FMO DATABASE

FMODB ID: 7GVVK

Calculation Name: 1NGM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NGM

Chain ID: B

ChEMBL ID:

UniProt ID: P13393

Base Structure: X-ray

Registration Date: 2023-06-20

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-314503.175957
FMO2-HF: Nuclear repulsion	285412.572676
FMO2-HF: Total energy	-29090.603281
FMO2-MP2: Total energy	-29175.994456

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(B:435:GLY)

Summations of interaction energy for fragment #1(B:435: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.
-9.13	-5.463	0.642	-1.902	-2.405	0.007

Interaction energy analysis for fragmet #1(B:435:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.002

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	B	437	TYR	0	0.022	0.020	3.471	0.060	2.003	-0.003	-1.019	-0.922	0.001
4	B	438	CYS	0	-0.033	-0.024	5.114	-0.419	-0.439	-0.001	-0.015	0.037	0.000
5	B	439	PRO	0	0.027	0.018	4.016	-1.428	-1.145	0.001	-0.094	-0.190	0.000
6	B	440	ARG	1	0.950	0.983	2.961	-9.063	-7.654	0.643	-0.754	-1.297	0.006
7	B	441	ASN	0	0.003	-0.002	3.910	0.110	0.162	0.002	-0.020	-0.033	0.000
8	B	442	LEU	0	0.027	-0.003	6.860	0.361	0.361	0.000	0.000	0.000	0.000
9	B	443	HIS	0	0.019	0.019	9.821	0.195	0.195	0.000	0.000	0.000	0.000
10	B	444	LEU	0	0.015	0.008	7.341	0.056	0.056	0.000	0.000	0.000	0.000
11	B	445	LEU	0	-0.079	-0.034	7.150	0.426	0.426	0.000	0.000	0.000	0.000
12	B	446	PRO	0	0.031	0.014	10.686	-0.158	-0.158	0.000	0.000	0.000	0.000
13	B	447	THR	0	0.020	0.020	14.438	-0.045	-0.045	0.000	0.000	0.000	0.000
14	B	448	THR	0	0.072	0.025	16.897	0.020	0.020	0.000	0.000	0.000	0.000
15	B	449	ASP	-1	-0.857	-0.931	20.000	0.172	0.172	0.000	0.000	0.000	0.000
16	B	450	THR	0	-0.111	-0.059	18.852	0.018	0.018	0.000	0.000	0.000	0.000
17	B	451	TYR	0	-0.085	-0.062	17.229	0.014	0.014	0.000	0.000	0.000	0.000
18	B	452	LEU	0	0.023	0.023	22.358	-0.012	-0.012	0.000	0.000	0.000	0.000
19	B	453	SER	0	0.019	0.021	24.411	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	454	LYS	1	0.911	0.947	22.839	-0.348	-0.348	0.000	0.000	0.000	0.000
21	B	455	VAL	0	-0.055	-0.023	26.545	0.001	0.001	0.000	0.000	0.000	0.000
22	B	456	SER	0	-0.009	0.004	29.626	0.000	0.000	0.000	0.000	0.000	0.000
23	B	457	ASP	-1	-0.901	-0.962	31.335	0.138	0.138	0.000	0.000	0.000	0.000
24	B	458	ASP	-1	-0.948	-0.962	34.215	0.086	0.086	0.000	0.000	0.000	0.000
25	B	459	PRO	0	-0.044	-0.018	37.988	0.000	0.000	0.000	0.000	0.000	0.000
26	B	460	ASP	-1	-0.950	-0.978	39.611	0.064	0.064	0.000	0.000	0.000	0.000
27	B	461	ASN	0	-0.060	-0.033	41.776	0.001	0.001	0.000	0.000	0.000	0.000
28	B	462	LEU	0	-0.049	-0.013	37.918	0.006	0.006	0.000	0.000	0.000	0.000
29	B	463	GLU	-1	-0.967	-0.980	40.396	0.082	0.082	0.000	0.000	0.000	0.000
30	B	464	ASP	-1	-0.947	-0.996	35.798	0.139	0.139	0.000	0.000	0.000	0.000
31	B	465	VAL	0	-0.055	-0.020	35.399	0.009	0.009	0.000	0.000	0.000	0.000
32	B	466	ASP	-1	-0.905	-0.952	37.803	0.096	0.096	0.000	0.000	0.000	0.000
33	B	467	ASP	-1	-0.964	-1.001	38.293	0.131	0.131	0.000	0.000	0.000	0.000
34	B	468	GLU	-1	-0.981	-0.986	40.896	0.092	0.092	0.000	0.000	0.000	0.000
