FMO DATABASE

FMODB ID: LNV79

Calculation Name: 2II7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2II7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YSC3

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-849574.573095
FMO2-HF: Nuclear repulsion	806016.907503
FMO2-HF: Total energy	-43557.665593
FMO2-MP2: Total energy	-43686.340171

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-26.149	-25.632	11.683	-6.572	-5.626	-0.063

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.043

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	SER	0	0.003	0.020	3.789	-1.388	0.157	-0.019	-0.601	-0.925	0.003
4	A	4	ILE	0	-0.017	-0.021	5.736	-0.284	-0.182	-0.001	-0.007	-0.094	0.000
5	A	5	GLY	0	0.010	0.012	8.761	-0.082	-0.082	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.915	0.961	12.177	-0.133	-0.133	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.033	0.012	12.989	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	8	CYS	0	0.003	0.007	15.080	-0.052	-0.052	0.000	0.000	0.000	0.000
9	A	9	TRP	0	-0.053	-0.026	15.068	0.020	0.020	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.039	0.011	20.568	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.057	-0.012	23.049	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.005	-0.013	26.402	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.842	-0.914	29.470	0.018	0.018	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.007	-0.010	29.592	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	TYR	0	0.016	0.017	31.568	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.040	-0.020	32.081	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.036	0.025	34.931	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	25	PRO	0	-0.028	-0.018	36.697	0.000	0.000	0.000	0.000	0.000	0.000
19	A	26	GLN	0	0.019	0.003	31.389	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	27	PHE	0	-0.020	-0.018	31.637	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	28	ILE	0	0.036	0.037	32.602	0.005	0.005	0.000	0.000	0.000	0.000
22	A	29	SER	0	0.023	0.026	28.430	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	30	HIS	0	0.020	-0.034	28.998	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.755	-0.858	28.257	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.047	-0.017	22.994	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	33	VAL	0	0.021	0.023	20.265	0.011	0.011	0.000	0.000	0.000	0.000
27	A	34	CYS	0	-0.054	-0.024	18.694	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	35	ILE	0	0.048	0.027	14.183	0.024	0.024	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.032	-0.019	9.784	-0.057	-0.057	0.000	0.000	0.000	0.000
30	A	37	ASN	0	0.018	0.013	8.272	0.151	0.151	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.055	-0.030	5.997	-0.186	-0.186	0.000	0.000	0.000	0.000
32	A	39	GLY	0	0.097	0.052	4.081	-0.599	-0.382	0.001	-0.060	-0.158	0.000
33	A	40	ASP	-1	-0.856	-0.945	1.746	-27.051	-28.454	11.703	-5.894	-4.405	-0.066
34	A	41	GLU	-1	-0.927	-0.971	4.429	0.222	0.278	-0.001	-0.010	-0.044	0.000
35	A	42	ASP	-1	-0.907	-0.952	7.469	-0.521	-0.521	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.005	-0.004	10.834	0.096	0.096	0.000	0.000	0.000	0.000
37	A	44	HIS	0	-0.044	-0.029	12.561	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.012	-0.011	15.982	0.039	0.039	0.000	0.000	0.000	0.000
39	A	46	GLU	-1	-0.951	-0.979	17.933	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	47	ILE	0	-0.015	-0.015	21.429	0.018	0.018	0.000	0.000	0.000	0.000
41	A	48	THR	0	0.008	0.024	23.914	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.021	-0.006	27.138	0.006	0.006	0.000	0.000	0.000	0.000
43	A	50	TYR	0	0.002	-0.020	27.984	0.002	0.002	0.000	0.000	0.000	0.000
44	A	51	TYR	0	0.034	-0.003	32.529	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	52	SER	0	0.029	0.011	36.092	0.003	0.003	0.000	0.000	0.000	0.000
46	A	53	ASP	-1	-0.916	-0.957	38.937	0.010	0.010	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.895	0.968	38.197	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	55	GLU	-1	-0.933	-0.981	36.582	0.025	0.025	0.000	0.000	0.000	0.000
49	A	56	PRO	0	-0.024	-0.014	31.579	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	57	VAL	0	-0.035	-0.008	31.894	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.001	-0.016	30.380	0.000	0.000	0.000	0.000	0.000	0.000
52	A	59	PRO	0	0.015	0.005	25.227	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	60	TYR	0	0.008	0.011	25.650	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	61	ARG	1	0.935	0.966	22.220	0.043	0.043	0.000	0.000	0.000	0.000
