FMO DATABASE

FMODB ID: R9L88

Calculation Name: 4K59-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4K59

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptAll
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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343645.380114
FMO2-HF: Nuclear repulsion	318544.406208
FMO2-HF: Total energy	-25100.973906
FMO2-MP2: Total energy	-25175.255066

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:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-22.423	-18.285	17.762	-9.369	-12.531	-0.061

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.006

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

Sort

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	GLY	0	-0.017	0.009	3.876	-3.822	-1.542	-0.025	-1.312	-0.944	0.001
4	A	6	PHE	0	0.001	-0.010	4.422	1.739	1.899	0.000	-0.017	-0.143	0.000
5	A	7	LEU	0	0.006	0.008	6.566	-0.191	-0.191	0.000	0.000	0.000	0.000
6	A	8	ILE	0	0.024	0.010	9.590	-0.097	-0.097	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.042	-0.016	12.345	0.025	0.025	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.013	0.002	15.538	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.709	0.818	17.014	-0.169	-0.169	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.871	0.917	19.859	-0.122	-0.122	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.912	-0.964	22.954	0.035	0.035	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.014	-0.006	24.469	0.003	0.003	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.832	-0.884	21.281	0.141	0.141	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.035	0.015	18.559	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.048	-0.037	13.236	0.018	0.018	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.029	0.026	15.300	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.044	-0.027	9.422	0.096	0.096	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.015	-0.008	12.379	-0.105	-0.105	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.002	-0.006	10.158	0.189	0.189	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.840	0.926	9.955	-1.387	-1.387	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.032	0.007	13.902	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.907	-0.949	15.374	0.445	0.445	0.000	0.000	0.000	0.000
23	A	25	TYR	0	-0.032	-0.018	9.961	0.062	0.062	0.000	0.000	0.000	0.000
24	A	26	PRO	0	0.007	0.010	13.452	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.050	0.007	13.373	0.045	0.045	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.758	-0.875	13.007	0.204	0.204	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.830	-0.915	11.203	0.243	0.243	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.023	0.005	8.474	0.127	0.127	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.024	-0.011	8.431	0.066	0.066	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.792	0.881	9.753	-0.211	-0.211	0.000	0.000	0.000	0.000
31	A	33	GLN	0	0.019	-0.004	4.856	0.264	0.264	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.026	-0.014	4.856	-0.149	-0.007	-0.001	-0.004	-0.137	0.000
33	A	35	ARG	1	0.835	0.923	6.584	-0.332	-0.332	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.965	-0.976	6.048	-0.109	-0.109	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.012	-0.009	2.697	-0.462	-0.322	0.749	-0.415	-0.473	0.000
36	A	38	GLY	0	-0.001	0.004	2.589	-0.943	-0.110	1.181	-0.779	-1.236	-0.015
37	A	39	ILE	0	-0.042	-0.028	3.718	-2.104	-1.478	0.007	-0.248	-0.385	-0.001
38	A	40	ARG	1	0.918	0.969	3.720	1.221	1.403	0.000	-0.026	-0.156	0.000
39	A	41	ILE	0	0.011	0.003	5.453	0.628	0.628	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.028	-0.011	8.762	-0.194	-0.194	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.015	0.009	11.178	0.106	0.106	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.040	-0.040	12.356	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.785	-0.873	14.940	-0.072	-0.072	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.008	-0.014	18.602	0.016	0.016	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.020	-0.002	21.541	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.024	0.012	24.414	0.012	0.012	0.000	0.000	0.000	0.000
47	A	49	ASN	0	-0.007	-0.005	25.805	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	50	GLN	0	0.002	0.002	21.010	0.010	0.010	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.059	0.042	18.643	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.822	0.900	16.042	0.027	0.027	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.031	0.021	12.257	-0.049	-0.049	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.009	0.007	10.176	0.070	0.070	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.031	-0.033	7.156	-0.144	-0.144	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.877	-0.941	1.938	-12.316	-14.335	12.102	-5.794	-4.289	-0.050
55	A	57	ALA	0	0.030	0.012	2.971	-2.649	-1.246	1.272	-0.955	-1.720	0.003
56	A	58	PRO	0	0.084	0.035	2.377	-0.326	0.321	2.409	-0.277	-2.778	0.001
57	A	59	ARG	1	0.954	0.950	3.150	-1.564	-1.820	0.068	0.458	-0.270	0.000
58	A	60	GLY	0	0.040	0.034	6.716	-0.356	-0.356	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.018	-0.002	6.287	-0.358	-0.358	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.063	-0.030	8.557	0.103	0.103	0.000	0.000	0.000	0.000
61	A	63	ILE	0	0.001	-0.006	7.722	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.002	-0.003	12.372	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.892	0.936	16.060	-0.307	-0.307	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.787	-0.884	18.148	0.266	0.266	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.799	-0.860	20.862	0.209	0.209	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.064	-0.018	19.833	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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