FMO DATABASE

FMODB ID: 7GRYK

Calculation Name: 4U1E-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U1E

Chain ID: G

ChEMBL ID:

UniProt ID: P38249

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	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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-425234.676943
FMO2-HF: Nuclear repulsion	390302.261831
FMO2-HF: Total energy	-34932.415112
FMO2-MP2: Total energy	-35036.717635

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(G:8:GLU)

Summations of interaction energy for fragment #1(G:8:GLU)

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.
-85.327	-82.66	-0.001	-1.08	-1.584	0.002

Interaction energy analysis for fragmet #1(G:8:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.964 / q_NPA : -0.985

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	G	10	ILE	0	0.035	0.023	3.439	-0.978	1.560	0.000	-1.031	-1.507	0.002
4	G	11	GLU	-1	-0.870	-0.934	5.313	22.363	22.434	-0.001	-0.003	-0.066	0.000
5	G	12	ASN	0	-0.054	-0.038	8.925	1.271	1.271	0.000	0.000	0.000	0.000
6	G	13	ALA	0	0.055	0.018	11.338	-0.799	-0.799	0.000	0.000	0.000	0.000
7	G	14	ASP	-1	-0.808	-0.856	14.156	19.230	19.230	0.000	0.000	0.000	0.000
8	G	15	GLY	0	0.010	0.001	14.473	-1.275	-1.275	0.000	0.000	0.000	0.000
9	G	16	SER	0	-0.155	-0.100	12.976	0.082	0.082	0.000	0.000	0.000	0.000
10	G	17	ARG	1	0.915	0.950	8.822	-24.000	-24.000	0.000	0.000	0.000	0.000
11	G	18	SER	0	-0.015	-0.022	7.663	-3.262	-3.262	0.000	0.000	0.000	0.000
12	G	19	ILE	0	0.055	0.039	3.814	4.080	4.138	0.000	-0.046	-0.011	0.000
13	G	20	ILE	0	-0.012	-0.009	4.826	-4.735	-4.735	0.000	0.000	0.000	0.000
14	G	21	THR	0	0.020	0.020	5.565	2.646	2.646	0.000	0.000	0.000	0.000
15	G	22	TYR	0	0.005	-0.019	7.664	-3.107	-3.107	0.000	0.000	0.000	0.000
16	G	23	LYS	1	0.848	0.922	11.056	-15.929	-15.929	0.000	0.000	0.000	0.000
17	G	24	ILE	0	-0.008	-0.016	14.020	-0.182	-0.182	0.000	0.000	0.000	0.000
18	G	25	GLU	-1	-0.833	-0.900	17.561	14.518	14.518	0.000	0.000	0.000	0.000
19	G	26	ASP	-1	-0.858	-0.925	20.408	11.777	11.777	0.000	0.000	0.000	0.000
20	G	27	GLY	0	-0.024	-0.005	22.646	-0.348	-0.348	0.000	0.000	0.000	0.000
21	G	28	VAL	0	-0.015	0.005	20.693	0.075	0.075	0.000	0.000	0.000	0.000
22	G	29	LYS	1	0.931	0.964	12.854	-21.129	-21.129	0.000	0.000	0.000	0.000
23	G	30	TYR	0	0.023	0.013	15.793	-0.155	-0.155	0.000	0.000	0.000	0.000
