FMO DATABASE

FMODB ID: G5621

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

Total energy (hartree)

FMO2-HF: Electronic energy	-548460.037566
FMO2-HF: Nuclear repulsion	516486.26382
FMO2-HF: Total energy	-31973.773746
FMO2-MP2: Total energy	-32068.064984

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.
-13.027	-6.924	12.564	-5.972	-12.693	-0.028

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 : -0.004 / q_NPA : 0.016

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	0.844	0.924	3.690	-6.938	-3.262	-0.037	-1.993	-1.646	0.003
4	A	14	ARG	1	0.877	0.934	5.178	0.028	0.112	-0.001	-0.004	-0.079	0.000
5	A	15	VAL	0	0.006	0.010	7.895	0.184	0.184	0.000	0.000	0.000	0.000
6	A	16	GLN	0	-0.018	-0.010	10.522	-0.270	-0.270	0.000	0.000	0.000	0.000
7	A	17	ILE	0	0.013	0.007	13.814	0.107	0.107	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.884	-0.918	16.602	-0.267	-0.267	0.000	0.000	0.000	0.000
9	A	19	TYR	0	0.027	0.017	19.280	0.030	0.030	0.000	0.000	0.000	0.000
10	A	20	CYS	0	-0.097	0.009	22.301	0.020	0.020	0.000	0.000	0.000	0.000
11	A	21	THR	0	0.040	0.007	25.011	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	22	GLN	0	0.041	0.007	26.217	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.950	0.976	27.560	0.326	0.326	0.000	0.000	0.000	0.000
14	A	25	TRP	0	-0.026	-0.025	24.409	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.068	0.042	19.615	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	27	PRO	0	0.024	0.010	20.579	-0.057	-0.057	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.950	0.985	20.573	0.285	0.285	0.000	0.000	0.000	0.000
18	A	29	ALA	0	0.045	0.020	18.782	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	30	ALA	0	-0.004	-0.008	16.298	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	31	TRP	0	-0.048	-0.027	15.641	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.032	0.013	15.876	-0.071	-0.071	0.000	0.000	0.000	0.000
22	A	33	ALA	0	0.031	0.009	12.463	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	34	GLN	0	0.017	0.016	11.370	-0.233	-0.233	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.862	-0.917	11.942	-0.790	-0.790	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.004	-0.021	11.450	0.012	0.012	0.000	0.000	0.000	0.000
26	A	37	LEU	0	-0.007	-0.004	6.096	0.078	0.078	0.000	0.000	0.000	0.000
27	A	38	THR	0	-0.033	-0.005	7.388	-0.656	-0.656	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.096	-0.055	9.584	0.113	0.113	0.000	0.000	0.000	0.000
29	A	40	PHE	0	-0.009	-0.011	7.447	0.246	0.246	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.942	-0.952	4.345	-5.268	-4.887	-0.001	-0.041	-0.339	0.000
31	A	42	THR	0	-0.013	-0.013	2.410	-7.458	-6.130	2.373	-1.550	-2.151	-0.012
32	A	43	GLU	-1	-0.887	-0.947	3.107	7.828	9.628	0.249	-0.473	-1.576	-0.004
33	A	44	LEU	0	-0.067	-0.045	3.161	-0.865	0.338	0.246	-0.601	-0.847	-0.005
34	A	45	THR	0	-0.005	-0.011	1.911	-2.799	-1.871	9.672	-5.285	-5.315	-0.004
35	A	46	GLU	-1	-0.871	-0.923	2.713	-0.462	-3.759	0.063	3.975	-0.740	-0.006
36	A	47	LEU	0	-0.002	0.003	5.581	0.841	0.841	0.000	0.000	0.000	0.000
37	A	48	ALA	0	-0.002	0.005	9.013	-0.097	-0.097	0.000	0.000	0.000	0.000
