FMO DATABASE

FMODB ID: 4JG7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-609087.075728
FMO2-HF: Nuclear repulsion	573826.07671
FMO2-HF: Total energy	-35260.999018
FMO2-MP2: Total energy	-35363.2355

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.
-1.723	0.653	0.004	-1.293	-1.086	0.002

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 : 0.048 / 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

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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	F	157	HIS	0	0.022	0.007	3.433	0.839	3.114	0.006	-1.266	-1.015	0.002
4	F	158	ALA	0	0.036	0.023	4.364	-0.926	-0.922	-0.001	-0.023	0.021	0.000
5	F	159	LYS	1	0.928	0.967	6.810	0.444	0.444	0.000	0.000	0.000	0.000
6	F	160	PRO	0	0.017	0.009	8.553	-0.018	-0.018	0.000	0.000	0.000	0.000
7	F	161	PRO	0	0.012	0.013	12.102	0.074	0.074	0.000	0.000	0.000	0.000
8	F	162	TYR	0	-0.013	-0.005	14.594	0.041	0.041	0.000	0.000	0.000	0.000
9	F	163	SER	0	0.006	-0.004	15.284	0.029	0.029	0.000	0.000	0.000	0.000
10	F	164	TYR	0	0.035	-0.015	13.536	0.004	0.004	0.000	0.000	0.000	0.000
11	F	165	ILE	0	0.087	0.057	18.212	0.004	0.004	0.000	0.000	0.000	0.000
12	F	166	SER	0	0.020	0.026	19.351	-0.003	-0.003	0.000	0.000	0.000	0.000
13	F	167	LEU	0	-0.020	-0.010	14.804	-0.007	-0.007	0.000	0.000	0.000	0.000
14	F	168	ILE	0	-0.013	0.004	19.324	0.004	0.004	0.000	0.000	0.000	0.000
15	F	169	THR	0	0.021	-0.002	22.112	0.000	0.000	0.000	0.000	0.000	0.000
16	F	170	MET	0	-0.046	-0.018	19.056	-0.010	-0.010	0.000	0.000	0.000	0.000
17	F	171	ALA	0	0.012	0.018	21.103	-0.001	-0.001	0.000	0.000	0.000	0.000
18	F	172	ILE	0	0.017	0.016	23.030	0.001	0.001	0.000	0.000	0.000	0.000
19	F	173	GLN	0	0.015	0.016	26.535	-0.009	-0.009	0.000	0.000	0.000	0.000
20	F	174	GLN	0	0.005	-0.004	22.698	0.001	0.001	0.000	0.000	0.000	0.000
21	F	175	SER	0	-0.036	-0.006	26.892	0.002	0.002	0.000	0.000	0.000	0.000
22	F	176	PRO	0	0.020	0.000	28.089	-0.004	-0.004	0.000	0.000	0.000	0.000
23	F	177	ASN	0	-0.010	-0.019	31.618	-0.007	-0.007	0.000	0.000	0.000	0.000
24	F	178	LYS	1	0.862	0.938	30.639	0.024	0.024	0.000	0.000	0.000	0.000
25	F	179	MET	0	-0.011	0.015	29.644	0.005	0.005	0.000	0.000	0.000	0.000
26	F	180	LEU	0	-0.006	0.010	23.831	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	181	THR	0	0.002	-0.037	26.029	0.013	0.013	0.000	0.000	0.000	0.000
28	F	182	LEU	0	-0.020	-0.013	21.932	0.000	0.000	0.000	0.000	0.000	0.000
29	F	183	SER	0	0.015	-0.011	21.687	0.017	0.017	0.000	0.000	0.000	0.000
30	F	184	GLU	-1	-0.790	-0.850	20.995	0.093	0.093	0.000	0.000	0.000	0.000
31	F	185	ILE	0	-0.002	0.008	19.985	-0.010	-0.010	0.000	0.000	0.000	0.000
32	F	186	TYR	0	-0.034	-0.054	17.298	0.007	0.007	0.000	0.000	0.000	0.000
33	F	187	GLN	0	-0.020	-0.021	16.425	0.041	0.041	0.000	0.000	0.000	0.000
34	F	188	TRP	0	0.069	0.027	17.077	-0.017	-0.017	0.000	0.000	0.000	0.000
35	F	189	ILE	0	-0.024	-0.015	13.399	-0.039	-0.039	0.000	0.000	0.000	0.000
36	F	190	MET	0	-0.041	-0.020	12.428	0.005	0.005	0.000	0.000	0.000	0.000
37	F	191	ASP	-1	-0.834	-0.894	12.911	0.024	0.024	0.000	0.000	0.000	0.000
38	F	192	LEU	0	-0.027	-0.009	14.895	-0.053	-0.053	0.000	0.000	0.000	0.000
39	F	193	PHE	0	-0.005	-0.010	11.163	-0.114	-0.114	0.000	0.000	0.000	0.000
40	F	194	PRO	0	0.018	-0.004	7.950	0.127	0.127	0.000	0.000	0.000	0.000
