FMO DATABASE

FMODB ID: 6Y26Z

Calculation Name: 3F8X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F8X

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D504

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1117440.703779
FMO2-HF: Nuclear repulsion	1066942.578525
FMO2-HF: Total energy	-50498.125254
FMO2-MP2: Total energy	-50645.8693

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:16:SER)

Summations of interaction energy for fragment #1(A:16:SER)

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.
-50.851	-50.748	17.073	-8.088	-9.086	0.007

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.019

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	18	ASN	0	-0.023	0.006	3.890	-1.429	-0.301	-0.011	-0.480	-0.637	0.001
4	A	19	ALA	0	0.081	0.030	6.547	-0.426	-0.426	0.000	0.000	0.000	0.000
5	A	20	ALA	0	0.012	0.027	8.748	-0.074	-0.074	0.000	0.000	0.000	0.000
6	A	21	VAL	0	0.011	0.009	7.412	-0.029	-0.029	0.000	0.000	0.000	0.000
7	A	22	GLN	0	-0.053	-0.022	5.807	0.205	0.205	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.024	-0.029	8.555	0.156	0.156	0.000	0.000	0.000	0.000
9	A	24	GLY	0	0.035	0.019	11.797	0.091	0.091	0.000	0.000	0.000	0.000
10	A	25	LEU	0	-0.026	-0.010	8.643	0.073	0.073	0.000	0.000	0.000	0.000
11	A	26	GLN	0	-0.050	-0.019	11.656	0.102	0.102	0.000	0.000	0.000	0.000
12	A	27	GLU	-1	-0.795	-0.883	13.967	-0.333	-0.333	0.000	0.000	0.000	0.000
13	A	28	TRP	0	0.002	-0.012	14.402	0.079	0.079	0.000	0.000	0.000	0.000
14	A	29	HIS	0	-0.010	-0.016	12.442	0.130	0.130	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.659	0.790	16.802	0.397	0.397	0.000	0.000	0.000	0.000
16	A	31	ILE	0	-0.001	0.002	19.498	0.041	0.041	0.000	0.000	0.000	0.000
17	A	32	ILE	0	-0.045	-0.021	18.896	0.040	0.040	0.000	0.000	0.000	0.000
18	A	33	ALA	0	-0.067	-0.029	20.843	0.030	0.030	0.000	0.000	0.000	0.000
19	A	34	GLU	-1	-0.918	-0.962	22.546	-0.290	-0.290	0.000	0.000	0.000	0.000
20	A	35	ALA	0	-0.028	-0.005	24.526	0.028	0.028	0.000	0.000	0.000	0.000
21	A	36	ASP	-1	-0.800	-0.880	24.213	-0.237	-0.237	0.000	0.000	0.000	0.000
22	A	37	TRP	0	0.051	-0.003	22.848	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.912	-0.968	25.845	-0.177	-0.177	0.000	0.000	0.000	0.000
24	A	39	ARG	1	0.854	0.928	23.098	0.218	0.218	0.000	0.000	0.000	0.000
25	A	40	LEU	0	0.008	0.017	19.779	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	41	PRO	0	0.022	-0.014	21.674	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	42	ASP	-1	-0.852	-0.899	22.382	-0.169	-0.169	0.000	0.000	0.000	0.000
28	A	43	LEU	0	-0.070	-0.022	15.229	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	44	LEU	0	-0.003	0.011	17.579	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	45	ALA	0	0.007	0.006	17.929	0.026	0.026	0.000	0.000	0.000	0.000
31	A	46	GLU	-1	-0.895	-0.969	19.851	-0.091	-0.091	0.000	0.000	0.000	0.000
32	A	47	ASP	-1	-0.925	-0.972	20.759	0.010	0.010	0.000	0.000	0.000	0.000
33	A	48	VAL	0	-0.065	-0.015	18.280	0.007	0.007	0.000	0.000	0.000	0.000
34	A	49	VAL	0	0.047	0.032	18.666	0.003	0.003	0.000	0.000	0.000	0.000
35	A	50	PHE	0	0.019	-0.009	19.232	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	51	SER	0	0.006	-0.001	20.666	0.037	0.037	0.000	0.000	0.000	0.000
