FMO DATABASE

FMODB ID: 66VVZ

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:

Apendix: None

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-314943.744841
FMO2-HF: Nuclear repulsion	285852.02942
FMO2-HF: Total energy	-29091.715421
FMO2-MP2: Total energy	-29177.040312

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.
-27.248	-31.267	16.515	-6.729	-5.768	0.026

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 : 0.047 / q_NPA : 0.036

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	B	437	TYR	0	0.022	0.009	3.494	0.962	3.082	-0.001	-1.132	-0.988	0.001
4	B	438	CYS	0	-0.016	0.007	4.163	0.053	0.163	-0.001	-0.020	-0.089	0.000
5	B	439	PRO	0	0.027	0.010	3.494	-2.634	-2.078	0.028	-0.313	-0.271	-0.002
6	B	440	ARG	1	0.917	0.924	1.896	-26.696	-33.561	16.478	-5.235	-4.378	0.027
7	B	441	ASN	0	0.016	0.006	3.702	-1.134	-1.074	0.011	-0.029	-0.042	0.000
8	B	442	LEU	0	0.032	0.006	7.094	0.485	0.485	0.000	0.000	0.000	0.000
9	B	443	HIS	0	0.024	0.017	9.775	0.101	0.101	0.000	0.000	0.000	0.000
10	B	444	LEU	0	-0.048	-0.014	8.057	0.004	0.004	0.000	0.000	0.000	0.000
11	B	445	LEU	0	-0.032	-0.023	7.325	0.772	0.772	0.000	0.000	0.000	0.000
12	B	446	PRO	0	0.014	0.010	10.808	-0.198	-0.198	0.000	0.000	0.000	0.000
13	B	447	THR	0	0.017	0.013	14.133	-0.016	-0.016	0.000	0.000	0.000	0.000
14	B	448	THR	0	0.055	0.014	16.793	0.007	0.007	0.000	0.000	0.000	0.000
15	B	449	ASP	-1	-0.815	-0.896	19.910	0.341	0.341	0.000	0.000	0.000	0.000
16	B	450	THR	0	-0.074	-0.025	18.551	0.020	0.020	0.000	0.000	0.000	0.000
17	B	451	TYR	0	-0.067	-0.050	17.652	0.009	0.009	0.000	0.000	0.000	0.000
18	B	452	LEU	0	0.015	0.022	22.487	-0.025	-0.025	0.000	0.000	0.000	0.000
19	B	453	SER	0	-0.003	-0.017	24.003	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	454	LYS	1	0.837	0.916	21.772	-0.474	-0.474	0.000	0.000	0.000	0.000
21	B	455	VAL	0	-0.019	-0.013	26.602	0.000	0.000	0.000	0.000	0.000	0.000
22	B	456	SER	0	-0.007	-0.025	29.769	0.007	0.007	0.000	0.000	0.000	0.000
23	B	457	ASP	-1	-0.952	-0.974	31.400	0.212	0.212	0.000	0.000	0.000	0.000
24	B	458	ASP	-1	-0.904	-0.941	33.978	0.126	0.126	0.000	0.000	0.000	0.000
25	B	459	PRO	0	-0.059	-0.027	37.784	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	460	ASP	-1	-0.947	-0.974	39.680	0.097	0.097	0.000	0.000	0.000	0.000
27	B	461	ASN	0	-0.126	-0.075	41.707	0.000	0.000	0.000	0.000	0.000	0.000
28	B	462	LEU	0	-0.032	-0.004	37.699	0.007	0.007	0.000	0.000	0.000	0.000
29	B	463	GLU	-1	-0.930	-0.963	40.267	0.106	0.106	0.000	0.000	0.000	0.000
30	B	464	ASP	-1	-0.900	-0.934	35.910	0.177	0.177	0.000	0.000	0.000	0.000
31	B	465	VAL	0	-0.054	-0.034	35.217	0.011	0.011	0.000	0.000	0.000	0.000
32	B	466	ASP	-1	-0.874	-0.910	37.799	0.118	0.118	0.000	0.000	0.000	0.000
33	B	467	ASP	-1	-0.880	-0.946	37.480	0.148	0.148	0.000	0.000	0.000	0.000
34	B	468	GLU	-1	-0.979	-0.992	40.395	0.105	0.105	0.000	0.000	0.000	0.000
35	B	469	GLU	-1	-0.959	-0.977	38.918	0.117	0.117	0.000	0.000	0.000	0.000
