FMO DATABASE

FMODB ID: 2N9GR

Calculation Name: 6B9X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6B9X

Chain ID: B

ChEMBL ID:

UniProt ID: Q6IAA8

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-993582.582175
FMO2-HF: Nuclear repulsion	945019.682639
FMO2-HF: Total energy	-48562.899536
FMO2-MP2: Total energy	-48701.113924

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:0:ALA)

Summations of interaction energy for fragment #1(B:0:ALA)

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.
-4.43	-1.38	0.497	-1.514	-2.034	-0.001

Interaction energy analysis for fragmet #1(B:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.000

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

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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	2	LEU	0	0.063	0.040	3.806	-0.463	1.111	-0.023	-0.806	-0.745	0.004
4	B	3	ARG	1	0.959	0.970	6.414	0.051	0.051	0.000	0.000	0.000	0.000
5	B	4	PRO	0	0.095	0.035	9.668	-0.013	-0.013	0.000	0.000	0.000	0.000
6	B	5	LYS	1	0.975	0.974	12.517	-0.052	-0.052	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.019	-0.003	11.527	0.015	0.015	0.000	0.000	0.000	0.000
8	B	7	LEU	0	0.053	0.042	11.149	0.005	0.005	0.000	0.000	0.000	0.000
9	B	8	THR	0	0.006	-0.005	13.146	0.006	0.006	0.000	0.000	0.000	0.000
10	B	9	GLN	0	0.001	0.007	16.382	0.002	0.002	0.000	0.000	0.000	0.000
11	B	10	VAL	0	0.055	0.040	13.529	0.009	0.009	0.000	0.000	0.000	0.000
12	B	11	LEU	0	0.004	0.004	16.019	0.008	0.008	0.000	0.000	0.000	0.000
13	B	12	SER	0	-0.082	-0.061	18.472	0.016	0.016	0.000	0.000	0.000	0.000
14	B	13	GLN	0	-0.049	-0.026	18.314	0.010	0.010	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.008	0.015	21.926	0.008	0.008	0.000	0.000	0.000	0.000
16	B	15	ASN	0	-0.003	0.010	23.433	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	16	THR	0	0.036	0.007	26.070	0.008	0.008	0.000	0.000	0.000	0.000
18	B	17	GLY	0	0.003	-0.011	29.034	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	18	GLY	0	0.026	0.011	32.049	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	19	VAL	0	-0.037	-0.021	26.056	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	20	GLN	0	-0.040	-0.021	28.878	0.009	0.009	0.000	0.000	0.000	0.000
22	B	21	SER	0	-0.058	-0.026	24.896	0.001	0.001	0.000	0.000	0.000	0.000
23	B	22	THR	0	0.025	0.002	19.979	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	23	LEU	0	-0.035	-0.027	20.269	0.000	0.000	0.000	0.000	0.000	0.000
25	B	24	LEU	0	0.018	0.013	12.965	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	25	LEU	0	0.002	-0.003	17.614	0.011	0.011	0.000	0.000	0.000	0.000
27	B	26	ASN	0	0.060	0.023	16.434	0.004	0.004	0.000	0.000	0.000	0.000
28	B	27	ASN	0	0.002	-0.024	17.952	0.062	0.062	0.000	0.000	0.000	0.000
29	B	28	GLU	-1	-0.915	-0.944	20.632	-0.206	-0.206	0.000	0.000	0.000	0.000
30	B	29	GLY	0	0.009	0.014	21.763	0.021	0.021	0.000	0.000	0.000	0.000
31	B	30	SER	0	-0.091	-0.042	19.244	0.018	0.018	0.000	0.000	0.000	0.000
32	B	31	LEU	0	-0.034	-0.018	19.200	-0.030	-0.030	0.000	0.000	0.000	0.000
33	B	32	LEU	0	-0.034	-0.017	12.868	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	33	ALA	0	-0.034	-0.018	14.923	0.007	0.007	0.000	0.000	0.000	0.000
35	B	34	TYR	0	-0.008	-0.005	17.005	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	35	SER	0	0.025	0.016	20.014	0.019	0.019	0.000	0.000	0.000	0.000
37	B	36	GLY	0	0.027	0.019	22.008	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	37	TYR	0	-0.025	-0.035	25.736	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	38	GLY	0	0.024	0.018	28.606	0.003	0.003	0.000	0.000	0.000	0.000
40	B	39	ASP	-1	-0.853	-0.920	31.498	-0.051	-0.051	0.000	0.000	0.000	0.000
41	B	40	THR	0	-0.095	-0.035	30.423	0.000	0.000	0.000	0.000	0.000	0.000
42	B	41	ASP	-1	-0.785	-0.873	27.898	-0.104	-0.104	0.000	0.000	0.000	0.000
43	B	42	ALA	0	0.068	0.019	24.000	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	43	ARG	1	0.870	0.900	24.345	0.087	0.087	0.000	0.000	0.000	0.000
45	B	44	VAL	0	0.008	0.016	25.900	-0.007	-0.007	0.000	0.000	0.000	0.000
46	B	45	THR	0	-0.013	-0.007	26.186	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	46	ALA	0	-0.007	-0.001	22.826	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	47	ALA	0	0.050	0.029	24.681	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	48	ILE	0	0.009	0.009	26.909	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	49	ALA	0	0.005	-0.004	25.031	0.000	0.000	0.000	0.000	0.000	0.000
51	B	50	SER	0	-0.016	-0.008	23.763	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	51	ASN	0	0.008	0.000	25.390	-0.006	-0.006	0.000	0.000	0.000	0.000
53	B	52	ILE	0	-0.025	-0.019	28.985	0.004	0.004	0.000	0.000	0.000	0.000
54	B	53	TRP	0	0.011	-0.004	23.377	0.005	0.005	0.000	0.000	0.000	0.000
55	B	54	ALA	0	0.043	0.019	26.394	0.001	0.001	0.000	0.000	0.000	0.000
56	B	55	ALA	0	-0.034	-0.003	27.576	0.005	0.005	0.000	0.000	0.000	0.000
57	B	56	TYR	0	-0.028	-0.029	30.271	0.007	0.007	0.000	0.000	0.000	0.000
58	B	57	ASP	-1	-0.941	-0.966	25.335	-0.206	-0.206	0.000	0.000	0.000	0.000
59	B	58	ARG	1	0.944	0.963	26.536	0.174	0.174	0.000	0.000	0.000	0.000
60	B	59	ASN	0	-0.053	-0.036	30.298	0.003	0.003	0.000	0.000	0.000	0.000
61	B	60	GLY	0	-0.009	0.009	32.030	0.007	0.007	0.000	0.000	0.000	0.000
62	B	61	ASN	0	0.007	0.018	29.708	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	62	GLN	0	-0.028	-0.013	31.619	0.008	0.008	0.000	0.000	0.000	0.000
64	B	63	ALA	0	0.001	-0.003	32.523	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	64	PHE	0	-0.065	-0.046	32.754	0.004	0.004	0.000	0.000	0.000	0.000
66	B	65	ASN	0	-0.002	0.002	31.839	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	66	GLU	-1	-0.826	-0.898	25.080	-0.211	-0.211	0.000	0.000	0.000	0.000
68	B	67	ASP	-1	-1.008	-0.983	28.182	-0.136	-0.136	0.000	0.000	0.000	0.000
69	B	68	ASN	0	-0.054	-0.035	24.319	0.009	0.009	0.000	0.000	0.000	0.000
70	B	69	LEU	0	0.014	0.003	26.649	0.006	0.006	0.000	0.000	0.000	0.000
71	B	70	LYS	1	0.929	0.958	24.565	0.166	0.166	0.000	0.000	0.000	0.000
72	B	71	PHE	0	-0.021	-0.036	24.005	-0.011	-0.011	0.000	0.000	0.000	0.000
73	B	72	ILE	0	0.020	0.034	26.629	0.010	0.010	0.000	0.000	0.000	0.000
74	B	73	LEU	0	-0.047	-0.023	28.331	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	74	MET	0	-0.008	0.000	31.033	0.001	0.001	0.000	0.000	0.000	0.000
76	B	75	ASP	-1	-0.862	-0.934	33.400	-0.072	-0.072	0.000	0.000	0.000	0.000
77	B	76	CYS	0	-0.035	-0.015	35.330	0.000	0.000	0.000	0.000	0.000	0.000
78	B	77	MET	0	0.025	-0.004	37.910	0.002	0.002	0.000	0.000	0.000	0.000
79	B	78	GLU	-1	-0.935	-0.950	38.780	-0.050	-0.050	0.000	0.000	0.000	0.000
80	B	79	GLY	0	-0.006	-0.009	34.757	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	80	ARG	1	0.779	0.901	32.771	0.072	0.072	0.000	0.000	0.000	0.000
