FMO DATABASE

FMODB ID: 1N3KZ

Calculation Name: 2DBS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SGN2

Base Structure: X-ray

Registration Date: 2023-09-23

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-498029.727205
FMO2-HF: Nuclear repulsion	467050.110507
FMO2-HF: Total energy	-30979.616698
FMO2-MP2: Total energy	-31071.155163

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-314.488	-316.737	49.566	-22.255	-25.063	-0.254

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.843

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	A	9	ALA	0	0.043	0.028	3.238	-0.962	0.864	0.007	-0.738	-1.095	0.001
4	A	10	GLU	-1	-0.826	-0.879	1.717	-132.764	-137.651	27.639	-12.325	-10.428	-0.152
5	A	11	LEU	0	-0.031	-0.026	2.230	2.305	3.757	3.589	-1.124	-3.917	0.002
6	A	12	ASP	-1	-0.889	-0.948	5.034	-22.385	-22.205	-0.001	-0.010	-0.169	0.000
7	A	13	GLY	0	-0.022	-0.005	7.368	3.484	3.484	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.024	-0.023	4.886	3.184	3.184	0.000	0.000	0.000	0.000
9	A	15	LEU	0	0.002	-0.001	8.145	2.698	2.698	0.000	0.000	0.000	0.000
10	A	16	MET	0	0.015	0.006	10.897	3.030	3.030	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.066	-0.032	10.289	-0.598	-0.598	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.011	-0.019	10.319	1.370	1.370	0.000	0.000	0.000	0.000
13	A	19	LEU	0	-0.001	-0.003	14.230	1.369	1.369	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.014	0.021	16.261	1.429	1.429	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.891	-0.931	14.883	-18.668	-18.668	0.000	0.000	0.000	0.000
16	A	22	ALA	0	-0.084	-0.065	16.662	-0.063	-0.063	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.911	-0.938	18.763	-12.722	-12.722	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.038	0.015	16.572	0.024	0.024	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.079	-0.034	19.121	0.280	0.280	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.777	0.893	21.088	12.432	12.432	0.000	0.000	0.000	0.000
21	A	27	GLU	-1	-0.885	-0.953	21.186	-13.965	-13.965	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.043	-0.006	16.699	-0.141	-0.141	0.000	0.000	0.000	0.000
23	A	29	PRO	0	-0.016	-0.004	21.007	0.572	0.572	0.000	0.000	0.000	0.000
24	A	30	PRO	0	-0.018	-0.014	22.344	-0.391	-0.391	0.000	0.000	0.000	0.000
25	A	31	THR	0	-0.025	-0.009	22.312	-0.115	-0.115	0.000	0.000	0.000	0.000
26	A	32	TYR	0	-0.008	-0.016	16.052	-0.148	-0.148	0.000	0.000	0.000	0.000
27	A	33	ARG	1	0.887	0.926	16.497	13.794	13.794	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.008	0.006	10.809	0.308	0.308	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.018	0.022	11.967	-0.744	-0.744	0.000	0.000	0.000	0.000
30	A	36	LEU	0	0.009	0.005	5.919	0.183	0.183	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.033	0.003	8.205	-0.814	-0.814	0.000	0.000	0.000	0.000
32	A	38	PRO	0	0.014	0.002	4.493	1.353	1.490	-0.001	-0.009	-0.128	0.000
33	A	39	LEU	0	-0.008	-0.003	7.045	1.309	1.309	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.823	-0.897	5.860	-40.520	-40.520	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.878	-0.934	1.864	-115.532	-118.334	17.216	-7.293	-7.120	-0.102
36	A	42	PRO	0	0.016	0.001	6.093	0.924	0.924	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.942	-0.968	7.016	-23.276	-23.276	0.000	0.000	0.000	0.000
38	A	44	VAL	0	-0.002	-0.007	2.455	0.474	1.530	0.903	-0.432	-1.527	-0.003
39	A	45	ALA	0	-0.011	-0.008	5.165	2.199	2.203	-0.001	-0.001	-0.001	0.000
40	A	46	ALA	0	0.012	0.000	7.999	2.196	2.196	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.011	0.001	7.165	2.275	2.275	0.000	0.000	0.000	0.000
42	A	48	ALA	0	-0.009	0.002	7.325	1.248	1.248	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.001	0.000	9.062	1.146	1.146	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.000	0.003	12.095	1.213	1.213	0.000	0.000	0.000	0.000
45	A	51	TRP	0	0.000	-0.015	9.173	0.825	0.825	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.037	-0.010	12.978	0.748	0.748	0.000	0.000	0.000	0.000
47	A	53	MET	0	-0.089	-0.025	15.244	0.683	0.683	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.955	-0.962	14.655	-14.287	-14.287	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.037	0.004	18.174	0.336	0.336	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.088	-0.017	19.663	-0.270	-0.270	0.000	0.000	0.000	0.000
51	A	57	ASN	0	0.033	-0.022	22.108	0.507	0.507	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.049	0.021	25.845	0.070	0.070	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.908	-0.978	26.119	-9.836	-9.836	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.024	0.000	24.708	-0.307	-0.307	0.000	0.000	0.000	0.000
55	A	61	TRP	0	-0.069	-0.051	19.703	0.025	0.025	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.018	0.023	21.282	-0.355	-0.355	0.000	0.000	0.000	0.000
57	A	63	SER	0	0.029	0.007	17.769	-0.546	-0.546	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.010	0.003	15.651	0.470	0.470	0.000	0.000	0.000	0.000
59	A	65	TYR	0	-0.023	-0.022	13.958	-1.361	-1.361	0.000	0.000	0.000	0.000
60	A	66	ALA	0	0.027	0.006	10.730	0.623	0.623	0.000	0.000	0.000	0.000
61	A	67	LEU	0	-0.032	-0.012	10.330	-2.087	-2.087	0.000	0.000	0.000	0.000
62	A	68	PHE	0	0.052	0.007	5.408	0.575	0.575	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.007	-0.008	6.979	1.863	1.863	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.073	-0.050	4.988	0.512	0.512	0.000	0.000	0.000	0.000
65	A	71	GLY	0	0.027	0.014	2.709	-1.561	-0.965	0.212	-0.342	-0.466	0.000
66	A	72	ARG	1	0.845	0.937	3.434	36.645	36.834	0.003	0.019	-0.212	0.000
67	A	73	PRO	0	0.018	0.027	6.883	0.501	0.501	0.000	0.000	0.000	0.000
68	A	74	ILE	0	-0.039	-0.035	10.114	1.760	1.760	0.000	0.000	0.000	0.000
69	A	75	ARG	1	0.909	0.946	12.399	19.504	19.504	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.057	0.040	13.892	-1.313	-1.313	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.067	-0.026	16.578	1.050	1.050	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.023	0.006	18.623	-0.403	-0.403	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.021	-0.005	19.476	0.519	0.519	0.000	0.000	0.000	0.000
74	A	80	GLY	0	-0.023	0.013	22.444	0.369	0.369	0.000	0.000	0.000	0.000
75	A	81	LYN	0	-0.020	-0.033	25.468	0.219	0.219	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.821	-0.877	19.586	-14.839	-14.839	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.030	-0.038	23.545	0.569	0.569	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.834	-0.905	22.021	-13.120	-13.120	0.000	0.000	0.000	0.000
79	A	85	VAL	0	-0.070	-0.042	23.542	0.569	0.569	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.018	-0.001	23.865	-0.136	-0.136	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)