FMO DATABASE

FMODB ID: 89K2Y

Calculation Name: 4ABM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ABM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H444

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479273.603064
FMO2-HF: Nuclear repulsion	447045.125355
FMO2-HF: Total energy	-32228.477708
FMO2-MP2: Total energy	-32323.124005

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.
-10.7	-8.845	9.668	-5.793	-5.73	-0.047

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 : 0.063 / q_NPA : 0.023

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	MET	0	0.047	0.027	3.572	-0.355	1.394	0.003	-0.943	-0.809	0.004
4	A	22	GLU	-1	-0.843	-0.925	1.950	-15.398	-16.272	9.642	-4.590	-4.178	-0.050
5	A	23	GLN	0	0.002	-0.007	3.065	2.654	3.504	0.024	-0.252	-0.622	-0.001
6	A	24	GLU	-1	-0.954	-0.961	5.089	-0.477	-0.347	-0.001	-0.008	-0.121	0.000
7	A	25	ALA	0	-0.015	-0.022	7.557	0.719	0.719	0.000	0.000	0.000	0.000
8	A	26	ILE	0	0.022	0.016	5.244	0.587	0.587	0.000	0.000	0.000	0.000
9	A	27	GLN	0	-0.011	-0.006	8.876	0.373	0.373	0.000	0.000	0.000	0.000
10	A	28	ARG	1	0.835	0.901	11.127	1.288	1.288	0.000	0.000	0.000	0.000
11	A	29	LEU	0	-0.004	0.009	10.564	0.185	0.185	0.000	0.000	0.000	0.000
12	A	30	ARG	1	0.962	0.972	9.731	1.023	1.023	0.000	0.000	0.000	0.000
13	A	31	ASP	-1	-0.796	-0.876	14.866	-0.620	-0.620	0.000	0.000	0.000	0.000
14	A	32	THR	0	-0.068	-0.034	16.745	0.098	0.098	0.000	0.000	0.000	0.000
15	A	33	GLU	-1	-0.763	-0.874	15.401	-0.466	-0.466	0.000	0.000	0.000	0.000
16	A	34	GLU	-1	-0.918	-0.936	19.152	-0.294	-0.294	0.000	0.000	0.000	0.000
17	A	35	MET	0	-0.077	-0.032	21.128	0.065	0.065	0.000	0.000	0.000	0.000
18	A	36	LEU	0	0.000	-0.035	20.746	0.044	0.044	0.000	0.000	0.000	0.000
19	A	37	SER	0	0.055	0.025	22.603	0.037	0.037	0.000	0.000	0.000	0.000
20	A	38	LYS	1	0.970	1.001	24.559	0.290	0.290	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.837	0.914	27.072	0.264	0.264	0.000	0.000	0.000	0.000
22	A	40	GLN	0	0.006	0.000	26.994	0.014	0.014	0.000	0.000	0.000	0.000
23	A	41	GLU	-1	-0.838	-0.907	27.736	-0.163	-0.163	0.000	0.000	0.000	0.000
24	A	42	PHE	0	-0.091	-0.049	31.160	0.018	0.018	0.000	0.000	0.000	0.000
25	A	43	LEU	0	-0.064	-0.049	31.182	0.015	0.015	0.000	0.000	0.000	0.000
26	A	44	GLU	-1	-0.844	-0.920	31.162	-0.130	-0.130	0.000	0.000	0.000	0.000
27	A	45	LYS	1	0.997	1.009	34.911	0.107	0.107	0.000	0.000	0.000	0.000
28	A	46	LYS	1	0.882	0.943	37.079	0.123	0.123	0.000	0.000	0.000	0.000
29	A	47	ILE	0	0.001	-0.004	35.944	0.009	0.009	0.000	0.000	0.000	0.000
30	A	48	GLU	-1	-0.921	-0.949	37.722	-0.086	-0.086	0.000	0.000	0.000	0.000
31	A	49	GLN	0	-0.052	-0.044	41.000	0.005	0.005	0.000	0.000	0.000	0.000
32	A	50	GLU	-1	-0.863	-0.938	42.664	-0.083	-0.083	0.000	0.000	0.000	0.000
33	A	51	LEU	0	-0.004	0.001	41.873	0.006	0.006	0.000	0.000	0.000	0.000
34	A	52	THR	0	-0.019	0.000	44.917	0.006	0.006	0.000	0.000	0.000	0.000
35	A	53	ALA	0	-0.049	-0.062	47.110	0.004	0.004	0.000	0.000	0.000	0.000
36	A	54	ALA	0	-0.010	-0.013	48.316	0.003	0.003	0.000	0.000	0.000	0.000
37	A	55	LYS	1	0.954	0.980	47.820	0.060	0.060	0.000	0.000	0.000	0.000
38	A	56	LYS	1	0.948	1.009	50.254	0.067	0.067	0.000	0.000	0.000	0.000
39	A	57	HIS	0	-0.059	-0.008	53.006	0.003	0.003	0.000	0.000	0.000	0.000
