FMO DATABASE

FMODB ID: QYLRY

Calculation Name: 5X2D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X2D

Chain ID: A

ChEMBL ID:

UniProt ID: Q2PMV7

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	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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-695127.726689
FMO2-HF: Nuclear repulsion	657047.479258
FMO2-HF: Total energy	-38080.24743
FMO2-MP2: Total energy	-38190.454018

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:83:PRO)

Summations of interaction energy for fragment #1(A:83:PRO)

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.
-2.259	1.104	0.1	-1.649	-1.814	0

Interaction energy analysis for fragmet #1(A:83:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.035

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	85	LEU	0	-0.004	0.008	3.815	-1.748	1.054	-0.027	-1.498	-1.277	0.001
4	A	86	PRO	0	-0.013	-0.004	6.498	-0.085	-0.085	0.000	0.000	0.000	0.000
5	A	87	PRO	0	0.006	0.004	8.621	-0.016	-0.016	0.000	0.000	0.000	0.000
6	A	88	GLU	-1	-0.919	-0.965	11.563	0.023	0.023	0.000	0.000	0.000	0.000
7	A	89	ILE	0	-0.067	-0.020	10.813	0.010	0.010	0.000	0.000	0.000	0.000
8	A	90	ILE	0	0.029	0.028	12.664	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	91	VAL	0	-0.033	-0.024	11.923	0.016	0.016	0.000	0.000	0.000	0.000
10	A	92	ILE	0	0.007	0.000	14.984	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	93	SER	0	-0.035	-0.029	17.606	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	94	ALA	0	0.009	-0.006	14.210	0.013	0.013	0.000	0.000	0.000	0.000
13	A	95	ASN	0	-0.061	-0.001	16.245	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	96	MET	0	0.023	0.002	12.335	0.005	0.005	0.000	0.000	0.000	0.000
15	A	97	SER	0	-0.002	-0.008	10.339	0.052	0.052	0.000	0.000	0.000	0.000
16	A	98	LEU	0	0.087	0.012	5.870	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	99	GLU	-1	-0.849	-0.902	6.122	0.687	0.687	0.000	0.000	0.000	0.000
18	A	100	ASP	-1	-0.814	-0.907	7.360	0.253	0.253	0.000	0.000	0.000	0.000
19	A	101	GLN	0	0.018	0.015	8.819	-0.113	-0.113	0.000	0.000	0.000	0.000
20	A	102	ILE	0	-0.004	-0.005	2.773	-0.638	-0.077	0.127	-0.151	-0.537	-0.001
21	A	103	LYS	1	0.742	0.856	7.056	-0.570	-0.570	0.000	0.000	0.000	0.000
22	A	104	ILE	0	0.030	0.030	9.590	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	105	ALA	0	0.005	0.015	8.532	-0.040	-0.040	0.000	0.000	0.000	0.000
24	A	106	ARG	1	0.901	0.932	8.870	-0.191	-0.191	0.000	0.000	0.000	0.000
25	A	107	GLU	-1	-0.906	-0.939	10.691	0.096	0.096	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.030	-0.031	13.790	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	109	ILE	0	-0.010	-0.019	11.095	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	110	PRO	0	-0.057	-0.017	14.065	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	111	ILE	0	0.007	-0.006	17.044	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	112	ALA	0	-0.007	0.003	18.504	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	113	PRO	0	-0.034	-0.021	18.671	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	114	GLY	0	-0.023	-0.002	21.646	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	115	ALA	0	-0.015	0.009	24.048	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	116	GLN	0	0.035	0.013	26.098	0.002	0.002	0.000	0.000	0.000	0.000
35	A	117	THR	0	-0.024	-0.024	28.919	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	118	SER	0	0.033	-0.003	30.212	0.002	0.002	0.000	0.000	0.000	0.000
37	A	119	GLU	-1	-0.976	-0.981	31.524	0.026	0.026	0.000	0.000	0.000	0.000
38	A	120	GLU	-1	-0.840	-0.904	27.934	0.028	0.028	0.000	0.000	0.000	0.000
39	A	121	LEU	0	0.018	0.007	25.376	0.004	0.004	0.000	0.000	0.000	0.000
40	A	122	GLY	0	0.000	0.004	26.952	0.004	0.004	0.000	0.000	0.000	0.000
41	A	123	ARG	1	0.974	0.966	28.095	-0.038	-0.038	0.000	0.000	0.000	0.000
42	A	124	LEU	0	0.013	0.031	21.253	0.003	0.003	0.000	0.000	0.000	0.000
43	A	125	THR	0	0.009	-0.002	23.163	0.006	0.006	0.000	0.000	0.000	0.000
44	A	126	GLU	-1	-0.903	-0.940	23.527	0.059	0.059	0.000	0.000	0.000	0.000
