FMO DATABASE

FMODB ID: 43RYN

Calculation Name: 3ZII-A-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-528316.047422
FMO2-HF: Nuclear repulsion	496582.886958
FMO2-HF: Total energy	-31733.160463
FMO2-MP2: Total energy	-31827.179455

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:60:ACE )

Summations of interaction energy for fragment #1(A:60:ACE )

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.
-0.356	1.512	-0.007	-0.927	-0.933	-0.003

Interaction energy analysis for fragmet #1(A:60:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.010

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	62	SER	0	0.027	0.026	3.820	-0.171	1.602	-0.007	-0.919	-0.847	-0.003
4	A	63	LYS	1	0.946	0.960	5.166	0.129	0.224	0.000	-0.008	-0.086	0.000
5	A	64	VAL	0	0.054	0.034	7.327	-0.115	-0.115	0.000	0.000	0.000	0.000
6	A	65	VAL	0	-0.046	-0.019	10.589	0.097	0.097	0.000	0.000	0.000	0.000
7	A	66	LEU	0	0.007	0.009	13.056	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	67	SER	0	0.008	0.002	16.037	0.000	0.000	0.000	0.000	0.000	0.000
9	A	68	GLU	-1	-0.814	-0.887	19.289	0.092	0.092	0.000	0.000	0.000	0.000
10	A	69	PRO	0	-0.029	-0.003	22.777	0.000	0.000	0.000	0.000	0.000	0.000
11	A	70	ARG	1	0.935	0.951	25.065	-0.087	-0.087	0.000	0.000	0.000	0.000
12	A	71	VAL	0	-0.013	-0.003	27.897	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	72	TYR	0	-0.004	-0.020	27.938	0.001	0.001	0.000	0.000	0.000	0.000
14	A	73	ALA	0	0.027	0.001	27.878	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	74	GLU	-1	-0.763	-0.868	24.069	0.071	0.071	0.000	0.000	0.000	0.000
16	A	75	ALA	0	-0.026	-0.015	23.126	0.002	0.002	0.000	0.000	0.000	0.000
17	A	76	GLN	0	-0.047	-0.039	23.779	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	77	GLU	-1	-0.882	-0.931	20.948	0.056	0.056	0.000	0.000	0.000	0.000
19	A	78	ILE	0	-0.061	-0.021	19.079	0.000	0.000	0.000	0.000	0.000	0.000
20	A	79	ALA	0	0.031	0.011	18.853	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	80	ASP	-1	-0.892	-0.938	18.682	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	81	HIS	0	0.021	0.004	14.473	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	82	LEU	0	0.010	0.022	14.752	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	83	LYS	1	0.951	0.974	16.851	0.019	0.019	0.000	0.000	0.000	0.000
25	A	84	ASN	0	-0.142	-0.063	13.371	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	85	ARG	1	0.855	0.915	12.119	0.204	0.204	0.000	0.000	0.000	0.000
27	A	86	ARG	1	0.843	0.925	9.739	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	87	ALA	0	0.079	0.045	11.863	0.013	0.013	0.000	0.000	0.000	0.000
29	A	88	VAL	0	-0.038	-0.025	13.222	0.047	0.047	0.000	0.000	0.000	0.000
30	A	89	VAL	0	0.009	0.011	15.548	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	90	VAL	0	0.003	-0.008	17.818	0.015	0.015	0.000	0.000	0.000	0.000
32	A	91	ASN	0	0.022	0.005	21.100	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	92	LEU	0	0.004	-0.025	23.539	0.002	0.002	0.000	0.000	0.000	0.000
34	A	93	GLN	0	0.012	-0.005	25.884	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	94	ARG	1	0.794	0.898	27.471	-0.078	-0.078	0.000	0.000	0.000	0.000
36	A	95	ILE	0	-0.040	-0.010	28.691	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	96	GLN	0	0.020	0.013	31.432	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	97	HIS	0	0.109	0.026	34.112	0.000	0.000	0.000	0.000	0.000	0.000
39	A	98	ASP	-1	-0.873	-0.930	34.844	0.012	0.012	0.000	0.000	0.000	0.000
