FMO DATABASE

FMODB ID: K9VY3

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:

Apendix: None

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-695430.709824
FMO2-HF: Nuclear repulsion	657350.048104
FMO2-HF: Total energy	-38080.66172
FMO2-MP2: Total energy	-38190.821775

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.
-1.114	1.565	0.034	-1.293	-1.42	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 : -0.027 / q_NPA : -0.033

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	0.002	0.015	3.786	-0.826	1.337	-0.011	-1.169	-0.983	0.001
4	A	86	PRO	0	0.001	0.000	6.513	-0.228	-0.228	0.000	0.000	0.000	0.000
5	A	87	PRO	0	0.011	0.007	8.464	-0.013	-0.013	0.000	0.000	0.000	0.000
6	A	88	GLU	-1	-0.860	-0.923	11.446	0.069	0.069	0.000	0.000	0.000	0.000
7	A	89	ILE	0	-0.044	-0.015	10.652	0.021	0.021	0.000	0.000	0.000	0.000
8	A	90	ILE	0	0.006	0.006	12.964	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	91	VAL	0	-0.026	-0.019	12.177	0.018	0.018	0.000	0.000	0.000	0.000
10	A	92	ILE	0	-0.006	0.009	15.255	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	93	SER	0	-0.037	-0.032	17.906	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	94	ALA	0	-0.003	-0.012	14.461	0.025	0.025	0.000	0.000	0.000	0.000
13	A	95	ASN	0	-0.042	0.000	16.441	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	96	MET	0	0.040	0.021	12.545	0.016	0.016	0.000	0.000	0.000	0.000
15	A	97	SER	0	-0.005	-0.018	9.659	0.073	0.073	0.000	0.000	0.000	0.000
16	A	98	LEU	0	0.068	0.009	5.734	0.011	0.011	0.000	0.000	0.000	0.000
17	A	99	GLU	-1	-0.848	-0.913	5.266	1.275	1.275	0.000	0.000	0.000	0.000
18	A	100	ASP	-1	-0.831	-0.881	6.944	0.381	0.381	0.000	0.000	0.000	0.000
19	A	101	GLN	0	0.012	-0.008	9.241	-0.106	-0.106	0.000	0.000	0.000	0.000
20	A	102	ILE	0	-0.006	0.000	3.046	-0.565	-0.049	0.045	-0.124	-0.437	-0.001
21	A	103	LYS	1	0.777	0.878	7.267	-0.943	-0.943	0.000	0.000	0.000	0.000
22	A	104	ILE	0	0.021	0.021	9.964	-0.093	-0.093	0.000	0.000	0.000	0.000
23	A	105	ALA	0	0.005	0.016	8.727	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	106	ARG	1	0.898	0.943	8.825	-0.367	-0.367	0.000	0.000	0.000	0.000
25	A	107	GLU	-1	-0.911	-0.949	10.486	0.175	0.175	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.022	-0.036	13.874	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	109	ILE	0	0.000	-0.006	10.929	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	110	PRO	0	-0.062	-0.027	14.080	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	111	ILE	0	-0.015	-0.011	16.999	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	112	ALA	0	0.002	0.000	18.518	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	113	PRO	0	-0.026	-0.008	18.665	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	114	GLY	0	-0.032	-0.005	21.627	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	115	ALA	0	-0.004	0.006	24.195	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	116	GLN	0	0.035	0.012	26.046	0.003	0.003	0.000	0.000	0.000	0.000
35	A	117	THR	0	-0.055	-0.031	28.852	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	118	SER	0	0.013	-0.014	30.530	0.003	0.003	0.000	0.000	0.000	0.000
37	A	119	GLU	-1	-0.958	-0.971	31.621	0.049	0.049	0.000	0.000	0.000	0.000
38	A	120	GLU	-1	-0.801	-0.882	27.918	0.057	0.057	0.000	0.000	0.000	0.000
39	A	121	LEU	0	0.026	0.005	25.585	0.008	0.008	0.000	0.000	0.000	0.000
40	A	122	GLY	0	0.005	0.008	27.044	0.006	0.006	0.000	0.000	0.000	0.000
41	A	123	ARG	1	0.953	0.961	28.007	-0.071	-0.071	0.000	0.000	0.000	0.000
42	A	124	LEU	0	-0.017	0.014	20.947	0.006	0.006	0.000	0.000	0.000	0.000
43	A	125	THR	0	-0.009	-0.007	23.031	0.011	0.011	0.000	0.000	0.000	0.000
44	A	126	GLU	-1	-0.869	-0.945	23.802	0.103	0.103	0.000	0.000	0.000	0.000
45	A	127	ASN	0	-0.070	-0.029	21.937	0.015	0.015	0.000	0.000	0.000	0.000
46	A	128	LEU	0	0.057	0.027	17.562	0.013	0.013	0.000	0.000	0.000	0.000
