FMO DATABASE

FMODB ID: 3Q11L

Calculation Name: 3ZII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZII

Chain ID: A

ChEMBL ID:

UniProt ID: O31728

Base Structure: X-ray

Registration Date: 2023-06-20

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-525082.678287
FMO2-HF: Nuclear repulsion	493519.889891
FMO2-HF: Total energy	-31562.788396
FMO2-MP2: Total energy	-31656.281148

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:61:SER)

Summations of interaction energy for fragment #1(A:61: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.
-3.631	-1.748	-0.014	-1.083	-0.786	0.003

Interaction energy analysis for fragmet #1(A:61:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.014

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	A	63	LYS	1	0.939	0.954	3.868	-2.596	-0.713	-0.014	-1.083	-0.786	0.003
4	A	64	VAL	0	0.043	0.031	6.673	-0.500	-0.500	0.000	0.000	0.000	0.000
5	A	65	VAL	0	-0.035	-0.012	10.030	0.119	0.119	0.000	0.000	0.000	0.000
6	A	66	LEU	0	0.013	0.008	13.171	-0.100	-0.100	0.000	0.000	0.000	0.000
7	A	67	SER	0	0.014	0.003	16.314	0.000	0.000	0.000	0.000	0.000	0.000
8	A	68	GLU	-1	-0.734	-0.828	19.786	0.226	0.226	0.000	0.000	0.000	0.000
9	A	69	PRO	0	-0.008	0.003	23.022	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	70	ARG	1	0.850	0.907	25.739	-0.271	-0.271	0.000	0.000	0.000	0.000
11	A	71	VAL	0	-0.031	-0.017	28.850	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	72	TYR	0	0.003	-0.017	28.460	0.009	0.009	0.000	0.000	0.000	0.000
13	A	73	ALA	0	0.039	0.022	28.097	0.004	0.004	0.000	0.000	0.000	0.000
14	A	74	GLU	-1	-0.745	-0.870	24.524	0.265	0.265	0.000	0.000	0.000	0.000
15	A	75	ALA	0	-0.022	-0.023	23.362	0.026	0.026	0.000	0.000	0.000	0.000
16	A	76	GLN	0	-0.029	-0.023	24.099	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	77	GLU	-1	-0.889	-0.941	21.078	0.353	0.353	0.000	0.000	0.000	0.000
18	A	78	ILE	0	-0.045	-0.017	18.858	0.045	0.045	0.000	0.000	0.000	0.000
19	A	79	ALA	0	0.049	0.022	18.500	0.019	0.019	0.000	0.000	0.000	0.000
20	A	80	ASP	-1	-0.845	-0.906	18.874	0.281	0.281	0.000	0.000	0.000	0.000
21	A	81	HIS	0	0.013	0.013	14.693	0.134	0.134	0.000	0.000	0.000	0.000
22	A	82	LEU	0	0.012	0.018	13.936	0.049	0.049	0.000	0.000	0.000	0.000
23	A	83	LYS	1	0.878	0.921	14.914	-0.272	-0.272	0.000	0.000	0.000	0.000
24	A	84	ASN	0	-0.144	-0.069	13.026	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	85	ARG	1	0.796	0.846	10.192	0.222	0.222	0.000	0.000	0.000	0.000
26	A	86	ARG	1	0.845	0.939	9.160	-0.926	-0.926	0.000	0.000	0.000	0.000
27	A	87	ALA	0	0.072	0.042	10.644	-0.138	-0.138	0.000	0.000	0.000	0.000
28	A	88	VAL	0	-0.053	-0.036	12.652	0.162	0.162	0.000	0.000	0.000	0.000
29	A	89	VAL	0	0.031	0.025	14.795	-0.080	-0.080	0.000	0.000	0.000	0.000
30	A	90	VAL	0	-0.010	-0.015	17.224	0.032	0.032	0.000	0.000	0.000	0.000
31	A	91	ASN	0	0.003	-0.003	20.761	-0.049	-0.049	0.000	0.000	0.000	0.000
32	A	92	LEU	0	0.039	0.008	23.585	0.009	0.009	0.000	0.000	0.000	0.000
33	A	93	GLN	0	0.015	0.005	25.931	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	94	ARG	1	0.751	0.856	27.095	-0.213	-0.213	0.000	0.000	0.000	0.000
35	A	95	ILE	0	-0.041	-0.004	29.038	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	96	GLN	0	0.044	0.029	31.823	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	97	HIS	0	0.160	0.056	34.141	0.008	0.008	0.000	0.000	0.000	0.000
38	A	98	ASP	-1	-0.843	-0.893	34.290	0.076	0.076	0.000	0.000	0.000	0.000