38	A	49	LEU	0	-0.003	-0.006	12.065	0.152	0.152	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.926	0.960	15.574	0.331	0.331	0.000	0.000	0.000	0.000
40	A	51	PRO	0	-0.019	-0.012	18.431	0.042	0.042	0.000	0.000	0.000	0.000
41	A	52	GLY	0	0.068	0.033	21.911	0.029	0.029	0.000	0.000	0.000	0.000
42	A	53	THR	0	-0.004	-0.026	24.376	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.045	0.010	28.141	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	55	GLY	0	-0.004	-0.025	29.672	0.013	0.013	0.000	0.000	0.000	0.000
45	A	56	VAL	0	-0.024	-0.006	23.871	0.008	0.008	0.000	0.000	0.000	0.000
46	A	57	PHE	0	0.013	-0.028	19.977	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	58	VAL	0	-0.021	0.002	19.820	0.026	0.026	0.000	0.000	0.000	0.000
48	A	59	VAL	0	0.025	0.019	15.063	-0.069	-0.069	0.000	0.000	0.000	0.000
49	A	60	ARG	1	0.868	0.906	15.379	0.181	0.181	0.000	0.000	0.000	0.000
50	A	61	VAL	0	0.040	0.010	10.159	-0.127	-0.127	0.000	0.000	0.000	0.000
51	A	62	ASP	-1	-0.742	-0.850	9.069	1.125	1.125	0.000	0.000	0.000	0.000
52	A	63	ASP	-1	-0.960	-0.979	11.925	0.089	0.089	0.000	0.000	0.000	0.000
53	A	64	GLU	-1	-0.848	-0.888	14.934	0.415	0.415	0.000	0.000	0.000	0.000
54	A	65	VAL	0	-0.085	-0.039	16.194	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	66	VAL	0	0.003	0.004	15.064	0.032	0.032	0.000	0.000	0.000	0.000
56	A	67	TRP	0	0.000	-0.022	18.178	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	68	ASP	-1	-0.807	-0.898	20.514	-0.126	-0.126	0.000	0.000	0.000	0.000
58	A	69	ARG	1	0.989	0.998	23.595	0.164	0.164	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.708	0.855	25.967	0.047	0.047	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.919	-0.961	26.499	0.031	0.031	0.000	0.000	0.000	0.000
61	A	72	GLN	0	0.038	0.024	21.988	0.008	0.008	0.000	0.000	0.000	0.000
62	A	73	GLY	0	-0.005	0.014	26.805	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	74	PHE	0	-0.048	-0.041	23.690	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	75	PRO	0	0.012	0.016	20.514	0.025	0.025	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.759	-0.860	21.666	-0.219	-0.219	0.000	0.000	0.000	0.000
66	A	77	PRO	0	0.041	0.023	19.222	0.022	0.022	0.000	0.000	0.000	0.000
67	A	78	THR	0	-0.028	-0.038	18.689	0.016	0.016	0.000	0.000	0.000	0.000
68	A	79	ALA	0	-0.077	-0.046	19.366	0.056	0.056	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.019	0.003	16.633	0.053	0.053	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.894	0.947	14.496	0.581	0.581	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.906	0.956	14.853	0.045	0.045	0.000	0.000	0.000	0.000
72	A	83	LEU	0	-0.008	0.000	16.517	0.086	0.086	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.006	-0.004	10.957	0.065	0.065	0.000	0.000	0.000	0.000
74	A	85	ARG	1	0.934	0.952	11.763	-0.318	-0.318	0.000	0.000	0.000	0.000
75	A	86	ASP	-1	-0.885	-0.913	12.620	0.672	0.672	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.766	0.859	12.061	-0.407	-0.407	0.000	0.000	0.000	0.000
77	A	88	VAL	0	-0.073	-0.043	6.661	0.277	0.277	0.000	0.000	0.000	0.000
78	A	89	ALA	0	-0.008	0.016	10.004	0.169	0.169	0.000	0.000	0.000	0.000

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