FMO DATABASE

FMODB ID: 895VY

Calculation Name: 3DEX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DEX

Chain ID: A

ChEMBL ID:

UniProt ID: Q82LK9

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-548553.208952
FMO2-HF: Nuclear repulsion	516579.045712
FMO2-HF: Total energy	-31974.16324
FMO2-MP2: Total energy	-32068.45038

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:11:HIS)

Summations of interaction energy for fragment #1(A:11:HIS)

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.
-26.532	-18.489	14.842	-8.209	-14.677	-0.053

Interaction energy analysis for fragmet #1(A:11:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.005

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	13	HIS	1	0.826	0.914	3.693	-6.994	-3.680	-0.033	-1.866	-1.415	0.002
4	A	14	ARG	1	0.790	0.878	4.830	-0.399	-0.301	-0.001	-0.005	-0.093	0.000
5	A	15	VAL	0	0.021	0.015	7.615	0.238	0.238	0.000	0.000	0.000	0.000
6	A	16	GLN	0	-0.013	-0.004	10.263	-0.233	-0.233	0.000	0.000	0.000	0.000
7	A	17	ILE	0	0.013	0.021	13.505	0.133	0.133	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.831	-0.900	16.211	-0.274	-0.274	0.000	0.000	0.000	0.000
9	A	19	TYR	0	0.022	0.006	19.169	0.033	0.033	0.000	0.000	0.000	0.000
10	A	20	CYS	0	-0.076	-0.003	22.431	0.020	0.020	0.000	0.000	0.000	0.000
11	A	21	THR	0	0.035	0.012	24.844	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	22	GLN	0	0.044	0.024	26.183	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.911	0.956	27.651	0.311	0.311	0.000	0.000	0.000	0.000
14	A	25	TRP	0	-0.033	-0.030	24.243	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.070	0.047	19.626	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	27	PRO	0	0.022	0.013	20.563	-0.062	-0.062	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.949	0.985	20.518	0.298	0.298	0.000	0.000	0.000	0.000
18	A	29	ALA	0	0.042	0.014	18.503	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	30	ALA	0	0.010	0.004	16.210	-0.084	-0.084	0.000	0.000	0.000	0.000
20	A	31	TRP	0	-0.047	-0.023	15.582	-0.108	-0.108	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.021	0.008	15.745	-0.079	-0.079	0.000	0.000	0.000	0.000
22	A	33	ALA	0	0.035	0.001	12.604	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	34	GLN	0	0.012	0.011	11.348	-0.273	-0.273	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.864	-0.918	11.797	-0.929	-0.929	0.000	0.000	0.000	0.000
25	A	36	LEU	0	0.007	0.001	11.133	0.065	0.065	0.000	0.000	0.000	0.000
26	A	37	LEU	0	0.034	0.009	6.159	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	38	THR	0	-0.055	-0.028	7.278	-0.657	-0.657	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.090	-0.053	9.563	0.294	0.294	0.000	0.000	0.000	0.000
29	A	40	PHE	0	-0.011	-0.004	7.461	0.448	0.448	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.937	-0.960	4.173	-5.152	-4.808	-0.001	-0.055	-0.289	0.000
31	A	42	THR	0	-0.007	-0.008	2.195	-13.885	-13.758	6.705	-3.042	-3.789	-0.021
32	A	43	GLU	-1	-0.873	-0.936	2.434	4.297	6.020	2.270	-0.861	-3.132	-0.010
33	A	44	LEU	0	-0.051	-0.028	2.983	0.818	1.902	0.663	-0.531	-1.216	-0.007
34	A	45	THR	0	-0.004	-0.010	2.195	-7.343	-5.188	5.186	-3.027	-4.314	-0.016
35	A	46	GLU	-1	-0.861	-0.915	3.171	-0.842	-1.644	0.053	1.178	-0.429	-0.001
36	A	47	LEU	0	-0.017	-0.007	5.642	0.684	0.684	0.000	0.000	0.000	0.000
