FMO DATABASE

FMODB ID: YVQQ2

Calculation Name: 3CYO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CYO

Chain ID: A

ChEMBL ID:

UniProt ID: Q70626

Base Structure: X-ray

Registration Date: 2023-09-20

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-420670.585401
FMO2-HF: Nuclear repulsion	390646.50489
FMO2-HF: Total energy	-30024.080511
FMO2-MP2: Total energy	-30112.922313

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:THR)

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

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.
-8.05	-4.755	4.719	-3.746	-4.268	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.008

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	5	GLN	0	0.042	-0.001	3.620	-2.509	-0.829	0.005	-0.592	-1.093	0.003
4	A	6	ALA	0	0.000	0.000	2.163	-0.131	-0.785	4.695	-2.181	-1.860	-0.004
5	A	7	ARG	1	0.932	0.975	3.608	-5.966	-3.869	0.020	-0.964	-1.153	0.003
6	A	8	GLN	0	-0.016	-0.009	5.281	-0.599	-0.427	-0.001	-0.009	-0.162	0.000
7	A	9	LEU	0	0.051	0.034	7.633	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.015	0.000	6.000	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.051	0.028	9.455	0.017	0.017	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.003	0.002	11.064	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.039	-0.022	11.930	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.028	0.010	12.369	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.024	0.002	15.012	0.014	0.014	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.033	0.016	17.035	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.050	-0.027	17.226	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.031	0.025	19.431	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.872	-0.941	21.106	0.118	0.118	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.073	-0.050	22.018	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.015	0.024	23.935	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.981	0.991	24.830	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.030	-0.008	27.147	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.004	-0.008	27.123	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.862	-0.924	28.702	0.055	0.055	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.041	-0.020	31.412	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	27	GLN	0	-0.017	-0.023	32.899	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	28	GLN	0	0.061	0.047	34.375	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	29	HIS	0	-0.016	-0.016	34.463	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.027	-0.019	36.648	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.023	0.017	37.460	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	32	GLN	0	0.065	0.041	40.297	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.039	-0.015	41.582	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.062	-0.030	43.057	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	35	VAL	0	0.021	0.016	43.713	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	36	TRP	0	0.010	0.000	46.298	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.011	-0.003	47.945	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.015	-0.019	47.622	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.890	0.953	48.511	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.093	-0.038	51.261	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.072	-0.015	54.053	0.000	0.000	0.000	0.000	0.000	0.000
40	A	52	MET	0	0.029	0.017	53.415	0.000	0.000	0.000	0.000	0.000	0.000
41	A	53	GLU	-1	-0.961	-0.996	50.467	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	54	TRP	0	0.071	0.042	48.378	0.000	0.000	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.844	-0.943	48.689	0.004	0.004	0.000	0.000	0.000	0.000
44	A	56	ARG	1	0.899	0.941	47.187	0.008	0.008	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.929	-0.970	45.812	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	58	ILE	0	0.030	0.026	44.126	0.000	0.000	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.019	0.008	43.167	0.002	0.002	0.000	0.000	0.000	0.000
48	A	60	ASN	0	-0.048	-0.023	41.901	0.001	0.001	0.000	0.000	0.000	0.000
49	A	61	TYR	0	0.030	0.013	39.003	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	62	THR	0	0.013	-0.016	38.324	0.001	0.001	0.000	0.000	0.000	0.000
51	A	63	SER	0	-0.025	0.000	38.091	0.003	0.003	0.000	0.000	0.000	0.000
52	A	64	LEU	0	0.013	0.016	34.861	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	ILE	0	-0.001	-0.011	32.564	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	66	HIS	0	-0.021	-0.024	33.151	0.006	0.006	0.000	0.000	0.000	0.000
55	A	67	SER	0	0.001	0.005	32.936	0.003	0.003	0.000	0.000	0.000	0.000
56	A	68	LEU	0	-0.073	-0.039	30.028	0.000	0.000	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.017	0.022	28.487	0.000	0.000	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.894	-0.915	27.902	0.032	0.032	0.000	0.000	0.000	0.000
59	A	71	LYS	1	0.942	0.965	25.527	0.041	0.041	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.064	-0.045	24.141	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	73	GLN	0	-0.002	-0.026	23.085	0.004	0.004	0.000	0.000	0.000	0.000
62	A	74	ASN	0	0.036	0.030	23.251	0.017	0.017	0.000	0.000	0.000	0.000
63	A	75	GLN	0	-0.124	-0.078	18.235	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	76	GLN	0	-0.097	-0.060	17.831	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.898	-0.949	18.197	0.115	0.115	0.000	0.000	0.000	0.000
66	A	78	LYS	1	0.877	0.950	16.998	0.031	0.031	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.016	-0.015	14.745	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	80	GLU	-1	-0.856	-0.941	13.330	0.245	0.245	0.000	0.000	0.000	0.000
69	A	81	GLN	0	-0.002	0.017	13.718	0.107	0.107	0.000	0.000	0.000	0.000
70	A	82	GLU	-1	-0.956	-0.989	12.137	0.018	0.018	0.000	0.000	0.000	0.000
71	A	83	LEU	0	-0.060	-0.008	7.772	0.044	0.044	0.000	0.000	0.000	0.000
72	A	84	LEU	0	-0.086	-0.046	8.671	0.383	0.383	0.000	0.000	0.000	0.000
73	A	85	GLU	-1	-0.996	-0.995	7.868	0.315	0.315	0.000	0.000	0.000	0.000

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