FMO DATABASE

FMODB ID: YY612

Calculation Name: 3ZIE-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIE

Chain ID: A

ChEMBL ID:

UniProt ID: O29476

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	-547076.209082
FMO2-HF: Nuclear repulsion	514787.103614
FMO2-HF: Total energy	-32289.105468
FMO2-MP2: Total energy	-32385.18357

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:37:VAL )

Summations of interaction energy for fragment #1(A:37:VAL )

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.
-9.822	-1.485	3.54	-4.228	-7.651	-0.03

Interaction energy analysis for fragmet #1(A:37:VAL )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.013

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	39	ILE	0	0.005	-0.003	3.164	-1.477	0.928	0.145	-0.974	-1.577	0.001
4	A	40	ARG	1	0.836	0.910	5.101	0.345	0.348	0.000	-0.003	0.000	0.000
5	A	41	VAL	0	0.010	0.002	8.544	0.001	0.001	0.000	0.000	0.000	0.000
6	A	42	ALA	0	-0.042	-0.012	11.783	0.040	0.040	0.000	0.000	0.000	0.000
7	A	43	GLU	-1	-0.861	-0.940	14.462	-0.179	-0.179	0.000	0.000	0.000	0.000
8	A	44	VAL	0	-0.048	-0.023	16.816	0.015	0.015	0.000	0.000	0.000	0.000
9	A	45	THR	0	-0.004	-0.004	19.488	0.006	0.006	0.000	0.000	0.000	0.000
10	A	46	GLY	0	-0.005	-0.013	22.239	0.010	0.010	0.000	0.000	0.000	0.000
11	A	47	LEU	0	-0.013	-0.024	22.092	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	48	ASN	0	-0.038	-0.017	21.561	0.002	0.002	0.000	0.000	0.000	0.000
13	A	49	GLU	-1	-0.770	-0.885	17.097	-0.084	-0.084	0.000	0.000	0.000	0.000
14	A	50	VAL	0	-0.014	-0.009	16.387	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	51	PRO	0	-0.046	-0.034	15.896	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	52	GLU	-1	-0.824	-0.920	12.274	0.008	0.008	0.000	0.000	0.000	0.000
17	A	53	ILE	0	0.030	0.024	11.517	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	54	LYS	1	0.939	0.962	10.926	0.010	0.010	0.000	0.000	0.000	0.000
19	A	55	ARG	1	0.894	0.953	11.594	-0.043	-0.043	0.000	0.000	0.000	0.000
20	A	56	GLU	-1	-0.716	-0.819	7.369	-0.116	-0.116	0.000	0.000	0.000	0.000
21	A	57	ILE	0	-0.041	-0.016	6.895	-0.155	-0.155	0.000	0.000	0.000	0.000
22	A	58	TYR	0	-0.076	-0.054	7.694	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	59	ASP	-1	-0.923	-0.943	6.508	0.384	0.384	0.000	0.000	0.000	0.000
24	A	60	GLY	0	-0.066	-0.030	4.208	0.353	0.512	0.000	-0.028	-0.131	0.000
25	A	61	ASN	0	0.011	-0.001	2.473	-8.612	-3.890	1.890	-2.889	-3.724	-0.032
26	A	62	ILE	0	-0.043	-0.027	2.503	0.307	0.552	1.264	-0.139	-1.370	0.001
27	A	63	VAL	0	0.014	0.005	4.913	-0.002	0.009	0.000	-0.003	-0.008	0.000
28	A	64	VAL	0	-0.039	-0.022	8.549	0.053	0.053	0.000	0.000	0.000	0.000
29	A	65	ALA	0	0.000	-0.015	11.094	0.021	0.021	0.000	0.000	0.000	0.000
30	A	66	ASP	-1	-0.811	-0.904	14.489	-0.153	-0.153	0.000	0.000	0.000	0.000
31	A	67	ILE	0	-0.029	-0.036	17.615	0.015	0.015	0.000	0.000	0.000	0.000
32	A	68	ALA	0	0.044	0.023	20.462	0.016	0.016	0.000	0.000	0.000	0.000
33	A	69	PHE	0	-0.066	-0.032	20.395	0.018	0.018	0.000	0.000	0.000	0.000
34	A	70	ILE	0	0.020	0.016	21.947	0.010	0.010	0.000	0.000	0.000	0.000
35	A	71	LYS	1	0.837	0.955	23.623	0.111	0.111	0.000	0.000	0.000	0.000
36	A	72	HIS	0	-0.053	-0.040	25.913	0.007	0.007	0.000	0.000	0.000	0.000
37	A	73	ASP	-1	-0.836	-0.858	28.367	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	74	LYS	1	0.986	0.962	28.213	0.063	0.063	0.000	0.000	0.000	0.000