82	B	81	VAL	0	0.014	-0.007	28.111	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	82	ALA	0	-0.011	-0.003	25.958	0.003	0.003	0.000	0.000	0.000	0.000
84	B	83	ILE	0	-0.010	-0.014	23.839	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	84	THR	0	-0.003	-0.008	20.557	0.005	0.005	0.000	0.000	0.000	0.000
86	B	85	ARG	1	0.982	1.003	18.630	0.265	0.265	0.000	0.000	0.000	0.000
87	B	86	VAL	0	-0.025	-0.008	13.529	0.022	0.022	0.000	0.000	0.000	0.000
88	B	87	ALA	0	0.046	0.040	11.484	-0.050	-0.050	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.067	-0.034	12.076	0.027	0.027	0.000	0.000	0.000	0.000
90	B	89	LEU	0	-0.080	-0.046	12.251	0.039	0.039	0.000	0.000	0.000	0.000
91	B	90	LEU	0	0.011	0.009	15.928	0.031	0.031	0.000	0.000	0.000	0.000
92	B	91	LEU	0	-0.011	-0.002	17.585	-0.009	-0.009	0.000	0.000	0.000	0.000
93	B	92	CYS	0	-0.034	-0.012	19.678	0.022	0.022	0.000	0.000	0.000	0.000
94	B	93	MET	0	-0.022	0.009	22.536	0.004	0.004	0.000	0.000	0.000	0.000
95	B	94	TYR	0	0.042	0.015	24.892	0.007	0.007	0.000	0.000	0.000	0.000
96	B	95	ALA	0	-0.020	-0.012	28.496	0.003	0.003	0.000	0.000	0.000	0.000
97	B	96	LYS	1	1.022	1.016	31.120	0.053	0.053	0.000	0.000	0.000	0.000
98	B	97	GLU	-1	-0.843	-0.919	34.593	-0.061	-0.061	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.023	-0.018	36.953	0.000	0.000	0.000	0.000	0.000	0.000
100	B	99	VAL	0	-0.058	-0.002	31.021	0.002	0.002	0.000	0.000	0.000	0.000
101	B	100	GLY	0	0.026	0.014	34.462	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	101	PHE	0	0.095	0.019	31.896	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	102	GLY	0	-0.040	-0.011	30.925	-0.007	-0.007	0.000	0.000	0.000	0.000
104	B	103	MET	0	0.025	0.013	29.521	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	104	LEU	0	0.024	0.014	27.331	-0.005	-0.005	0.000	0.000	0.000	0.000
106	B	105	LYS	1	0.969	0.988	26.375	0.102	0.102	0.000	0.000	0.000	0.000
107	B	106	ALA	0	0.000	0.009	25.222	-0.012	-0.012	0.000	0.000	0.000	0.000
108	B	107	LYS	1	0.891	0.945	23.982	0.078	0.078	0.000	0.000	0.000	0.000
109	B	108	ALA	0	0.025	0.012	21.931	-0.011	-0.011	0.000	0.000	0.000	0.000
110	B	109	GLN	0	0.008	-0.019	20.512	-0.011	-0.011	0.000	0.000	0.000	0.000
111	B	110	ALA	0	-0.014	0.005	20.042	-0.013	-0.013	0.000	0.000	0.000	0.000
112	B	111	LEU	0	-0.010	-0.009	17.216	-0.011	-0.011	0.000	0.000	0.000	0.000
113	B	112	VAL	0	0.002	0.002	15.818	-0.031	-0.031	0.000	0.000	0.000	0.000
114	B	113	GLN	0	-0.028	-0.016	15.421	-0.043	-0.043	0.000	0.000	0.000	0.000
115	B	114	TYR	0	-0.037	-0.011	12.190	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	115	LEU	0	-0.007	-0.027	11.406	-0.025	-0.025	0.000	0.000	0.000	0.000
117	B	116	GLU	-1	-0.813	-0.902	10.692	-0.571	-0.571	0.000	0.000	0.000	0.000
118	B	117	GLU	-1	-0.899	-0.934	8.202	-0.459	-0.459	0.000	0.000	0.000	0.000
119	B	118	PRO	0	-0.022	-0.011	6.079	-0.210	-0.210	0.000	0.000	0.000	0.000
120	B	119	LEU	0	-0.026	-0.035	5.721	-0.406	-0.406	0.000	0.000	0.000	0.000
121	B	120	THR	0	0.012	-0.005	7.922	-0.150	-0.150	0.000	0.000	0.000	0.000
122	B	121	GLN	0	-0.090	-0.034	3.397	-0.336	0.005	0.038	-0.088	-0.291	0.000
123	B	122	VAL	0	-0.086	-0.046	2.592	-2.352	-1.271	0.481	-0.612	-0.950	-0.005
124	B	123	ALA	0	-0.002	0.017	4.029	0.159	0.213	0.001	-0.008	-0.048	0.000
125	B	124	ALA	0	-0.010	0.007	7.335	0.171	0.171	0.000	0.000	0.000	0.000
126	B	125	SER	0	0.024	0.020	9.387	0.207	0.207	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:ALA)