FMO DATABASE

FMODB ID: Q17LY

Calculation Name: 4D3G-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3G

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G229

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-491812.875923
FMO2-HF: Nuclear repulsion	459986.575924
FMO2-HF: Total energy	-31826.299999
FMO2-MP2: Total energy	-31916.246698

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:-1:ACE )

Summations of interaction energy for fragment #1(A:-1: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.
0.583	2.309	0.036	-0.865	-0.897	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.004

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	1	MET	0	0.011	0.017	3.849	1.159	1.820	-0.005	-0.318	-0.339	0.000
4	A	2	LYS	1	0.935	0.975	7.122	0.628	0.628	0.000	0.000	0.000	0.000
5	A	3	MET	0	0.015	0.009	9.973	0.032	0.032	0.000	0.000	0.000	0.000
6	A	4	ILE	0	0.003	0.006	13.348	0.030	0.030	0.000	0.000	0.000	0.000
7	A	5	ILE	0	-0.010	-0.008	16.223	0.005	0.005	0.000	0.000	0.000	0.000
8	A	6	ALA	0	0.023	0.002	19.842	0.012	0.012	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.024	-0.013	21.905	0.000	0.000	0.000	0.000	0.000	0.000
10	A	8	VAL	0	0.006	0.001	25.566	0.007	0.007	0.000	0.000	0.000	0.000
11	A	9	GLN	0	0.109	0.041	27.455	0.001	0.001	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.784	-0.900	30.882	-0.046	-0.046	0.000	0.000	0.000	0.000
13	A	11	GLN	0	-0.045	0.014	32.939	0.000	0.000	0.000	0.000	0.000	0.000
14	A	12	ASP	-1	-0.762	-0.876	29.914	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	13	SER	0	-0.086	-0.071	28.562	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	14	GLN	0	-0.064	-0.043	28.470	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.770	-0.889	29.500	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	16	LEU	0	-0.012	0.008	22.544	0.002	0.002	0.000	0.000	0.000	0.000
19	A	17	ALA	0	-0.042	-0.033	24.466	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.912	-0.952	25.166	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.057	-0.053	24.356	0.003	0.003	0.000	0.000	0.000	0.000
22	A	20	LEU	0	0.005	0.001	19.154	0.003	0.003	0.000	0.000	0.000	0.000
23	A	21	VAL	0	0.012	0.014	20.332	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	22	LYS	1	0.887	0.952	21.846	0.018	0.018	0.000	0.000	0.000	0.000
25	A	23	ASN	0	-0.009	0.005	18.460	0.019	0.019	0.000	0.000	0.000	0.000
26	A	24	ASN	0	-0.058	-0.017	16.539	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	25	PHE	0	0.032	0.013	13.546	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	26	ARG	1	0.973	0.985	16.638	0.168	0.168	0.000	0.000	0.000	0.000
29	A	27	ALA	0	0.026	0.019	17.657	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	28	THR	0	-0.059	-0.037	20.164	0.008	0.008	0.000	0.000	0.000	0.000
31	A	29	LYS	1	0.954	0.987	22.961	0.058	0.058	0.000	0.000	0.000	0.000
32	A	30	LEU	0	0.001	-0.005	24.292	0.001	0.001	0.000	0.000	0.000	0.000
33	A	31	ALA	0	-0.006	-0.001	27.854	0.005	0.005	0.000	0.000	0.000	0.000
34	A	32	THR	0	-0.014	-0.025	30.729	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	33	THR	0	-0.053	-0.005	32.826	0.002	0.002	0.000	0.000	0.000	0.000
36	A	34	NME	0	0.059	0.049	35.625	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	40	ACE	0	-0.057	-0.050	36.003	0.000	0.000	0.000	0.000	0.000	0.000
38	A	41	ASN	0	-0.057	-0.054	30.469	0.000	0.000	0.000	0.000	0.000	0.000
39	A	42	THR	0	0.026	0.023	28.987	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	43	THR	0	0.026	0.015	24.583	0.000	0.000	0.000	0.000	0.000	0.000
41	A	44	PHE	0	-0.028	-0.014	22.137	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.006	-0.001	19.838	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.055	-0.038	16.623	0.011	0.011	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.063	0.047	13.484	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.030	-0.013	10.815	0.039	0.039	0.000	0.000	0.000	0.000
46	A	49	ASN	0	0.028	0.000	5.101	-0.272	-0.276	0.000	-0.002	0.007	0.000
47	A	50	ASP	-1	-0.926	-0.964	3.396	-1.623	-0.758	0.041	-0.532	-0.374	-0.004
48	A	51	ASP	-1	-0.878	-0.941	4.805	1.255	1.459	0.000	-0.013	-0.191	0.000
49	A	52	ARG	1	0.837	0.920	7.476	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.004	-0.003	9.688	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	54	ASP	-1	-0.859	-0.939	12.105	0.125	0.125	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.948	-0.971	13.903	0.055	0.055	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.001	-0.010	14.688	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.002	-0.007	15.778	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.003	0.010	18.335	0.003	0.003	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.018	-0.007	19.501	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.011	-0.017	19.266	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	61	ASN	0	-0.018	-0.001	22.514	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	62	GLN	0	-0.062	-0.025	24.190	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.080	-0.017	25.367	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.117	-0.059	26.674	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.054	0.022	27.166	0.001	0.001	0.000	0.000	0.000	0.000
63	A	66	ASN	0	-0.032	-0.031	29.199	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.926	0.983	30.945	0.013	0.013	0.000	0.000	0.000	0.000
65	A	68	NME	0	-0.025	0.017	34.016	0.001	0.001	0.000	0.000	0.000	0.000
66	A	92	ACE	0	0.001	-0.038	37.270	0.000	0.000	0.000	0.000	0.000	0.000
67	A	93	VAL	0	-0.013	-0.017	35.592	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	94	GLY	0	0.062	0.055	32.598	0.002	0.002	0.000	0.000	0.000	0.000
69	A	95	GLY	0	-0.043	-0.023	29.941	0.000	0.000	0.000	0.000	0.000	0.000
70	A	96	ALA	0	0.013	0.006	24.850	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	97	THR	0	-0.043	-0.020	24.264	0.005	0.005	0.000	0.000	0.000	0.000
72	A	98	VAL	0	-0.001	0.001	18.218	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	99	PHE	0	-0.022	0.004	18.700	0.007	0.007	0.000	0.000	0.000	0.000
74	A	100	VAL	0	0.025	0.007	12.217	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	101	MET	0	-0.046	-0.029	14.122	0.013	0.013	0.000	0.000	0.000	0.000
76	A	102	PRO	0	-0.005	-0.006	10.604	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	103	VAL	0	0.009	0.003	9.947	0.092	0.092	0.000	0.000	0.000	0.000
78	A	104	ASP	-1	-0.881	-0.927	9.639	-0.698	-0.698	0.000	0.000	0.000	0.000
79	A	105	ALA	0	-0.058	-0.042	10.710	-0.112	-0.112	0.000	0.000	0.000	0.000
80	A	106	PHE	0	-0.009	0.001	10.641	0.067	0.067	0.000	0.000	0.000	0.000
81	A	107	HIS	0	-0.014	-0.015	12.496	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	108	GLN	0	-0.062	-0.036	15.043	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	109	PHE	-1	-0.905	-0.935	17.084	-0.151	-0.151	0.000	0.000	0.000	0.000

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