55	A	62	LEU	0	-0.002	0.006	18.492	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	63	THR	0	-0.001	-0.005	15.107	0.006	0.006	0.000	0.000	0.000	0.000
57	A	64	VAL	0	-0.052	-0.029	12.691	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	65	PRO	0	0.020	0.006	12.526	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	66	ALA	0	0.052	0.030	7.059	0.042	0.042	0.000	0.000	0.000	0.000
60	A	67	ARG	1	0.833	0.930	4.985	2.635	2.635	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.894	0.957	7.776	0.842	0.842	0.000	0.000	0.000	0.000
62	A	69	THR	0	0.032	0.012	11.385	0.059	0.059	0.000	0.000	0.000	0.000
63	A	70	LYS	1	0.930	0.949	13.953	0.175	0.175	0.000	0.000	0.000	0.000
64	A	71	HIS	0	-0.042	-0.003	17.364	0.036	0.036	0.000	0.000	0.000	0.000
65	A	72	VAL	0	0.031	0.015	20.472	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	73	ARG	1	0.910	0.964	22.953	0.084	0.084	0.000	0.000	0.000	0.000
67	A	74	PHE	0	0.086	0.018	25.767	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	75	ASN	0	-0.040	-0.038	28.342	0.005	0.005	0.000	0.000	0.000	0.000
69	A	76	ASP	-1	-0.922	-0.962	27.599	-0.077	-0.077	0.000	0.000	0.000	0.000
70	A	77	LEU	0	-0.065	-0.012	25.382	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	78	ASN	0	-0.042	-0.047	29.126	0.003	0.003	0.000	0.000	0.000	0.000
72	A	79	ASP	-1	-0.894	-0.886	29.270	-0.055	-0.055	0.000	0.000	0.000	0.000
73	A	80	PRO	0	-0.003	-0.022	28.754	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	81	ALA	0	0.010	-0.021	31.940	0.000	0.000	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.016	-0.006	32.718	0.000	0.000	0.000	0.000	0.000	0.000
76	A	83	ILE	0	0.003	0.019	30.472	0.003	0.003	0.000	0.000	0.000	0.000
77	A	84	PRO	0	-0.044	-0.018	34.381	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	85	HIS	1	0.850	0.921	35.442	0.029	0.029	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.930	-0.960	38.240	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	87	THR	0	-0.021	-0.020	37.529	0.002	0.002	0.000	0.000	0.000	0.000
81	A	88	ASP	-1	-0.900	-0.939	36.155	0.010	0.010	0.000	0.000	0.000	0.000
82	A	89	PHE	0	-0.122	-0.056	29.401	0.000	0.000	0.000	0.000	0.000	0.000
83	A	90	ALA	0	0.026	0.031	30.275	0.003	0.003	0.000	0.000	0.000	0.000
84	A	91	SER	0	-0.008	-0.017	26.216	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	92	VAL	0	0.014	0.015	23.368	0.011	0.011	0.000	0.000	0.000	0.000
86	A	93	ILE	0	-0.018	-0.006	18.617	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	94	GLN	0	-0.002	-0.005	18.624	0.028	0.028	0.000	0.000	0.000	0.000
88	A	95	SER	0	-0.040	-0.058	12.840	-0.058	-0.058	0.000	0.000	0.000	0.000
89	A	96	ASN	0	0.056	0.045	12.107	0.040	0.040	0.000	0.000	0.000	0.000
90	A	97	VAL	0	0.017	0.017	8.789	0.106	0.106	0.000	0.000	0.000	0.000
91	A	98	PRO	0	-0.032	0.009	8.314	-0.120	-0.120	0.000	0.000	0.000	0.000
92	A	99	ILE	0	0.026	0.030	9.682	-0.051	-0.051	0.000	0.000	0.000	0.000
93	A	100	VAL	0	-0.011	-0.025	11.176	0.064	0.064	0.000	0.000	0.000	0.000
94	A	101	VAL	0	-0.006	-0.005	13.773	-0.057	-0.057	0.000	0.000	0.000	0.000
95	A	102	GLN	0	0.008	0.006	17.399	0.028	0.028	0.000	0.000	0.000	0.000
96	A	103	HIS	0	-0.014	-0.015	20.065	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	104	THR	0	-0.034	-0.002	23.767	0.010	0.010	0.000	0.000	0.000	0.000
98	A	105	ARG	1	0.887	0.942	26.647	-0.039	-0.039	0.000	0.000	0.000	0.000
99	A	106	LEU	0	0.103	0.066	29.564	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	107	ASP	-1	-0.823	-0.902	32.294	0.026	0.026	0.000	0.000	0.000	0.000
101	A	108	SER	0	-0.039	-0.042	30.376	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	109	ARG	1	0.942	0.965	29.513	0.005	0.005	0.000	0.000	0.000	0.000
103	A	110	GLN	0	-0.051	-0.033	31.915	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	111	ALA	0	0.002	0.002	35.205	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.919	-0.958	29.760	0.000	0.000	0.000	0.000	0.000	0.000
106	A	113	ASN	0	0.036	0.007	32.898	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	114	ALA	0	-0.020	0.043	35.599	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.011	-0.011	35.962	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.022	-0.006	32.654	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	117	SER	0	-0.091	-0.081	36.999	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	118	THR	0	-0.078	-0.049	39.791	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	119	ILE	0	-0.034	0.009	41.123	-0.001	-0.001	0.000	0.000	0.000	0.000

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