FMO DATABASE

FMODB ID: 1481Z

Calculation Name: 2GBO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GBO

Chain ID: A

ChEMBL ID:

UniProt ID: Q831P3

Base Structure: X-ray

Registration Date: 2023-06-19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-414427.418957
FMO2-HF: Nuclear repulsion	380272.219557
FMO2-HF: Total energy	-34155.1994
FMO2-MP2: Total energy	-34251.92932

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:1:MET)

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

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.
-0.677	3.427	2.595	-2.072	-4.628	-0.006

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.015

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	3	GLU	-1	-0.819	-0.896	2.294	-8.158	-4.346	2.596	-2.023	-4.385	-0.006
4	A	4	GLY	0	-0.027	-0.015	4.160	1.687	1.979	-0.001	-0.049	-0.243	0.000
5	A	5	ILE	0	-0.018	-0.006	6.027	1.003	1.003	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.029	-0.001	6.054	0.765	0.765	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.933	0.977	8.175	1.512	1.512	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.948	0.965	9.233	2.059	2.059	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.035	0.024	11.311	0.223	0.223	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.036	0.015	12.447	0.179	0.179	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.047	-0.032	13.381	0.124	0.124	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.019	0.007	15.960	0.138	0.138	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.020	0.003	16.790	0.071	0.071	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.005	0.004	17.571	0.076	0.076	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.957	-0.979	20.009	-0.510	-0.510	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.822	-0.892	21.738	-0.406	-0.406	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.839	-0.918	21.870	-0.401	-0.401	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.026	-0.014	24.419	0.045	0.045	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.797	-0.895	26.393	-0.246	-0.246	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.782	0.873	22.948	0.451	0.451	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.003	0.000	27.949	0.028	0.028	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.858	0.909	28.289	0.315	0.315	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.047	-0.018	31.837	0.020	0.020	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.016	0.012	31.690	0.016	0.016	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.004	-0.003	33.441	0.016	0.016	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.831	0.910	32.300	0.244	0.244	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.025	-0.012	37.870	0.011	0.011	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.031	0.016	39.082	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.907	0.951	40.608	0.137	0.137	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.017	-0.003	41.560	0.010	0.010	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.026	0.026	43.721	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.010	0.012	45.354	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.006	-0.009	46.330	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.079	0.029	48.290	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.009	0.000	50.767	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	GLN	0	0.018	0.000	51.292	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.050	-0.023	51.593	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.772	0.863	54.559	0.073	0.073	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.076	0.040	56.666	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	PHE	0	-0.013	-0.011	57.639	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.789	-0.879	58.923	-0.065	-0.065	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.916	-0.950	60.795	-0.064	-0.064	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.027	-0.012	62.311	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.013	-0.004	62.949	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.842	-0.916	65.130	-0.054	-0.054	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.054	-0.029	66.751	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.077	-0.034	67.500	0.003	0.003	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.014	0.013	68.289	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	TYR	0	0.004	-0.013	70.077	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.026	-0.001	72.861	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.001	-0.009	74.156	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.048	0.033	75.355	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.920	0.952	77.094	0.040	0.040	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.026	0.002	78.975	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.035	0.046	79.138	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.027	-0.006	80.761	0.002	0.002	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.056	-0.041	83.167	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.036	0.010	84.546	0.001	0.001	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.002	-0.008	85.075	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.826	0.911	86.195	0.033	0.033	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.024	-0.006	88.260	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.001	0.018	90.802	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.079	-0.035	87.853	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.028	0.003	83.845	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.004	-0.039	88.415	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.002	-0.041	87.886	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.890	-0.931	86.340	-0.030	-0.030	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.823	-0.877	85.017	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.012	0.006	83.462	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.024	-0.019	81.267	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.879	0.915	78.443	0.035	0.035	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.011	-0.004	78.939	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.025	-0.020	77.038	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.000	0.015	75.924	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.774	-0.863	75.224	-0.039	-0.039	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.028	-0.004	72.389	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.928	-0.980	71.246	-0.041	-0.041	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.848	0.900	71.052	0.039	0.039	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.954	-0.970	67.788	-0.049	-0.049	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.031	-0.015	66.784	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.106	-0.030	65.815	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.065	-0.027	62.777	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:1:MET)