24	G	31	LYS	1	0.918	0.958	9.937	-25.354	-25.354	0.000	0.000	0.000	0.000
25	G	32	ILE	0	0.005	0.001	10.752	-1.398	-1.398	0.000	0.000	0.000	0.000
26	G	33	THR	0	-0.012	-0.015	9.683	2.966	2.966	0.000	0.000	0.000	0.000
27	G	34	GLN	0	-0.006	0.010	9.018	-0.908	-0.908	0.000	0.000	0.000	0.000
28	G	35	LYS	1	0.882	0.934	9.570	-18.083	-18.083	0.000	0.000	0.000	0.000
29	G	36	VAL	0	0.028	0.021	11.766	-1.676	-1.676	0.000	0.000	0.000	0.000
30	G	37	LYS	1	0.938	0.956	13.492	-15.384	-15.384	0.000	0.000	0.000	0.000
31	G	38	GLU	-1	-0.860	-0.910	16.141	13.697	13.697	0.000	0.000	0.000	0.000
32	G	39	VAL	0	-0.009	0.000	18.932	-0.110	-0.110	0.000	0.000	0.000	0.000
33	G	40	LYS	1	0.969	0.951	22.181	-10.927	-10.927	0.000	0.000	0.000	0.000
34	G	41	VAL	0	0.018	0.027	23.283	0.127	0.127	0.000	0.000	0.000	0.000
35	G	42	LEU	0	-0.039	-0.014	25.241	-0.428	-0.428	0.000	0.000	0.000	0.000
36	G	43	GLU	-1	-0.747	-0.876	27.165	8.953	8.953	0.000	0.000	0.000	0.000
37	G	44	LYS	1	0.828	0.916	21.144	-13.437	-13.437	0.000	0.000	0.000	0.000
38	G	45	VAL	0	0.020	0.027	26.136	-0.321	-0.321	0.000	0.000	0.000	0.000
39	G	46	HIS	0	0.048	0.024	25.066	0.602	0.602	0.000	0.000	0.000	0.000
40	G	47	LYS	1	0.933	0.941	22.436	-11.752	-11.752	0.000	0.000	0.000	0.000
41	G	48	SER	0	0.054	0.030	25.522	-0.326	-0.326	0.000	0.000	0.000	0.000
42	G	49	VAL	0	-0.007	-0.010	28.931	-0.298	-0.298	0.000	0.000	0.000	0.000
43	G	50	ALA	0	0.029	0.012	27.198	-0.248	-0.248	0.000	0.000	0.000	0.000
44	G	51	GLU	-1	-0.839	-0.910	27.084	10.269	10.269	0.000	0.000	0.000	0.000
45	G	52	ARG	1	0.923	0.956	30.372	-9.139	-9.139	0.000	0.000	0.000	0.000
46	G	53	LYS	1	0.790	0.883	31.177	-9.361	-9.361	0.000	0.000	0.000	0.000
47	G	54	ASN	0	-0.079	-0.041	30.097	-0.146	-0.146	0.000	0.000	0.000	0.000
48	G	55	TRP	0	-0.031	0.000	33.843	-0.169	-0.169	0.000	0.000	0.000	0.000
49	G	56	HIS	0	0.035	0.026	36.754	-0.157	-0.157	0.000	0.000	0.000	0.000
50	G	57	LYS	1	0.823	0.919	39.870	-7.032	-7.032	0.000	0.000	0.000	0.000
51	G	58	TYR	0	0.007	-0.005	41.858	-0.130	-0.130	0.000	0.000	0.000	0.000
52	G	59	GLY	0	0.036	0.015	45.855	-0.040	-0.040	0.000	0.000	0.000	0.000
53	G	60	SER	0	0.020	-0.001	49.464	-0.001	-0.001	0.000	0.000	0.000	0.000
54	G	61	GLU	-1	-0.756	-0.838	46.096	6.481	6.481	0.000	0.000	0.000	0.000
55	G	62	LYS	1	0.931	1.011	46.643	-6.153	-6.153	0.000	0.000	0.000	0.000
56	G	63	GLY	0	0.005	-0.019	46.197	-0.135	-0.135	0.000	0.000	0.000	0.000
