU	0	-0.043	-0.013	10.935	-0.023	-0.023	0.000	0.000	0.000	0.000
71	B	71	ARG	1	0.901	0.956	14.708	0.052	0.052	0.000	0.000	0.000	0.000
72	B	72	GLY	0	0.027	0.004	17.458	0.016	0.016	0.000	0.000	0.000	0.000
73	B	73	ILE	0	-0.028	-0.019	14.777	-0.007	-0.007	0.000	0.000	0.000	0.000
74	B	74	THR	0	0.016	0.000	18.814	0.011	0.011	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.823	-0.890	20.608	0.021	0.021	0.000	0.000	0.000	0.000
76	B	76	THR	0	-0.088	-0.046	16.062	0.008	0.008	0.000	0.000	0.000	0.000
77	B	77	TRP	0	0.049	0.034	19.111	0.006	0.006	0.000	0.000	0.000	0.000
78	B	78	ILE	0	-0.026	-0.029	17.635	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	79	ILE	0	0.004	0.015	18.896	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.790	-0.886	20.024	0.045	0.045	0.000	0.000	0.000	0.000
81	B	81	VAL	0	-0.007	-0.008	21.727	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	82	SER	0	-0.028	-0.018	23.495	0.003	0.003	0.000	0.000	0.000	0.000
83	B	83	VAL	0	0.002	-0.004	26.117	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	84	VAL	0	-0.020	-0.014	28.492	0.002	0.002	0.000	0.000	0.000	0.000
85	B	85	ASN	0	0.057	0.033	31.241	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	86	PRO	0	0.011	-0.002	33.446	0.001	0.001	0.000	0.000	0.000	0.000
87	B	87	ALA	0	0.012	0.007	36.604	0.000	0.000	0.000	0.000	0.000	0.000
88	B	88	ASN	0	0.009	-0.006	31.495	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	89	SER	0	-0.004	0.005	33.942	0.001	0.001	0.000	0.000	0.000	0.000
90	B	90	THR	0	-0.002	0.003	28.373	0.002	0.002	0.000	0.000	0.000	0.000
91	B	91	MET	0	-0.052	-0.011	27.316	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	92	LYS	1	0.973	1.001	24.183	-0.043	-0.043	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.037	-0.041	22.652	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.021	-0.027	15.009	0.001	0.001	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.013	-0.017	17.632	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	96	ARG	1	0.931	0.971	14.259	0.028	0.028	0.000	0.000	0.000	0.000
97	B	97	ASN	0	-0.003	0.006	11.811	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.011	-0.002	15.273	-0.026	-0.026	0.000	0.000	0.000	0.000
99	B	99	ASP	-1	-0.747	-0.877	16.171	-0.016	-0.016	0.000	0.000	0.000	0.000
100	B	100	HIS	0	0.064	0.008	13.475	-0.009	-0.009	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.025	-0.008	11.060	-0.021	-0.021	0.000	0.000	0.000	0.000
102	B	102	GLY	0	0.014	0.022	9.312	-0.100	-0.100	0.000	0.000	0.000	0.000
103	B	103	ILE	0	-0.050	-0.020	8.232	-0.203	-0.203	0.000	0.000	0.000	0.000
104	B	104	MET	0	-0.009	0.006	4.146	-0.601	-0.251	0.020	-0.082	-0.289	0.001
105	B	105	LYS	1	0.913	0.974	7.503	0.296	0.296	0.000	0.000	0.000	0.000
106	B	106	VAL	0	-0.007	-0.017	8.212	-0.053	-0.053	0.000	0.000	0.000	0.000
107	B	107	GLU	-1	-0.787	-0.860	10.461	-0.079	-0.079	0.000	0.000	0.000	0.000
108	B	108	GLU	-1	-0.818	-0.859	12.519	0.080	0.080	0.000	0.000	0.000	0.000
109	B	109	TYR	0	-0.045	-0.054	13.738	-0.004	-0.004	0.000	0.000	0.000	0.000
110	B	110	THR	0	0.009	-0.005	17.617	0.009	0.009	0.000	0.000	0.000	0.000
111	B	111	THR	0	-0.046	-0.007	20.587	-0.005	-0.005	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.011	0.011	23.081	0.003	0.003	0.000	0.000	0.000	0.000
113	B	113	GLN	0	0.012	-0.010	27.120	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	114	PHE	0	-0.005	-0.003	29.740	0.001	0.001	0.000	0.000	0.000	0.000
115	B	115	ASP	-1	-0.769	-0.846	32.845	0.035	0.035	0.000	0.000	0.000	0.000
116	B	116	SER	0	0.008	-0.009	34.367	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	117	ALA	0	-0.054	-0.017	37.080	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	118	THR	0	-0.052	-0.058	34.501	0.000	0.000	0.000	0.000	0.000	0.000
