FMO DATABASE

FMODB ID: N3MGQ

Calculation Name: 2DYJ-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJV1

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	93
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-664901.453573
FMO2-HF: Nuclear repulsion	628999.375341
FMO2-HF: Total energy	-35902.078232
FMO2-MP2: Total energy	-36009.404089

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:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
1.74	2.776	0.002	-0.496	-0.542	0

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.007

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].
3	A	5	LYS	1	0.894	0.957	3.851	1.519	2.319	-0.005	-0.434	-0.361
4	A	6	ALA	0	0.062	0.029	7.043	0.268	0.268	0.000	0.000	0.000
5	A	7	HIS	0	0.011	0.006	3.718	-0.005	0.231	0.007	-0.062	-0.181
6	A	8	LEU	0	0.011	0.003	5.709	0.300	0.300	0.000	0.000	0.000
7	A	9	GLU	-1	-0.796	-0.905	7.640	-0.308	-0.308	0.000	0.000	0.000
8	A	10	ALA	0	0.033	0.024	9.065	0.060	0.060	0.000	0.000	0.000
9	A	11	GLN	0	-0.033	-0.016	7.799	0.228	0.228	0.000	0.000	0.000
10	A	12	LEU	0	0.006	-0.005	11.031	-0.003	-0.003	0.000	0.000	0.000
11	A	13	LYS	1	0.941	0.991	13.374	0.028	0.028	0.000	0.000	0.000
12	A	14	ARG	1	0.938	0.970	14.330	-0.107	-0.107	0.000	0.000	0.000
13	A	15	ALA	0	0.009	0.001	15.214	0.000	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.030	0.004	16.957	-0.006	-0.006	0.000	0.000	0.000
15	A	17	ALA	0	-0.020	-0.006	18.856	-0.004	-0.004	0.000	0.000	0.000
16	A	18	GLU	-1	-0.864	-0.925	19.567	0.109	0.109	0.000	0.000	0.000
17	A	19	GLU	-1	-0.881	-0.953	20.580	0.066	0.066	0.000	0.000	0.000
18	A	20	ILE	0	-0.057	-0.036	22.836	-0.006	-0.006	0.000	0.000	0.000
19	A	21	GLN	0	-0.028	-0.011	24.706	-0.004	-0.004	0.000	0.000	0.000
20	A	22	ALA	0	0.007	0.023	25.957	0.000	0.000	0.000	0.000	0.000
21	A	23	LEU	0	-0.122	-0.055	27.167	-0.003	-0.003	0.000	0.000	0.000
22	A	24	GLU	-1	-0.838	-0.932	29.696	0.023	0.023	0.000	0.000	0.000
23	A	25	ASP	-1	-0.887	-0.915	32.621	-0.004	-0.004	0.000	0.000	0.000
24	A	26	PRO	0	0.092	0.034	33.543	-0.001	-0.001	0.000	0.000	0.000
25	A	27	ARG	1	0.722	0.846	34.300	0.006	0.006	0.000	0.000	0.000
26	A	28	LEU	0	-0.025	-0.017	28.675	-0.004	-0.004	0.000	0.000	0.000
27	A	29	PHE	0	0.030	0.025	30.566	0.002	0.002	0.000	0.000	0.000
28	A	30	LEU	0	-0.035	-0.032	30.696	-0.003	-0.003	0.000	0.000	0.000
29	A	31	LEU	0	-0.037	0.012	25.581	-0.003	-0.003	0.000	0.000	0.000
30	A	32	THR	0	0.003	0.006	24.314	0.004	0.004	0.000	0.000	0.000
31	A	33	VAL	0	-0.005	-0.009	19.283	-0.007	-0.007	0.000	0.000	0.000
32	A	34	GLU	-1	-0.847	-0.929	20.857	-0.070	-0.070	0.000	0.000	0.000
33	A	35	ALA	0	-0.051	-0.038	17.410	-0.007	-0.007	0.000	0.000	0.000
34	A	36	VAL	0	-0.016	-0.002	13.970	0.014	0.014	0.000	0.000	0.000
35	A	37	ARG	1	0.923	0.979	14.607	0.154	0.154	0.000	0.000	0.000
36	A	38	LEU	0	-0.045	-0.020	10.973	0.029	0.029	0.000	0.000	0.000
37	A	39	SER	0	-0.015	-0.008	14.522	-0.044	-0.044	0.000	0.000	0.000
38	A	40	LYS	1	0.949	0.950	14.228	0.206	0.206	0.000	0.000	0.000
39	A	41	ASP	-1	-0.790	-0.876	13.304	-0.258	-0.258	0.000	0.000	0.000
40	A	42	GLY	0	-0.030	-0.012	13.325	0.019	0.019	0.000	0.000	0.000
41	A	43	SER	0	-0.052	-0.046	14.024	0.046	0.046	0.000	0.000	0.000
42	A	44	VAL	0	-0.008	-0.012	17.535	0.027	0.027	0.000	0.000	0.000
43	A	45	LEU	0	-0.022	-0.004	14.442	-0.034	-0.034	0.000	0.000	0.000
44	A	46	SER	0	-0.031	-0.006	17.633	0.015	0.015	0.000	0.000	0.000
45	A	47	VAL	0	-0.019	-0.025	18.544	-0.010	-0.010	0.000	0.000	0.000
46	A	48	TYR	0	0.004	0.006	19.086	-0.004	-0.004	0.000	0.000	0.000
47	A	49	VAL	0	-0.006	-0.010	22.269	0.006	0.006	0.000	0.000	0.000
48	A	50	GLU	-1	-0.874	-0.935	24.870	-0.025	-0.025	0.000	0.000	0.000
49	A	51	ALA	0	-0.020	-0.011	27.624	0.006	0.006	0.000	0.000	0.000
50	A	52	PHE	0	0.054	0.039	30.685	-0.001	-0.001	0.000	0.000	0.000
51	A	53	ARG	1	0.925	0.944	33.445	0.007	0.007	0.000	0.000	0.000
52	A	54	GLU	-1	-0.910	-0.943	35.048	-0.020	-0.020	0.000	0.000	0.000
53	A	55	GLU	-1	-0.754	-0.887	31.140	-0.039	-0.039	0.000	0.000	0.000
54	A	56	GLU	-1	-0.902	-0.945	32.503	-0.028	-0.028	0.000	0.000	0.000
55	A	57	GLY	0	-0.026	-0.031	34.030	0.000	0.000	0.000	0.000	0.000
56	A	58	ALA	0	0.039	0.024	30.546	0.002	0.002	0.000	0.000	0.000
57	A	59	LEU	0	0.014	0.005	27.995	0.001	0.001	0.000	0.000	0.000
58	A	60	ARG	1	0.934	0.961	30.159	0.021	0.021	0.000	0.000	0.000
59	A	61	ALA	0	-0.034	-0.011	31.695	0.001	0.001	0.000	0.000	0.000
60	A	62	LEU	0	0.031	0.017	25.498	0.003	0.003	0.000	0.000	0.000
61	A	63	SER	0	0.011	-0.002	27.855	-0.001	-0.001	0.000	0.000	0.000
62	A	64	ARG	1	0.893	0.954	29.091	0.005	0.005	0.000	0.000	0.000
63	A	65	ALA	0	-0.060	-0.024	28.183	0.003	0.003	0.000	0.000	0.000
64	A	66	GLU	-1	-0.674	-0.804	23.661	-0.023	-0.023	0.000	0.000	0.000
65	A	67	ARG	1	0.976	0.969	24.753	0.016	0.016	0.000	0.000	0.000
66	A	68	ARG	1	0.944	0.972	25.450	-0.001	-0.001	0.000	0.000	0.000
67	A	69	LEU	0	0.072	0.041	22.786	0.008	0.008	0.000	0.000	0.000
68	A	70	VAL	0	-0.002	0.007	20.000	0.009	0.009	0.000	0.000	0.000
69	A	71	ALA	0	-0.049	-0.025	20.639	0.010	0.010	0.000	0.000	0.000
70	A	72	ALA	0	-0.017	-0.009	22.096	0.011	0.011	0.000	0.000	0.000
71	A	73	LEU	0	0.038	0.015	16.813	0.017	0.017	0.000	0.000	0.000
72	A	74	ALA	0	-0.046	-0.026	17.212	0.022	0.022	0.000	0.000	0.000
73	A	75	ARG	1	0.907	0.962	18.333	-0.046	-0.046	0.000	0.000	0.000
74	A	76	ARG	1	0.807	0.902	16.566	-0.110	-0.110	0.000	0.000	0.000
75	A	77	VAL	0	-0.006	0.014	11.425	0.046	0.046	0.000	0.000	0.000
76	A	78	ARG	1	0.935	0.970	10.848	-0.266	-0.266	0.000	0.000	0.000
77	A	79	MET	0	0.032	0.011	10.804	0.018	0.018	0.000	0.000	0.000
78	A	80	ARG	1	0.887	0.950	12.931	-0.097	-0.097	0.000	0.000	0.000
79	A	81	ARG	1	1.007	0.993	15.358	0.026	0.026	0.000	0.000	0.000
80	A	82	LEU	0	0.006	0.010	14.837	-0.016	-0.016	0.000	0.000	0.000
81	A	83	PRO	0	0.005	0.027	14.593	-0.005	-0.005	0.000	0.000	0.000
82	A	84	ARG	1	0.771	0.858	17.390	0.047	0.047	0.000	0.000	0.000
83	A	85	LEU	0	-0.003	-0.019	19.044	-0.014	-0.014	0.000	0.000	0.000
84	A	86	GLU	-1	-0.865	-0.922	21.730	-0.092	-0.092	0.000	0.000	0.000
85	A	87	PHE	0	-0.026	-0.023	22.762	-0.004	-0.004	0.000	0.000	0.000
86	A	88	LEU	0	-0.006	0.000	23.126	0.000	0.000	0.000	0.000	0.000
87	A	89	PRO	0	0.033	0.023	25.618	0.003	0.003	0.000	0.000	0.000
88	A	90	TRP	0	0.052	0.005	24.722	-0.009	-0.009	0.000	0.000	0.000
89	A	91	ARG	1	0.878	0.937	25.192	0.043	0.043	0.000	0.000	0.000
90	A	92	ALA	0	-0.054	-0.027	25.723	-0.004	-0.004	0.000	0.000	0.000
91	A	93	SER	0	-0.043	-0.024	20.637	-0.014	-0.014	0.000	0.000	0.000
92	A	94	PRO	0	-0.081	-0.038	18.482	-0.005	-0.005	0.000	0.000	0.000
93	A	95	NME	0	0.043	0.026	19.074	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )