FMO DATABASE

FMODB ID: 1N7LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-548491.449982
FMO2-HF: Nuclear repulsion	516518.270253
FMO2-HF: Total energy	-31973.179729
FMO2-MP2: Total energy	-32067.543475

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.
-7.253	-5.828	16.818	-4.934	-13.308	-0.016

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 : 0.010 / q_NPA : 0.021

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	0.849	0.927	3.636	-7.508	-3.631	-0.042	-2.103	-1.732	0.003
4	A	14	ARG	1	0.973	1.002	5.041	-0.264	-0.192	-0.001	-0.004	-0.066	0.000
5	A	15	VAL	0	0.015	0.020	7.498	0.035	0.035	0.000	0.000	0.000	0.000
6	A	16	GLN	0	-0.033	-0.017	10.255	-0.254	-0.254	0.000	0.000	0.000	0.000
7	A	17	ILE	0	0.018	0.011	13.343	0.059	0.059	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.936	-0.969	16.442	-0.057	-0.057	0.000	0.000	0.000	0.000
9	A	19	TYR	0	0.032	0.021	19.695	0.023	0.023	0.000	0.000	0.000	0.000
10	A	20	CYS	0	-0.100	-0.003	22.456	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	21	THR	0	0.017	0.015	25.585	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	22	GLN	0	0.047	0.002	26.763	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.960	0.981	28.396	0.196	0.196	0.000	0.000	0.000	0.000
14	A	25	TRP	0	-0.024	-0.022	24.714	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.067	0.036	20.730	0.003	0.003	0.000	0.000	0.000	0.000
16	A	27	PRO	0	0.008	0.006	21.693	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.966	0.989	21.713	0.109	0.109	0.000	0.000	0.000	0.000
18	A	29	ALA	0	0.035	0.015	19.177	0.012	0.012	0.000	0.000	0.000	0.000
19	A	30	ALA	0	-0.006	-0.009	17.421	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	31	TRP	0	-0.041	-0.012	16.785	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.048	0.012	16.330	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	33	ALA	0	0.015	0.005	13.625	0.029	0.029	0.000	0.000	0.000	0.000
23	A	34	GLN	0	0.017	0.015	12.386	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.930	-0.969	12.498	-0.387	-0.387	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.014	-0.032	11.541	0.024	0.024	0.000	0.000	0.000	0.000
26	A	37	LEU	0	0.004	-0.003	7.174	0.182	0.182	0.000	0.000	0.000	0.000
27	A	38	THR	0	-0.063	-0.012	7.591	-0.466	-0.466	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.055	-0.029	9.352	0.007	0.007	0.000	0.000	0.000	0.000
29	A	40	PHE	0	-0.031	-0.020	7.363	0.042	0.042	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.959	-0.968	3.787	-5.682	-5.030	0.002	-0.226	-0.428	-0.001
31	A	42	THR	0	0.018	0.003	2.364	-4.688	-3.829	3.343	-1.665	-2.538	-0.014
32	A	43	GLU	-1	-0.890	-0.942	2.953	7.966	10.021	0.628	-0.654	-2.029	-0.005
33	A	44	LEU	0	-0.070	-0.050	3.135	-2.340	-0.770	0.287	-0.797	-1.059	-0.006
34	A	45	THR	0	-0.055	-0.014	1.794	-4.462	-2.521	12.608	-9.571	-4.978	0.011
35	A	46	GLU	-1	-0.903	-0.972	2.398	7.035	-2.566	-0.007	10.086	-0.478	-0.004
36	A	47	LEU	0	-0.005	0.008	5.980	0.496	0.496	0.000	0.000	0.000	0.000
37	A	48	ALA	0	-0.013	-0.008	9.300	-0.185	-0.185	0.000	0.000	0.000	0.000
38	A	49	LEU	0	0.004	-0.002	12.434	0.109	0.109	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.931	0.958	16.079	0.065	0.065	0.000	0.000	0.000	0.000
40	A	51	PRO	0	-0.045	-0.024	18.667	0.031	0.031	0.000	0.000	0.000	0.000
41	A	52	GLY	0	0.088	0.042	22.305	0.021	0.021	0.000	0.000	0.000	0.000
42	A	53	THR	0	0.010	-0.016	24.440	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.034	0.003	28.133	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	55	GLY	0	-0.004	-0.023	29.548	0.012	0.012	0.000	0.000	0.000	0.000
45	A	56	VAL	0	-0.019	-0.011	23.516	0.011	0.011	0.000	0.000	0.000	0.000
46	A	57	PHE	0	0.012	-0.026	20.446	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	58	VAL	0	-0.001	0.009	19.364	0.016	0.016	0.000	0.000	0.000	0.000
48	A	59	VAL	0	0.002	0.013	15.136	-0.044	-0.044	0.000	0.000	0.000	0.000
49	A	60	ARG	1	0.895	0.942	14.998	-0.131	-0.131	0.000	0.000	0.000	0.000
50	A	61	VAL	0	0.032	0.009	10.121	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	62	ASP	-1	-0.752	-0.858	9.288	1.513	1.513	0.000	0.000	0.000	0.000
52	A	63	ASP	-1	-0.958	-0.982	11.894	0.350	0.350	0.000	0.000	0.000	0.000
53	A	64	GLU	-1	-0.881	-0.909	14.912	0.602	0.602	0.000	0.000	0.000	0.000
54	A	65	VAL	0	-0.084	-0.046	16.169	0.010	0.010	0.000	0.000	0.000	0.000
55	A	66	VAL	0	-0.008	0.001	15.013	0.015	0.015	0.000	0.000	0.000	0.000
56	A	67	TRP	0	-0.007	-0.021	18.154	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	68	ASP	-1	-0.865	-0.930	20.507	0.069	0.069	0.000	0.000	0.000	0.000
58	A	69	ARG	1	1.003	1.012	23.597	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.821	0.923	25.981	-0.099	-0.099	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.958	-0.984	26.101	0.160	0.160	0.000	0.000	0.000	0.000
61	A	72	GLN	0	0.042	0.016	22.453	0.016	0.016	0.000	0.000	0.000	0.000
62	A	73	GLY	0	-0.008	0.017	26.803	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	74	PHE	0	-0.046	-0.044	24.399	0.000	0.000	0.000	0.000	0.000	0.000
64	A	75	PRO	0	0.006	0.011	20.568	0.018	0.018	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.793	-0.909	21.763	0.019	0.019	0.000	0.000	0.000	0.000
66	A	77	PRO	0	0.048	0.023	19.332	0.036	0.036	0.000	0.000	0.000	0.000
67	A	78	THR	0	-0.021	-0.005	18.696	0.047	0.047	0.000	0.000	0.000	0.000
68	A	79	ALA	0	-0.051	-0.026	19.353	0.064	0.064	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.011	0.003	16.381	0.055	0.055	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.968	0.985	14.391	0.149	0.149	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.912	0.950	14.828	-0.157	-0.157	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.000	0.011	16.470	0.077	0.077	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.014	-0.004	10.903	0.060	0.060	0.000	0.000	0.000	0.000
74	A	85	ARG	1	0.945	0.963	11.711	-0.519	-0.519	0.000	0.000	0.000	0.000
75	A	86	ASP	-1	-0.898	-0.927	12.547	0.849	0.849	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.801	0.872	12.091	-0.658	-0.658	0.000	0.000	0.000	0.000
77	A	88	VAL	0	-0.060	-0.028	6.627	0.273	0.273	0.000	0.000	0.000	0.000
78	A	89	ALA	0	-0.018	0.009	9.919	0.159	0.159	0.000	0.000	0.000	0.000

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