37	A	52	ASN	0	0.030	0.014	21.542	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.018	-0.009	23.852	0.013	0.013	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.040	-0.021	25.479	0.008	0.008	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.032	-0.013	27.569	0.015	0.015	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.048	-0.011	24.941	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	57	ASP	-1	-0.921	-0.966	25.472	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	58	PRO	0	-0.041	-0.008	22.609	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	59	TYR	0	-0.022	-0.015	24.696	0.016	0.016	0.000	0.000	0.000	0.000
45	A	60	HIS	0	0.003	-0.011	23.615	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	61	GLY	0	0.017	0.023	23.599	0.006	0.006	0.000	0.000	0.000	0.000
47	A	62	LYS	1	0.821	0.907	22.494	0.110	0.110	0.000	0.000	0.000	0.000
48	A	63	GLY	0	-0.009	0.004	25.179	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	64	PRO	0	0.020	-0.006	27.083	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	65	LEU	0	0.019	0.026	20.555	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	66	MET	0	0.001	-0.002	25.260	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.031	0.001	27.279	0.000	0.000	0.000	0.000	0.000	0.000
53	A	68	ILE	0	-0.032	-0.017	26.840	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.001	0.007	21.429	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	70	PRO	0	0.051	0.025	25.775	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.002	0.011	27.905	0.001	0.001	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.007	-0.006	25.742	0.003	0.003	0.000	0.000	0.000	0.000
58	A	73	PHE	0	0.045	0.006	21.130	0.004	0.004	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.081	-0.029	27.114	0.004	0.004	0.000	0.000	0.000	0.000
60	A	75	VAL	0	-0.047	-0.035	30.240	0.012	0.012	0.000	0.000	0.000	0.000
61	A	76	LEU	0	-0.044	-0.006	24.865	0.003	0.003	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.811	-0.886	28.214	-0.187	-0.187	0.000	0.000	0.000	0.000
63	A	78	ASN	0	-0.087	-0.074	28.278	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	79	PHE	0	0.024	0.031	19.893	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	80	GLN	0	-0.047	-0.023	21.770	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	81	TYR	0	0.000	-0.035	16.336	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	82	ALA	0	-0.025	-0.019	17.356	0.029	0.029	0.000	0.000	0.000	0.000
68	A	83	ARG	1	0.750	0.849	14.834	0.368	0.368	0.000	0.000	0.000	0.000
69	A	84	HIS	0	-0.002	0.005	10.078	-0.121	-0.121	0.000	0.000	0.000	0.000
70	A	85	PHE	0	-0.013	-0.007	8.441	0.016	0.016	0.000	0.000	0.000	0.000
71	A	86	SER	0	-0.008	-0.007	3.794	-0.623	-0.237	0.006	-0.142	-0.249	-0.001
72	A	87	SER	0	-0.020	-0.030	4.193	-0.405	0.042	-0.001	-0.216	-0.230	-0.001
73	A	88	LYS	1	0.809	0.877	1.955	-47.159	-48.781	17.068	-7.525	-7.920	0.008
74	A	89	SER	0	-0.010	-0.039	3.284	0.234	-0.002	0.011	0.275	-0.050	0.000
75	A	90	GLY	0	0.065	0.037	5.586	0.080	0.080	0.000	0.000	0.000	0.000
76	A	91	TYR	0	-0.031	-0.014	5.264	-0.957	-0.957	0.000	0.000	0.000	0.000
77	A	92	VAL	0	-0.006	0.004	8.485	0.333	0.333	0.000	0.000	0.000	0.000
78	A	93	LEU	0	0.000	-0.001	10.989	-0.152	-0.152	0.000	0.000	0.000	0.000
79	A	94	GLU	-1	-0.772	-0.853	13.837	-0.362	-0.362	0.000	0.000	0.000	0.000
80	A	95	PHE	0	0.000	0.006	16.987	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	96	ASN	0	-0.053	-0.040	20.036	0.055	0.055	0.000	0.000	0.000	0.000
82	A	97	ALA	0	0.055	0.033	23.692	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	98	ASN	0	-0.068	-0.043	26.711	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	99	MET	0	0.030	0.030	30.457	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	100	GLY	0	0.013	0.003	33.292	0.010	0.010	0.000	0.000	0.000	0.000