57	G	64	SER	0	-0.080	-0.060	45.982	-0.049	-0.049	0.000	0.000	0.000	0.000
58	G	65	PRO	0	0.022	0.025	43.600	0.144	0.144	0.000	0.000	0.000	0.000
59	G	66	ALA	0	0.033	0.007	39.137	-0.026	-0.026	0.000	0.000	0.000	0.000
60	G	67	GLY	0	0.027	0.013	41.145	-0.049	-0.049	0.000	0.000	0.000	0.000
61	G	68	PRO	0	-0.013	-0.009	42.474	-0.069	-0.069	0.000	0.000	0.000	0.000
62	G	69	SER	0	-0.001	-0.033	45.381	-0.068	-0.068	0.000	0.000	0.000	0.000
63	G	70	ALA	0	0.022	-0.011	48.469	0.005	0.005	0.000	0.000	0.000	0.000
64	G	71	VAL	0	-0.019	0.004	49.708	-0.073	-0.073	0.000	0.000	0.000	0.000
65	G	72	THR	0	-0.051	-0.015	45.944	0.069	0.069	0.000	0.000	0.000	0.000
66	G	73	ALA	0	0.034	0.027	49.403	-0.017	-0.017	0.000	0.000	0.000	0.000
67	G	74	ARG	1	0.904	0.929	47.368	-6.253	-6.253	0.000	0.000	0.000	0.000
68	G	75	LEU	0	-0.028	-0.009	47.046	0.146	0.146	0.000	0.000	0.000	0.000
69	G	76	GLY	0	-0.001	0.006	47.647	-0.073	-0.073	0.000	0.000	0.000	0.000
70	G	77	GLU	-1	-0.948	-0.974	48.571	5.663	5.663	0.000	0.000	0.000	0.000
71	G	78	GLU	-1	-0.957	-0.975	49.326	6.471	6.471	0.000	0.000	0.000	0.000
72	G	79	VAL	0	-0.006	-0.002	50.632	-0.139	-0.139	0.000	0.000	0.000	0.000
73	G	80	GLU	-1	-0.813	-0.879	50.931	5.789	5.789	0.000	0.000	0.000	0.000
74	G	81	LEU	0	-0.005	-0.012	48.156	-0.060	-0.060	0.000	0.000	0.000	0.000
75	G	82	ARG	1	0.954	0.990	50.303	-5.497	-5.497	0.000	0.000	0.000	0.000
76	G	83	LEU	0	-0.011	-0.007	47.755	-0.120	-0.120	0.000	0.000	0.000	0.000
77	G	84	SER	0	0.038	0.001	51.881	0.009	0.009	0.000	0.000	0.000	0.000
78	G	85	ARG	1	0.970	0.979	54.476	-5.520	-5.520	0.000	0.000	0.000	0.000
79	G	86	ASN	0	-0.055	-0.026	56.708	-0.094	-0.094	0.000	0.000	0.000	0.000
80	G	87	TRP	0	0.034	0.028	56.435	-0.075	-0.075	0.000	0.000	0.000	0.000
81	G	88	LYS	1	0.853	0.904	58.609	-4.830	-4.830	0.000	0.000	0.000	0.000
82	G	89	GLN	0	0.029	0.003	61.980	-0.013	-0.013	0.000	0.000	0.000	0.000
83	G	90	ALA	0	0.022	0.022	60.063	-0.046	-0.046	0.000	0.000	0.000	0.000
84	G	91	GLU	-1	-0.862	-0.922	59.743	5.265	5.265	0.000	0.000	0.000	0.000
85	G	92	GLU	-1	-0.824	-0.910	62.679	4.695	4.695	0.000	0.000	0.000	0.000
86	G	93	GLU	-1	-0.991	-0.986	64.956	4.856	4.856	0.000	0.000	0.000	0.000
87	G	94	ARG	1	0.719	0.811	57.476	-5.410	-5.410	0.000	0.000	0.000	0.000
88	G	95	ILE	0	-0.071	-0.014	64.959	-0.033	-0.033	0.000	0.000	0.000	0.000
89	G	96	GLN	0	-0.014	0.007	67.493	-0.050	-0.050	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(G:8:GLU)