37	A	48	ALA	0	-0.003	0.014	8.831	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	49	LEU	0	-0.007	-0.014	11.928	0.102	0.102	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.885	0.939	15.450	0.370	0.370	0.000	0.000	0.000	0.000
40	A	51	PRO	0	-0.012	-0.006	18.678	0.030	0.030	0.000	0.000	0.000	0.000
41	A	52	GLY	0	0.060	0.031	22.225	0.027	0.027	0.000	0.000	0.000	0.000
42	A	53	THR	0	-0.005	-0.013	24.567	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.068	-0.002	28.359	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	55	GLY	0	-0.002	0.003	29.837	0.012	0.012	0.000	0.000	0.000	0.000
45	A	56	VAL	0	0.026	0.012	23.727	0.001	0.001	0.000	0.000	0.000	0.000
46	A	57	PHE	0	-0.007	-0.026	19.534	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	58	VAL	0	-0.023	0.002	20.007	0.029	0.029	0.000	0.000	0.000	0.000
48	A	59	VAL	0	0.025	0.012	15.105	-0.072	-0.072	0.000	0.000	0.000	0.000
49	A	60	ARG	1	0.854	0.897	15.249	0.235	0.235	0.000	0.000	0.000	0.000
50	A	61	VAL	0	0.018	-0.004	10.125	-0.155	-0.155	0.000	0.000	0.000	0.000
51	A	62	ASP	-1	-0.753	-0.860	8.859	1.145	1.145	0.000	0.000	0.000	0.000
52	A	63	ASP	-1	-0.859	-0.928	11.519	-0.120	-0.120	0.000	0.000	0.000	0.000
53	A	64	GLU	-1	-0.812	-0.853	14.789	0.320	0.320	0.000	0.000	0.000	0.000
54	A	65	VAL	0	-0.055	-0.029	16.059	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	66	VAL	0	-0.008	-0.001	14.946	0.046	0.046	0.000	0.000	0.000	0.000
56	A	67	TRP	0	0.012	-0.016	18.081	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	68	ASP	-1	-0.779	-0.868	20.389	-0.159	-0.159	0.000	0.000	0.000	0.000
58	A	69	ARG	1	0.905	0.948	23.464	0.184	0.184	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.621	0.774	25.939	0.071	0.071	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.849	-0.907	26.259	0.001	0.001	0.000	0.000	0.000	0.000
61	A	72	GLN	0	0.034	0.019	21.612	0.005	0.005	0.000	0.000	0.000	0.000
62	A	73	GLY	0	0.012	0.030	26.578	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	74	PHE	0	-0.037	-0.032	23.484	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	75	PRO	0	0.002	0.013	20.445	0.023	0.023	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.755	-0.866	21.641	-0.284	-0.284	0.000	0.000	0.000	0.000
66	A	77	PRO	0	0.034	0.019	18.643	0.021	0.021	0.000	0.000	0.000	0.000
67	A	78	THR	0	0.013	-0.023	18.189	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	79	ALA	0	-0.071	-0.029	19.630	0.058	0.058	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.007	0.005	16.510	0.048	0.048	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.859	0.929	13.809	0.806	0.806	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.853	0.925	15.248	0.139	0.139	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.027	0.013	16.447	0.086	0.086	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.011	-0.005	11.093	0.064	0.064	0.000	0.000	0.000	0.000
74	A	85	ARG	1	0.910	0.932	12.131	-0.149	-0.149	0.000	0.000	0.000	0.000
75	A	86	ASP	-1	-0.882	-0.924	13.075	0.579	0.579	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.758	0.862	12.033	-0.354	-0.354	0.000	0.000	0.000	0.000
77	A	88	VAL	0	-0.053	-0.022	7.220	0.341	0.341	0.000	0.000	0.000	0.000
78	A	89	ALA	0	-0.017	0.003	10.197	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:HIS)