FMO DATABASE

FMODB ID: 8N2VY

Calculation Name: 3Q47-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q47

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WUD1

Base Structure: X-ray

Registration Date: 2023-09-26

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1173533.257305
FMO2-HF: Nuclear repulsion	1119853.901023
FMO2-HF: Total energy	-53679.356282
FMO2-MP2: Total energy	-53834.401672

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:24:SER)

Summations of interaction energy for fragment #1(B:24: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.
-9.759	-7.846	0.603	-1.071	-1.445	0.003

Interaction energy analysis for fragmet #1(B:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.029

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	26	SER	0	0.012	-0.039	3.881	0.174	1.134	-0.009	-0.429	-0.522	0.001
4	B	27	ALA	0	0.048	0.004	6.649	0.625	0.625	0.000	0.000	0.000	0.000
5	B	28	GLN	0	0.057	0.049	9.337	0.250	0.250	0.000	0.000	0.000	0.000
6	B	29	GLU	-1	-0.749	-0.842	6.863	-1.238	-1.238	0.000	0.000	0.000	0.000
7	B	30	LEU	0	-0.054	-0.013	5.466	0.303	0.303	0.000	0.000	0.000	0.000
8	B	31	LYS	1	0.833	0.895	9.273	-0.049	-0.049	0.000	0.000	0.000	0.000
9	B	32	GLU	-1	-0.858	-0.918	12.462	0.019	0.019	0.000	0.000	0.000	0.000
10	B	33	GLN	0	-0.042	-0.018	8.932	0.271	0.271	0.000	0.000	0.000	0.000
11	B	34	GLY	0	0.052	0.024	12.429	-0.013	-0.013	0.000	0.000	0.000	0.000
12	B	35	ASN	0	0.019	0.017	14.681	-0.024	-0.024	0.000	0.000	0.000	0.000
13	B	36	ARG	1	0.956	0.980	11.733	-0.544	-0.544	0.000	0.000	0.000	0.000
14	B	37	LEU	0	0.009	0.006	13.727	-0.029	-0.029	0.000	0.000	0.000	0.000
15	B	38	PHE	0	0.014	0.002	17.685	-0.040	-0.040	0.000	0.000	0.000	0.000
16	B	39	VAL	0	-0.022	-0.007	20.375	-0.032	-0.032	0.000	0.000	0.000	0.000
17	B	40	GLY	0	-0.022	-0.012	20.761	-0.028	-0.028	0.000	0.000	0.000	0.000
18	B	41	ARG	1	0.907	0.956	21.972	-0.269	-0.269	0.000	0.000	0.000	0.000
19	B	42	LYS	1	0.805	0.901	18.916	-0.535	-0.535	0.000	0.000	0.000	0.000
20	B	43	TYR	0	0.068	0.020	18.893	0.054	0.054	0.000	0.000	0.000	0.000
21	B	44	PRO	0	0.087	0.032	19.368	0.025	0.025	0.000	0.000	0.000	0.000
22	B	45	GLU	-1	-0.742	-0.862	15.375	0.690	0.690	0.000	0.000	0.000	0.000
23	B	46	ALA	0	-0.010	0.001	14.480	0.135	0.135	0.000	0.000	0.000	0.000
24	B	47	ALA	0	0.018	0.004	15.184	0.035	0.035	0.000	0.000	0.000	0.000
25	B	48	ALA	0	0.027	0.016	13.320	0.017	0.017	0.000	0.000	0.000	0.000
26	B	49	CYS	0	-0.099	-0.043	10.722	0.275	0.275	0.000	0.000	0.000	0.000
27	B	50	TYR	0	0.025	-0.031	11.078	0.030	0.030	0.000	0.000	0.000	0.000
28	B	51	GLY	0	0.032	0.023	13.430	-0.069	-0.069	0.000	0.000	0.000	0.000
