FMO DATABASE

FMODB ID: GNK21

Calculation Name: 5CLV-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CLV

Chain ID: E

ChEMBL ID:

UniProt ID: P03052

Base Structure: X-ray

Registration Date: 2023-06-20

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-355695.123554
FMO2-HF: Nuclear repulsion	331388.423599
FMO2-HF: Total energy	-24306.699955
FMO2-MP2: Total energy	-24379.591482

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(E:2:LYS)

Summations of interaction energy for fragment #1(E:2: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.
-8.102	-6.31	-0.025	-0.77	-0.995	-0.001

Interaction energy analysis for fragmet #1(E:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.971 / q_NPA : 0.960

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	E	4	ARG	1	0.846	0.912	3.763	25.916	27.708	-0.025	-0.770	-0.995	-0.001
4	E	5	LEU	0	0.000	0.019	6.018	-0.028	-0.028	0.000	0.000	0.000	0.000
5	E	6	THR	0	0.027	0.011	9.822	0.687	0.687	0.000	0.000	0.000	0.000
6	E	7	GLU	-1	-0.914	-0.984	12.654	-13.251	-13.251	0.000	0.000	0.000	0.000
7	E	8	SER	0	0.012	0.022	15.203	0.470	0.470	0.000	0.000	0.000	0.000
8	E	9	GLN	0	0.083	0.026	12.456	-0.336	-0.336	0.000	0.000	0.000	0.000
9	E	10	PHE	0	-0.008	-0.003	12.531	0.137	0.137	0.000	0.000	0.000	0.000
10	E	11	GLN	0	-0.010	-0.007	14.769	0.257	0.257	0.000	0.000	0.000	0.000
11	E	12	GLU	-1	-0.941	-0.965	18.169	-13.390	-13.390	0.000	0.000	0.000	0.000
12	E	13	ALA	0	-0.021	-0.011	15.632	0.354	0.354	0.000	0.000	0.000	0.000
13	E	14	ILE	0	-0.055	-0.039	16.893	0.363	0.363	0.000	0.000	0.000	0.000
14	E	15	GLN	0	-0.007	0.010	19.251	0.728	0.728	0.000	0.000	0.000	0.000
15	E	16	GLY	0	0.006	0.002	22.628	-0.149	-0.149	0.000	0.000	0.000	0.000
16	E	17	LEU	0	-0.034	-0.009	18.491	0.071	0.071	0.000	0.000	0.000	0.000
17	E	18	GLU	-1	-0.888	-0.938	22.653	-9.934	-9.934	0.000	0.000	0.000	0.000
18	E	19	VAL	0	-0.079	-0.043	19.157	-0.229	-0.229	0.000	0.000	0.000	0.000
19	E	20	GLY	0	0.035	0.013	22.308	0.233	0.233	0.000	0.000	0.000	0.000
20	E	21	GLN	0	0.034	0.006	21.293	-0.178	-0.178	0.000	0.000	0.000	0.000
21	E	22	GLN	0	0.027	0.003	19.469	-0.318	-0.318	0.000	0.000	0.000	0.000
22	E	23	THR	0	-0.037	-0.020	16.705	-0.560	-0.560	0.000	0.000	0.000	0.000
23	E	24	ILE	0	0.076	0.047	16.014	-0.846	-0.846	0.000	0.000	0.000	0.000
24	E	25	GLU	-1	-0.853	-0.940	15.630	-13.200	-13.200	0.000	0.000	0.000	0.000
25	E	26	ILE	0	-0.053	-0.026	13.079	-0.665	-0.665	0.000	0.000	0.000	0.000
26	E	27	ALA	0	0.000	-0.003	11.457	-1.039	-1.039	0.000	0.000	0.000	0.000
27	E	28	ARG	1	0.974	1.008	10.924	12.403	12.403	0.000	0.000	0.000	0.000
28	E	29	GLY	0	0.006	-0.019	11.458	-0.571	-0.571	0.000	0.000	0.000	0.000