40	A	58	GLY	0	0.069	0.045	54.107	0.002	0.002	0.000	0.000	0.000	0.000
41	A	59	THR	0	-0.024	-0.023	55.703	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	60	LYS	1	0.957	0.999	56.957	0.055	0.055	0.000	0.000	0.000	0.000
43	A	61	ASN	0	0.022	-0.018	56.970	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	62	LYS	1	1.061	1.033	55.559	0.052	0.052	0.000	0.000	0.000	0.000
45	A	63	ARG	1	0.997	1.000	53.946	0.061	0.061	0.000	0.000	0.000	0.000
46	A	64	ALA	0	0.059	0.014	53.127	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	65	ALA	0	0.004	0.004	51.473	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	66	LEU	0	0.001	-0.004	50.523	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	67	GLN	0	-0.071	-0.039	49.285	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	68	ALA	0	0.056	0.032	47.153	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	69	LEU	0	-0.008	0.004	45.718	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	70	LYS	1	0.934	0.960	44.899	0.083	0.083	0.000	0.000	0.000	0.000
53	A	71	ARG	1	0.838	0.920	42.814	0.084	0.084	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.972	0.996	41.142	0.076	0.076	0.000	0.000	0.000	0.000
55	A	73	LYS	1	0.987	0.990	40.159	0.078	0.078	0.000	0.000	0.000	0.000
56	A	74	ARG	1	0.918	0.985	37.630	0.131	0.131	0.000	0.000	0.000	0.000
57	A	75	TYR	0	0.011	-0.006	36.529	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	76	GLU	-1	-0.813	-0.917	35.237	-0.104	-0.104	0.000	0.000	0.000	0.000
59	A	77	LYS	1	0.934	0.974	34.830	0.131	0.131	0.000	0.000	0.000	0.000
60	A	78	GLN	0	-0.047	-0.037	32.642	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	79	LEU	0	0.059	0.029	30.304	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	80	ALA	0	0.038	0.027	30.038	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	81	GLN	0	-0.064	-0.035	29.039	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	82	ILE	0	-0.023	-0.014	25.820	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	83	ASP	-1	-0.786	-0.881	25.139	-0.197	-0.197	0.000	0.000	0.000	0.000
66	A	84	GLY	0	-0.029	-0.010	24.879	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	85	THR	0	-0.067	-0.046	21.560	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	86	LEU	0	0.024	0.013	20.344	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	87	SER	0	0.035	0.033	19.826	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	88	THR	0	-0.058	-0.021	18.781	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	89	ILE	0	-0.099	-0.053	15.648	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.848	-0.929	15.038	-0.363	-0.363	0.000	0.000	0.000	0.000
73	A	91	PHE	0	-0.016	-0.019	14.726	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	92	GLN	0	-0.058	-0.027	11.857	-0.071	-0.071	0.000	0.000	0.000	0.000
75	A	93	ARG	1	0.812	0.881	10.367	0.390	0.390	0.000	0.000	0.000	0.000
76	A	94	GLU	-1	-0.928	-0.973	9.774	-0.371	-0.371	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.078	-0.033	10.636	0.106	0.106	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.063	-0.024	6.454	-0.039	-0.039	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.966	-0.975	5.459	-0.559	-0.559	0.000	0.000	0.000	0.000

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