FMO DATABASE

FMODB ID: K93Z3

Calculation Name: 3GNA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNA

Chain ID: A

ChEMBL ID:

UniProt ID: P15919

Base Structure: X-ray

Registration Date: 2023-06-21

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-368230.806997
FMO2-HF: Nuclear repulsion	340712.420737
FMO2-HF: Total energy	-27518.38626
FMO2-MP2: Total energy	-27598.920095

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:389:GLY)

Summations of interaction energy for fragment #1(A:389: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.
1.067	2.17	-0.015	-0.633	-0.454	0.002

Interaction energy analysis for fragmet #1(A:389:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.012

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	391	ARG	1	0.906	0.950	3.863	0.599	1.702	-0.015	-0.633	-0.454	0.002
4	A	392	PRO	0	0.049	0.022	6.761	-0.402	-0.402	0.000	0.000	0.000	0.000
5	A	393	ARG	1	0.934	0.963	8.408	0.580	0.580	0.000	0.000	0.000	0.000
6	A	394	GLN	0	0.087	0.059	11.303	0.052	0.052	0.000	0.000	0.000	0.000
7	A	395	HIS	0	0.162	0.079	14.566	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	396	LEU	0	0.018	0.022	17.663	0.004	0.004	0.000	0.000	0.000	0.000
9	A	397	LEU	0	0.024	0.011	19.487	0.004	0.004	0.000	0.000	0.000	0.000
10	A	398	SER	0	-0.034	-0.017	18.743	0.016	0.016	0.000	0.000	0.000	0.000
11	A	399	LEU	0	-0.026	-0.011	15.978	0.008	0.008	0.000	0.000	0.000	0.000
12	A	400	THR	0	0.080	0.036	20.266	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	401	ARG	1	1.052	1.015	21.979	0.009	0.009	0.000	0.000	0.000	0.000
14	A	402	ARG	1	0.881	0.935	19.425	0.097	0.097	0.000	0.000	0.000	0.000
15	A	403	ALA	0	0.038	0.013	17.576	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	404	GLN	0	-0.028	-0.026	18.718	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	405	LYS	1	0.988	0.985	21.021	0.064	0.064	0.000	0.000	0.000	0.000
18	A	406	HIS	0	0.005	0.020	15.821	0.034	0.034	0.000	0.000	0.000	0.000
19	A	407	ARG	1	0.844	0.904	14.641	0.131	0.131	0.000	0.000	0.000	0.000
20	A	408	LEU	0	0.029	0.024	17.862	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	409	ARG	1	0.840	0.925	20.129	0.211	0.211	0.000	0.000	0.000	0.000
22	A	410	GLU	-1	-0.782	-0.891	18.848	-0.222	-0.222	0.000	0.000	0.000	0.000
23	A	411	LEU	0	0.050	0.038	21.818	0.011	0.011	0.000	0.000	0.000	0.000
24	A	412	LYS	1	0.949	0.968	23.681	0.102	0.102	0.000	0.000	0.000	0.000
25	A	413	ILE	0	-0.014	-0.002	23.655	0.011	0.011	0.000	0.000	0.000	0.000
26	A	414	GLN	0	0.043	0.019	23.638	0.007	0.007	0.000	0.000	0.000	0.000
27	A	415	VAL	0	0.008	0.001	27.494	0.008	0.008	0.000	0.000	0.000	0.000
28	A	416	LYS	1	0.741	0.849	29.570	0.081	0.081	0.000	0.000	0.000	0.000
29	A	417	GLU	-1	-0.874	-0.930	29.015	-0.110	-0.110	0.000	0.000	0.000	0.000
30	A	418	PHE	0	0.007	0.003	31.626	0.003	0.003	0.000	0.000	0.000	0.000
31	A	419	ALA	0	0.043	0.013	33.468	0.005	0.005	0.000	0.000	0.000	0.000
32	A	420	ASP	-1	-0.824	-0.895	35.139	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	421	LYS	1	0.793	0.899	32.372	0.097	0.097	0.000	0.000	0.000	0.000
34	A	422	GLU	-1	-0.922	-0.959	36.495	-0.065	-0.065	0.000	0.000	0.000	0.000
35	A	423	GLU	-1	-0.944	-0.963	37.478	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	424	GLY	0	-0.024	-0.009	39.997	0.002	0.002	0.000	0.000	0.000	0.000
37	A	425	GLY	0	0.006	-0.002	37.633	0.002	0.002	0.000	0.000	0.000	0.000
38	A	426	ASP	-1	-0.858	-0.920	37.415	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	427	VAL	0	-0.009	-0.031	31.979	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	428	LYS	1	0.912	0.979	34.420	0.033	0.033	0.000	0.000	0.000	0.000
41	A	429	ALA	0	0.058	0.025	36.407	0.001	0.001	0.000	0.000	0.000	0.000
42	A	430	VAL	0	0.049	0.044	33.058	0.000	0.000	0.000	0.000	0.000	0.000
43	A	431	CYS	0	-0.100	-0.065	31.539	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	432	LEU	0	-0.005	0.004	33.185	0.001	0.001	0.000	0.000	0.000	0.000
45	A	433	THR	0	0.037	0.006	35.953	0.003	0.003	0.000	0.000	0.000	0.000
46	A	434	LEU	0	-0.017	-0.011	30.636	0.000	0.000	0.000	0.000	0.000	0.000
47	A	435	PHE	0	-0.053	-0.021	31.239	0.000	0.000	0.000	0.000	0.000	0.000
48	A	436	LEU	0	0.024	0.013	32.984	0.002	0.002	0.000	0.000	0.000	0.000
49	A	437	LEU	0	0.019	0.008	35.409	0.003	0.003	0.000	0.000	0.000	0.000
50	A	438	ALA	0	-0.034	-0.014	30.831	0.001	0.001	0.000	0.000	0.000	0.000
51	A	439	LEU	0	-0.026	-0.009	32.915	0.002	0.002	0.000	0.000	0.000	0.000
52	A	440	ARG	1	0.763	0.833	34.630	0.026	0.026	0.000	0.000	0.000	0.000
53	A	441	ALA	0	-0.025	0.002	34.246	0.002	0.002	0.000	0.000	0.000	0.000
54	A	442	ARG	1	0.771	0.875	29.258	0.030	0.030	0.000	0.000	0.000	0.000
55	A	443	ASN	0	-0.002	0.003	34.401	0.004	0.004	0.000	0.000	0.000	0.000
56	A	444	GLU	-1	-0.825	-0.893	32.670	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	445	HIS	0	-0.009	-0.022	37.075	0.000	0.000	0.000	0.000	0.000	0.000
58	A	446	ARG	1	1.000	1.007	40.427	0.005	0.005	0.000	0.000	0.000	0.000
59	A	447	GLN	0	0.012	0.011	33.579	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	448	ALA	0	-0.005	0.005	38.145	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	449	ASP	-1	-0.809	-0.899	39.225	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	450	GLU	-1	-0.955	-0.985	40.046	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	451	LEU	0	-0.041	-0.021	35.818	0.000	0.000	0.000	0.000	0.000	0.000
64	A	452	GLU	-1	-0.805	-0.908	39.860	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	453	ALA	0	-0.006	0.009	42.688	0.000	0.000	0.000	0.000	0.000	0.000
66	A	454	ILE	0	-0.056	-0.021	39.986	0.001	0.001	0.000	0.000	0.000	0.000
67	A	455	MET	0	-0.118	-0.057	38.265	0.000	0.000	0.000	0.000	0.000	0.000
68	A	456	GLN	0	-0.044	-0.012	42.558	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:389:GLY)