FMO DATABASE

FMODB ID: MVR9Z

Calculation Name: 5GNJ-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5GNJ

Chain ID: G

ChEMBL ID:

UniProt ID: Q39204

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-355837.012465
FMO2-HF: Nuclear repulsion	326877.257705
FMO2-HF: Total energy	-28959.75476
FMO2-MP2: Total energy	-29045.437677

3D Structure Molmil

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(G:452:ASN)

Summations of interaction energy for fragment #1(G:452:ASN)

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.
-6.886	-29.096	24.59	5.559	-7.939	0.016

Interaction energy analysis for fragmet #1(G:452:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : 0.018

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	G	454	VAL	0	0.022	0.000	2.650	10.632	-0.091	0.084	11.728	-1.090	-0.004
4	G	455	GLU	-1	-0.944	-0.990	2.182	-5.383	-4.170	1.277	-0.950	-1.539	-0.001
5	G	456	ALA	0	0.034	0.002	1.761	-5.284	-16.382	22.930	-6.985	-4.848	0.019
6	G	457	GLU	-1	-0.863	-0.925	2.920	1.023	-0.579	0.299	1.766	-0.462	0.002
7	G	458	ARG	1	0.898	0.938	5.868	-2.464	-2.464	0.000	0.000	0.000	0.000
8	G	459	GLN	0	0.019	0.021	5.843	-0.506	-0.506	0.000	0.000	0.000	0.000
9	G	460	ARG	1	0.930	0.973	7.502	-1.934	-1.934	0.000	0.000	0.000	0.000
10	G	461	ARG	1	0.931	0.959	9.492	-2.014	-2.014	0.000	0.000	0.000	0.000
11	G	462	GLU	-1	-0.893	-0.944	10.989	0.123	0.123	0.000	0.000	0.000	0.000
12	G	463	LYS	1	0.967	0.990	11.960	-0.159	-0.159	0.000	0.000	0.000	0.000
13	G	464	LEU	0	-0.013	-0.006	13.737	-0.083	-0.083	0.000	0.000	0.000	0.000
14	G	465	ASN	0	0.026	-0.006	15.547	-0.040	-0.040	0.000	0.000	0.000	0.000
15	G	466	GLN	0	0.029	0.028	15.516	-0.028	-0.028	0.000	0.000	0.000	0.000
16	G	467	ARG	1	0.913	0.935	16.491	-0.133	-0.133	0.000	0.000	0.000	0.000
17	G	468	PHE	0	0.019	0.007	19.338	-0.004	-0.004	0.000	0.000	0.000	0.000
18	G	469	TYR	0	-0.002	0.004	21.723	-0.012	-0.012	0.000	0.000	0.000	0.000
19	G	470	ALA	0	0.027	0.007	23.003	-0.018	-0.018	0.000	0.000	0.000	0.000
20	G	471	LEU	0	0.004	0.008	24.535	-0.011	-0.011	0.000	0.000	0.000	0.000
21	G	472	ARG	1	0.849	0.910	25.652	-0.205	-0.205	0.000	0.000	0.000	0.000
22	G	473	ALA	0	-0.034	-0.002	27.963	-0.008	-0.008	0.000	0.000	0.000	0.000
23	G	474	VAL	0	-0.026	-0.004	28.818	-0.014	-0.014	0.000	0.000	0.000	0.000
24	G	475	VAL	0	-0.021	0.000	30.798	-0.003	-0.003	0.000	0.000	0.000	0.000
25	G	476	PRO	0	0.016	0.010	33.003	0.003	0.003	0.000	0.000	0.000	0.000
26	G	477	ASN	0	-0.004	-0.002	36.112	0.002	0.002	0.000	0.000	0.000	0.000
27	G	478	VAL	0	0.034	0.030	30.734	0.010	0.010	0.000	0.000	0.000	0.000
28	G	479	SER	0	0.001	-0.013	31.032	0.012	0.012	0.000	0.000	0.000	0.000
29	G	480	LYS	1	0.947	0.963	30.502	-0.108	-0.108	0.000	0.000	0.000	0.000
30	G	481	MET	0	-0.005	0.022	31.074	0.010	0.010	0.000	0.000	0.000	0.000
31	G	482	ASP	-1	-0.786	-0.891	27.411	0.322	0.322	0.000	0.000	0.000	0.000
32	G	483	LYS	1	0.892	0.941	19.158	-0.490	-0.490	0.000	0.000	0.000	0.000
33	G	484	ALA	0	0.006	0.005	25.775	-0.008	-0.008	0.000	0.000	0.000	0.000
