FMO DATABASE

FMODB ID: 2JQGR

Calculation Name: 5G4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5G4D

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTB8

Base Structure: X-ray

Registration Date: 2023-09-19

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-535945.740294
FMO2-HF: Nuclear repulsion	503110.625416
FMO2-HF: Total energy	-32835.114878
FMO2-MP2: Total energy	-32929.89111

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:-2:ALA)

Summations of interaction energy for fragment #1(A:-2: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.
-16.003	-13.21	15.122	-7.389	-10.525	-0.042

Interaction energy analysis for fragmet #1(A:-2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.015

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	0	ASP	-1	-0.830	-0.895	3.813	-1.853	-0.315	-0.008	-0.669	-0.861	0.003
4	A	1	MET	0	-0.040	-0.023	2.429	0.221	0.479	0.783	-0.179	-0.862	0.000
5	A	2	TYR	0	-0.024	-0.054	2.143	-0.209	-0.143	3.521	-0.901	-2.685	-0.008
6	A	3	VAL	0	-0.017	-0.006	3.745	-0.774	-0.736	0.021	0.027	-0.086	0.000
7	A	4	VAL	0	0.006	-0.003	7.493	0.233	0.233	0.000	0.000	0.000	0.000
8	A	5	ILE	0	-0.044	-0.019	10.540	-0.131	-0.131	0.000	0.000	0.000	0.000
9	A	6	VAL	0	0.021	0.005	13.733	0.028	0.028	0.000	0.000	0.000	0.000
10	A	7	TYR	0	-0.026	-0.024	17.195	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	8	ASP	-1	-0.901	-0.938	20.345	0.176	0.176	0.000	0.000	0.000	0.000
12	A	9	VAL	0	-0.033	-0.017	23.036	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.104	0.058	25.850	0.007	0.007	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.004	-0.013	28.902	0.002	0.002	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.913	-0.963	30.674	0.065	0.065	0.000	0.000	0.000	0.000
16	A	13	ARG	1	0.754	0.828	27.117	-0.065	-0.065	0.000	0.000	0.000	0.000
17	A	14	VAL	0	0.015	0.031	24.558	0.003	0.003	0.000	0.000	0.000	0.000
18	A	15	ASN	0	-0.004	-0.020	24.112	0.023	0.023	0.000	0.000	0.000	0.000
19	A	16	ARG	1	0.928	0.954	24.503	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	17	VAL	0	0.104	0.074	19.960	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.930	0.974	19.812	-0.145	-0.145	0.000	0.000	0.000	0.000
22	A	19	LYS	1	0.886	0.929	19.571	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	20	PHE	0	0.004	0.011	16.410	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	21	LEU	0	0.075	0.034	14.289	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.959	0.977	14.760	-0.147	-0.147	0.000	0.000	0.000	0.000
26	A	23	ARG	1	0.841	0.933	15.949	0.006	0.006	0.000	0.000	0.000	0.000
27	A	24	HIS	1	0.805	0.899	11.990	0.055	0.055	0.000	0.000	0.000	0.000
28	A	25	LEU	0	-0.018	0.012	8.730	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	26	HIS	0	0.026	0.016	8.701	-0.178	-0.178	0.000	0.000	0.000	0.000
30	A	27	TRP	0	-0.053	-0.025	12.501	0.033	0.033	0.000	0.000	0.000	0.000
31	A	28	VAL	0	-0.020	-0.002	13.173	0.013	0.013	0.000	0.000	0.000	0.000
32	A	29	GLN	0	0.020	-0.004	16.025	-0.057	-0.057	0.000	0.000	0.000	0.000
33	A	30	ASN	0	-0.041	-0.019	19.325	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	31	SER	0	0.028	0.013	20.215	0.006	0.006	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.016	0.016	14.604	0.014	0.014	0.000	0.000	0.000	0.000
36	A	33	PHE	0	-0.014	-0.015	13.077	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.758	-0.810	8.884	1.787	1.787	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.044	0.011	6.852	-0.222	-0.222	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.893	-0.932	2.029	-9.336	-7.794	6.381	-4.584	-3.340	-0.032
40	A	37	VAL	0	-0.027	-0.013	3.611	-0.623	-0.493	0.001	0.024	-0.156	0.000
41	A	38	THR	0	0.057	0.022	4.933	-0.733	-0.736	-0.001	-0.004	0.009	0.000
42	A	39	LEU	0	0.016	-0.017	7.343	0.441	0.441	0.000	0.000	0.000	0.000
43	A	40	ALA	0	-0.002	-0.001	9.635	0.212	0.212	0.000	0.000	0.000	0.000
44	A	41	GLU	-1	-0.795	-0.875	9.124	-0.247	-0.247	0.000	0.000	0.000	0.000
45	A	42	PHE	0	0.036	0.005	9.036	0.193	0.193	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.798	-0.897	10.933	-0.145	-0.145	0.000	0.000	0.000	0.000
47	A	44	ARG	1	0.869	0.931	12.633	0.588	0.588	0.000	0.000	0.000	0.000
48	A	45	ILE	0	-0.050	-0.025	10.600	0.065	0.065	0.000	0.000	0.000	0.000
49	A	46	LYS	1	0.841	0.905	14.586	0.222	0.222	0.000	0.000	0.000	0.000
50	A	47	ALA	0	0.033	0.013	16.249	0.023	0.023	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.021	0.004	18.164	0.014	0.014	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.075	-0.056	15.930	0.027	0.027	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.009	0.001	19.947	0.009	0.009	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.909	-0.932	22.255	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.186	-0.098	21.385	0.009	0.009	0.000	0.000	0.000	0.000
56	A	53	ILE	0	-0.068	-0.032	21.652	0.015	0.015	0.000	0.000	0.000	0.000
57	A	54	ASP	-1	-0.869	-0.940	25.375	0.018	0.018	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.975	-1.003	24.485	0.005	0.005	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.931	-0.951	26.931	0.029	0.029	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.938	-0.942	29.064	0.063	0.063	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.773	-0.846	24.719	0.090	0.090	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.008	-0.003	22.894	0.002	0.002	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.009	-0.019	16.805	0.025	0.025	0.000	0.000	0.000	0.000
64	A	61	VAL	0	-0.001	0.009	15.709	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	62	ILE	0	-0.010	-0.015	10.920	0.048	0.048	0.000	0.000	0.000	0.000
66	A	63	TYR	0	0.002	0.003	11.253	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.901	0.958	7.824	0.223	0.223	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.023	-0.013	5.886	-0.122	-0.122	0.000	0.000	0.000	0.000
69	A	66	ARG	1	0.986	0.979	4.328	-0.374	-0.171	0.000	-0.040	-0.163	0.000
70	A	67	SER	0	0.048	0.018	2.108	-1.890	-1.678	4.421	-2.496	-2.137	-0.005
71	A	68	MET	0	-0.002	0.012	3.170	-0.709	-1.902	0.004	1.435	-0.246	0.000
72	A	69	PRO	0	-0.026	0.015	5.062	-0.661	-0.659	-0.001	-0.002	0.002	0.000
73	A	70	LYS	1	1.005	0.988	8.382	-0.828	-0.828	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.762	0.832	9.147	-1.672	-1.672	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.944	-0.965	14.222	0.464	0.464	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.014	-0.007	17.290	0.003	0.003	0.000	0.000	0.000	0.000
77	A	74	LEU	0	0.029	0.021	19.697	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	75	GLY	0	0.014	0.016	23.368	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	76	MET	0	-0.033	-0.024	20.898	0.019	0.019	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ALA)