FMO DATABASE

FMODB ID: GNZ31

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	OptAll
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	-414916.393756
FMO2-HF: Nuclear repulsion	380760.903656
FMO2-HF: Total energy	-34155.4901
FMO2-MP2: Total energy	-34252.168441

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.
-2.3	4.246	2.372	-3.825	-5.093	0

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 : 0.057 / q_NPA : 0.027

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

Sort

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].
3	A	3	GLU	-1	-0.812	-0.884	2.192	-8.810	-2.636	2.370	-3.723	-4.821
4	A	4	GLY	0	-0.057	-0.030	3.996	1.342	1.714	0.002	-0.102	-0.272
5	A	5	ILE	0	-0.025	-0.014	6.259	0.958	0.958	0.000	0.000	0.000
6	A	6	SER	0	0.024	-0.010	5.955	0.591	0.591	0.000	0.000	0.000
7	A	7	LYS	1	0.947	0.976	8.168	1.414	1.414	0.000	0.000	0.000
8	A	8	LYS	1	0.924	0.957	9.189	1.826	1.826	0.000	0.000	0.000
9	A	9	PHE	0	0.032	0.018	11.622	0.195	0.195	0.000	0.000	0.000
10	A	10	ALA	0	0.052	0.021	12.622	0.152	0.152	0.000	0.000	0.000
11	A	11	ILE	0	-0.046	-0.022	13.471	0.108	0.108	0.000	0.000	0.000
12	A	12	GLN	0	0.007	-0.002	16.185	0.113	0.113	0.000	0.000	0.000
13	A	13	LEU	0	-0.013	0.009	16.899	0.058	0.058	0.000	0.000	0.000
14	A	14	LEU	0	0.002	0.000	17.765	0.069	0.069	0.000	0.000	0.000
15	A	15	GLU	-1	-0.939	-0.970	20.151	-0.452	-0.452	0.000	0.000	0.000
16	A	16	ASP	-1	-0.839	-0.896	21.964	-0.368	-0.368	0.000	0.000	0.000
17	A	17	ASP	-1	-0.824	-0.911	21.969	-0.368	-0.368	0.000	0.000	0.000
18	A	18	ALA	0	-0.031	-0.010	24.451	0.039	0.039	0.000	0.000	0.000
19	A	19	GLU	-1	-0.785	-0.878	26.401	-0.218	-0.218	0.000	0.000	0.000
20	A	20	ARG	1	0.785	0.869	23.170	0.406	0.406	0.000	0.000	0.000
21	A	21	ILE	0	0.008	0.002	27.916	0.024	0.024	0.000	0.000	0.000
22	A	22	LYS	1	0.873	0.919	28.563	0.280	0.280	0.000	0.000	0.000
23	A	23	MET	0	-0.046	-0.012	31.756	0.018	0.018	0.000	0.000	0.000
24	A	24	LEU	0	0.030	0.020	31.920	0.015	0.015	0.000	0.000	0.000
25	A	25	ILE	0	-0.019	-0.007	33.424	0.014	0.014	0.000	0.000	0.000
26	A	26	ARG	1	0.822	0.884	32.101	0.225	0.225	0.000	0.000	0.000
27	A	27	ASN	0	-0.020	0.000	37.790	0.011	0.011	0.000	0.000	0.000
28	A	28	GLN	0	0.049	0.010	39.177	0.010	0.010	0.000	0.000	0.000
29	A	29	LYS	1	0.891	0.939	40.464	0.128	0.128	0.000	0.000	0.000
30	A	30	ASN	0	-0.048	-0.016	41.341	0.010	0.010	0.000	0.000	0.000
31	A	31	SER	0	0.018	0.018	43.592	0.004	0.004	0.000	0.000	0.000
32	A	32	LEU	0	0.023	0.004	45.362	0.004	0.004	0.000	0.000	0.000
33	A	33	CYS	0	-0.025	0.003	46.762	0.006	0.006	0.000	0.000	0.000
34	A	34	ILE	0	0.084	0.030	48.195	0.004	0.004	0.000	0.000	0.000
35	A	35	SER	0	-0.014	0.005	50.920	0.004	0.004	0.000	0.000	0.000
36	A	36	GLN	0	0.034	0.004	51.678	0.005	0.005	0.000	0.000	0.000
37	A	37	CYS	0	-0.053	-0.022	51.862	0.003	0.003	0.000	0.000	0.000
38	A	38	LYS	1	0.809	0.876	54.830	0.069	0.069	0.000	0.000	0.000
39	A	39	ALA	0	0.053	0.031	56.941	0.003	0.003	0.000	0.000	0.000