34	G	485	SER	0	0.045	0.006	27.773	-0.017	-0.017	0.000	0.000	0.000	0.000
35	G	486	LEU	0	-0.038	0.011	25.699	-0.012	-0.012	0.000	0.000	0.000	0.000
36	G	487	LEU	0	0.000	-0.011	23.946	-0.013	-0.013	0.000	0.000	0.000	0.000
37	G	488	GLY	0	0.002	0.008	28.434	-0.012	-0.012	0.000	0.000	0.000	0.000
38	G	489	ASP	-1	-0.819	-0.927	31.925	0.143	0.143	0.000	0.000	0.000	0.000
39	G	490	ALA	0	-0.047	-0.018	29.757	-0.016	-0.016	0.000	0.000	0.000	0.000
40	G	491	ILE	0	-0.027	-0.014	29.955	-0.014	-0.014	0.000	0.000	0.000	0.000
41	G	492	ALA	0	0.003	0.002	33.087	-0.012	-0.012	0.000	0.000	0.000	0.000
42	G	493	TYR	0	0.022	0.005	34.141	-0.012	-0.012	0.000	0.000	0.000	0.000
43	G	494	ILE	0	0.001	-0.005	30.970	-0.012	-0.012	0.000	0.000	0.000	0.000
44	G	495	ASN	0	-0.046	-0.036	35.534	-0.013	-0.013	0.000	0.000	0.000	0.000
45	G	496	GLU	-1	-0.938	-0.960	38.547	0.063	0.063	0.000	0.000	0.000	0.000
46	G	497	LEU	0	0.000	-0.007	36.219	-0.008	-0.008	0.000	0.000	0.000	0.000
47	G	498	LYS	1	0.930	0.959	37.039	-0.099	-0.099	0.000	0.000	0.000	0.000
48	G	499	SER	0	0.007	0.015	40.753	-0.007	-0.007	0.000	0.000	0.000	0.000
49	G	500	LYS	1	0.987	0.996	43.417	-0.046	-0.046	0.000	0.000	0.000	0.000
50	G	501	VAL	0	-0.005	0.001	41.439	-0.005	-0.005	0.000	0.000	0.000	0.000
51	G	502	VAL	0	0.049	0.027	44.608	-0.004	-0.004	0.000	0.000	0.000	0.000
52	G	503	LYS	1	0.929	0.968	46.897	-0.046	-0.046	0.000	0.000	0.000	0.000
53	G	504	THR	0	-0.021	-0.010	47.827	-0.003	-0.003	0.000	0.000	0.000	0.000
54	G	505	GLU	-1	-0.952	-0.988	46.379	0.021	0.021	0.000	0.000	0.000	0.000
55	G	506	SER	0	-0.026	-0.007	50.099	-0.002	-0.002	0.000	0.000	0.000	0.000
56	G	507	GLU	-1	-0.921	-0.970	52.670	0.029	0.029	0.000	0.000	0.000	0.000
57	G	508	LYS	1	0.954	0.982	50.124	-0.009	-0.009	0.000	0.000	0.000	0.000
58	G	509	LEU	0	-0.005	-0.001	54.427	-0.003	-0.003	0.000	0.000	0.000	0.000
59	G	510	GLN	0	-0.003	0.001	56.118	-0.001	-0.001	0.000	0.000	0.000	0.000
60	G	511	ILE	0	0.038	0.015	56.711	-0.001	-0.001	0.000	0.000	0.000	0.000
61	G	512	LYS	1	0.854	0.928	57.270	-0.006	-0.006	0.000	0.000	0.000	0.000
62	G	513	ASN	0	-0.014	-0.029	59.377	-0.003	-0.003	0.000	0.000	0.000	0.000
63	G	514	GLN	0	-0.010	-0.001	62.054	0.001	0.001	0.000	0.000	0.000	0.000
64	G	515	LEU	0	-0.015	0.004	60.995	-0.001	-0.001	0.000	0.000	0.000	0.000
65	G	516	GLU	-1	-0.883	-0.931	63.015	-0.002	-0.002	0.000	0.000	0.000	0.000
66	G	517	GLU	-1	-0.867	-0.934	65.106	0.006	0.006	0.000	0.000	0.000	0.000
67	G	518	VAL	0	0.039	0.022	67.032	-0.001	-0.001	0.000	0.000	0.000	0.000
68	G	519	LYS	1	0.823	0.909	64.719	0.002	0.002	0.000	0.000	0.000	0.000
69	G	520	LEU	0	-0.039	-0.033	68.874	-0.001	-0.001	0.000	0.000	0.000	0.000
70	G	521	GLU	-1	-0.918	-0.950	71.234	0.004	0.004	0.000	0.000	0.000	0.000
71	G	522	LEU	0	-0.072	-0.026	70.969	-0.001	-0.001	0.000	0.000	0.000	0.000
72	G	523	ALA	0	-0.079	-0.032	72.536	-0.001	-0.001	0.000	0.000	0.000	0.000
73	G	524	GLY	0	-0.015	0.003	74.477	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:452:ASN)