FMO DATABASE

FMODB ID: QV5QY

Calculation Name: 5X07-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X07

Chain ID: F

ChEMBL ID:

UniProt ID: Q9Y261

Base Structure: X-ray

Registration Date: 2023-09-23

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608752.39444
FMO2-HF: Nuclear repulsion	573492.707921
FMO2-HF: Total energy	-35259.686518
FMO2-MP2: Total energy	-35362.061081

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(F:155:GLY)

Summations of interaction energy for fragment #1(F:155:GLY)

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.
1.425	2.882	0.013	-0.648	-0.82	0

Interaction energy analysis for fragmet #1(F:155:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.016

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].
3	F	157	HIS	0	0.033	0.019	3.196	1.042	2.406	0.015	-0.631	-0.747
4	F	158	ALA	0	0.040	0.020	4.469	-0.840	-0.837	-0.001	-0.014	0.012
5	F	159	LYS	1	0.931	0.964	7.204	0.902	0.902	0.000	0.000	0.000
6	F	160	PRO	0	0.003	0.011	8.777	0.087	0.087	0.000	0.000	0.000
7	F	161	PRO	0	0.019	0.010	11.926	0.033	0.033	0.000	0.000	0.000
8	F	162	TYR	0	0.021	0.015	14.815	0.054	0.054	0.000	0.000	0.000
9	F	163	SER	0	0.008	0.004	15.537	-0.023	-0.023	0.000	0.000	0.000
10	F	164	TYR	0	0.066	0.001	13.429	-0.006	-0.006	0.000	0.000	0.000
11	F	165	ILE	0	0.071	0.044	18.070	0.010	0.010	0.000	0.000	0.000
12	F	166	SER	0	0.014	0.019	19.611	0.015	0.015	0.000	0.000	0.000
13	F	167	LEU	0	-0.037	-0.024	14.376	0.008	0.008	0.000	0.000	0.000
14	F	168	ILE	0	0.003	0.001	18.937	0.013	0.013	0.000	0.000	0.000
15	F	169	THR	0	0.013	-0.002	21.587	0.017	0.017	0.000	0.000	0.000
16	F	170	MET	0	-0.053	-0.022	18.549	0.006	0.006	0.000	0.000	0.000
17	F	171	ALA	0	0.012	0.012	20.920	0.011	0.011	0.000	0.000	0.000
18	F	172	ILE	0	0.030	0.026	22.854	0.012	0.012	0.000	0.000	0.000
19	F	173	GLN	0	-0.017	0.036	26.310	0.003	0.003	0.000	0.000	0.000
20	F	174	GLN	0	-0.017	-0.020	23.460	0.005	0.005	0.000	0.000	0.000
21	F	175	SER	0	-0.047	-0.042	26.789	0.007	0.007	0.000	0.000	0.000
22	F	176	PRO	0	0.014	-0.011	28.081	0.000	0.000	0.000	0.000	0.000
23	F	177	ASN	0	-0.003	-0.012	31.264	0.001	0.001	0.000	0.000	0.000
24	F	178	LYS	1	0.919	0.984	30.544	0.082	0.082	0.000	0.000	0.000
25	F	179	MET	0	-0.016	0.017	29.519	0.002	0.002	0.000	0.000	0.000
26	F	180	LEU	0	-0.006	0.012	23.704	0.000	0.000	0.000	0.000	0.000
27	F	181	THR	0	0.056	0.035	26.133	0.002	0.002	0.000	0.000	0.000
28	F	182	LEU	0	0.005	-0.013	21.590	-0.007	-0.007	0.000	0.000	0.000
29	F	183	SER	0	0.030	0.008	21.400	-0.006	-0.006	0.000	0.000	0.000
30	F	184	GLU	-1	-0.842	-0.915	20.958	-0.046	-0.046	0.000	0.000	0.000
31	F	185	ILE	0	0.008	0.010	19.442	-0.014	-0.014	0.000	0.000	0.000
32	F	186	TYR	0	-0.034	-0.039	17.336	-0.012	-0.012	0.000	0.000	0.000
33	F	187	GLN	0	-0.022	-0.018	16.425	0.000	0.000	0.000	0.000	0.000
34	F	188	TRP	0	0.068	0.039	17.286	-0.024	-0.024	0.000	0.000	0.000
35	F	189	ILE	0	-0.012	-0.010	13.161	-0.031	-0.031	0.000	0.000	0.000
36	F	190	MET	0	-0.064	-0.030	12.458	-0.033	-0.033	0.000	0.000	0.000
37	F	191	ASP	-1	-0.860	-0.929	12.942	-0.088	-0.088	0.000	0.000	0.000
38	F	192	LEU	0	-0.053	-0.011	14.987	-0.020	-0.020	0.000	0.000	0.000
