FMO DATABASE

FMODB ID: V5N61

Calculation Name: 2YWX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWX

Chain ID: A

ChEMBL ID:

UniProt ID: Q58033

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	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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1377495.038095
FMO2-HF: Nuclear repulsion	1318124.684314
FMO2-HF: Total energy	-59370.353782
FMO2-MP2: Total energy	-59543.094882

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.
-7.738	-5.004	18.112	-3.877	-16.972	-0.05

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 : -0.011 / q_NPA : 0.024

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	3	CYS	0	-0.026	-0.008	3.593	0.372	3.379	0.368	-1.131	-2.245	-0.005
4	A	4	ILE	0	0.009	0.011	4.747	-0.690	-0.633	-0.001	-0.013	-0.043	0.000
5	A	5	ILE	0	-0.002	-0.004	8.396	-0.022	-0.022	0.000	0.000	0.000	0.000
6	A	6	MET	0	-0.026	-0.005	10.996	-0.062	-0.062	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.018	0.009	14.621	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.048	-0.042	17.475	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.858	-0.917	18.386	0.179	0.179	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.054	-0.039	19.432	0.002	0.002	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.877	-0.955	17.518	0.249	0.249	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.048	0.024	15.714	0.053	0.053	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.977	0.995	17.216	-0.184	-0.184	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.045	-0.036	16.980	0.018	0.018	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.048	0.013	13.339	0.051	0.051	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.887	-0.954	13.390	0.444	0.444	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.828	0.930	15.308	-0.308	-0.308	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.013	0.014	11.611	0.017	0.017	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.027	0.016	9.966	0.135	0.135	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.006	-0.016	11.497	0.058	0.058	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.033	0.039	11.934	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.019	-0.016	6.422	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.926	0.957	9.200	-0.352	-0.352	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.996	-0.980	11.192	0.468	0.468	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.067	-0.044	10.065	-0.112	-0.112	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.042	-0.009	9.960	0.060	0.060	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.027	-0.011	4.987	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.900	-0.959	2.112	-5.101	-4.701	3.893	-1.521	-2.773	-0.009
29	A	29	PHE	0	-0.056	-0.062	2.603	1.104	2.126	7.451	-4.415	-4.058	-0.017
30	A	30	GLU	-1	-0.876	-0.929	2.847	-1.815	-5.556	2.715	3.871	-2.846	-0.013
31	A	31	VAL	0	-0.020	-0.017	4.910	-0.161	-0.114	0.000	-0.004	-0.044	0.000
32	A	32	ARG	1	0.939	0.966	8.128	-0.565	-0.565	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.020	0.017	10.778	0.016	0.016	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.014	0.001	14.109	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.058	-0.046	15.837	0.015	0.015	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.052	0.016	18.337	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.049	0.055	19.358	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.881	0.926	21.417	-0.110	-0.110	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.027	0.023	18.274	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.023	0.025	18.472	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.795	-0.923	18.073	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.022	0.021	14.698	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.030	-0.023	13.597	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.843	-0.913	12.858	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.961	-0.970	13.135	-0.168	-0.168	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.047	-0.031	8.621	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.036	-0.027	8.709	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.826	0.899	9.292	0.027	0.027	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.054	-0.017	9.414	-0.108	-0.108	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.009	0.024	4.502	-0.268	-0.156	-0.001	-0.007	-0.104	0.000
51	A	51	LYS	1	0.895	0.933	3.014	0.488	1.210	0.048	-0.150	-0.621	0.001
52	A	52	ALA	0	-0.035	-0.012	2.233	-2.799	-1.332	3.480	-2.197	-2.750	-0.006
53	A	53	ASP	-1	-0.869	-0.935	2.975	0.524	-0.393	0.149	1.815	-1.046	-0.001
54	A	54	VAL	0	-0.031	-0.022	4.760	0.661	0.869	-0.001	-0.024	-0.183	0.000
55	A	55	PHE	0	0.037	0.015	5.456	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.005	0.004	7.736	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.002	0.008	10.100	0.061	0.061	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.026	-0.015	12.799	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.043	0.012	15.582	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.067	0.035	18.881	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.035	-0.023	22.604	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.064	0.047	24.875	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.023	-0.012	20.280	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.018	-0.008	20.974	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.030	-0.005	13.991	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.036	0.004	15.024	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.088	0.032	15.760	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.008	-0.005	16.565	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.008	-0.001	10.871	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.026	0.002	13.328	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.087	-0.032	14.904	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.021	-0.006	13.804	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.022	-0.002	9.896	-0.062	-0.062	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.007	0.010	12.776	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.831	0.928	7.316	0.984	0.984	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.014	0.004	8.987	0.075	0.075	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.031	0.026	10.015	