40	A	40	PHE	0	-0.016	-0.012	57.885	0.002	0.002	0.000	0.000	0.000
41	A	41	GLU	-1	-0.796	-0.876	58.877	-0.062	-0.062	0.000	0.000	0.000
42	A	42	GLU	-1	-0.902	-0.946	60.994	-0.059	-0.059	0.000	0.000	0.000
43	A	43	VAL	0	-0.029	-0.003	62.613	0.003	0.003	0.000	0.000	0.000
44	A	44	VAL	0	-0.011	-0.009	62.866	0.002	0.002	0.000	0.000	0.000
45	A	45	ASP	-1	-0.839	-0.927	65.201	-0.050	-0.050	0.000	0.000	0.000
46	A	46	THR	0	-0.089	-0.051	66.808	0.003	0.003	0.000	0.000	0.000
47	A	47	GLN	0	-0.069	-0.035	67.956	0.003	0.003	0.000	0.000	0.000
48	A	48	MET	0	0.011	0.025	68.452	0.002	0.002	0.000	0.000	0.000
49	A	49	TYR	0	0.018	-0.001	69.768	0.003	0.003	0.000	0.000	0.000
50	A	50	GLY	0	-0.011	0.000	72.888	0.002	0.002	0.000	0.000	0.000
51	A	51	PHE	0	0.004	-0.007	74.177	0.002	0.002	0.000	0.000	0.000
52	A	52	SER	0	0.036	0.028	75.311	0.002	0.002	0.000	0.000	0.000
53	A	53	ARG	1	0.920	0.959	77.077	0.038	0.038	0.000	0.000	0.000
54	A	54	GLN	0	0.022	0.006	78.869	0.002	0.002	0.000	0.000	0.000
55	A	55	VAL	0	0.029	0.029	79.136	0.001	0.001	0.000	0.000	0.000
56	A	56	THR	0	-0.021	-0.011	80.595	0.001	0.001	0.000	0.000	0.000
57	A	57	TYR	0	-0.064	-0.039	83.082	0.001	0.001	0.000	0.000	0.000
58	A	58	ALA	0	0.043	0.017	84.634	0.001	0.001	0.000	0.000	0.000
59	A	59	THR	0	-0.007	-0.017	84.842	0.001	0.001	0.000	0.000	0.000
60	A	60	ARG	1	0.814	0.905	86.534	0.031	0.031	0.000	0.000	0.000
61	A	61	LEU	0	-0.037	-0.012	88.124	0.001	0.001	0.000	0.000	0.000
62	A	62	GLY	0	-0.007	0.010	90.846	0.001	0.001	0.000	0.000	0.000
63	A	63	ILE	0	-0.070	-0.030	87.921	0.000	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.019	0.003	84.133	0.000	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.010	-0.031	88.674	0.000	0.000	0.000	0.000	0.000
66	A	66	ASN	0	0.006	-0.030	87.560	-0.001	-0.001	0.000	0.000	0.000
67	A	67	ASP	-1	-0.886	-0.927	86.215	-0.028	-0.028	0.000	0.000	0.000
68	A	68	GLU	-1	-0.825	-0.884	85.168	-0.031	-0.031	0.000	0.000	0.000
69	A	69	GLY	0	0.028	0.016	83.367	-0.001	-0.001	0.000	0.000	0.000
70	A	70	HIS	0	-0.038	-0.024	80.940	-0.001	-0.001	0.000	0.000	0.000
71	A	71	ARG	1	0.869	0.907	78.413	0.034	0.034	0.000	0.000	0.000
72	A	72	LEU	0	-0.014	-0.012	79.061	-0.001	-0.001	0.000	0.000	0.000
73	A	73	LEU	0	-0.026	-0.018	77.214	-0.001	-0.001	0.000	0.000	0.000
74	A	74	SER	0	-0.031	-0.015	76.001	-0.001	-0.001	0.000	0.000	0.000
75	A	75	ASP	-1	-0.793	-0.858	75.171	-0.038	-0.038	0.000	0.000	0.000
76	A	76	LEU	0	-0.032	-0.010	72.416	-0.001	-0.001	0.000	0.000	0.000
77	A	77	GLU	-1	-0.849	-0.929	71.175	-0.040	-0.040	0.000	0.000	0.000
78	A	78	ARG	1	0.878	0.924	70.836	0.038	0.038	0.000	0.000	0.000
79	A	79	GLU	-1	-0.945	-0.967	67.890	-0.047	-0.047	0.000	0.000	0.000
80	A	80	LEU	0	-0.039	-0.016	66.636	-0.002	-0.002	0.000	0.000	0.000
81	A	81	ASN	0	-0.101	-0.038	65.944	-0.002	-0.002	0.000	0.000	0.000
82	A	82	GLN	0	-0.115	-0.053	63.012	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)