36	B	470	LEU	0	0.022	0.016	38.476	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	471	ASN	0	-0.086	-0.075	41.359	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	472	ALA	0	-0.020	-0.004	44.394	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	473	HIS	0	-0.118	-0.058	38.808	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	474	LEU	0	-0.057	-0.010	44.534	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	475	LEU	0	-0.041	-0.016	47.888	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	476	ASN	0	0.063	0.025	50.751	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	477	GLU	-1	-0.761	-0.884	54.380	0.048	0.048	0.000	0.000	0.000	0.000
44	B	478	GLU	-1	-0.957	-0.963	57.682	0.047	0.047	0.000	0.000	0.000	0.000
45	B	479	ALA	0	0.029	0.002	53.266	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	480	SER	0	0.009	0.010	54.051	0.000	0.000	0.000	0.000	0.000	0.000
47	B	481	LYS	1	0.853	0.901	55.010	-0.048	-0.048	0.000	0.000	0.000	0.000
48	B	482	LEU	0	-0.038	-0.010	55.582	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	483	LYS	1	0.970	0.979	48.131	-0.064	-0.064	0.000	0.000	0.000	0.000
50	B	484	GLU	-1	-0.921	-0.960	54.434	0.042	0.042	0.000	0.000	0.000	0.000
51	B	485	ARG	1	0.940	0.969	56.685	-0.037	-0.037	0.000	0.000	0.000	0.000
52	B	486	ILE	0	-0.012	-0.008	54.028	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	487	TRP	0	0.004	0.010	50.979	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	488	ILE	0	0.033	0.007	55.011	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	489	GLY	0	-0.033	-0.014	58.470	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	490	LEU	0	-0.052	-0.033	52.236	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	491	ASN	0	-0.049	-0.024	52.607	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	492	ALA	0	0.013	0.005	56.075	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	493	ASP	-1	-0.930	-0.958	56.941	0.020	0.020	0.000	0.000	0.000	0.000
60	B	494	PHE	0	0.079	0.030	53.132	0.000	0.000	0.000	0.000	0.000	0.000
61	B	495	LEU	0	-0.039	-0.026	56.854	0.000	0.000	0.000	0.000	0.000	0.000
62	B	496	LEU	0	0.021	0.026	59.422	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	497	GLU	-1	-0.909	-0.953	56.427	0.020	0.020	0.000	0.000	0.000	0.000
64	B	498	GLN	0	-0.039	-0.007	55.337	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	499	GLU	-1	-0.941	-0.968	59.867	0.023	0.023	0.000	0.000	0.000	0.000
66	B	500	SER	0	-0.010	-0.007	63.165	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	501	LYS	1	0.844	0.904	56.761	-0.025	-0.025	0.000	0.000	0.000	0.000
68	B	502	ARG	1	0.899	0.946	62.270	-0.026	-0.026	0.000	0.000	0.000	0.000
69	B	503	LEU	0	0.030	0.013	64.169	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	504	LYS	1	0.882	0.945	64.212	-0.015	-0.015	0.000	0.000	0.000	0.000
71	B	505	GLN	0	-0.073	-0.033	60.723	0.000	0.000	0.000	0.000	0.000	0.000
72	B	506	GLU	-1	-0.916	-0.932	65.545	0.022	0.022	0.000	0.000	0.000	0.000

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