29	E	30	VAL	0	-0.038	-0.008	6.547	-1.015	-1.015	0.000	0.000	0.000	0.000
30	E	31	LEU	0	-0.032	-0.014	6.328	-2.154	-2.154	0.000	0.000	0.000	0.000
31	E	32	VAL	0	0.050	0.042	7.802	-1.159	-1.159	0.000	0.000	0.000	0.000
32	E	33	ASP	-1	-0.872	-0.930	9.923	-16.834	-16.834	0.000	0.000	0.000	0.000
33	E	34	GLY	0	-0.054	-0.010	5.942	-0.471	-0.471	0.000	0.000	0.000	0.000
34	E	35	LYS	1	0.863	0.936	6.781	14.985	14.985	0.000	0.000	0.000	0.000
35	E	36	PRO	0	0.034	0.007	7.709	-0.871	-0.871	0.000	0.000	0.000	0.000
36	E	37	GLN	0	0.102	0.040	7.890	2.224	2.224	0.000	0.000	0.000	0.000
37	E	38	ALA	0	-0.029	-0.016	10.567	1.159	1.159	0.000	0.000	0.000	0.000
38	E	39	THR	0	-0.007	0.005	12.100	1.182	1.182	0.000	0.000	0.000	0.000
39	E	40	PHE	0	0.090	0.055	11.345	0.809	0.809	0.000	0.000	0.000	0.000
40	E	41	ALA	0	-0.034	-0.023	14.782	0.636	0.636	0.000	0.000	0.000	0.000
41	E	42	THR	0	-0.051	-0.032	16.670	0.640	0.640	0.000	0.000	0.000	0.000
42	E	43	SER	0	-0.010	-0.021	18.082	0.331	0.331	0.000	0.000	0.000	0.000
43	E	44	LEU	0	-0.051	-0.017	17.714	0.451	0.451	0.000	0.000	0.000	0.000
44	E	45	GLY	0	0.024	0.036	20.493	0.451	0.451	0.000	0.000	0.000	0.000
45	E	46	LEU	0	-0.037	-0.006	18.495	0.234	0.234	0.000	0.000	0.000	0.000
46	E	47	THR	0	0.061	0.016	19.221	-0.612	-0.612	0.000	0.000	0.000	0.000
47	E	48	ARG	1	1.004	0.966	13.785	17.697	17.697	0.000	0.000	0.000	0.000
48	E	49	GLY	0	0.007	0.015	14.621	-0.833	-0.833	0.000	0.000	0.000	0.000
49	E	50	ALA	0	0.051	0.031	16.214	-0.323	-0.323	0.000	0.000	0.000	0.000
50	E	51	VAL	0	0.009	0.007	12.221	-0.049	-0.049	0.000	0.000	0.000	0.000
51	E	52	SER	0	-0.013	-0.002	11.860	-0.557	-0.557	0.000	0.000	0.000	0.000
52	E	53	GLN	0	-0.013	-0.008	12.756	-0.014	-0.014	0.000	0.000	0.000	0.000
53	E	54	ALA	0	-0.044	-0.024	15.316	0.114	0.114	0.000	0.000	0.000	0.000
54	E	55	VAL	0	0.014	-0.005	8.694	0.051	0.051	0.000	0.000	0.000	0.000
55	E	56	HIS	0	-0.013	0.003	11.607	-1.134	-1.134	0.000	0.000	0.000	0.000
56	E	57	ARG	1	0.966	0.976	12.582	13.698	13.698	0.000	0.000	0.000	0.000
57	E	58	VAL	0	0.019	0.009	13.460	0.254	0.254	0.000	0.000	0.000	0.000
58	E	59	TRP	0	-0.029	-0.020	7.810	-1.216	-1.216	0.000	0.000	0.000	0.000
59	E	60	ALA	0	0.031	-0.003	12.220	-0.120	-0.120	0.000	0.000	0.000	0.000
60	E	61	ALA	0	0.039	0.038	14.440	0.458	0.458	0.000	0.000	0.000	0.000
61	E	62	PHE	0	-0.017	-0.025	11.163	0.499	0.499	0.000	0.000	0.000	0.000
62	E	63	GLU	-1	-0.942	-0.976	11.278	-22.399	-22.399	0.000	0.000	0.000	0.000
63	E	64	ASP	-1	-0.905	-0.952	14.794	-14.392	-14.392	0.000	0.000	0.000	0.000
64	E	65	LYS	1	0.782	0.911	18.223	13.471	13.471	0.000	0.000	0.000	0.000
65	E	66	ASN	0	-0.058	-0.013	14.310	-0.218	-0.218	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:2:LYS)