119	B	119	SER	0	-0.046	-0.015	37.050	0.000	0.000	0.000	0.000	0.000	0.000
120	B	120	SER	0	-0.024	-0.016	33.255	0.000	0.000	0.000	0.000	0.000	0.000
121	B	121	THR	0	-0.054	-0.032	29.568	0.000	0.000	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.020	0.022	26.509	0.002	0.002	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.009	-0.014	24.634	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.834	-0.884	21.565	0.068	0.068	0.000	0.000	0.000	0.000
125	B	125	SER	0	-0.011	-0.028	17.722	-0.003	-0.003	0.000	0.000	0.000	0.000
126	B	126	ARG	1	0.825	0.920	14.301	-0.050	-0.050	0.000	0.000	0.000	0.000
127	B	127	VAL	0	0.028	0.013	10.692	-0.008	-0.008	0.000	0.000	0.000	0.000
128	B	128	LYS	1	0.856	0.920	7.836	0.094	0.094	0.000	0.000	0.000	0.000
129	B	129	PHE	0	0.048	0.023	5.353	0.065	0.065	0.000	0.000	0.000	0.000
130	B	130	SER	0	-0.044	-0.046	4.466	-0.569	-0.387	-0.001	-0.061	-0.120	0.000
131	B	131	SER	0	-0.015	-0.030	3.035	0.575	1.937	0.070	-0.476	-0.954	0.000
132	B	132	GLY	0	0.090	0.046	1.917	-7.412	-9.569	8.378	-3.456	-2.766	-0.036
133	B	133	PHE	0	0.027	0.032	4.081	0.307	0.437	-0.001	-0.022	-0.108	0.000
134	B	134	ASN	0	-0.058	-0.039	3.964	-0.603	-0.291	0.000	-0.043	-0.269	0.000
135	B	135	MET	0	0.020	0.007	5.557	0.247	0.247	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.063	0.030	8.365	0.076	0.076	0.000	0.000	0.000	0.000
137	B	137	ILE	0	-0.030	-0.022	7.891	0.076	0.076	0.000	0.000	0.000	0.000
138	B	138	LYS	1	0.955	0.969	7.078	1.104	1.104	0.000	0.000	0.000	0.000
139	B	139	SER	0	0.020	0.025	11.587	0.061	0.061	0.000	0.000	0.000	0.000
140	B	140	LYS	1	0.928	0.973	12.528	0.274	0.274	0.000	0.000	0.000	0.000
141	B	141	VAL	0	0.013	0.009	12.469	0.031	0.031	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.841	-0.888	15.263	-0.153	-0.153	0.000	0.000	0.000	0.000
143	B	143	ASP	-1	-0.776	-0.882	17.704	-0.182	-0.182	0.000	0.000	0.000	0.000
144	B	144	TRP	0	-0.008	0.012	18.454	0.023	0.023	0.000	0.000	0.000	0.000
145	B	145	SER	0	-0.022	-0.032	18.346	0.020	0.020	0.000	0.000	0.000	0.000
146	B	146	ARG	1	0.797	0.871	20.285	0.179	0.179	0.000	0.000	0.000	0.000
147	B	147	THR	0	-0.015	-0.015	23.133	0.018	0.018	0.000	0.000	0.000	0.000
148	B	148	LYS	1	0.846	0.907	23.747	0.126	0.126	0.000	0.000	0.000	0.000
149	B	149	PHE	0	0.019	0.009	25.211	0.010	0.010	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.789	-0.879	27.007	-0.071	-0.071	0.000	0.000	0.000	0.000
151	B	151	GLU	-1	-0.844	-0.906	27.819	-0.092	-0.092	0.000	0.000	0.000	0.000
152	B	152	ASN	0	-0.001	-0.019	27.652	0.009	0.009	0.000	0.000	0.000	0.000
153	B	153	VAL	0	0.001	0.007	30.869	0.007	0.007	0.000	0.000	0.000	0.000
154	B	154	LYS	1	0.780	0.878	32.255	0.079	0.079	0.000	0.000	0.000	0.000
155	B	155	LYS	1	0.945	0.971	31.466	0.078	0.078	0.000	0.000	0.000	0.000
156	B	156	SER	0	-0.012	0.007	34.558	0.005	0.005	0.000	0.000	0.000	0.000
157	B	157	ARG	1	0.994	0.998	36.336	0.057	0.057	0.000	0.000	0.000	0.000
158	B	158	MET	0	-0.019	-0.014	38.683	0.002	0.002	0.000	0.000	0.000	0.000
159	B	159	GLY	0	0.028	0.022	39.317	0.003	0.003	0.000	0.000	0.000	0.000
160	B	160	MET	0	0.007	-0.004	39.821	0.002	0.002	0.000	0.000	0.000	0.000
161	B	161	ALA	0	0.004	0.007	42.278	0.002	0.002	0.000	0.000	0.000	0.000
162	B	162	PHE	0	0.005	0.006	44.097	0.002	0.002	0.000	0.000	0.000	0.000
163	B	163	VAL	0	-0.036	-0.026	43.575	0.002	0.002	0.000	0.000	0.000	0.000
164	B	164	ILE	0	0.036	0.012	45.249	0.001	0.001	0.000	0.000	0.000	0.000
165	B	165	GLN	0	0.008	0.010	48.246	0.001	0.001	0.000	0.000	0.000	0.000
166	B	166	LYS	1	0.896	0.954	46.990	0.036	0.036	0.000	0.000	0.000	0.000
167	B	167	LEU	0	-0.077	-0.037	49.183	0.001	0.001	0.000	0.000	0.000	0.000
168	B	168	GLU	-1	-1.000	-0.986	52.288	-0.024	-0.024	0.000	0.000	0.000	0.000

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