FMO DATABASE

FMODB ID: R8YR8

Calculation Name: 2F9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F9S

Chain ID: A

ChEMBL ID:

UniProt ID: P35160

Base Structure: X-ray

Registration Date: 2023-09-22

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1297783.583721
FMO2-HF: Nuclear repulsion	1242937.837997
FMO2-HF: Total energy	-54845.745724
FMO2-MP2: Total energy	-55003.529152

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:38:GLU)

Summations of interaction energy for fragment #1(A:38: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.
20.87	24.699	0.346	-1.628	-2.548	0.01

Interaction energy analysis for fragmet #1(A:38:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.953 / q_NPA : -0.986

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	40	SER	0	-0.062	-0.026	3.448	-4.366	-2.635	0.008	-0.843	-0.896	0.006
4	A	41	ASP	-1	-0.923	-0.972	6.939	26.714	26.714	0.000	0.000	0.000	0.000
5	A	42	ALA	0	0.025	0.022	9.172	-0.793	-0.793	0.000	0.000	0.000	0.000
6	A	43	PRO	0	-0.008	0.005	11.672	-0.825	-0.825	0.000	0.000	0.000	0.000
7	A	44	ASN	0	0.009	0.000	15.198	0.385	0.385	0.000	0.000	0.000	0.000
8	A	45	PHE	0	0.005	-0.002	16.984	-0.529	-0.529	0.000	0.000	0.000	0.000
9	A	46	VAL	0	0.030	0.007	20.461	0.101	0.101	0.000	0.000	0.000	0.000
10	A	47	LEU	0	-0.029	-0.005	22.634	-0.301	-0.301	0.000	0.000	0.000	0.000
11	A	48	GLU	-1	-0.905	-0.954	25.489	9.796	9.796	0.000	0.000	0.000	0.000
12	A	49	ASP	-1	-0.769	-0.879	27.633	10.665	10.665	0.000	0.000	0.000	0.000
13	A	50	THR	0	-0.050	-0.049	28.912	-0.318	-0.318	0.000	0.000	0.000	0.000
14	A	51	ASN	0	-0.085	-0.045	32.030	-0.583	-0.583	0.000	0.000	0.000	0.000
15	A	52	GLY	0	-0.038	-0.007	32.409	-0.238	-0.238	0.000	0.000	0.000	0.000
16	A	53	LYS	1	0.927	0.981	27.318	-11.344	-11.344	0.000	0.000	0.000	0.000
17	A	54	ARG	1	0.944	0.971	27.033	-10.318	-10.318	0.000	0.000	0.000	0.000
18	A	55	ILE	0	-0.008	-0.006	21.692	0.002	0.002	0.000	0.000	0.000	0.000
19	A	56	GLU	-1	-0.860	-0.923	19.700	13.476	13.476	0.000	0.000	0.000	0.000
20	A	57	LEU	0	-0.009	0.015	13.904	0.313	0.313	0.000	0.000	0.000	0.000
21	A	58	SER	0	-0.018	-0.030	15.295	0.851	0.851	0.000	0.000	0.000	0.000
22	A	59	ASP	-1	-0.892	-0.940	16.344	14.092	14.092	0.000	0.000	0.000	0.000
23	A	60	LEU	0	-0.108	-0.057	16.360	-0.280	-0.280	0.000	0.000	0.000	0.000
24	A	61	LYS	1	0.958	0.974	11.650	-19.726	-19.726	0.000	0.000	0.000	0.000
25	A	62	GLY	0	-0.050	-0.022	12.449	-1.334	-1.334	0.000	0.000	0.000	0.000
26	A	63	LYS	1	0.897	0.951	13.733	-16.861	-16.861	0.000	0.000	0.000	0.000
27	A	64	GLY	0	0.042	0.043	11.450	1.258	1.258	0.000	0.000	0.000	0.000
28	A	65	VAL	0	-0.038	-0.029	11.930	-2.404	-2.404	0.000	0.000	0.000	0.000
