FMO DATABASE

FMODB ID: QYY6Y

Calculation Name: 5DCK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DCK

Chain ID: A

ChEMBL ID:

UniProt ID: P16087

Base Structure: X-ray

Registration Date: 2023-06-21

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-437906.828475
FMO2-HF: Nuclear repulsion	408846.682753
FMO2-HF: Total energy	-29060.145721
FMO2-MP2: Total energy	-29142.877721

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:141:HIS)

Summations of interaction energy for fragment #1(A:141:HIS)

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.
2.297	3.781	0	-0.636	-0.848	0.002

Interaction energy analysis for fragmet #1(A:141:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.016

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].	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	143	VAL	0	0.022	0.017	3.672	-1.637	-0.153	-0.636	-0.848	0.002
4	A	144	GLN	0	0.012	-0.003	6.105	0.463	0.463	0.000	0.000	0.000
5	A	145	LEU	0	0.004	0.030	8.287	-0.088	-0.088	0.000	0.000	0.000
6	A	146	ARG	1	0.935	0.964	10.534	0.244	0.244	0.000	0.000	0.000
7	A	147	GLN	0	-0.037	-0.028	14.415	0.012	0.012	0.000	0.000	0.000
8	A	148	GLY	0	0.027	0.007	18.126	-0.036	-0.036	0.000	0.000	0.000
9	A	149	ALA	0	-0.008	-0.026	20.010	0.006	0.006	0.000	0.000	0.000
10	A	150	LYS	1	0.947	0.965	22.813	0.003	0.003	0.000	0.000	0.000
11	A	151	GLU	-1	-0.784	-0.855	19.658	0.148	0.148	0.000	0.000	0.000
12	A	152	ASP	-1	-0.822	-0.897	23.776	0.095	0.095	0.000	0.000	0.000
13	A	153	TYR	0	0.007	-0.043	21.154	0.019	0.019	0.000	0.000	0.000
14	A	154	SER	0	0.020	-0.001	22.271	0.018	0.018	0.000	0.000	0.000
15	A	155	SER	0	0.036	0.037	22.093	0.021	0.021	0.000	0.000	0.000
16	A	156	PHE	0	-0.022	-0.003	15.172	0.028	0.028	0.000	0.000	0.000
17	A	157	ILE	0	-0.022	-0.019	17.889	0.037	0.037	0.000	0.000	0.000
18	A	158	ASP	-1	-0.906	-0.939	18.866	0.376	0.376	0.000	0.000	0.000
19	A	159	ARG	1	0.823	0.886	14.899	-0.144	-0.144	0.000	0.000	0.000
20	A	160	LEU	0	-0.055	-0.024	12.809	0.077	0.077	0.000	0.000	0.000
21	A	161	PHE	0	-0.012	-0.038	14.005	0.099	0.099	0.000	0.000	0.000
22	A	162	ALA	0	0.081	0.066	15.656	0.068	0.068	0.000	0.000	0.000
23	A	163	GLN	0	-0.061	-0.034	7.793	0.080	0.080	0.000	0.000	0.000
24	A	164	ILE	0	-0.041	-0.033	10.993	0.216	0.216	0.000	0.000	0.000
25	A	165	ASP	-1	-0.846	-0.901	12.075	0.752	0.752	0.000	0.000	0.000
26	A	166	GLN	0	-0.038	-0.038	13.048	-0.034	-0.034	0.000	0.000	0.000
27	A	167	GLU	-1	-0.897	-0.922	6.822	3.601	3.601	0.000	0.000	0.000
28	A	168	GLN	0	-0.020	-0.014	8.277	-0.121	-0.121	0.000	0.000	0.000
29	A	169	ASN	0	0.087	0.044	11.752	0.052	0.052	0.000	0.000	0.000
30	A	170	THR	0	-0.023	-0.028	14.529	-0.056	-0.056	0.000	0.000	0.000
31	A	171	ALA	0	0.013	0.007	15.779	0.022	0.022	0.000	0.000	0.000