45	A	127	ASN	0	-0.102	-0.051	22.126	0.008	0.008	0.000	0.000	0.000	0.000
46	A	128	LEU	0	0.055	0.030	17.744	0.007	0.007	0.000	0.000	0.000	0.000
47	A	129	LYS	1	0.794	0.874	19.978	-0.057	-0.057	0.000	0.000	0.000	0.000
48	A	130	SER	0	-0.032	-0.024	22.028	0.003	0.003	0.000	0.000	0.000	0.000
49	A	131	PHE	0	-0.010	0.004	13.452	0.003	0.003	0.000	0.000	0.000	0.000
50	A	132	ALA	0	0.012	0.017	17.683	0.011	0.011	0.000	0.000	0.000	0.000
51	A	133	ASP	-1	-0.719	-0.846	18.730	0.087	0.087	0.000	0.000	0.000	0.000
52	A	134	LYS	1	0.879	0.950	19.789	-0.089	-0.089	0.000	0.000	0.000	0.000
53	A	135	THR	0	-0.078	-0.053	15.129	0.006	0.006	0.000	0.000	0.000	0.000
54	A	136	PHE	0	-0.021	-0.017	12.649	0.013	0.013	0.000	0.000	0.000	0.000
55	A	137	GLY	0	0.020	0.039	17.676	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	138	GLY	0	0.025	0.008	21.404	0.002	0.002	0.000	0.000	0.000	0.000
57	A	139	CYS	0	-0.055	-0.014	24.158	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	140	TRP	0	0.002	0.009	17.217	0.001	0.001	0.000	0.000	0.000	0.000
59	A	141	GLN	0	-0.038	-0.025	23.559	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	142	VAL	0	0.000	-0.001	20.843	0.003	0.003	0.000	0.000	0.000	0.000
61	A	143	MET	0	-0.033	-0.009	23.119	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	144	VAL	0	0.013	0.006	22.113	0.003	0.003	0.000	0.000	0.000	0.000
63	A	145	VAL	0	-0.044	-0.023	24.133	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	146	ASP	-1	-0.889	-0.948	25.077	0.019	0.019	0.000	0.000	0.000	0.000
65	A	147	GLY	0	0.003	-0.001	26.984	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	148	SER	0	-0.019	-0.003	26.918	0.000	0.000	0.000	0.000	0.000	0.000
67	A	149	TYR	0	-0.047	-0.042	22.705	0.000	0.000	0.000	0.000	0.000	0.000
68	A	150	TRP	0	0.026	0.000	28.401	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	151	ILE	0	-0.005	0.006	25.846	0.001	0.001	0.000	0.000	0.000	0.000
70	A	152	THR	0	-0.007	0.008	29.562	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	153	GLN	0	-0.004	0.001	28.536	0.004	0.004	0.000	0.000	0.000	0.000
72	A	154	THR	0	0.002	-0.019	28.642	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	155	PHE	0	0.002	0.004	26.354	0.002	0.002	0.000	0.000	0.000	0.000
74	A	156	VAL	0	0.007	-0.005	24.059	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	157	PRO	0	-0.047	-0.007	24.440	0.005	0.005	0.000	0.000	0.000	0.000
76	A	158	ASN	0	-0.020	-0.014	22.675	0.003	0.003	0.000	0.000	0.000	0.000
77	A	159	MET	0	0.014	0.012	16.657	0.009	0.009	0.000	0.000	0.000	0.000
78	A	160	SER	0	-0.001	-0.007	18.365	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	161	PHE	0	-0.004	-0.003	11.481	0.014	0.014	0.000	0.000	0.000	0.000
80	A	162	GLN	0	0.014	0.020	16.663	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	163	PHE	0	0.020	0.020	14.688	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	164	GLU	-1	-0.886	-0.940	16.673	0.011	0.011	0.000	0.000	0.000	0.000
83	A	165	LEU	0	-0.020	-0.008	14.719	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	166	TYR	0	-0.009	-0.034	15.887	0.002	0.002	0.000	0.000	0.000	0.000
85	A	167	ASN	0	-0.028	-0.011	20.249	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	168	ARG	1	0.897	0.958	21.219	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	169	ALA	0	0.007	0.016	20.486	0.004	0.004	0.000	0.000	0.000	0.000
88	A	170	TYR	0	0.018	0.004	17.966	0.002	0.002	0.000	0.000	0.000	0.000
89	A	171	LEU	0	-0.033	-0.011	19.061	0.004	0.004	0.000	0.000	0.000	0.000
90	A	172	PHE	0	0.004	-0.011	17.358	0.002	0.002	0.000	0.000	0.000	0.000
91	A	173	TRP	0	0.035	0.010	19.948	0.001	0.001	0.000	0.000	0.000	0.000
92	A	174	GLN	0	0.050	0.037	20.518	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	175	THR	0	-0.057	-0.058	22.490	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	176	SER	0	-0.041	-0.035	25.477	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	177	GLU	-1	-0.943	-0.956	23.266	0.098	0.098	0.000	0.000	0.000	0.000

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Highlights

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Interactive mode: IFIE and PIEDA for fragment #1(A:83:PRO)