29	B	52	ARG	1	0.895	0.948	5.619	-3.398	-3.398	0.000	0.000	0.000	0.000
30	B	53	ALA	0	-0.021	-0.006	8.731	0.037	0.037	0.000	0.000	0.000	0.000
31	B	54	ILE	0	-0.003	-0.001	10.498	-0.129	-0.129	0.000	0.000	0.000	0.000
32	B	55	THR	0	-0.067	-0.046	9.549	-0.048	-0.048	0.000	0.000	0.000	0.000
33	B	56	ARG	1	0.866	0.923	2.389	-5.790	-4.837	0.612	-0.642	-0.923	0.002
34	B	57	ASN	0	0.015	0.004	9.744	-0.185	-0.185	0.000	0.000	0.000	0.000
35	B	58	PRO	0	0.041	0.034	13.080	0.029	0.029	0.000	0.000	0.000	0.000
36	B	59	LEU	0	0.051	0.033	16.116	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	60	VAL	0	-0.003	0.006	15.772	-0.028	-0.028	0.000	0.000	0.000	0.000
38	B	61	ALA	0	0.099	0.046	18.455	0.050	0.050	0.000	0.000	0.000	0.000
39	B	62	VAL	0	0.000	0.003	18.832	0.024	0.024	0.000	0.000	0.000	0.000
40	B	63	TYR	0	-0.001	-0.009	13.245	0.026	0.026	0.000	0.000	0.000	0.000
41	B	64	TYR	0	-0.002	-0.009	17.326	0.068	0.068	0.000	0.000	0.000	0.000
42	B	65	THR	0	-0.001	-0.006	19.979	0.008	0.008	0.000	0.000	0.000	0.000
43	B	66	ASN	0	-0.027	-0.015	18.187	-0.033	-0.033	0.000	0.000	0.000	0.000
44	B	67	ARG	1	0.867	0.909	16.399	-0.488	-0.488	0.000	0.000	0.000	0.000
45	B	68	ALA	0	0.034	0.023	19.790	0.006	0.006	0.000	0.000	0.000	0.000
46	B	69	LEU	0	-0.020	0.005	23.400	-0.008	-0.008	0.000	0.000	0.000	0.000
47	B	70	CYS	0	-0.094	-0.049	19.974	0.012	0.012	0.000	0.000	0.000	0.000
48	B	71	TYR	0	0.031	0.000	20.229	0.011	0.011	0.000	0.000	0.000	0.000
49	B	72	LEU	0	0.018	0.009	24.215	-0.011	-0.011	0.000	0.000	0.000	0.000
50	B	73	LYS	1	0.874	0.946	24.851	-0.241	-0.241	0.000	0.000	0.000	0.000
51	B	74	MET	0	-0.108	-0.030	21.259	0.016	0.016	0.000	0.000	0.000	0.000
52	B	75	GLN	0	0.004	0.008	26.233	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	76	GLN	0	-0.007	0.000	24.658	0.018	0.018	0.000	0.000	0.000	0.000
54	B	77	PRO	0	0.078	0.034	27.297	0.013	0.013	0.000	0.000	0.000	0.000
55	B	78	GLU	-1	-0.843	-0.933	29.418	0.208	0.208	0.000	0.000	0.000	0.000
56	B	79	GLN	0	-0.024	-0.011	24.031	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	80	ALA	0	0.002	0.000	24.705	0.009	0.009	0.000	0.000	0.000	0.000
58	B	81	LEU	0	0.043	0.029	25.829	-0.009	-0.009	0.000	0.000	0.000	0.000
59	B	82	ALA	0	0.000	-0.007	25.550	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	83	ASP	-1	-0.774	-0.850	20.887	0.373	0.373	0.000	0.000	0.000	0.000
61	B	84	CYS	0	-0.075	-0.040	23.708	-0.014	-0.014	0.000	0.000	0.000	0.000
62	B	85	ARG	1	0.920	0.964	26.483	-0.150	-0.150	0.000	0.000	0.000	0.000
63	B	86	ARG	1	0.978	0.976	21.415	-0.292	-0.292	0.000	0.000	0.000	0.000
