FMO DATABASE

FMODB ID: Q18ZY

Calculation Name: 5DTC-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12024

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	88
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-617300.853235
FMO2-HF: Nuclear repulsion	582795.087251
FMO2-HF: Total energy	-34505.765984
FMO2-MP2: Total energy	-34608.559822

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:5:LYS )

Summations of interaction energy for fragment #1(A:5:LYS )

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.
-22.205	-18.056	0.916	-2.198	-2.868	-0.012

Interaction energy analysis for fragmet #1(A:5:LYS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.004 / q_NPA : 0.982

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	7	GLN	0	-0.009	-0.004	3.097	3.203	5.446	-0.014	-0.976	-1.254	0.000
4	A	8	VAL	0	0.037	0.023	4.553	-4.478	-4.359	0.000	-0.016	-0.103	0.000
5	A	9	LYS	1	0.943	0.988	7.287	21.226	21.226	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.002	0.003	10.269	-0.175	-0.175	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.981	0.989	13.535	15.257	15.257	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.024	0.013	17.126	-0.214	-0.214	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.021	0.021	20.030	0.443	0.443	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.038	0.010	23.458	0.001	0.001	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.943	0.971	26.377	9.830	9.830	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.824	-0.908	29.385	-8.807	-8.807	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.943	0.961	31.407	7.723	7.723	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.910	-0.946	33.606	-8.131	-8.131	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.861	-0.927	32.646	-8.291	-8.291	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.015	-0.008	32.101	-0.191	-0.191	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.050	-0.025	29.479	-0.233	-0.233	0.000	0.000	0.000	0.000
18	A	22	HIS	0	-0.035	0.002	27.944	-0.446	-0.446	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.007	0.014	22.534	0.066	0.066	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.013	-0.025	23.506	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.900	-0.955	22.224	-12.408	-12.408	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.054	-0.012	18.408	-0.527	-0.527	0.000	0.000	0.000	0.000
23	A	27	PRO	0	-0.054	-0.025	14.651	-0.419	-0.419	0.000	0.000	0.000	0.000
24	A	28	MET	0	0.015	0.012	13.861	0.444	0.444	0.000	0.000	0.000	0.000
25	A	29	TYR	0	-0.017	-0.017	7.301	-0.348	-0.348	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.033	0.024	9.593	1.204	1.204	0.000	0.000	0.000	0.000
27	A	31	PRO	0	0.038	0.011	8.000	-2.270	-2.270	0.000	0.000	0.000	0.000
28	A	32	ILE	0	0.028	0.007	4.282	1.718	1.907	0.000	-0.040	-0.149	0.000
29	A	33	SER	0	-0.015	-0.007	8.237	1.012	1.012	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.020	0.007	10.546	1.585	1.585	0.000	0.000	0.000	0.000
31	A	35	LYS	1	1.009	0.984	13.590	15.387	15.387	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.944	0.986	16.504	11.855	11.855	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.011	-0.010	19.871	0.290	0.290	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.074	0.041	17.287	0.240	0.240	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.002	-0.001	14.692	0.043	0.043	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.035	0.010	18.302	0.431	0.431	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.960	-0.966	20.113	-12.271	-12.271	0.000	0.000	0.000	0.000
38	A	42	ILE	0	-0.015	-0.012	15.168	0.156	0.156	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.010	0.005	19.650	0.289	0.289	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.007	-0.015	22.206	0.760	0.760	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.012	0.014	21.773	0.439	0.439	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.063	-0.040	19.631	0.222	0.222	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.046	-0.011	23.820	0.222	0.222	0.000	0.000	0.000	0.000
44	A	48	GLY	0	-0.026	0.011	26.801	0.338	0.338	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.060	-0.049	28.330	0.322	0.322	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.927	-0.949	30.238	-7.925	-7.925	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.908	0.944	32.616	7.792	7.792	0.000	0.000	0.000	0.000
48	A	52	PRO	0	-0.006	0.004	27.918	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	53	VAL	0	0.019	0.002	28.743	0.245	0.245	0.000	0.000	0.000	0.000
50	A	54	PRO	0	-0.035	-0.005	27.298	-0.403	-0.403	0.000	0.000	0.000	0.000
51	A	55	PHE	0	0.056	0.024	24.002	0.181	0.181	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.853	-0.940	23.613	-11.582	-11.582	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.005	-0.012	19.343	-0.055	-0.055	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.023	-0.005	20.925	-0.089	-0.089	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.011	-0.004	14.705	-0.326	-0.326	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.910	-0.958	18.619	-14.346	-14.346	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.014	0.016	21.237	0.305	0.305	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.906	-0.941	20.157	-14.059	-14.059	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.021	-0.014	20.827	-0.395	-0.395	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.006	-0.008	15.219	-0.379	-0.379	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.923	0.960	19.295	12.376	12.376	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.050	-0.034	15.765	0.349	0.349	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.012	0.003	11.905	-0.246	-0.246	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.050	0.023	10.395	-0.037	-0.037	0.000	0.000	0.000	0.000
65	A	69	HIS	0	0.034	0.004	6.769	-2.122	-2.122	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.860	-0.931	9.115	-21.337	-21.337	0.000	0.000	0.000	0.000
67	A	71	TYR	0	-0.019	-0.005	12.201	0.581	0.581	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.004	-0.018	6.834	0.345	0.345	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.005	0.002	9.404	-1.214	-1.214	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.889	0.953	10.987	16.845	16.845	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.822	0.904	13.721	17.072	17.072	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.008	0.026	11.367	0.513	0.513	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.035	-0.012	10.357	-0.417	-0.417	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.049	0.020	5.244	-1.314	-1.314	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.002	-0.018	2.628	-1.840	-0.301	0.930	-1.163	-1.306	-0.012
76	A	80	GLU	-1	-0.966	-0.986	5.036	-39.023	-38.964	0.000	-0.003	-0.056	0.000
77	A	81	ALA	0	-0.041	-0.003	6.942	3.472	3.472	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.040	-0.032	9.409	0.097	0.097	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.037	-0.022	10.695	0.843	0.843	0.000	0.000	0.000	0.000
80	A	84	ASN	0	0.021	-0.001	13.803	0.418	0.418	0.000	0.000	0.000	0.000
81	A	85	VAL	0	-0.041	-0.020	15.291	0.017	0.017	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.877	-0.935	18.255	-10.935	-10.935	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.067	-0.075	21.566	-0.472	-0.472	0.000	0.000	0.000	0.000
84	A	88	THR	0	0.005	0.008	23.576	0.468	0.468	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.893	0.947	26.750	8.429	8.429	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.043	-0.034	27.771	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.037	-0.017	27.582	0.299	0.299	0.000	0.000	0.000	0.000
88	A	1	NME	0	-0.031	-0.006	30.056	0.322	0.322	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS )