FMO DATABASE

FMODB ID: 664GZ

Calculation Name: 3D0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D0W

Chain ID: A

ChEMBL ID:

UniProt ID: O34306

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptHSide
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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-566318.780945
FMO2-HF: Nuclear repulsion	532422.352548
FMO2-HF: Total energy	-33896.428398
FMO2-MP2: Total energy	-33997.078757

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:19:GLY)

Summations of interaction energy for fragment #1(A:19:GLY)

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.
-4.358	-2.317	0.045	-0.909	-1.175	0.002

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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	21	ILE	0	-0.020	-0.002	3.130	-1.997	-0.073	0.047	-0.852	-1.118	0.002
4	A	22	LYS	1	0.867	0.919	4.190	-0.447	-0.415	-0.001	-0.043	0.013	0.000
5	A	23	GLU	-1	-0.875	-0.950	6.812	-1.323	-1.323	0.000	0.000	0.000	0.000
6	A	24	ASP	-1	-0.795	-0.888	7.623	-0.715	-0.715	0.000	0.000	0.000	0.000
7	A	25	ILE	0	0.019	0.018	8.721	0.126	0.126	0.000	0.000	0.000	0.000
8	A	26	LEU	0	-0.028	-0.005	3.932	0.122	0.207	-0.001	-0.014	-0.070	0.000
9	A	27	LYS	1	0.830	0.897	8.625	0.553	0.553	0.000	0.000	0.000	0.000
10	A	28	ASP	-1	-0.854	-0.922	11.565	-0.272	-0.272	0.000	0.000	0.000	0.000
11	A	29	PHE	0	0.004	0.004	11.129	0.111	0.111	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-0.839	-0.918	10.923	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	31	GLU	-1	-0.830	-0.895	13.599	-0.251	-0.251	0.000	0.000	0.000	0.000
14	A	32	PHE	0	0.018	0.021	16.245	0.043	0.043	0.000	0.000	0.000	0.000
15	A	33	LYS	1	0.798	0.875	13.070	0.100	0.100	0.000	0.000	0.000	0.000
16	A	34	GLY	0	0.002	-0.008	17.616	0.021	0.021	0.000	0.000	0.000	0.000
17	A	35	TYR	0	0.009	-0.012	19.501	0.012	0.012	0.000	0.000	0.000	0.000
18	A	36	LEU	0	0.035	0.025	19.802	0.014	0.014	0.000	0.000	0.000	0.000
19	A	37	LYS	1	0.845	0.909	19.580	0.019	0.019	0.000	0.000	0.000	0.000
20	A	38	LYS	1	0.804	0.922	23.072	0.085	0.085	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.016	0.012	25.528	0.001	0.001	0.000	0.000	0.000	0.000
22	A	40	VAL	0	0.025	0.015	25.571	0.006	0.006	0.000	0.000	0.000	0.000
23	A	41	ASN	0	0.003	-0.004	25.734	0.008	0.008	0.000	0.000	0.000	0.000
24	A	42	ARG	1	0.980	0.995	28.880	0.041	0.041	0.000	0.000	0.000	0.000
25	A	43	GLY	0	0.070	0.041	30.850	0.002	0.002	0.000	0.000	0.000	0.000
26	A	44	LYS	1	0.846	0.905	29.152	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	45	LYS	1	0.800	0.903	30.922	0.020	0.020	0.000	0.000	0.000	0.000
28	A	46	LEU	0	0.055	0.034	34.818	0.000	0.000	0.000	0.000	0.000	0.000
29	A	47	GLY	0	0.018	0.018	36.514	0.001	0.001	0.000	0.000	0.000	0.000
30	A	48	LEU	0	-0.024	-0.008	36.709	0.002	0.002	0.000	0.000	0.000	0.000
31	A	49	ASP	-1	-0.926	-0.963	38.642	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	50	ASP	-1	-0.875	-0.921	41.012	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	51	GLY	0	-0.029	-0.008	42.340	0.002	0.002	0.000	0.000	0.000	0.000
34	A	52	LYS	1	0.774	0.875	40.594	0.005	0.005	0.000	0.000	0.000	0.000
35	A	53	LEU	0	-0.018	-0.008	36.800	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	54	VAL	0	0.054	0.032	34.028	0.002	0.002	0.000	0.000	0.000	0.000