64	B	87	ALA	0	-0.055	-0.032	23.561	-0.013	-0.013	0.000	0.000	0.000	0.000
65	B	88	LEU	0	-0.038	-0.020	24.445	-0.019	-0.019	0.000	0.000	0.000	0.000
66	B	89	GLU	-1	-0.945	-0.973	25.749	0.134	0.134	0.000	0.000	0.000	0.000
67	B	90	LEU	0	-0.086	-0.022	20.848	-0.012	-0.012	0.000	0.000	0.000	0.000
68	B	91	ASP	-1	-0.816	-0.912	24.956	0.044	0.044	0.000	0.000	0.000	0.000
69	B	92	GLY	0	0.040	0.025	26.993	0.010	0.010	0.000	0.000	0.000	0.000
70	B	93	GLN	0	0.005	-0.004	29.907	0.001	0.001	0.000	0.000	0.000	0.000
71	B	94	SER	0	-0.005	-0.010	26.443	0.004	0.004	0.000	0.000	0.000	0.000
72	B	95	VAL	0	-0.019	0.002	28.929	0.010	0.010	0.000	0.000	0.000	0.000
73	B	96	LYS	1	0.933	0.962	23.094	-0.163	-0.163	0.000	0.000	0.000	0.000
74	B	97	ALA	0	0.045	0.030	26.660	0.012	0.012	0.000	0.000	0.000	0.000
75	B	98	HIS	0	0.001	-0.001	28.010	0.005	0.005	0.000	0.000	0.000	0.000
76	B	99	PHE	0	0.003	-0.008	30.451	0.002	0.002	0.000	0.000	0.000	0.000
77	B	100	PHE	0	0.002	-0.017	24.869	0.004	0.004	0.000	0.000	0.000	0.000
78	B	101	LEU	0	0.032	0.037	29.572	0.008	0.008	0.000	0.000	0.000	0.000
79	B	102	GLY	0	0.027	0.009	31.185	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	103	GLN	0	-0.022	-0.021	31.349	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	104	CYS	0	-0.064	-0.025	29.538	0.007	0.007	0.000	0.000	0.000	0.000
82	B	105	GLN	0	0.010	-0.004	32.204	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	106	LEU	0	-0.052	-0.027	35.646	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	107	GLU	-1	-0.940	-0.982	31.935	0.196	0.196	0.000	0.000	0.000	0.000
85	B	108	MET	0	-0.042	-0.008	33.510	0.007	0.007	0.000	0.000	0.000	0.000
86	B	109	GLU	-1	-0.783	-0.847	37.058	0.104	0.104	0.000	0.000	0.000	0.000
87	B	110	SER	0	0.039	0.022	37.937	-0.007	-0.007	0.000	0.000	0.000	0.000
88	B	111	TYR	0	-0.053	-0.086	39.774	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	112	ASP	-1	-0.796	-0.866	41.664	0.076	0.076	0.000	0.000	0.000	0.000
90	B	113	GLU	-1	-0.824	-0.903	37.668	0.110	0.110	0.000	0.000	0.000	0.000
91	B	114	ALA	0	0.000	0.012	37.100	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	115	ILE	0	-0.025	-0.025	38.073	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	116	ALA	0	-0.008	0.001	40.053	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	117	ASN	0	0.010	-0.004	34.709	-0.008	-0.008	0.000	0.000	0.000	0.000
95	B	118	LEU	0	0.018	0.007	35.180	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	119	GLN	0	0.019	0.011	37.253	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	120	ARG	1	0.819	0.906	35.841	-0.053	-0.053	0.000	0.000	0.000	0.000
98	B	121	ALA	0	0.027	0.010	33.871	-0.004	-0.004	0.000	0.000	0.000	0.000
99	B	122	TYR	0	0.011	0.006	35.253	-0.007	-0.007	0.000	0.000	0.000	0.000
100	B	123	SER	0	-0.047	-0.043	38.182	-0.007	-0.007	0.000	0.000	0.000	0.000
101	B	124	LEU	0	-0.023	0.002	32.762	-0.006	-0.006	0.000	0.000	0.000	0.000
102	B	125	ALA	0	0.002	0.001	34.705	-0.006	-0.006	0.000	0.000	0.000	0.000
103	B	126	LYS	1	0.916	0.957	35.646	-0.041	-0.041	0.000	0.000	0.000	0.000
104	B	127	GLU	-1	-0.871	-0.903	37.180	0.027	0.027	0.000	0.000	0.000	0.000
105	B	128	GLN	0	-0.046	-0.037	31.684	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	129	ARG	1	0.906	0.960	35.104	-0.006	-0.006	0.000	0.000	0.000	0.000
107	B	130	LEU	0	0.001	0.018	30.840	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	131	ASN	0	-0.008	-0.018	34.145	0.005	0.005	0.000	0.000	0.000	0.000
109	B	132	PHE	0	0.014	-0.002	30.066	0.003	0.003	0.000	0.000	0.000	0.000
110	B	133	GLY	0	0.053	0.030	35.014	0.005	0.005	0.000	0.000	0.000	0.000
111	B	134	ASP	-1	-0.765	-0.856	38.340	0.062	0.062	0.000	0.000	0.000	0.000
112	B	135	ASP	-1	-0.883	-0.915	34.223	0.100	0.100	0.000	0.000	0.000	0.000
113	B	136	ILE	0	-0.022	-0.020	34.251	0.005	0.005	0.000	0.000	0.000	0.000
114	B	137	PRO	0	0.007	0.001	37.407	0.001	0.001	0.000	0.000	0.000	0.000
115	B	138	SER	0	-0.010	-0.016	38.880	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	139	ALA	0	0.010	0.011	36.496	0.002	0.002	0.000	0.000	0.000	0.000
117	B	140	LEU	0	-0.010	-0.003	38.580	0.000	0.000	0.000	0.000	0.000	0.000
118	B	141	ARG	1	0.758	0.836	41.443	-0.072	-0.072	0.000	0.000	0.000	0.000
119	B	142	ILE	0	0.010	0.021	39.391	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	143	ALA	0	0.046	0.017	39.841	0.000	0.000	0.000	0.000	0.000	0.000
121	B	144	LYS	1	0.885	0.932	41.748	-0.068	-0.068	0.000	0.000	0.000	0.000
122	B	145	LYS	1	0.900	0.963	45.199	-0.079	-0.079	0.000	0.000	0.000	0.000
123	B	146	LYS	1	0.868	0.924	42.068	-0.107	-0.107	0.000	0.000	0.000	0.000
124	B	147	ARG	1	0.853	0.900	44.802	-0.074	-0.074	0.000	0.000	0.000	0.000
125	B	148	TRP	0	-0.007	0.006	46.133	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	149	ASN	0	0.008	-0.012	47.298	-0.004	-0.004	0.000	0.000	0.000	0.000
127	B	150	SER	0	-0.057	-0.032	46.115	0.000	0.000	0.000	0.000	0.000	0.000
128	B	151	ILE	0	0.011	-0.001	48.167	-0.001	-0.001	0.000	0.000	0.000	0.000
129	B	152	GLU	-1	-0.807	-0.883	51.664	0.063	0.063	0.000	0.000	0.000	0.000
130	B	153	GLU	-1	-0.842	-0.915	47.031	0.097	0.097	0.000	0.000	0.000	0.000
131	B	154	ARG	1	0.746	0.875	45.627	-0.094	-0.094	0.000	0.000	0.000	0.000
132	B	155	ARG	1	0.814	0.916	53.036	-0.066	-0.066	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:24:SER)