35	B	469	GLU	-1	-0.985	-1.001	38.914	0.112	0.112	0.000	0.000	0.000	0.000
36	B	470	LEU	0	0.054	0.042	39.536	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	471	ASN	0	-0.030	-0.025	41.619	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	472	ALA	0	-0.017	0.005	44.458	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	473	HIS	0	-0.055	-0.019	39.978	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	474	LEU	0	-0.032	-0.013	45.199	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	475	LEU	0	-0.035	-0.013	48.574	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	476	ASN	0	0.066	0.009	51.477	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	477	GLU	-1	-0.837	-0.922	55.010	0.039	0.039	0.000	0.000	0.000	0.000
44	B	478	GLU	-1	-0.944	-0.978	58.384	0.041	0.041	0.000	0.000	0.000	0.000
45	B	479	ALA	0	-0.012	-0.004	53.936	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	480	SER	0	-0.026	-0.004	54.469	0.000	0.000	0.000	0.000	0.000	0.000
47	B	481	LYS	1	0.917	0.946	55.393	-0.039	-0.039	0.000	0.000	0.000	0.000
48	B	482	LEU	0	-0.007	-0.003	56.076	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	483	LYS	1	0.967	0.988	48.822	-0.054	-0.054	0.000	0.000	0.000	0.000
50	B	484	GLU	-1	-0.916	-0.939	55.082	0.033	0.033	0.000	0.000	0.000	0.000
51	B	485	ARG	1	0.964	0.975	57.186	-0.034	-0.034	0.000	0.000	0.000	0.000
52	B	486	ILE	0	-0.022	-0.012	54.782	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	487	TRP	0	-0.014	-0.014	51.387	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	488	ILE	0	0.022	0.009	55.315	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	489	GLY	0	-0.016	-0.002	58.687	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	490	LEU	0	-0.048	-0.031	52.523	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	491	ASN	0	-0.033	-0.019	52.861	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	492	ALA	0	-0.002	0.006	56.386	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	493	ASP	-1	-0.953	-0.965	56.971	0.017	0.017	0.000	0.000	0.000	0.000
60	B	494	PHE	0	0.088	0.036	54.284	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	495	LEU	0	-0.068	-0.056	57.151	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	496	LEU	0	0.026	0.031	59.767	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	497	GLU	-1	-0.911	-0.955	57.708	0.015	0.015	0.000	0.000	0.000	0.000
64	B	498	GLN	0	-0.092	-0.052	55.866	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	499	GLU	-1	-0.950	-0.975	60.155	0.017	0.017	0.000	0.000	0.000	0.000
66	B	500	SER	0	0.022	0.005	63.584	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	501	LYS	1	0.857	0.933	56.921	-0.017	-0.017	0.000	0.000	0.000	0.000
68	B	502	ARG	1	0.966	0.982	62.621	-0.020	-0.020	0.000	0.000	0.000	0.000
69	B	503	LEU	0	0.070	0.046	64.782	0.000	0.000	0.000	0.000	0.000	0.000
70	B	504	LYS	1	0.886	0.938	64.631	-0.008	-0.008	0.000	0.000	0.000	0.000
71	B	505	GLN	0	-0.061	-0.030	61.324	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	506	GLU	-1	-0.985	-0.963	65.865	0.014	0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:435:GLY)