FMO DATABASE

FMODB ID: VRJ31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-414167.033269
FMO2-HF: Nuclear repulsion	380012.373739
FMO2-HF: Total energy	-34154.65953
FMO2-MP2: Total energy	-34251.433621

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.
-1.262	3.036	3.024	-2.308	-5.015	-0.009

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 : 0.036 / q_NPA : 0.017

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	-0.832	-0.926	2.225	-8.793	-4.792	3.025	-2.255	-4.771	-0.009
4	A	4	GLY	0	-0.035	-0.022	4.187	1.646	1.943	-0.001	-0.053	-0.244	0.000
5	A	5	ILE	0	-0.013	-0.003	5.982	0.984	0.984	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.047	0.031	6.402	0.789	0.789	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.935	0.981	8.238	1.510	1.510	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.947	0.963	9.467	2.185	2.185	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.030	0.022	11.308	0.221	0.221	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.030	0.006	12.482	0.174	0.174	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.040	-0.027	13.532	0.120	0.120	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.024	0.014	16.000	0.162	0.162	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.026	0.006	16.816	0.065	0.065	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.013	0.003	17.850	0.076	0.076	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.967	-0.982	20.275	-0.514	-0.514	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.797	-0.895	21.758	-0.405	-0.405	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.875	-0.939	21.764	-0.417	-0.417	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.034	-0.023	24.474	0.046	0.046	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.894	-0.944	26.428	-0.274	-0.274	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.806	0.897	23.263	0.447	0.447	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.009	0.006	27.981	0.028	0.028	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.869	0.918	28.622	0.316	0.316	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.064	-0.022	31.775	0.021	0.021	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.016	0.010	32.202	0.017	0.017	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.008	-0.002	33.636	0.016	0.016	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.938	0.961	33.022	0.235	0.235	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.024	-0.012	37.922	0.013	0.013	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.036	0.021	39.159	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.893	0.941	40.588	0.141	0.141	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.010	0.005	41.535	0.010	0.010	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.029	0.027	43.839	0.005	0.005	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.004	0.006	45.408	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.014	-0.013	46.209	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.082	0.029	48.495	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.011	0.002	50.840	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.012	-0.008	51.319	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.049	-0.021	51.642	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.841	0.915	54.617	0.074	0.074	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.079	0.047	56.728	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	PHE	0	-0.023	-0.018	57.691	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.827	-0.917	59.004	-0.065	-0.065	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.914	-0.950	60.859	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.050	-0.024	62.265	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.008	-0.006	62.994	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.848	-0.916	64.985	-0.056	-0.056	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.034	-0.017	67.025	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.078	-0.038	67.265	0.003	0.003	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.009	0.012	67.989	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	TYR	0	0.004	-0.014	70.393	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.035	-0.005	72.915	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.011	-0.005	74.204	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.050	0.032	75.412	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.918	0.957	77.154	0.041	0.041	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.021	-0.006	79.027	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.041	0.050	79.144	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.013	-0.006	81.044	0.002	0.002	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.076	-0.045	83.227	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.045	0.013	84.599	0.001	0.001	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.019	0.006	85.220	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.817	0.903	86.156	0.034	0.034	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.027	-0.009	88.399	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.002	0.019	90.864	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.077	-0.033	87.704	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.017	0.007	83.808	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.018	-0.006	88.468	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.001	-0.041	87.951	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.881	-0.924	86.416	-0.030	-0.030	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.882	-0.926	85.089	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.010	0.006	83.522	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.025	-0.021	81.824	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.998	0.996	79.625	0.035	0.035	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.003	0.003	78.801	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.042	-0.023	77.091	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.018	0.021	76.001	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.897	-0.964	75.260	-0.039	-0.039	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.040	-0.018	72.413	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.973	-0.986	71.320	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.865	0.922	71.140	0.039	0.039	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.963	-0.972	67.899	-0.049	-0.049	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.022	-0.017	66.451	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.105	-0.035	65.901	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.025	-0.001	61.895	0.001	0.001	0.000	0.000	0.000	0.000

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