29	A	66	PHE	0	0.031	0.001	12.473	1.703	1.703	0.000	0.000	0.000	0.000
30	A	67	LEU	0	0.020	0.015	14.093	-1.594	-1.594	0.000	0.000	0.000	0.000
31	A	68	ASN	0	-0.041	-0.030	15.781	-0.289	-0.289	0.000	0.000	0.000	0.000
32	A	69	PHE	0	0.045	0.022	16.621	-0.819	-0.819	0.000	0.000	0.000	0.000
33	A	70	TRP	0	-0.025	-0.030	20.794	-0.369	-0.369	0.000	0.000	0.000	0.000
34	A	71	GLY	0	0.078	0.030	24.217	-0.189	-0.189	0.000	0.000	0.000	0.000
35	A	72	THR	0	-0.128	-0.113	27.964	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	73	TRP	0	0.011	0.000	28.712	-0.134	-0.134	0.000	0.000	0.000	0.000
37	A	74	CYS	0	-0.077	-0.005	26.817	0.014	0.014	0.000	0.000	0.000	0.000
38	A	75	GLU	-1	-0.826	-0.924	28.974	9.840	9.840	0.000	0.000	0.000	0.000
39	A	76	PRO	0	-0.001	-0.013	24.722	0.109	0.109	0.000	0.000	0.000	0.000
40	A	77	CYS	0	0.021	0.028	24.647	0.541	0.541	0.000	0.000	0.000	0.000
41	A	78	LYS	1	0.891	0.957	25.716	-9.375	-9.375	0.000	0.000	0.000	0.000
42	A	79	LYS	1	0.892	0.955	26.562	-11.558	-11.558	0.000	0.000	0.000	0.000
43	A	80	GLU	-1	-0.789	-0.912	21.076	15.016	15.016	0.000	0.000	0.000	0.000
44	A	81	PHE	0	0.038	0.010	23.723	0.276	0.276	0.000	0.000	0.000	0.000
45	A	82	PRO	0	-0.001	-0.005	25.477	0.132	0.132	0.000	0.000	0.000	0.000
46	A	83	TYR	0	-0.001	0.003	22.696	-0.069	-0.069	0.000	0.000	0.000	0.000
47	A	84	MET	0	0.015	0.017	20.054	0.396	0.396	0.000	0.000	0.000	0.000
48	A	85	ALA	0	0.025	0.025	22.126	0.270	0.270	0.000	0.000	0.000	0.000
49	A	86	ASN	0	-0.063	-0.042	24.837	-0.350	-0.350	0.000	0.000	0.000	0.000
50	A	87	GLN	0	0.029	-0.005	19.736	0.621	0.621	0.000	0.000	0.000	0.000
51	A	88	TYR	0	-0.056	-0.050	20.612	0.062	0.062	0.000	0.000	0.000	0.000
52	A	89	LYS	1	0.884	0.935	22.094	-11.096	-11.096	0.000	0.000	0.000	0.000
53	A	90	HIS	0	-0.028	0.002	19.575	-0.763	-0.763	0.000	0.000	0.000	0.000
54	A	91	PHE	0	0.034	0.006	15.725	0.153	0.153	0.000	0.000	0.000	0.000
55	A	92	LYS	1	1.000	1.020	18.748	-12.235	-12.235	0.000	0.000	0.000	0.000
56	A	93	SER	0	-0.075	-0.046	20.584	0.375	0.375	0.000	0.000	0.000	0.000
57	A	94	GLN	0	0.000	0.011	16.782	0.678	0.678	0.000	0.000	0.000	0.000
58	A	95	GLY	0	0.033	0.024	16.071	1.107	1.107	0.000	0.000	0.000	0.000
59	A	96	VAL	0	-0.002	0.002	13.910	1.310	1.310	0.000	0.000	0.000	0.000
60	A	97	GLU	-1	-0.854	-0.910	16.246	13.403	13.403	0.000	0.000	0.000	0.000
61	A	98	ILE	0	-0.015	-0.003	16.773	1.136	1.136	0.000	0.000	0.000	0.000
62	A	99	VAL	0	-0.002	-0.005	18.243	-0.812	-0.812	0.000	0.000	0.000	0.000
63	A	100	ALA	0	0.007	0.007	19.134	0.545	0.545	0.000	0.000	0.000	0.000
64	A	101	VAL	0	0.025	0.005	19.897	-0.761	-0.761	0.000	0.000	0.000	0.000
65	A	102	ASN	0	-0.054	-0.037	22.562	-0.130	-0.130	0.000	0.000	0.000	0.000
66	A	103	VAL	0	0.026	-0.002	24.066	-0.063	-0.063	0.000	0.000	0.000	0.000
67	A	104	GLY	0	0.017	0.019	26.584	-0.319	-0.319	0.000	0.000	0.000	0.000
68	A	105	GLU	-1	-0.792	-0.836	29.868	9.633	9.633	0.000	0.000	0.000	0.000
69	A	106	SER	0	0.009	0.001	32.046	0.078	0.078	0.000	0.000	0.000	0.000
70	A	107	LYS	1	1.019	0.997	33.618	-8.922	-8.922	0.000	0.000	0.000	0.000
71	A	108	ILE	0	-0.014	-0.001	34.662	0.105	0.105	0.000	0.000	0.000	0.000
72	A	109	ALA	0	0.018	0.011	34.516	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	110	VAL	0	0.065	0.032	29.504	0.094	0.094	0.000	0.000	0.000	0.000
74	A	111	HIS	0	-0.013	-0.009	32.205	0.158	0.158	0.000	0.000	0.000	0.000
75	A	112	ASN	0	-0.005	-0.019	34.315	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	113	PHE	0	0.043	0.027	28.279	-0.132	-0.132	0.000	0.000	0.000	0.000
77	A	114	MET	0	0.021	0.000	28.597	0.041	0.041	0.000	0.000	0.000	0.000
78	A	115	LYS	1	0.885	0.951	31.503	-8.977	-8.977	0.000	0.000	0.000	0.000
79	A	116	SER	0	-0.041	-0.015	34.572	-0.158	-0.158	0.000	0.000	0.000	0.000
80	A	117	TYR	0	-0.014	-0.006	29.633	-0.106	-0.106	0.000	0.000	0.000	0.000
81	A	118	GLY	0	-0.050	-0.007	30.047	0.297	0.297	0.000	0.000	0.000	0.000
82	A	119	VAL	0	-0.027	-0.012	26.609	0.281	0.281	0.000	0.000	0.000	0.000
83	A	120	ASN	0	-0.064	-0.032	26.109	-0.084	-0.084	0.000	0.000	0.000	0.000
84	A	121	PHE	0	0.012	0.008	22.855	0.122	0.122	0.000	0.000	0.000	0.000
85	A	122	PRO	0	-0.023	-0.012	22.472	-0.581	-0.581	0.000	0.000	0.000	0.000
86	A	123	VAL	0	0.015	0.010	23.348	0.423	0.423	0.000	0.000	0.000	0.000
87	A	124	VAL	0	-0.018	-0.012	22.617	-0.372	-0.372	0.000	0.000	0.000	0.000
88	A	125	LEU	0	-0.022	-0.023	25.594	0.044	0.044	0.000	0.000	0.000	0.000
89	A	126	ASP	-1	-0.751	-0.877	24.063	12.452	12.452	0.000	0.000	0.000	0.000
90	A	127	THR	0	-0.042	-0.041	26.219	-0.158	-0.158	0.000	0.000	0.000	0.000
91	A	128	ASP	-1	-0.905	-0.962	28.132	10.432	10.432	0.000	0.000	0.000	0.000
92	A	129	ARG	1	0.906	0.960	25.863	-11.145	-11.145	0.000	0.000	0.000	0.000
93	A	130	GLN	0	0.060	0.050	24.881	0.494	0.494	0.000	0.000	0.000	0.000
94	A	131	VAL	0	-0.019	-0.016	19.509	0.567	0.567	0.000	0.000	0.000	0.000
95	A	132	LEU	0	-0.051	-0.038	19.923	0.703	0.703	0.000	0.000	0.000	0.000
96	A	133	ASP	-1	-0.915	-0.956	20.523	12.533	12.533	0.000	0.000	0.000	0.000
97	A	134	ALA	0	-0.057	-0.023	18.721	0.420	0.420	0.000	0.000	0.000	0.000
98	A	135	TYR	0	-0.105	-0.077	13.050	1.508	1.508	0.000	0.000	0.000	0.000
99	A	136	ASP	-1	-0.942	-0.960	16.383	16.046	16.046	0.000	0.000	0.000	0.000
100	A	137	VAL	0	-0.046	-0.015	17.801	0.285	0.285	0.000	0.000	0.000	0.000
101	A	138	SER	0	0.019	0.002	19.689	-0.889	-0.889	0.000	0.000	0.000	0.000
102	A	139	PRO	0	-0.074	-0.025	20.673	-0.534	-0.534	0.000	0.000	0.000	0.000
