FMO DATABASE

FMODB ID: 4N74N

Calculation Name: 2GN5-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GN5

Chain ID: A

ChEMBL ID:

UniProt ID: P69542

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-552466.676678
FMO2-HF: Nuclear repulsion	518605.348887
FMO2-HF: Total energy	-33861.327791
FMO2-MP2: Total energy	-33963.061509

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.
-8.028	-1.894	0.33	-2.094	-4.37	-0.015

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 : -0.041 / q_NPA : -0.039

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	LYN	0	0.013	0.003	3.051	-2.961	1.336	0.170	-1.360	-3.108	-0.007
4	A	4	VAL	0	0.036	0.021	5.427	0.463	0.463	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.901	-0.938	6.190	-0.620	-0.620	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.051	0.040	7.373	0.254	0.254	0.000	0.000	0.000	0.000
7	A	7	LYN	0	0.200	0.063	5.288	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.088	0.008	8.129	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.286	0.011	11.704	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.027	-0.053	13.691	0.038	0.038	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.173	0.131	16.396	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.064	0.000	19.398	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.095	-0.067	15.592	0.007	0.007	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.045	-0.092	18.702	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.051	0.043	20.707	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	16	ARG	1	1.045	1.011	23.498	0.124	0.124	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.115	-0.085	25.237	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.016	-0.011	28.355	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.101	0.055	29.688	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.043	-0.015	32.062	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.873	0.961	35.234	0.081	0.081	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.040	-0.063	36.737	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.026	-0.022	39.050	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.985	0.963	39.811	0.073	0.073	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.024	0.000	40.449	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.103	0.052	39.160	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.122	-0.031	35.696	0.006	0.006	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.038	-0.070	33.402	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.021	0.075	30.718	0.011	0.011	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.800	-0.908	28.009	-0.172	-0.172	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.271	-0.113	23.896	0.009	0.009	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.046	0.002	24.050	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.059	0.003	18.691	0.015	0.015	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.004	0.009	20.148	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.046	0.019	13.754	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.980	-1.007	14.361	-0.221	-0.221	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.024	-0.044	11.363	-0.059	-0.059	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.041	0.065	9.616	0.092	0.092	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.070	0.086	10.693	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.989	-0.975	12.700	-0.266	-0.266	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.013	-0.068	14.839	0.053	0.053	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.033	-0.025	12.446	-0.038	-0.038	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.080	0.060	13.455	0.019	0.019	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.020	0.002	15.762	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.089	-0.047	16.732	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	LYN	0	-0.018	-0.010	18.558	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.053	0.010	15.151	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.006	-0.014	19.740	0.029	0.029	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.064	-0.106	19.422	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.687	-0.849	21.555	-0.272	-0.272	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.796	-0.881	24.223	-0.185	-0.185	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.043	-0.048	26.522	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.200	-0.100	22.777	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.090	0.048	22.435	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.021	0.023	20.765	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.030	0.003	15.666	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.012	-0.004	16.349	0.040	0.040	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.108	-0.084	15.107	-0.059	-0.059	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.105	0.050	11.968	0.054	0.054	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.171	0.038	4.688	-0.026	0.054	0.000	-0.004	-0.076	0.000
61	A	61	TYR	0	-0.124	-0.200	8.133	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	62	THR	-1	-0.659	-0.835	6.198	-2.067	-2.067	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.031	0.030	8.280	0.379	0.379	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.034	0.008	11.183	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.002	0.015	13.441	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.213	-0.104	16.348	0.048	0.048	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.026	0.007	16.243	-0.062	-0.062	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.153	-0.013	12.752	0.029	0.029	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.829	0.887	19.145	0.226	0.226	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.099	-0.135	22.764	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.048	-0.002	25.729	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.012	-0.009	28.394	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.068	0.009	28.512	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.036	0.026	25.642	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.111	0.112	19.182	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.070	-0.083	22.122	0.014	0.014	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.139	0.221	15.732	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.071	0.069	20.227	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.934	-0.854	22.372	-0.237	-0.237	0.000	0.000	0.000	0.000
80	A	80	ARG	0	0.304	0.026	19.946	0.016	0.016	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.259	-0.074	13.867	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.836	0.832	15.819	0.378	0.378	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.097	0.004	10.908	-0.110	-0.110	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.020	-0.030	10.056	0.133	0.133	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.067	0.045	8.780	-0.173	-0.173	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.019	0.045	3.705	-0.348	-0.203	0.004	-0.034	-0.114	0.000
87	A	87	LYS	0	-0.120	-0.058	2.930	-2.539	-0.927	0.156	-0.696	-1.072	-0.008

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