86	A	101	ASP	-1	-0.947	-0.975	34.818	-0.139	-0.139	0.000	0.000	0.000	0.000
87	A	102	GLH	0	-0.082	-0.068	34.052	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	103	LEU	0	-0.012	-0.011	30.136	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	104	LEU	0	-0.032	-0.013	25.617	0.010	0.010	0.000	0.000	0.000	0.000
90	A	105	THR	0	-0.011	0.001	23.022	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	106	GLY	0	0.021	-0.003	21.620	0.035	0.035	0.000	0.000	0.000	0.000
92	A	107	VAL	0	-0.052	-0.016	16.226	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	108	ASP	-1	-0.735	-0.846	16.033	-0.409	-0.409	0.000	0.000	0.000	0.000
94	A	109	LEU	0	-0.054	-0.027	12.032	-0.119	-0.119	0.000	0.000	0.000	0.000
95	A	110	ILE	0	0.026	0.004	11.791	0.097	0.097	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.779	-0.840	8.331	-0.887	-0.887	0.000	0.000	0.000	0.000
97	A	112	PHE	0	0.013	0.005	9.960	0.028	0.028	0.000	0.000	0.000	0.000
98	A	113	ASN	0	0.046	0.027	10.524	0.103	0.103	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.865	-0.957	10.339	0.664	0.664	0.000	0.000	0.000	0.000
100	A	115	ALA	0	-0.034	-0.018	12.132	-0.054	-0.054	0.000	0.000	0.000	0.000
101	A	116	GLY	0	-0.003	-0.004	12.300	-0.045	-0.045	0.000	0.000	0.000	0.000
102	A	117	LYS	1	0.799	0.899	13.354	0.222	0.222	0.000	0.000	0.000	0.000
103	A	118	ILE	0	0.008	0.015	14.148	0.035	0.035	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.013	-0.042	13.979	0.052	0.052	0.000	0.000	0.000	0.000
105	A	120	ASP	-1	-0.889	-0.915	14.200	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.004	0.003	14.730	-0.094	-0.094	0.000	0.000	0.000	0.000
107	A	122	VAL	0	-0.020	-0.015	16.447	0.058	0.058	0.000	0.000	0.000	0.000
108	A	123	VAL	0	0.018	0.020	17.410	-0.050	-0.050	0.000	0.000	0.000	0.000
109	A	124	MET	0	-0.032	-0.021	20.108	0.040	0.040	0.000	0.000	0.000	0.000
110	A	125	MET	0	0.007	0.002	21.634	-0.024	-0.024	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.872	0.950	23.974	0.247	0.247	0.000	0.000	0.000	0.000
112	A	127	PRO	0	0.045	0.010	26.735	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	128	ALA	0	0.073	0.007	29.610	0.000	0.000	0.000	0.000	0.000	0.000
114	A	129	SER	0	-0.009	0.003	30.513	0.001	0.001	0.000	0.000	0.000	0.000
115	A	130	VAL	0	0.078	0.044	31.066	0.004	0.004	0.000	0.000	0.000	0.000
116	A	131	VAL	0	0.011	0.014	27.581	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	132	ILE	0	-0.019	0.009	30.468	0.004	0.004	0.000	0.000	0.000	0.000
118	A	133	ASP	-1	-0.844	-0.896	33.737	-0.113	-0.113	0.000	0.000	0.000	0.000
119	A	134	LEU	0	0.012	0.001	28.171	0.003	0.003	0.000	0.000	0.000	0.000
120	A	135	SER	0	0.001	-0.015	31.216	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	136	VAL	0	-0.042	-0.011	32.831	0.006	0.006	0.000	0.000	0.000	0.000
122	A	137	GLU	-1	-0.814	-0.882	34.870	-0.115	-0.115	0.000	0.000	0.000	0.000
123	A	138	VAL	0	0.021	0.001	30.426	0.002	0.002	0.000	0.000	0.000	0.000
124	A	139	GLY	0	0.020	0.016	33.678	0.003	0.003	0.000	0.000	0.000	0.000
125	A	140	LYS	1	0.821	0.899	36.080	0.110	0.110	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.818	0.896	33.965	0.152	0.152	0.000	0.000	0.000	0.000
127	A	142	ILE	0	0.038	0.022	31.430	0.001	0.001	0.000	0.000	0.000	0.000
128	A	143	ALA	0	-0.035	-0.012	35.676	0.005	0.005	0.000	0.000	0.000	0.000
129	A	144	ALA	0	-0.043	-0.029	39.392	0.004	0.004	0.000	0.000	0.000	0.000
130	A	145	ALA	0	-0.025	0.003	36.387	0.001	0.001	0.000	0.000	0.000	0.000
131	A	146	GLN	0	-0.098	-0.041	35.705	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)