41	F	195	PHE	0	-0.018	0.002	4.666	0.464	0.561	-0.001	-0.004	-0.092	0.000
42	F	196	TYR	0	0.020	0.000	6.359	0.575	0.575	0.000	0.000	0.000	0.000
43	F	197	ARG	1	0.851	0.934	8.203	0.072	0.072	0.000	0.000	0.000	0.000
44	F	198	GLN	0	0.088	0.054	5.294	-0.030	-0.030	0.000	0.000	0.000	0.000
45	F	199	ASN	0	-0.001	-0.024	6.099	-0.717	-0.717	0.000	0.000	0.000	0.000
46	F	200	GLN	0	0.027	0.012	9.404	-0.194	-0.194	0.000	0.000	0.000	0.000
47	F	201	GLN	0	0.001	0.000	12.318	-0.060	-0.060	0.000	0.000	0.000	0.000
48	F	202	ARG	1	0.909	0.955	8.942	-1.501	-1.501	0.000	0.000	0.000	0.000
49	F	203	TRP	0	0.007	0.006	10.592	-0.190	-0.190	0.000	0.000	0.000	0.000
50	F	204	GLN	0	0.069	0.047	14.095	-0.109	-0.109	0.000	0.000	0.000	0.000
51	F	205	ASN	0	0.017	0.025	16.668	-0.081	-0.081	0.000	0.000	0.000	0.000
52	F	206	SER	0	-0.011	-0.010	16.212	-0.024	-0.024	0.000	0.000	0.000	0.000
53	F	207	ILE	0	0.002	0.014	17.152	-0.044	-0.044	0.000	0.000	0.000	0.000
54	F	208	ARG	1	0.926	0.961	19.635	-0.327	-0.327	0.000	0.000	0.000	0.000
55	F	209	HIS	0	-0.003	0.019	21.279	-0.006	-0.006	0.000	0.000	0.000	0.000
56	F	210	SER	0	-0.020	-0.021	20.975	-0.025	-0.025	0.000	0.000	0.000	0.000
57	F	211	LEU	0	-0.012	-0.011	23.015	-0.016	-0.016	0.000	0.000	0.000	0.000
58	F	212	SER	0	-0.055	-0.032	25.573	-0.010	-0.010	0.000	0.000	0.000	0.000
59	F	213	PHE	0	-0.049	-0.016	25.508	-0.001	-0.001	0.000	0.000	0.000	0.000
60	F	214	ASN	0	-0.033	-0.023	24.383	-0.017	-0.017	0.000	0.000	0.000	0.000
61	F	215	ASP	-1	-0.842	-0.922	28.478	0.046	0.046	0.000	0.000	0.000	0.000
62	F	216	CYS	0	-0.032	-0.014	29.033	-0.003	-0.003	0.000	0.000	0.000	0.000
63	F	217	PHE	0	-0.051	-0.021	24.648	-0.004	-0.004	0.000	0.000	0.000	0.000
64	F	218	LEU	0	0.081	0.044	29.925	0.006	0.006	0.000	0.000	0.000	0.000
65	F	219	LYS	1	0.896	0.966	30.828	-0.095	-0.095	0.000	0.000	0.000	0.000
66	F	220	VAL	0	0.044	0.015	32.324	-0.004	-0.004	0.000	0.000	0.000	0.000
67	F	221	PRO	0	-0.035	-0.020	34.070	0.007	0.007	0.000	0.000	0.000	0.000
68	F	222	ARG	0	-0.001	0.001	30.262	-0.003	-0.003	0.000	0.000	0.000	0.000
69	F	223	SER	0	-0.010	-0.014	36.021	-0.004	-0.004	0.000	0.000	0.000	0.000
70	F	224	PRO	0	0.016	-0.006	38.614	0.001	0.001	0.000	0.000	0.000	0.000
71	F	225	ASP	-1	-0.814	-0.894	41.243	0.041	0.041	0.000	0.000	0.000	0.000
72	F	226	LYS	1	0.837	0.923	36.723	-0.039	-0.039	0.000	0.000	0.000	0.000
73	F	227	PRO	0	-0.011	0.016	36.430	0.004	0.004	0.000	0.000	0.000	0.000
74	F	228	GLY	0	0.064	-0.010	34.140	-0.002	-0.002	0.000	0.000	0.000	0.000
75	F	229	LYN	0	-0.043	0.000	27.499	0.005	0.005	0.000	0.000	0.000	0.000
76	F	230	GLY	0	0.013	0.001	29.558	-0.001	-0.001	0.000	0.000	0.000	0.000
77	F	231	SER	0	-0.084	-0.054	29.771	-0.009	-0.009	0.000	0.000	0.000	0.000
78	F	232	PHE	0	0.030	0.028	29.386	0.007	0.007	0.000	0.000	0.000	0.000
79	F	233	TRP	0	-0.035	-0.028	27.018	0.004	0.004	0.000	0.000	0.000	0.000
80	F	234	THR	0	0.017	-0.031	28.771	-0.006	-0.006	0.000	0.000	0.000	0.000
81	F	235	LEU	0	-0.022	-0.009	27.731	0.004	0.004	0.000	0.000	0.000	0.000
82	F	236	HIS	0	0.015	0.015	31.313	-0.001	-0.001	0.000	0.000	0.000	0.000
83	F	237	PRO	0	-0.014	-0.021	34.048	-0.004	-0.004	0.000	0.000	0.000	0.000
84	F	238	ASP	-1	-0.922	-0.949	34.404	-0.009	-0.009	0.000	0.000	0.000	0.000
85	F	239	SER	0	-0.078	-0.030	31.847	-0.002	-0.002	0.000	0.000	0.000	0.000

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