FMO DATABASE

FMODB ID: VQ6L1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-498907.840828
FMO2-HF: Nuclear repulsion	467929.062695
FMO2-HF: Total energy	-30978.778133
FMO2-MP2: Total energy	-31070.434613

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.
-262.696	-259.632	27.34	-11.234	-19.167	-0.108

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 : 0.943 / q_NPA : 0.968

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	3.343	-0.780	0.989	0.006	-0.680	-1.095	0.001
4	A	10	GLU	-1	-0.940	-0.966	2.698	-68.335	-65.133	0.289	-1.348	-2.143	-0.008
5	A	11	LEU	0	-0.060	-0.040	2.139	0.827	1.860	5.061	-1.487	-4.606	0.000
6	A	12	ASP	-1	-0.933	-0.964	4.728	-22.046	-21.820	-0.001	-0.022	-0.204	0.000
7	A	13	GLY	0	0.013	0.011	7.230	3.443	3.443	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.027	-0.020	4.842	2.978	2.978	0.000	0.000	0.000	0.000
9	A	15	LEU	0	-0.001	-0.008	8.075	2.623	2.623	0.000	0.000	0.000	0.000
10	A	16	MET	0	0.021	0.019	10.575	3.046	3.046	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.027	-0.007	10.002	-0.681	-0.681	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.009	-0.019	9.676	1.544	1.544	0.000	0.000	0.000	0.000
13	A	19	LEU	0	0.002	-0.007	13.939	1.336	1.336	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.011	0.011	15.957	1.422	1.422	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.915	-0.959	14.853	-18.375	-18.375	0.000	0.000	0.000	0.000
16	A	22	ALA	0	-0.086	-0.064	16.318	-0.081	-0.081	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.980	-0.980	18.468	-12.813	-12.813	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.027	0.014	16.091	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.065	-0.036	18.789	0.293	0.293	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.870	0.950	20.602	12.200	12.200	0.000	0.000	0.000	0.000
21	A	27	GLU	-1	-0.894	-0.957	20.797	-13.739	-13.739	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.055	-0.012	16.219	-0.147	-0.147	0.000	0.000	0.000	0.000
23	A	29	PRO	0	-0.017	-0.011	20.608	0.529	0.529	0.000	0.000	0.000	0.000
24	A	30	PRO	0	-0.012	0.001	21.670	-0.405	-0.405	0.000	0.000	0.000	0.000
25	A	31	THR	0	-0.012	-0.014	21.949	-0.086	-0.086	0.000	0.000	0.000	0.000
26	A	32	TYR	0	-0.017	-0.019	15.731	-0.210	-0.210	0.000	0.000	0.000	0.000
27	A	33	ARG	1	0.949	0.967	16.296	13.798	13.798	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.026	0.012	10.029	0.155	0.155	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.019	0.031	11.403	-0.756	-0.756	0.000	0.000	0.000	0.000
30	A	36	LEU	0	0.015	-0.005	5.501	0.319	0.319	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.017	-0.005	7.539	-1.028	-1.028	0.000	0.000	0.000	0.000
32	A	38	PRO	0	0.024	0.018	4.307	1.426	1.608	-0.001	-0.015	-0.165	0.000
33	A	39	LEU	0	-0.002	-0.004	6.620	1.359	1.359	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.875	-0.929	4.938	-45.568	-45.514	-0.001	-0.002	-0.051	0.000
35	A	41	GLU	-1	-0.869	-0.952	1.974	-118.402	-123.241	20.350	-7.229	-8.282	-0.100
36	A	42	PRO	0	0.004	0.004	5.881	1.112	1.112	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.938	-0.975	6.919	-24.108	-24.108	0.000	0.000	0.000	0.000
38	A	44	VAL	0	-0.013	-0.006	2.458	0.111	1.300	1.031	-0.452	-1.767	-0.003
39	A	45	ALA	0	-0.022	-0.017	5.130	2.563	2.571	-0.001	-0.002	-0.004	0.000
40	A	46	ALA	0	0.025	0.004	8.021	2.452	2.452	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.018	0.004	7.121	2.315	2.315	0.000	0.000	0.000	0.000
42	A	48	ALA	0	-0.011	0.001	7.400	1.423	1.423	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.009	-0.002	9.061	1.285	1.285	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.002	0.002	12.067	1.301	1.301	0.000	0.000	0.000	0.000
45	A	51	TRP	0	-0.028	-0.023	9.353	0.796	0.796	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.037	-0.009	12.978	0.791	0.791	0.000	0.000	0.000	0.000
47	A	53	MET	0	-0.083	-0.020	15.248	0.664	0.664	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.930	-0.952	14.628	-14.707	-14.707	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.014	-0.016	18.196	0.349	0.349	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.123	-0.046	19.793	-0.211	-0.211	0.000	0.000	0.000	0.000
51	A	57	ASN	0	0.021	-0.030	22.241	0.571	0.571	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.066	0.021	25.968	0.065	0.065	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.871	-0.957	25.719	-9.970	-9.970	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.025	-0.005	24.689	-0.318	-0.318	0.000	0.000	0.000	0.000
55	A	61	TRP	0	-0.069	-0.044	19.972	0.036	0.036	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.010	0.018	20.814	-0.388	-0.388	0.000	0.000	0.000	0.000
57	A	63	SER	0	0.080	0.040	17.265	-0.541	-0.541	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.005	0.006	14.797	0.513	0.513	0.000	0.000	0.000	0.000
59	A	65	TYR	0	-0.037	-0.018	13.307	-1.272	-1.272	0.000	0.000	0.000	0.000
60	A	66	ALA	0	0.039	0.007	9.750	0.772	0.772	0.000	0.000	0.000	0.000
61	A	67	LEU	0	-0.032	-0.011	9.841	-2.279	-2.279	0.000	0.000	0.000	0.000
62	A	68	PHE	0	0.030	-0.002	5.919	0.667	0.667	0.000	0.000	0.000	0.000
63	A	69	LEU	0	0.010	-0.009	7.282	1.743	1.743	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.045	-0.021	5.065	-2.265	-2.265	0.000	0.000	0.000	0.000
65	A	71	GLY	0	0.023	0.011	2.935	-0.332	0.093	0.596	-0.423	-0.598	0.001
66	A	72	ARG	1	0.875	0.959	3.634	35.105	34.920	0.011	0.426	-0.252	0.001
67	A	73	PRO	0	0.003	0.016	6.985	0.233	0.233	0.000	0.000	0.000	0.000
68	A	74	ILE	0	-0.023	-0.017	10.077	1.820	1.820	0.000	0.000	0.000	0.000
69	A	75	ARG	1	0.909	0.944	12.867	19.924	19.924	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.052	0.041	13.634	-1.365	-1.365	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.069	-0.031	16.115	1.076	1.076	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.021	0.004	18.018	-0.377	-0.377	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.048	-0.011	19.095	0.467	0.467	0.000	0.000	0.000	0.000
74	A	80	GLY	0	-0.029	0.011	21.786	0.380	0.380	0.000	0.000	0.000	0.000
75	A	81	LYN	0	-0.012	-0.024	24.820	0.222	0.222	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.856	-0.920	19.652	-14.551	-14.551	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.013	-0.033	23.266	0.587	0.587	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.866	-0.923	21.568	-13.632	-13.632	0.000	0.000	0.000	0.000
79	A	85	VAL	0	-0.050	-0.035	23.449	0.576	0.576	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.022	0.000	23.855	-0.111	-0.111	0.000	0.000	0.000	0.000

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