37	A	55	LYS	1	0.962	0.970	32.220	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	56	SER	0	0.045	-0.002	27.170	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	57	ALA	0	0.068	0.036	28.449	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	58	ALA	0	0.022	0.022	29.424	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	59	ILE	0	-0.014	0.003	29.403	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	60	LEU	0	-0.013	-0.019	24.127	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	61	GLY	0	0.054	0.037	28.155	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	62	ASP	-1	-0.880	-0.947	30.659	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	63	TYR	0	-0.151	-0.085	24.555	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	64	LEU	0	0.078	0.044	25.195	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	65	ALA	0	-0.065	-0.021	29.260	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	66	LYS	1	0.851	0.928	31.620	0.022	0.022	0.000	0.000	0.000	0.000
49	A	67	HIS	0	-0.041	-0.014	30.841	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.860	-0.935	28.363	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.908	-0.951	28.278	-0.076	-0.076	0.000	0.000	0.000	0.000
52	A	70	PRO	0	-0.025	-0.013	24.081	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	71	GLN	0	-0.076	-0.050	22.943	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	72	ASN	0	-0.028	-0.018	18.054	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.034	0.009	17.928	0.021	0.021	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.914	-0.961	14.255	-0.146	-0.146	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.822	-0.916	18.336	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	76	MET	0	-0.020	0.002	21.673	0.009	0.009	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.012	-0.002	18.719	0.014	0.014	0.000	0.000	0.000	0.000
60	A	78	LEU	0	-0.018	-0.021	21.056	0.014	0.014	0.000	0.000	0.000	0.000
61	A	79	GLN	0	0.018	0.008	23.482	0.008	0.008	0.000	0.000	0.000	0.000
62	A	80	GLU	-1	-0.914	-0.949	25.294	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	81	LEU	0	-0.032	-0.012	22.216	0.008	0.008	0.000	0.000	0.000	0.000
64	A	82	TRP	0	-0.001	-0.007	26.615	0.006	0.006	0.000	0.000	0.000	0.000
65	A	83	SER	0	-0.082	-0.055	29.080	0.001	0.001	0.000	0.000	0.000	0.000
66	A	84	VAL	0	-0.040	-0.021	29.210	0.000	0.000	0.000	0.000	0.000	0.000
67	A	85	ALA	0	-0.037	0.014	29.858	0.004	0.004	0.000	0.000	0.000	0.000
68	A	86	ASP	-1	-0.857	-0.927	31.900	0.033	0.033	0.000	0.000	0.000	0.000
69	A	87	GLU	-1	-0.954	-1.006	33.826	0.020	0.020	0.000	0.000	0.000	0.000
70	A	88	ASP	-1	-0.858	-0.925	34.254	0.043	0.043	0.000	0.000	0.000	0.000
71	A	89	GLU	-1	-0.895	-0.949	30.171	0.053	0.053	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.808	0.913	29.406	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	91	GLU	-1	-0.945	-0.963	29.807	0.031	0.031	0.000	0.000	0.000	0.000
74	A	92	HIS	0	-0.052	-0.043	28.399	0.008	0.008	0.000	0.000	0.000	0.000
75	A	93	LEU	0	-0.005	0.003	23.252	0.010	0.010	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.031	0.013	24.822	0.001	0.001	0.000	0.000	0.000	0.000
77	A	95	GLN	0	-0.057	-0.040	25.904	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.049	-0.023	20.742	0.007	0.007	0.000	0.000	0.000	0.000
79	A	97	LEU	0	0.055	0.028	20.163	0.010	0.010	0.000	0.000	0.000	0.000
80	A	98	VAL	0	-0.005	-0.001	21.429	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.898	0.953	21.105	-0.133	-0.133	0.000	0.000	0.000	0.000
82	A	100	LEU	0	-0.031	0.002	16.099	0.014	0.014	0.000	0.000	0.000	0.000
83	A	101	VAL	0	0.030	0.005	17.330	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-0.970	-0.970	18.971	0.007	0.007	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.970	1.007	12.224	-0.293	-0.293	0.000	0.000	0.000	0.000
86	A	104	GLN	0	-0.047	-0.031	10.306	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)