FMO DATABASE

FMODB ID: VQ221

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	OptHSide
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	-419926.014079
FMO2-HF: Nuclear repulsion	389901.280622
FMO2-HF: Total energy	-30024.733456
FMO2-MP2: Total energy	-30113.470059

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.
-6.255	-2.656	3.944	-3.447	-4.095	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 : 0.046 / q_NPA : 0.010

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	0.043	0.004	3.508	-2.336	-0.666	0.007	-0.578	-1.098	0.002
4	A	6	ALA	0	-0.005	-0.003	2.139	0.058	-0.251	3.914	-1.904	-1.701	-0.003
5	A	7	ARG	1	0.876	0.936	3.615	-5.559	-3.486	0.024	-0.956	-1.142	0.003
6	A	8	GLN	0	-0.007	-0.005	5.105	-0.167	-0.002	-0.001	-0.009	-0.154	0.000
7	A	9	LEU	0	0.031	0.025	7.642	0.089	0.089	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.020	0.003	5.648	0.098	0.098	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.054	0.030	9.152	0.136	0.136	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.010	0.000	10.822	0.032	0.032	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.045	-0.028	11.673	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.026	0.012	12.313	0.013	0.013	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.024	-0.007	14.598	0.038	0.038	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.019	0.002	16.725	0.016	0.016	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.044	-0.023	16.819	0.005	0.005	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.011	0.017	19.049	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.858	-0.927	20.778	0.028	0.028	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.055	-0.036	21.473	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.004	0.018	23.519	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.958	0.987	23.779	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.037	-0.013	26.783	0.001	0.001	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.005	-0.014	26.648	0.000	0.000	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.841	-0.916	27.903	0.016	0.016	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.050	-0.026	31.061	0.002	0.002	0.000	0.000	0.000	0.000
25	A	27	GLN	0	-0.019	-0.024	32.496	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	28	GLN	0	0.041	0.033	33.963	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	29	HIS	0	0.001	-0.007	34.189	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.032	-0.016	36.413	0.000	0.000	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.028	0.020	36.883	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	32	GLN	0	0.047	0.023	39.893	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.003	0.006	41.188	0.001	0.001	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.060	-0.025	42.989	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	VAL	0	0.008	0.007	43.778	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	36	TRP	0	0.018	0.007	45.893	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.016	0.003	47.552	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.027	-0.025	47.075	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.799	0.894	48.559	0.008	0.008	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.094	-0.044	51.176	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.067	-0.012	53.815	0.000	0.000	0.000	0.000	0.000	0.000
40	A	52	MET	0	0.044	0.019	53.337	0.000	0.000	0.000	0.000	0.000	0.000
41	A	53	GLU	-1	-0.843	-0.923	50.184	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	54	TRP	0	0.056	0.044	47.718	0.001	0.001	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.787	-0.899	48.349	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	56	ARG	1	0.818	0.884	47.896	0.020	0.020	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.937	-0.972	45.500	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	58	ILE	0	0.019	0.014	43.807	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.002	0.009	42.838	0.001	0.001	0.000	0.000	0.000	0.000
48	A	60	ASN	0	-0.048	-0.013	41.662	0.001	0.001	0.000	0.000	0.000	0.000
49	A	61	TYR	0	0.019	-0.002	39.138	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	62	THR	0	0.012	0.001	38.008	0.000	0.000	0.000	0.000	0.000	0.000
51	A	63	SER	0	-0.010	0.008	37.780	0.002	0.002	0.000	0.000	0.000	0.000
52	A	64	LEU	0	0.013	0.014	34.836	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	ILE	0	-0.004	-0.014	32.203	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	66	HIS	0	-0.030	-0.029	32.833	0.003	0.003	0.000	0.000	0.000	0.000
55	A	67	SER	0	-0.024	0.001	32.655	0.001	0.001	0.000	0.000	0.000	0.000
56	A	68	LEU	0	-0.040	-0.031	29.702	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.019	0.020	28.200	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.886	-0.917	27.604	0.011	0.011	0.000	0.000	0.000	0.000
59	A	71	LYS	1	0.962	0.984	25.173	0.063	0.063	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.062	-0.036	23.864	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	73	GLN	0	0.011	-0.019	22.801	0.003	0.003	0.000	0.000	0.000	0.000
62	A	74	ASN	0	-0.030	-0.013	22.989	0.015	0.015	0.000	0.000	0.000	0.000
63	A	75	GLN	0	-0.099	-0.074	18.024	0.009	0.009	0.000	0.000	0.000	0.000
64	A	76	GLN	0	-0.109	-0.073	17.448	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.896	-0.950	17.922	0.088	0.088	0.000	0.000	0.000	0.000
66	A	78	LYS	1	0.782	0.890	17.015	0.026	0.026	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.017	-0.010	14.556	0.010	0.010	0.000	0.000	0.000	0.000
68	A	80	GLU	-1	-0.813	-0.906	13.099	0.130	0.130	0.000	0.000	0.000	0.000
69	A	81	GLN	0	-0.057	-0.026	13.619	0.079	0.079	0.000	0.000	0.000	0.000
70	A	82	GLU	-1	-0.850	-0.929	12.287	0.066	0.066	0.000	0.000	0.000	0.000
71	A	83	LEU	0	-0.050	-0.004	7.679	0.043	0.043	0.000	0.000	0.000	0.000
72	A	84	LEU	0	-0.078	-0.033	8.572	0.381	0.381	0.000	0.000	0.000	0.000
73	A	85	GLU	-1	-0.905	-0.931	8.054	0.462	0.462	0.000	0.000	0.000	0.000

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