47	A	129	LYS	1	0.821	0.895	19.799	-0.094	-0.094	0.000	0.000	0.000	0.000
48	A	130	SER	0	-0.019	-0.015	22.149	0.003	0.003	0.000	0.000	0.000	0.000
49	A	131	PHE	0	-0.020	-0.011	13.372	0.002	0.002	0.000	0.000	0.000	0.000
50	A	132	ALA	0	0.021	0.023	18.016	0.017	0.017	0.000	0.000	0.000	0.000
51	A	133	ASP	-1	-0.754	-0.867	19.038	0.139	0.139	0.000	0.000	0.000	0.000
52	A	134	LYS	1	0.882	0.949	20.079	-0.153	-0.153	0.000	0.000	0.000	0.000
53	A	135	THR	0	-0.095	-0.064	15.525	0.009	0.009	0.000	0.000	0.000	0.000
54	A	136	PHE	0	-0.028	-0.011	12.990	0.031	0.031	0.000	0.000	0.000	0.000
55	A	137	GLY	0	0.006	0.024	17.892	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	138	GLY	0	0.030	0.012	21.608	0.004	0.004	0.000	0.000	0.000	0.000
57	A	139	CYS	0	-0.072	-0.027	24.831	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	140	TRP	0	0.000	0.004	17.780	0.002	0.002	0.000	0.000	0.000	0.000
59	A	141	GLN	0	-0.009	0.003	23.884	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	142	VAL	0	-0.018	-0.006	20.875	0.008	0.008	0.000	0.000	0.000	0.000
61	A	143	MET	0	-0.039	-0.013	23.148	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	144	VAL	0	0.010	0.000	22.460	0.008	0.008	0.000	0.000	0.000	0.000
63	A	145	VAL	0	-0.038	-0.017	24.309	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	146	ASP	-1	-0.854	-0.919	25.184	0.047	0.047	0.000	0.000	0.000	0.000
65	A	147	GLY	0	0.010	-0.001	26.712	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	148	SER	0	-0.016	-0.003	26.869	0.003	0.003	0.000	0.000	0.000	0.000
67	A	149	TYR	0	-0.036	-0.039	22.915	0.000	0.000	0.000	0.000	0.000	0.000
68	A	150	TRP	0	0.014	0.002	28.210	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	151	ILE	0	0.007	0.002	26.102	0.001	0.001	0.000	0.000	0.000	0.000
70	A	152	THR	0	-0.033	-0.007	29.697	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	153	GLN	0	0.012	0.008	28.058	0.005	0.005	0.000	0.000	0.000	0.000
72	A	154	THR	0	-0.001	-0.015	28.158	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	155	PHE	0	0.003	0.007	25.746	0.004	0.004	0.000	0.000	0.000	0.000
74	A	156	VAL	0	0.017	0.003	23.737	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	157	PRO	0	-0.051	-0.011	24.031	0.006	0.006	0.000	0.000	0.000	0.000
76	A	158	ASN	0	-0.006	-0.004	22.685	0.001	0.001	0.000	0.000	0.000	0.000
77	A	159	MET	0	0.017	0.010	16.689	0.015	0.015	0.000	0.000	0.000	0.000
78	A	160	SER	0	-0.013	-0.010	18.421	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	161	PHE	0	-0.017	-0.020	11.801	0.028	0.028	0.000	0.000	0.000	0.000
80	A	162	GLN	0	0.041	0.034	17.088	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	163	PHE	0	-0.003	0.000	15.063	0.003	0.003	0.000	0.000	0.000	0.000
82	A	164	GLU	-1	-0.879	-0.932	17.065	0.033	0.033	0.000	0.000	0.000	0.000
83	A	165	LEU	0	-0.022	-0.017	14.606	0.008	0.008	0.000	0.000	0.000	0.000
84	A	166	TYR	0	-0.063	-0.061	15.267	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	167	ASN	0	-0.039	-0.012	19.896	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	168	ARG	1	0.823	0.916	21.211	-0.067	-0.067	0.000	0.000	0.000	0.000
87	A	169	ALA	0	0.033	0.020	20.482	0.009	0.009	0.000	0.000	0.000	0.000
88	A	170	TYR	0	0.017	0.008	18.189	0.000	0.000	0.000	0.000	0.000	0.000
89	A	171	LEU	0	-0.033	-0.008	19.367	0.006	0.006	0.000	0.000	0.000	0.000
90	A	172	PHE	0	0.017	0.000	17.551	0.002	0.002	0.000	0.000	0.000	0.000
91	A	173	TRP	0	0.031	-0.001	20.302	0.004	0.004	0.000	0.000	0.000	0.000
92	A	174	GLN	0	0.040	0.023	20.440	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	175	THR	0	-0.056	-0.046	22.909	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	176	SER	0	-0.033	-0.030	26.012	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	177	GLU	-1	-0.939	-0.951	22.939	0.128	0.128	0.000	0.000	0.000	0.000

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