32	A	172	GLU	-1	-0.854	-0.933	18.133	0.390	0.390	0.000	0.000	0.000
33	A	173	VAL	0	-0.006	0.011	12.952	-0.032	-0.032	0.000	0.000	0.000
34	A	174	LYS	1	0.798	0.882	11.810	-1.231	-1.231	0.000	0.000	0.000
35	A	175	LEU	0	0.019	0.025	14.753	-0.030	-0.030	0.000	0.000	0.000
36	A	176	TYR	0	0.026	0.018	16.098	-0.042	-0.042	0.000	0.000	0.000
37	A	177	LEU	0	0.009	0.013	9.874	-0.060	-0.060	0.000	0.000	0.000
38	A	178	LYS	1	0.848	0.898	13.915	-0.635	-0.635	0.000	0.000	0.000
39	A	179	GLN	0	0.018	0.007	16.142	-0.062	-0.062	0.000	0.000	0.000
40	A	180	SER	0	-0.013	0.000	14.819	-0.065	-0.065	0.000	0.000	0.000
41	A	181	LEU	0	-0.020	-0.011	10.346	-0.063	-0.063	0.000	0.000	0.000
42	A	182	SER	0	-0.023	-0.009	14.904	-0.058	-0.058	0.000	0.000	0.000
43	A	183	ILE	0	0.061	0.040	18.315	-0.029	-0.029	0.000	0.000	0.000
44	A	184	ALA	0	-0.026	-0.022	14.941	-0.033	-0.033	0.000	0.000	0.000
45	A	185	ASN	0	-0.058	-0.052	10.983	-0.085	-0.085	0.000	0.000	0.000
46	A	186	ALA	0	0.046	0.039	15.461	-0.011	-0.011	0.000	0.000	0.000
47	A	187	ASN	0	-0.030	-0.021	18.987	-0.029	-0.029	0.000	0.000	0.000
48	A	188	ALA	0	0.025	-0.008	20.952	0.008	0.008	0.000	0.000	0.000
49	A	189	ASP	-1	-0.873	-0.931	23.507	0.000	0.000	0.000	0.000	0.000
50	A	190	CYS	0	-0.002	0.017	23.095	0.010	0.010	0.000	0.000	0.000
51	A	191	LYS	1	0.877	0.948	17.609	0.021	0.021	0.000	0.000	0.000
52	A	192	LYS	1	0.956	0.982	23.857	0.003	0.003	0.000	0.000	0.000
53	A	193	ALA	0	-0.011	0.010	27.444	0.001	0.001	0.000	0.000	0.000
54	A	194	MET	0	-0.012	0.001	22.040	0.013	0.013	0.000	0.000	0.000
55	A	195	SER	0	-0.044	-0.023	26.516	0.004	0.004	0.000	0.000	0.000
56	A	196	HIS	0	-0.049	-0.015	27.735	-0.006	-0.006	0.000	0.000	0.000
57	A	197	LEU	0	-0.077	-0.035	26.354	0.007	0.007	0.000	0.000	0.000
58	A	198	LYS	1	1.002	1.000	24.710	-0.119	-0.119	0.000	0.000	0.000
59	A	199	PRO	0	0.028	-0.004	19.847	0.007	0.007	0.000	0.000	0.000
60	A	200	GLU	-1	-0.855	-0.924	21.933	0.166	0.166	0.000	0.000	0.000
61	A	201	SER	0	-0.053	-0.007	24.292	-0.004	-0.004	0.000	0.000	0.000
62	A	202	THR	0	-0.035	-0.067	25.397	0.018	0.018	0.000	0.000	0.000
63	A	203	LEU	0	0.025	-0.005	22.576	-0.007	-0.007	0.000	0.000	0.000
64	A	204	GLU	-1	-0.837	-0.930	25.706	0.171	0.171	0.000	0.000	0.000
65	A	205	GLU	-1	-0.906	-0.899	28.990	0.110	0.110	0.000	0.000	0.000
66	A	206	LYS	1	0.814	0.902	21.359	-0.219	-0.219	0.000	0.000	0.000
67	A	207	LEU	0	-0.021	-0.023	24.908	-0.009	-0.009	0.000	0.000	0.000
68	A	208	ARG	1	0.950	0.984	27.452	-0.101	-0.101	0.000	0.000	0.000
69	A	209	ALA	0	-0.057	-0.025	28.493	-0.009	-0.009	0.000	0.000	0.000
70	A	210	CYS	0	-0.045	-0.026	24.720	-0.014	-0.014	0.000	0.000	0.000
71	A	211	GLN	0	-0.030	0.016	28.357	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:141:HIS)