103	A	140	LEU	0	0.009	0.026	21.463	0.571	0.571	0.000	0.000	0.000	0.000
104	A	141	PRO	0	-0.010	-0.030	20.529	-0.613	-0.613	0.000	0.000	0.000	0.000
105	A	142	THR	0	0.016	-0.008	15.867	0.336	0.336	0.000	0.000	0.000	0.000
106	A	143	THR	0	-0.012	-0.006	14.083	-0.890	-0.890	0.000	0.000	0.000	0.000
107	A	144	PHE	0	0.015	0.014	11.327	1.338	1.338	0.000	0.000	0.000	0.000
108	A	145	LEU	0	-0.059	-0.022	8.756	-1.197	-1.197	0.000	0.000	0.000	0.000
109	A	146	ILE	0	0.029	0.013	7.923	4.085	4.085	0.000	0.000	0.000	0.000
110	A	147	ASN	0	0.068	0.029	3.864	-7.713	-7.458	0.001	-0.039	-0.217	0.000
111	A	148	PRO	0	0.051	0.022	7.844	-2.083	-2.083	0.000	0.000	0.000	0.000
112	A	149	GLU	-1	-0.910	-0.954	6.123	32.874	32.874	0.000	0.000	0.000	0.000
113	A	150	GLY	0	-0.113	-0.047	8.177	-1.838	-1.838	0.000	0.000	0.000	0.000
114	A	151	LYS	1	0.889	0.954	3.751	-37.882	-37.516	0.000	-0.104	-0.262	0.000
115	A	152	VAL	0	0.015	0.008	6.657	2.013	2.013	0.000	0.000	0.000	0.000
116	A	153	VAL	0	0.012	-0.003	2.568	-0.517	0.757	0.338	-0.636	-0.977	0.004
117	A	154	LYS	1	0.912	0.966	4.469	-28.309	-28.106	-0.001	-0.006	-0.196	0.000
118	A	155	VAL	0	0.030	0.023	7.737	-2.054	-2.054	0.000	0.000	0.000	0.000
119	A	156	VAL	0	-0.038	-0.021	11.182	0.261	0.261	0.000	0.000	0.000	0.000
120	A	157	THR	0	0.010	0.008	14.279	-0.696	-0.696	0.000	0.000	0.000	0.000
121	A	158	GLY	0	0.013	0.015	17.810	-0.144	-0.144	0.000	0.000	0.000	0.000
122	A	159	THR	0	-0.069	-0.042	19.569	0.379	0.379	0.000	0.000	0.000	0.000
123	A	160	MET	0	-0.023	0.003	16.848	0.985	0.985	0.000	0.000	0.000	0.000
124	A	161	THR	0	-0.003	-0.040	19.798	-0.646	-0.646	0.000	0.000	0.000	0.000
125	A	162	GLU	-1	-0.801	-0.908	19.719	13.716	13.716	0.000	0.000	0.000	0.000
126	A	163	SER	0	-0.009	-0.005	19.521	0.274	0.274	0.000	0.000	0.000	0.000
127	A	164	MET	0	0.022	0.053	16.051	0.331	0.331	0.000	0.000	0.000	0.000
128	A	165	ILE	0	0.015	0.004	14.978	1.403	1.403	0.000	0.000	0.000	0.000
129	A	166	HIS	0	-0.056	-0.034	15.585	1.254	1.254	0.000	0.000	0.000	0.000
130	A	167	ASP	-1	-0.913	-0.958	12.798	21.269	21.269	0.000	0.000	0.000	0.000
131	A	168	TYR	0	-0.061	-0.047	10.970	2.240	2.240	0.000	0.000	0.000	0.000
132	A	169	MET	0	0.007	0.003	11.031	1.631	1.631	0.000	0.000	0.000	0.000
133	A	170	ASN	0	0.019	-0.003	12.532	0.153	0.153	0.000	0.000	0.000	0.000
134	A	171	LEU	0	-0.073	-0.018	5.285	0.225	0.225	0.000	0.000	0.000	0.000
135	A	172	ILE	0	-0.032	-0.014	7.689	4.282	4.282	0.000	0.000	0.000	0.000
136	A	173	LYS	1	0.848	0.930	9.417	-22.562	-22.562	0.000	0.000	0.000	0.000
137	A	174	PRO	0	-0.188	-0.066	10.697	2.330	2.330	0.000	0.000	0.000	0.000
138	A	175	GLY	0	0.156	0.078	10.608	-2.755	-2.755	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:GLU)