FMO DATABASE

FMODB ID: 1NJJZ

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	OptAll
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	-421243.348392
FMO2-HF: Nuclear repulsion	391218.362346
FMO2-HF: Total energy	-30024.986047
FMO2-MP2: Total energy	-30113.675104

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.
-6.375	-2.239	0.209	-1.586	-2.757	0.006

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 : 0.045 / q_NPA : 0.012

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	0.039	0.009	3.572	-1.991	-0.554	0.007	-0.495	-0.949	0.001
4	A	6	ALA	0	0.012	0.016	2.883	-0.148	0.456	0.149	-0.221	-0.531	0.000
5	A	7	ARG	1	0.884	0.923	3.288	-6.126	-4.189	0.054	-0.863	-1.128	0.005
6	A	8	GLN	0	0.009	0.006	5.202	-0.188	-0.030	-0.001	-0.007	-0.149	0.000
7	A	9	LEU	0	0.009	0.013	7.983	0.032	0.032	0.000	0.000	0.000	0.000
8	A	10	LEU	0	-0.003	-0.008	5.603	0.068	0.068	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.051	0.020	9.078	0.108	0.108	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.024	-0.001	10.945	0.012	0.012	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.037	-0.023	11.653	0.002	0.002	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.034	0.016	12.327	0.009	0.009	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.020	-0.013	14.685	0.041	0.041	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.014	0.002	16.784	0.011	0.011	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.035	-0.018	16.622	0.007	0.007	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.010	0.012	18.902	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.807	-0.892	20.717	0.066	0.066	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.055	-0.026	21.556	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.004	0.013	23.367	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.882	0.913	23.094	-0.067	-0.067	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.048	-0.013	26.648	0.000	0.000	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.006	-0.001	26.732	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.832	-0.914	27.877	0.034	0.034	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.036	-0.016	30.917	0.001	0.001	0.000	0.000	0.000	0.000
25	A	27	GLN	0	-0.032	-0.026	32.252	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	GLN	0	0.041	0.020	33.752	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	29	HIS	0	0.003	0.000	33.914	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.028	-0.012	36.334	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.016	0.013	36.612	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	32	GLN	0	0.049	0.018	39.608	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.002	0.007	40.900	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.064	-0.036	42.801	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.003	-0.004	43.413	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	36	TRP	0	-0.011	-0.005	45.606	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.021	0.009	47.372	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.021	-0.018	47.072	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.822	0.895	48.132	0.002	0.002	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.066	-0.026	51.063	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.080	-0.024	53.849	0.000	0.000	0.000	0.000	0.000	0.000
40	A	52	MET	0	0.056	0.024	52.953	0.000	0.000	0.000	0.000	0.000	0.000
41	A	53	GLU	-1	-0.852	-0.923	50.315	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	54	TRP	0	0.084	0.048	47.717	0.001	0.001	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.800	-0.889	48.201	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	56	ARG	1	0.821	0.889	47.835	0.017	0.017	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.923	-0.957	45.403	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	58	ILE	0	0.031	0.018	43.719	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.042	-0.016	42.810	0.002	0.002	0.000	0.000	0.000	0.000
48	A	60	ASN	0	-0.041	-0.008	41.384	0.001	0.001	0.000	0.000	0.000	0.000
49	A	61	TYR	0	0.003	-0.016	39.239	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	62	THR	0	-0.001	-0.001	38.033	0.000	0.000	0.000	0.000	0.000	0.000
51	A	63	SER	0	-0.014	0.001	37.782	0.002	0.002	0.000	0.000	0.000	0.000
52	A	64	LEU	0	-0.001	0.002	34.631	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	ILE	0	0.000	-0.003	32.057	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	66	HIS	0	-0.017	-0.018	32.481	0.004	0.004	0.000	0.000	0.000	0.000
55	A	67	SER	0	0.015	0.027	32.209	0.001	0.001	0.000	0.000	0.000	0.000
56	A	68	LEU	0	-0.040	-0.029	29.637	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.006	0.022	28.032	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.894	-0.936	27.445	0.018	0.018	0.000	0.000	0.000	0.000
59	A	71	LYS	1	0.925	0.962	25.388	0.056	0.056	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.051	-0.042	23.867	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	73	GLN	0	-0.023	-0.025	22.745	0.004	0.004	0.000	0.000	0.000	0.000
62	A	74	ASN	0	0.005	-0.002	22.525	0.014	0.014	0.000	0.000	0.000	0.000
63	A	75	GLN	0	-0.092	-0.053	17.886	0.005	0.005	0.000	0.000	0.000	0.000
64	A	76	GLN	0	-0.070	-0.052	17.398	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.901	-0.957	17.713	0.113	0.113	0.000	0.000	0.000	0.000
66	A	78	LYS	1	0.781	0.883	16.809	0.039	0.039	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.022	-0.018	14.442	0.014	0.014	0.000	0.000	0.000	0.000
68	A	80	GLU	-1	-0.810	-0.891	13.000	0.181	0.181	0.000	0.000	0.000	0.000
69	A	81	GLN	0	-0.035	-0.018	13.269	0.099	0.099	0.000	0.000	0.000	0.000
70	A	82	GLU	-1	-0.835	-0.918	12.076	0.070	0.070	0.000	0.000	0.000	0.000
71	A	83	LEU	0	-0.052	-0.010	7.854	0.074	0.074	0.000	0.000	0.000	0.000
72	A	84	LEU	0	-0.050	-0.015	8.275	0.443	0.443	0.000	0.000	0.000	0.000
73	A	85	GLU	-1	-0.940	-0.934	7.407	0.711	0.711	0.000	0.000	0.000	0.000

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