FMO DATABASE

FMODB ID: 94RL2

Calculation Name: 4XP8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XP8

Chain ID: A

ChEMBL ID:

UniProt ID: C7BUG6

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	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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-598516.168338
FMO2-HF: Nuclear repulsion	563862.898214
FMO2-HF: Total energy	-34653.270124
FMO2-MP2: Total energy	-34753.065392

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:18:MET)

Summations of interaction energy for fragment #1(A:18:MET)

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.
-5.07	-0.392	8.825	-3.42	-10.082	-0.022

Interaction energy analysis for fragmet #1(A:18:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.022

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	20	CYS	0	0.016	-0.025	3.109	-3.067	-0.925	0.110	-1.132	-1.120	-0.003
4	A	21	PHE	0	0.010	0.013	5.769	0.737	0.737	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.901	-0.962	2.256	-3.445	-2.786	3.057	-1.001	-2.714	-0.005
6	A	23	ILE	0	-0.046	-0.024	2.287	-2.472	-0.528	4.342	-1.909	-4.377	-0.014
7	A	24	THR	0	-0.028	-0.019	3.061	2.153	1.457	0.052	0.959	-0.315	-0.001
8	A	25	GLY	0	0.005	-0.008	5.803	0.481	0.481	0.000	0.000	0.000	0.000
9	A	26	LYS	1	0.943	0.974	2.369	-1.977	-1.419	1.265	-0.331	-1.492	0.001
10	A	27	ALA	0	-0.053	-0.015	4.743	0.426	0.497	-0.001	-0.006	-0.064	0.000
11	A	28	TYR	0	0.007	-0.006	7.333	0.212	0.212	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.057	-0.011	8.632	0.089	0.089	0.000	0.000	0.000	0.000
13	A	30	ILE	0	-0.025	-0.009	8.919	0.073	0.073	0.000	0.000	0.000	0.000
14	A	31	ASP	-1	-0.845	-0.929	8.593	-0.920	-0.920	0.000	0.000	0.000	0.000
15	A	32	PRO	0	0.074	0.022	5.470	0.030	0.030	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.021	-0.003	8.098	0.009	0.009	0.000	0.000	0.000	0.000
17	A	34	ILE	0	0.011	0.009	11.273	0.091	0.091	0.000	0.000	0.000	0.000
18	A	35	LEU	0	0.009	0.008	8.344	0.058	0.058	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.927	0.972	6.899	1.725	1.725	0.000	0.000	0.000	0.000
20	A	37	ALA	0	0.013	0.008	12.691	0.095	0.095	0.000	0.000	0.000	0.000
21	A	38	ILE	0	-0.027	-0.013	15.219	0.070	0.070	0.000	0.000	0.000	0.000
22	A	39	ALA	0	0.057	0.014	14.224	0.058	0.058	0.000	0.000	0.000	0.000
23	A	40	TRP	0	-0.010	0.008	16.162	0.073	0.073	0.000	0.000	0.000	0.000
24	A	41	ASN	0	-0.067	-0.055	18.071	0.073	0.073	0.000	0.000	0.000	0.000
25	A	42	GLU	-1	-0.970	-0.974	19.523	-0.338	-0.338	0.000	0.000	0.000	0.000
26	A	43	SER	0	-0.040	-0.043	18.249	0.027	0.027	0.000	0.000	0.000	0.000
27	A	44	LYS	1	0.848	0.935	19.636	0.371	0.371	0.000	0.000	0.000	0.000
28	A	45	ASN	0	-0.011	-0.013	13.003	0.069	0.069	0.000	0.000	0.000	0.000
29	A	46	LYS	1	0.932	0.989	16.667	0.361	0.361	0.000	0.000	0.000	0.000
30	A	47	ASN	0	0.022	-0.009	16.313	0.013	0.013	0.000	0.000	0.000	0.000
31	A	48	GLY	0	0.029	0.017	18.531	0.047	0.047	0.000	0.000	0.000	0.000
32	A	49	ILE	0	-0.054	-0.022	21.712	0.044	0.044	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.956	0.982	23.373	0.230	0.230	0.000	0.000	0.000	0.000
34	A	51	SER	0	-0.030	-0.020	26.089	0.012	0.012	0.000	0.000	0.000	0.000
35	A	52	LYS	1	0.964	0.978	27.614	0.205	0.205	0.000	0.000	0.000	0.000
36	A	53	ILE	0	-0.011	0.015	30.510	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	54	ASN	0	-0.031	-0.016	28.194	0.009	0.009	0.000	0.000	0.000	0.000
38	A	55	LYS	1	0.987	0.976	32.469	0.148	0.148	0.000	0.000	0.000	0.000
39	A	56	ASN	0	0.015	0.030	31.252	0.002	0.002	0.000	0.000	0.000	0.000
40	A	57	GLY	0	0.033	0.022	34.836	0.004	0.004	0.000	0.000	0.000	0.000