39	F	193	PHE	0	-0.009	-0.014	10.688	-0.094	-0.094	0.000	0.000	0.000
40	F	194	PRO	0	0.018	-0.008	7.788	0.051	0.051	0.000	0.000	0.000
41	F	195	PHE	0	-0.011	-0.004	4.736	0.239	0.329	-0.001	-0.003	-0.085
42	F	196	TYR	0	-0.024	-0.020	6.444	0.120	0.120	0.000	0.000	0.000
43	F	197	ARG	1	0.937	0.990	7.922	0.176	0.176	0.000	0.000	0.000
44	F	198	GLN	0	0.052	0.017	5.540	0.090	0.090	0.000	0.000	0.000
45	F	199	ASN	0	-0.014	-0.010	6.283	-0.094	-0.094	0.000	0.000	0.000
46	F	200	GLN	0	0.060	0.011	9.731	-0.060	-0.060	0.000	0.000	0.000
47	F	201	GLN	0	-0.002	0.002	12.482	-0.040	-0.040	0.000	0.000	0.000
48	F	202	ARG	1	0.949	0.976	8.248	0.049	0.049	0.000	0.000	0.000
49	F	203	TRP	0	0.012	0.020	10.606	-0.041	-0.041	0.000	0.000	0.000
50	F	204	GLN	0	0.050	0.032	14.032	-0.012	-0.012	0.000	0.000	0.000
51	F	205	ASN	0	-0.026	-0.020	16.647	-0.006	-0.006	0.000	0.000	0.000
52	F	206	SER	0	0.005	-0.003	16.545	-0.008	-0.008	0.000	0.000	0.000
53	F	207	ILE	0	0.001	0.013	16.703	-0.009	-0.009	0.000	0.000	0.000
54	F	208	ARG	1	0.929	0.972	19.306	0.004	0.004	0.000	0.000	0.000
55	F	209	HIS	0	0.001	0.009	21.495	0.010	0.010	0.000	0.000	0.000
56	F	210	SER	0	-0.016	-0.016	20.946	0.001	0.001	0.000	0.000	0.000
57	F	211	LEU	0	-0.025	0.000	22.998	-0.001	-0.001	0.000	0.000	0.000
58	F	212	SER	0	-0.029	-0.011	25.419	0.006	0.006	0.000	0.000	0.000
59	F	213	PHE	0	-0.062	-0.016	25.822	0.003	0.003	0.000	0.000	0.000
60	F	214	ASN	0	-0.048	-0.045	24.262	-0.003	-0.003	0.000	0.000	0.000
61	F	215	ASP	-1	-0.812	-0.903	28.301	-0.061	-0.061	0.000	0.000	0.000
62	F	216	CYS	0	-0.079	-0.030	28.831	0.001	0.001	0.000	0.000	0.000
63	F	217	PHE	0	-0.055	-0.031	24.388	-0.005	-0.005	0.000	0.000	0.000
64	F	218	LEU	0	0.075	0.040	29.475	0.007	0.007	0.000	0.000	0.000
65	F	219	LYS	1	0.921	0.985	30.820	0.027	0.027	0.000	0.000	0.000
66	F	220	VAL	0	0.021	0.001	32.298	0.001	0.001	0.000	0.000	0.000
67	F	221	PRO	0	-0.011	-0.007	34.040	0.001	0.001	0.000	0.000	0.000
68	F	222	ARG	0	-0.021	0.183	30.830	0.002	0.002	0.000	0.000	0.000
69	F	223	SER	0	0.041	-0.053	36.358	-0.002	-0.002	0.000	0.000	0.000
70	F	224	PRO	0	-0.077	-0.028	38.695	0.001	0.001	0.000	0.000	0.000
71	F	225	ASP	-1	-0.894	-0.933	41.439	-0.013	-0.013	0.000	0.000	0.000
72	F	226	LYS	1	0.976	0.985	36.834	0.023	0.023	0.000	0.000	0.000
73	F	227	PRO	0	-0.065	0.012	36.558	-0.002	-0.002	0.000	0.000	0.000
74	F	228	GLY	0	0.130	-0.067	34.452	0.001	0.001	0.000	0.000	0.000
75	F	229	LYN	0	-0.033	-0.082	27.711	0.002	0.002	0.000	0.000	0.000
76	F	230	GLY	0	-0.020	0.014	29.359	-0.004	-0.004	0.000	0.000	0.000
77	F	231	SER	0	-0.062	-0.053	29.802	0.001	0.001	0.000	0.000	0.000
78	F	232	PHE	0	0.030	0.018	29.455	-0.001	-0.001	0.000	0.000	0.000
79	F	233	TRP	0	-0.049	-0.039	26.859	0.002	0.002	0.000	0.000	0.000
80	F	234	THR	0	-0.056	-0.076	28.719	-0.005	-0.005	0.000	0.000	0.000
81	F	235	LEU	0	0.013	-0.010	27.319	-0.004	-0.004	0.000	0.000	0.000
82	F	236	HIS	0	0.023	0.032	31.093	0.003	0.003	0.000	0.000	0.000
83	F	237	PRO	0	0.004	-0.009	33.790	-0.004	-0.004	0.000	0.000	0.000
84	F	238	ASP	-1	-0.976	-0.974	34.029	-0.084	-0.084	0.000	0.000	0.000
85	F	239	SER	0	-0.036	-0.022	32.362	-0.005	-0.005	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(F:155:GLY)