FMO DATABASE

FMODB ID: 2NKRR

Calculation Name: 3LLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HX36

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-538672.78055
FMO2-HF: Nuclear repulsion	507269.258273
FMO2-HF: Total energy	-31403.522277
FMO2-MP2: Total energy	-31497.08514

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:1:SER)

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

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.
-0.365	2.972	0.078	-1.651	-1.766	0.002

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.005

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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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	3	ILE	0	0.038	0.040	3.432	-1.716	0.381	-0.011	-1.022	-1.065	0.000
4	A	4	LYS	1	0.897	0.948	3.502	-0.505	-0.073	0.008	-0.255	-0.185	-0.002
5	A	5	PRO	0	0.057	0.044	5.979	0.225	0.225	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.047	-0.037	9.138	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.003	-0.012	12.305	0.034	0.034	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.064	-0.053	15.487	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.020	0.016	15.261	0.028	0.028	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.774	-0.806	14.311	-0.283	-0.283	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.045	0.012	8.426	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.086	-0.040	8.368	0.094	0.094	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.066	0.029	7.472	-0.326	-0.326	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.870	0.923	2.845	1.757	2.565	0.081	-0.374	-0.516	0.004
15	A	15	ALA	0	0.015	0.014	8.275	0.082	0.082	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.021	-0.016	5.616	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.054	-0.047	7.042	-0.141	-0.141	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.046	0.040	7.625	0.047	0.047	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.036	0.024	10.553	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.826	-0.917	11.421	-0.079	-0.079	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.007	-0.001	7.504	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.045	-0.042	9.661	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.041	0.015	11.012	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.874	-0.915	11.285	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.164	-0.078	5.152	0.105	0.105	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.069	-0.066	9.425	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.021	0.031	14.211	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.100	-0.058	16.231	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.908	-0.959	18.061	-0.070	-0.070	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.105	-0.052	16.468	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.083	0.034	18.704	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.917	-0.965	16.513	-0.064	-0.064	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.951	-0.961	18.109	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-1.004	-0.995	21.439	-0.047	-0.047	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.078	-0.053	17.860	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.857	-0.908	15.068	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.058	-0.050	11.835	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.059	0.023	11.334	0.018	0.018	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.051	-0.033	13.193	0.024	0.024	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.008	0.009	15.025	0.030	0.030	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.055	0.052	16.649	0.014	0.014	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.007	-0.015	16.733	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.069	-0.044	18.734	0.015	0.015	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.039	-0.009	20.836	0.019	0.019	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.021	0.024	22.322	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.037	-0.028	20.333	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.050	0.039	24.696	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.734	0.839	25.089	0.117	0.117	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.012	0.002	20.309	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.026	0.016	20.289	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.940	0.958	21.751	0.090	0.090	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.918	0.932	17.851	0.214	0.214	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.060	-0.046	20.501	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.738	-0.811	22.137	-0.117	-0.117	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.018	-0.033	21.252	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.015	0.019	20.774	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.826	-0.896	21.272	-0.164	-0.164	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.013	0.004	19.914	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.052	0.032	20.961	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.890	-0.952	21.220	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.001	-0.005	16.297	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.860	0.918	19.260	0.179	0.179	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.001	0.000	14.867	-0.047	-0.047	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.919	0.957	17.133	0.267	0.267	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.010	0.010	16.546	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.041	-0.017	12.888	0.038	0.038	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.045	-0.033	13.944	0.055	0.055	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.104	0.056	15.602	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.796	-0.874	17.693	-0.079	-0.079	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.023	-0.028	19.618	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.884	0.939	19.603	0.052	0.052	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.991	1.001	13.600	0.058	0.058	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.042	0.016	14.720	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.076	-0.055	12.141	-0.032	-0.032	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.046	-0.024	8.791	-0.140	-0.140	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.034	0.025	11.810	0.120	0.120	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.805	0.886	11.961	0.220	0.220	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.016	0.026	12.631	0.040	0.040	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.020	-0.054	14.516	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.024	0.022	16.925	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.057	-0.020	19.271	0.010	0.010	0.000	0.000	0.000	0.000

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