39	A	99	GLN	0	0.010	0.003	33.482	0.004	0.004	0.000	0.000	0.000	0.000
40	A	100	ALA	0	0.022	0.020	30.245	0.007	0.007	0.000	0.000	0.000	0.000
41	A	101	LYS	1	0.841	0.884	29.846	-0.077	-0.077	0.000	0.000	0.000	0.000
42	A	102	ARG	1	0.881	0.941	31.246	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	103	ILE	0	-0.002	0.009	26.165	0.001	0.001	0.000	0.000	0.000	0.000
44	A	104	VAL	0	0.039	0.024	26.526	0.005	0.005	0.000	0.000	0.000	0.000
45	A	105	ASP	-1	-0.799	-0.860	27.148	0.069	0.069	0.000	0.000	0.000	0.000
46	A	106	PHE	0	0.008	-0.001	24.684	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	107	LEU	0	-0.008	-0.005	21.955	0.002	0.002	0.000	0.000	0.000	0.000
48	A	108	SER	0	0.019	-0.005	23.622	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	109	LYS	1	0.776	0.862	25.426	-0.079	-0.079	0.000	0.000	0.000	0.000
50	A	110	THR	0	-0.064	-0.036	21.197	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	111	VAL	0	-0.001	-0.006	19.356	0.002	0.002	0.000	0.000	0.000	0.000
52	A	112	TYR	0	0.027	0.026	21.010	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	113	ALA	0	-0.054	-0.028	23.478	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	114	ILE	0	-0.087	-0.037	17.086	0.003	0.003	0.000	0.000	0.000	0.000
55	A	115	GLY	0	-0.004	0.002	18.616	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	116	GLY	0	-0.011	-0.004	17.608	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	117	ASP	-1	-0.878	-0.935	18.235	0.005	0.005	0.000	0.000	0.000	0.000
58	A	118	ILE	0	-0.065	-0.050	19.317	0.046	0.046	0.000	0.000	0.000	0.000
59	A	119	GLN	0	0.042	0.031	18.429	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	120	ARG	1	0.749	0.826	21.817	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	121	ILE	0	-0.025	-0.022	18.920	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	122	GLY	0	0.061	0.021	22.674	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	123	SER	0	-0.028	-0.012	25.672	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	124	ASP	-1	-0.905	-0.952	27.328	0.132	0.132	0.000	0.000	0.000	0.000
65	A	125	ILE	0	-0.041	-0.003	20.650	0.022	0.022	0.000	0.000	0.000	0.000
66	A	126	PHE	0	0.024	-0.001	22.008	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	127	LEU	0	-0.011	0.005	14.427	0.056	0.056	0.000	0.000	0.000	0.000
68	A	128	CYS	0	-0.024	0.009	17.551	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	129	THR	0	0.044	0.002	13.658	0.096	0.096	0.000	0.000	0.000	0.000
70	A	130	PRO	0	-0.007	0.010	12.300	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	131	ASP	-1	-0.721	-0.834	14.207	-0.131	-0.131	0.000	0.000	0.000	0.000
72	A	132	ASN	0	-0.078	-0.032	8.741	0.001	0.001	0.000	0.000	0.000	0.000
73	A	133	VAL	0	-0.074	-0.048	9.233	-0.090	-0.090	0.000	0.000	0.000	0.000
74	A	134	ASP	-1	-0.850	-0.909	11.258	-0.244	-0.244	0.000	0.000	0.000	0.000
75	A	135	VAL	0	-0.033	-0.020	12.703	0.053	0.053	0.000	0.000	0.000	0.000
76	A	136	SER	0	0.002	0.009	14.824	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	137	GLY	0	-0.013	0.000	16.948	0.019	0.019	0.000	0.000	0.000	0.000
78	A	138	THR	0	-0.067	-0.058	19.505	0.007	0.007	0.000	0.000	0.000	0.000
79	A	139	ILE	0	-0.005	0.007	20.106	0.002	0.002	0.000	0.000	0.000	0.000
80	A	140	SER	0	-0.029	-0.007	24.028	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	141	GLU	-1	-0.781	-0.851	27.819	0.066	0.066	0.000	0.000	0.000	0.000
82	A	142	LEU	0	-0.020	-0.006	30.466	-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:61:SER)