39	A	75	LEU	0	0.033	0.045	28.186	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	76	THR	0	-0.054	-0.090	25.011	0.000	0.000	0.000	0.000	0.000	0.000
41	A	77	LEU	0	-0.004	0.008	22.451	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	78	ASP	-1	-0.889	-0.949	23.321	-0.080	-0.080	0.000	0.000	0.000	0.000
43	A	79	ARG	1	0.851	0.929	24.329	0.046	0.046	0.000	0.000	0.000	0.000
44	A	80	VAL	0	0.060	0.027	19.115	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	81	LEU	0	-0.021	-0.019	19.294	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	82	LYS	1	0.920	0.974	19.928	0.052	0.052	0.000	0.000	0.000	0.000
47	A	83	ASP	-1	-0.926	-0.958	19.163	-0.071	-0.071	0.000	0.000	0.000	0.000
48	A	84	LEU	0	-0.016	-0.031	14.457	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	85	ARG	1	0.945	0.966	15.525	0.107	0.107	0.000	0.000	0.000	0.000
50	A	86	GLN	0	-0.031	0.001	17.703	0.002	0.002	0.000	0.000	0.000	0.000
51	A	87	LEU	0	0.005	0.001	11.871	0.008	0.008	0.000	0.000	0.000	0.000
52	A	88	ALA	0	0.001	-0.002	13.057	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	89	GLU	-1	-0.958	-0.979	14.112	-0.080	-0.080	0.000	0.000	0.000	0.000
54	A	90	ASP	-1	-0.920	-0.950	16.184	-0.055	-0.055	0.000	0.000	0.000	0.000
55	A	91	VAL	0	-0.074	-0.037	10.654	0.017	0.017	0.000	0.000	0.000	0.000
56	A	92	LYS	1	0.925	0.972	12.130	0.042	0.042	0.000	0.000	0.000	0.000
57	A	93	GLY	0	0.015	0.030	10.613	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	94	ASP	-1	-0.805	-0.891	10.610	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	95	ILE	0	-0.021	-0.023	11.602	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	96	VAL	0	-0.081	-0.036	13.516	0.035	0.035	0.000	0.000	0.000	0.000
61	A	97	GLY	0	0.022	0.016	15.343	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	98	LEU	0	-0.041	-0.024	14.086	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	99	GLY	0	-0.060	-0.049	17.287	0.005	0.005	0.000	0.000	0.000	0.000
64	A	100	GLU	-1	-0.873	-0.947	20.897	-0.105	-0.105	0.000	0.000	0.000	0.000
65	A	101	ASP	-1	-0.858	-0.940	20.612	-0.124	-0.124	0.000	0.000	0.000	0.000
66	A	102	TYR	0	0.034	0.034	15.362	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	103	VAL	0	-0.061	-0.015	14.633	0.014	0.014	0.000	0.000	0.000	0.000
68	A	104	ILE	0	-0.007	0.009	9.642	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	105	MET	0	-0.005	0.002	10.163	0.060	0.060	0.000	0.000	0.000	0.000
70	A	106	THR	0	-0.024	-0.036	6.769	-0.105	-0.105	0.000	0.000	0.000	0.000
71	A	107	PRO	0	0.052	0.040	3.873	0.070	0.218	0.001	-0.021	-0.128	0.000
72	A	108	THR	0	-0.006	-0.035	7.162	0.073	0.073	0.000	0.000	0.000	0.000
73	A	109	GLY	0	-0.050	-0.017	7.123	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	110	ILE	0	-0.017	-0.004	2.858	-0.654	-0.010	0.240	-0.171	-0.713	0.000
75	A	111	LYS	1	0.952	0.986	7.323	0.145	0.145	0.000	0.000	0.000	0.000
76	A	112	VAL	0	0.026	0.023	9.355	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	113	ASP	-1	-0.899	-0.950	11.746	-0.128	-0.128	0.000	0.000	0.000	0.000
78	A	114	ARG	1	0.795	0.865	14.501	0.172	0.172	0.000	0.000	0.000	0.000
79	A	115	ASN	0	-0.062	-0.007	17.428	0.014	0.014	0.000	0.000	0.000	0.000
80	A	116	LYS	1	0.958	0.969	18.108	0.143	0.143	0.000	0.000	0.000	0.000
81	A	117	ILE	0	0.052	0.041	16.178	0.012	0.012	0.000	0.000	0.000	0.000
82	A	118	ARG	1	0.945	0.951	20.032	0.108	0.108	0.000	0.000	0.000	0.000
83	A	119	SER	0	0.002	0.001	23.604	0.001	0.001	0.000	0.000	0.000	0.000
84	A	1	NME	0	0.016	0.025	26.540	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:VAL )