40	A	99	GLN	0	-0.040	-0.018	33.485	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	100	ALA	0	0.049	0.037	30.523	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	101	LYS	1	0.983	0.983	30.547	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	102	ARG	1	0.881	0.934	32.237	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	103	ILE	0	0.010	0.016	26.664	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	104	VAL	0	0.038	0.020	27.320	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	105	ASP	-1	-0.865	-0.917	28.449	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	106	PHE	0	0.013	-0.001	25.379	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	107	LEU	0	-0.012	-0.023	22.824	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	108	SER	0	0.009	-0.003	25.082	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	109	LYS	1	0.846	0.922	27.321	0.007	0.007	0.000	0.000	0.000	0.000
51	A	110	THR	0	-0.058	-0.025	22.687	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	111	VAL	0	0.008	-0.006	21.141	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	112	TYR	0	0.020	0.030	23.395	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	113	ALA	0	-0.048	-0.021	26.178	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	114	ILE	0	-0.099	-0.048	19.754	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	115	GLY	0	0.015	0.018	21.825	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	116	GLY	0	-0.031	-0.028	20.563	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	117	ASP	-1	-0.840	-0.916	20.734	-0.047	-0.047	0.000	0.000	0.000	0.000
59	A	118	ILE	0	-0.078	-0.056	21.363	0.007	0.007	0.000	0.000	0.000	0.000
60	A	119	GLN	0	0.032	0.026	21.835	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	120	ARG	1	0.926	0.968	23.394	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	121	ILE	0	-0.011	-0.012	19.754	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	122	GLY	0	0.054	0.015	23.868	0.005	0.005	0.000	0.000	0.000	0.000
64	A	123	SER	0	-0.055	-0.027	26.291	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	124	ASP	-1	-0.886	-0.938	27.759	0.042	0.042	0.000	0.000	0.000	0.000
66	A	125	ILE	0	-0.039	-0.001	20.455	0.006	0.006	0.000	0.000	0.000	0.000
67	A	126	PHE	0	0.003	-0.007	23.058	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	127	LEU	0	0.008	0.013	16.003	0.015	0.015	0.000	0.000	0.000	0.000
69	A	128	CYS	0	-0.034	-0.010	18.838	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	129	THR	0	0.018	-0.006	15.797	0.004	0.004	0.000	0.000	0.000	0.000
71	A	130	PRO	0	-0.007	0.013	14.286	0.009	0.009	0.000	0.000	0.000	0.000
72	A	131	ASP	-1	-0.751	-0.879	17.400	-0.196	-0.196	0.000	0.000	0.000	0.000
73	A	132	ASN	0	-0.071	-0.025	12.110	0.028	0.028	0.000	0.000	0.000	0.000
74	A	133	VAL	0	-0.096	-0.056	12.301	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	134	ASP	-1	-0.884	-0.930	14.837	-0.113	-0.113	0.000	0.000	0.000	0.000
76	A	135	VAL	0	-0.031	-0.010	16.360	0.005	0.005	0.000	0.000	0.000	0.000
77	A	136	SER	0	0.009	0.008	18.514	0.006	0.006	0.000	0.000	0.000	0.000
78	A	137	GLY	0	-0.011	-0.004	20.537	0.011	0.011	0.000	0.000	0.000	0.000
79	A	138	THR	0	-0.040	-0.039	22.964	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	139	ILE	0	-0.005	0.005	22.072	0.004	0.004	0.000	0.000	0.000	0.000
81	A	140	SER	0	0.000	0.004	26.254	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	141	GLU	-1	-0.973	-0.986	29.761	0.013	0.013	0.000	0.000	0.000	0.000
83	A	142	LEU	0	-0.037	-0.027	32.020	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	143	NME	0	0.013	0.020	34.050	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:60:ACE )