41	A	58	THR	0	-0.034	-0.014	29.539	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	59	TYR	0	-0.031	-0.049	27.225	0.014	0.014	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.035	0.029	24.034	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	61	ILE	0	0.021	0.010	21.425	0.012	0.012	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.062	0.047	19.328	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	63	ILE	0	-0.023	0.011	13.509	0.025	0.025	0.000	0.000	0.000	0.000
47	A	64	MET	0	0.002	0.028	13.496	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	65	GLN	0	-0.040	-0.023	17.287	0.084	0.084	0.000	0.000	0.000	0.000
49	A	66	ILE	0	0.029	0.030	16.803	0.042	0.042	0.000	0.000	0.000	0.000
50	A	67	ASN	0	-0.003	0.002	21.008	0.035	0.035	0.000	0.000	0.000	0.000
51	A	68	SER	0	0.066	0.011	24.383	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	69	SER	0	-0.056	-0.040	26.705	0.006	0.006	0.000	0.000	0.000	0.000
53	A	70	HIS	1	0.835	0.910	22.582	0.319	0.319	0.000	0.000	0.000	0.000
54	A	71	LEU	0	0.031	0.018	23.869	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	72	ASP	-1	-0.897	-0.933	25.476	-0.177	-0.177	0.000	0.000	0.000	0.000
56	A	73	LEU	0	-0.025	-0.010	21.362	0.006	0.006	0.000	0.000	0.000	0.000
57	A	74	LEU	0	0.009	-0.012	19.297	0.004	0.004	0.000	0.000	0.000	0.000
58	A	75	SER	0	0.019	0.015	22.626	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	76	LYS	1	0.917	0.967	24.712	0.191	0.191	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.056	-0.031	19.969	0.018	0.018	0.000	0.000	0.000	0.000
61	A	78	ASN	0	-0.035	-0.009	20.833	0.003	0.003	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.010	0.007	17.528	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	80	SER	0	-0.041	-0.023	21.223	0.027	0.027	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.849	-0.954	22.159	-0.302	-0.302	0.000	0.000	0.000	0.000
65	A	82	ASP	-1	-0.913	-0.960	22.874	-0.372	-0.372	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.762	-0.880	18.738	-0.447	-0.447	0.000	0.000	0.000	0.000
67	A	84	LEU	0	-0.040	-0.020	18.205	-0.068	-0.068	0.000	0.000	0.000	0.000
68	A	85	LEU	0	-0.044	-0.011	18.863	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	86	ASN	0	0.026	-0.003	19.750	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	87	ASP	-1	-0.852	-0.910	14.120	-0.933	-0.933	0.000	0.000	0.000	0.000
71	A	88	ALA	0	0.011	-0.006	12.876	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	90	ILE	0	0.067	0.053	10.996	-0.036	-0.036	0.000	0.000	0.000	0.000
73	A	91	ASN	0	-0.043	-0.034	13.792	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.000	-0.019	9.169	0.068	0.068	0.000	0.000	0.000	0.000
75	A	93	SER	0	-0.019	-0.013	10.030	0.093	0.093	0.000	0.000	0.000	0.000
76	A	94	VAL	0	0.014	0.004	11.316	0.126	0.126	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.002	-0.007	13.845	0.082	0.082	0.000	0.000	0.000	0.000
78	A	96	GLY	0	0.013	0.005	11.629	0.058	0.058	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.007	0.006	12.637	0.102	0.102	0.000	0.000	0.000	0.000
80	A	98	ILE	0	-0.049	-0.029	14.906	0.073	0.073	0.000	0.000	0.000	0.000
81	A	99	LEU	0	-0.057	-0.032	14.315	0.050	0.050	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.010	0.012	13.793	0.037	0.037	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.036	0.007	15.919	0.060	0.060	0.000	0.000	0.000	0.000
84	A	102	ASN	0	-0.011	-0.017	19.246	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	103	ILE	0	-0.032	-0.008	20.976	0.021	0.021	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.939	0.965	22.762	0.157	0.157	0.000	0.000	0.000	0.000
87	A	105	TYR	0	0.046	0.023	17.716	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:18:MET)