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.020	-0.014	10.665	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.011	0.007	13.048	0.034	0.034	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.034	-0.028	14.812	0.010	0.010	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.001	0.011	17.421	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.025	0.002	19.573	0.014	0.014	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.853	-0.917	22.200	0.166	0.166	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.017	0.013	25.550	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.904	0.930	27.365	-0.104	-0.104	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.036	0.001	29.629	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.871	-0.940	30.263	0.121	0.121	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.018	0.000	26.702	0.009	0.009	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.012	-0.009	26.563	0.007	0.007	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.878	-0.943	27.562	0.100	0.100	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.005	-0.006	22.354	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.020	0.010	22.792	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.053	-0.008	23.900	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.013	-0.003	23.684	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.081	-0.045	19.488	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.020	0.013	20.959	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.043	-0.015	22.862	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.044	0.002	19.241	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.008	0.003	23.049	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.009	-0.026	24.020	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.003	0.005	23.395	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.030	-0.005	18.413	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.009	0.004	17.885	0.015	0.015	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.050	0.018	16.058	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.034	0.001	14.923	0.004	0.004	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.041	0.017	16.414	0.032	0.032	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.033	0.000	16.796	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.002	-0.022	19.620	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.088	0.040	20.951	0.029	0.029	0.000	0.000	0.000	0.000
110	A	110	ASH	0	-0.097	-0.094	20.789	0.010	0.010	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.832	0.925	19.585	-0.270	-0.270	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.095	0.043	15.855	0.021	0.021	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.905	-0.958	14.448	0.536	0.536	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.027	-0.011	14.986	0.081	0.081	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.009	0.011	13.486	0.004	0.004	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.022	0.014	10.493	0.050	0.050	0.000	0.000	0.000	0.000
117	A	117	ILE	0	0.001	0.001	10.699	0.159	0.159	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.013	0.016	12.449	0.028	0.028	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.035	0.002	7.743	-0.054	-0.054	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.010	0.004	7.739	0.151	0.151	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.946	-0.986	9.204	0.464	0.464	0.000	0.000	0.000	0.000
122	A	122	ILE	0	-0.034	-0.008	8.140	-0.107	-0.107	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.009	-0.002	3.665	-0.507	-0.157	0.011	-0.101	-0.259	0.000
124	A	124	ALA	0	-0.025	-0.007	7.084	-0.142	-0.142	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.057	-0.014	10.319	-0.140	-0.140	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.900	0.948	7.566	0.233	0.233	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.836	-0.913	7.628	1.260	1.260	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.854	-0.956	9.718	0.324	0.324	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.034	-0.008	10.304	-0.172	-0.172	0.000	0.000	0.000	0.000
130	A	130	ILE	0	-0.024	-0.008	6.575	-0.054	-0.054	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.051	0.023	11.143	-0.084	-0.084	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.913	0.964	13.887	-0.381	-0.381	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.927	0.963	12.044	-0.836	-0.836	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.012	0.019	12.196	-0.064	-0.064	0.000	0.000	0.000	0.000
135	A	135	ILE	0	-0.004	0.001	15.776	-0.065	-0.065	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.908	-0.972	18.103	0.374	0.374	0.000	0.000	0.000	0.000
137	A	137	TYR	0	-0.027	-0.008	16.935	-0.042	-0.042	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.985	0.981	18.909	-0.408	-0.408	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.880	-0.940	21.505	0.200	0.200	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.943	0.956	19.220	-0.428	-0.428	0.000	0.000	0.000	0.000
141	A	141	MET	0	-0.009	-0.007	21.488	-0.021	-0.021	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.915	0.966	24.399	-0.238	-0.238	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.898	0.965	26.640	-0.223	-0.223	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.963	0.995	23.336	-0.289	-0.289	0.000	0.000	0.000	0.000
145	A	145	VAL	0	0.017	0.014	28.182	-0.012	-0.012	0.000	0.000	0.000	0.000
146	A	146	TYR	0	0.022	-0.003	30.588	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.037	0.028	31.714	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.063	-0.030	31.623	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.875	-0.929	34.209	0.112	0.112	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.865	-0.943	36.555	0.107	0.107	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.926	0.967	35.254	-0.138	-0.138	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.001	-0.034	37.702	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.826	0.923	39.652	-0.115	-0.115	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.961	-0.989	42.217	0.081	0.081	0.000	0.000	0.000	0.000
155	A	155	MET	0	-0.114	-0.030	40.011	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	156	PHE	0	-0.006	-0.006	42.707	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.932	0.991	46.849	-0.081	-0.081	0.000	0.000	0.000	0.000

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