FMO DATABASE

FMODB ID: QY14Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-368310.818949
FMO2-HF: Nuclear repulsion	340792.617356
FMO2-HF: Total energy	-27518.201593
FMO2-MP2: Total energy	-27598.77406

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.
0.37	1.485	-0.016	-0.629	-0.471	0.003

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 : 0.033 / q_NPA : 0.010

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	0.901	0.945	3.808	-0.491	0.624	-0.016	-0.629	-0.471	0.003
4	A	392	PRO	0	0.061	0.029	6.472	-0.299	-0.299	0.000	0.000	0.000	0.000
5	A	393	ARG	1	0.926	0.963	8.414	0.823	0.823	0.000	0.000	0.000	0.000
6	A	394	GLN	0	0.088	0.059	11.691	0.051	0.051	0.000	0.000	0.000	0.000
7	A	395	HIS	0	0.171	0.079	14.873	-0.061	-0.061	0.000	0.000	0.000	0.000
8	A	396	LEU	0	0.019	0.011	17.970	0.015	0.015	0.000	0.000	0.000	0.000
9	A	397	LEU	0	0.038	0.010	19.819	0.013	0.013	0.000	0.000	0.000	0.000
10	A	398	SER	0	-0.031	-0.010	19.093	0.014	0.014	0.000	0.000	0.000	0.000
11	A	399	LEU	0	-0.065	-0.016	16.159	0.010	0.010	0.000	0.000	0.000	0.000
12	A	400	THR	0	0.094	0.044	20.276	0.000	0.000	0.000	0.000	0.000	0.000
13	A	401	ARG	1	1.061	1.020	22.174	0.023	0.023	0.000	0.000	0.000	0.000
14	A	402	ARG	1	0.894	0.954	19.641	0.050	0.050	0.000	0.000	0.000	0.000
15	A	403	ALA	0	0.027	0.002	17.771	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	404	GLN	0	-0.015	-0.024	18.938	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	405	LYS	1	0.968	0.980	21.123	0.048	0.048	0.000	0.000	0.000	0.000
18	A	406	HIS	0	0.002	0.005	15.440	0.027	0.027	0.000	0.000	0.000	0.000
19	A	407	ARG	1	0.849	0.903	14.834	0.252	0.252	0.000	0.000	0.000	0.000
20	A	408	LEU	0	0.034	0.030	18.076	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	409	ARG	1	0.841	0.916	19.982	0.168	0.168	0.000	0.000	0.000	0.000
22	A	410	GLU	-1	-0.777	-0.877	19.197	-0.194	-0.194	0.000	0.000	0.000	0.000
23	A	411	LEU	0	0.047	0.031	22.111	0.009	0.009	0.000	0.000	0.000	0.000
24	A	412	LYS	1	0.920	0.948	24.010	0.104	0.104	0.000	0.000	0.000	0.000
25	A	413	ILE	0	-0.006	0.000	23.877	0.013	0.013	0.000	0.000	0.000	0.000
26	A	414	GLN	0	0.043	0.027	24.368	0.004	0.004	0.000	0.000	0.000	0.000
27	A	415	VAL	0	0.004	0.003	27.902	0.008	0.008	0.000	0.000	0.000	0.000
28	A	416	LYS	1	0.742	0.851	29.892	0.079	0.079	0.000	0.000	0.000	0.000
29	A	417	GLU	-1	-0.862	-0.935	29.295	-0.108	-0.108	0.000	0.000	0.000	0.000
30	A	418	PHE	0	0.007	0.012	32.091	0.003	0.003	0.000	0.000	0.000	0.000
31	A	419	ALA	0	0.056	0.017	33.881	0.005	0.005	0.000	0.000	0.000	0.000
32	A	420	ASP	-1	-0.850	-0.892	35.406	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	421	LYS	1	0.807	0.894	32.787	0.099	0.099	0.000	0.000	0.000	0.000
34	A	422	GLU	-1	-0.930	-0.961	37.113	-0.072	-0.072	0.000	0.000	0.000	0.000
35	A	423	GLU	-1	-0.952	-0.969	38.114	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	424	GLY	0	-0.011	0.003	40.376	0.003	0.003	0.000	0.000	0.000	0.000
37	A	425	GLY	0	-0.009	-0.020	37.740	0.002	0.002	0.000	0.000	0.000	0.000
38	A	426	ASP	-1	-0.871	-0.919	38.214	-0.054	-0.054	0.000	0.000	0.000	0.000
39	A	427	VAL	0	-0.012	-0.030	32.456	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	428	LYS	1	0.929	0.981	35.028	0.041	0.041	0.000	0.000	0.000	0.000
41	A	429	ALA	0	0.070	0.040	36.637	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	430	VAL	0	0.072	0.056	33.520	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	431	CYS	0	-0.105	-0.075	31.947	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	432	LEU	0	-0.017	-0.004	33.430	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	433	THR	0	0.046	0.007	36.163	0.001	0.001	0.000	0.000	0.000	0.000
46	A	434	LEU	0	-0.029	-0.010	30.807	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	435	PHE	0	-0.044	-0.016	31.465	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	436	LEU	0	0.032	0.015	33.217	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	437	LEU	0	0.018	0.001	35.774	0.001	0.001	0.000	0.000	0.000	0.000
50	A	438	ALA	0	-0.048	-0.022	31.018	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	439	LEU	0	-0.040	-0.016	33.110	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	440	ARG	1	0.792	0.851	34.845	0.051	0.051	0.000	0.000	0.000	0.000
53	A	441	ALA	0	-0.029	0.007	34.083	0.002	0.002	0.000	0.000	0.000	0.000
54	A	442	ARG	1	0.791	0.885	28.934	0.088	0.088	0.000	0.000	0.000	0.000
55	A	443	ASN	0	-0.027	-0.010	34.762	0.005	0.005	0.000	0.000	0.000	0.000
56	A	444	GLU	-1	-0.838	-0.901	33.309	-0.071	-0.071	0.000	0.000	0.000	0.000
57	A	445	HIS	0	0.033	-0.004	37.689	0.001	0.001	0.000	0.000	0.000	0.000
58	A	446	ARG	1	0.997	1.002	41.066	0.036	0.036	0.000	0.000	0.000	0.000
59	A	447	GLN	0	0.010	0.008	34.316	0.001	0.001	0.000	0.000	0.000	0.000
60	A	448	ALA	0	-0.004	-0.001	38.498	0.000	0.000	0.000	0.000	0.000	0.000
61	A	449	ASP	-1	-0.804	-0.898	39.528	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	450	GLU	-1	-0.958	-0.975	40.645	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	451	LEU	0	-0.058	-0.032	36.165	0.001	0.001	0.000	0.000	0.000	0.000
64	A	452	GLU	-1	-0.842	-0.931	40.147	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	453	ALA	0	-0.018	0.017	42.984	0.002	0.002	0.000	0.000	0.000	0.000
66	A	454	ILE	0	-0.071	-0.043	39.867	0.002	0.002	0.000	0.000	0.000	0.000
67	A	455	MET	0	-0.110	-0.049	38.645	0.001	0.001	0.000	0.000	0.000	0.000
68	A	456	GLN	0	-0.011	0.011	43.120	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:389:GLY)