FMO DATABASE

FMODB ID: QVJ8Y

Calculation Name: 2X3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X3D

Chain ID: A

ChEMBL ID:

UniProt ID: Q97ZR0

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-591028.751409
FMO2-HF: Nuclear repulsion	555565.149384
FMO2-HF: Total energy	-35463.602025
FMO2-MP2: Total energy	-35563.280675

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-1.366	0.39	-0.012	-0.831	-0.913	-0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.023

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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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	2	ALA	0	-0.002	0.011	3.735	-0.063	1.501	-0.013	-0.777	-0.774	-0.001
4	A	3	ILE	0	0.045	0.028	5.836	0.489	0.489	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.841	0.933	6.815	-0.062	-0.062	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.814	0.894	10.690	0.058	0.058	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.023	-0.002	14.295	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	7	VAL	0	0.024	0.016	16.885	0.006	0.006	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.048	-0.032	19.771	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.823	-0.898	22.874	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.034	-0.045	25.352	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.026	0.026	28.102	0.009	0.009	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.886	0.925	31.133	0.082	0.082	0.000	0.000	0.000	0.000
14	A	13	PRO	0	0.048	0.035	33.001	0.008	0.008	0.000	0.000	0.000	0.000
15	A	14	ILE	0	-0.034	-0.021	36.196	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.894	0.942	38.234	0.058	0.058	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.022	0.001	36.455	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	17	THR	0	-0.010	-0.023	30.550	0.007	0.007	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.047	-0.013	33.485	0.002	0.002	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.111	0.022	30.187	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.006	0.016	29.334	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.862	-0.936	29.258	-0.108	-0.108	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.041	-0.014	26.524	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	23	ALA	0	0.017	0.000	25.134	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.898	-0.940	24.260	-0.143	-0.143	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.918	0.959	24.348	0.128	0.128	0.000	0.000	0.000	0.000
27	A	26	ILE	0	0.068	0.022	20.029	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.089	-0.056	19.834	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.839	0.923	19.820	0.162	0.162	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.013	0.009	17.149	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.884	-0.943	13.299	-0.537	-0.537	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.040	-0.019	11.812	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.045	-0.013	12.455	0.025	0.025	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.936	-0.976	12.575	-0.209	-0.209	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.031	-0.018	16.551	0.047	0.047	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.004	-0.001	18.846	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	36	ASN	0	-0.075	-0.031	21.566	0.017	0.017	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.028	0.020	24.375	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.036	-0.014	26.958	0.010	0.010	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.008	-0.011	29.856	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.034	-0.015	30.295	0.004	0.004	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.918	-0.963	33.278	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	42	MET	0	-0.035	-0.024	35.935	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.888	-0.907	38.552	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.049	-0.047	41.258	0.000	0.000	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.964	-0.987	40.611	-0.054	-0.054	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.021	-0.007	36.379	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	47	MET	0	-0.048	-0.023	34.281	0.003	0.003	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.076	0.046	32.674	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.038	-0.034	28.824	0.003	0.003	0.000	0.000	0.000	0.000
51	A	50	MET	0	0.064	0.049	24.995	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.032	-0.025	22.039	0.000	0.000	0.000	0.000	0.000	0.000
53	A	52	ILE	0	0.010	0.004	19.605	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.004	-0.003	16.565	0.000	0.000	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.831	-0.923	14.936	-0.063	-0.063	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.052	0.019	12.799	0.001	0.001	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.094	-0.062	6.899	0.078	0.078	0.000	0.000	0.000	0.000
58	A	57	SER	0	-0.057	-0.039	6.211	-0.194	-0.194	0.000	0.000	0.000	0.000
59	A	58	LEU	0	-0.002	0.022	8.022	0.129	0.129	0.000	0.000	0.000	0.000
60	A	59	ASN	0	0.039	0.023	11.287	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	60	PHE	0	0.025	-0.003	13.236	0.085	0.085	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.889	-0.940	15.636	-0.320	-0.320	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.934	-0.970	16.490	-0.426	-0.426	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.017	-0.009	16.074	0.045	0.045	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.943	0.965	19.470	0.229	0.229	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.938	0.971	21.003	0.293	0.293	0.000	0.000	0.000	0.000
67	A	66	MET	0	0.022	0.020	22.293	0.020	0.020	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.020	-0.024	22.858	0.021	0.021	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.938	-0.959	25.457	-0.155	-0.155	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.977	-0.982	26.427	-0.183	-0.183	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.934	-0.936	27.825	-0.131	-0.131	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.072	-0.035	30.079	0.010	0.010	0.000	0.000	0.000	0.000
73	A	72	CYS	0	-0.105	-0.052	27.841	0.011	0.011	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.030	0.016	28.491	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.025	-0.017	22.086	0.001	0.001	0.000	0.000	0.000	0.000
76	A	75	HIS	0	-0.086	-0.026	26.336	0.004	0.004	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.028	-0.036	25.558	0.003	0.003	0.000	0.000	0.000	0.000
78	A	77	ILE	0	-0.041	-0.014	18.722	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.831	-0.896	21.984	-0.056	-0.056	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.948	-0.984	17.631	0.003	0.003	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.025	-0.010	13.200	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.002	0.018	11.270	0.053	0.053	0.000	0.000	0.000	0.000
83	A	82	SER	0	0.007	-0.010	8.108	-0.183	-0.183	0.000	0.000	0.000	0.000
84	A	83	GLY	0	0.001	0.005	5.321	0.243	0.243	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.021	-0.033	3.902	0.263	0.455	0.001	-0.054	-0.139	0.000
86	A	85	ARG	1	0.943	0.964	5.984	-0.696	-0.696	0.000	0.000	0.000	0.000
87	A	86	ILE	0	0.071	0.045	9.701	-0.032	-0.032	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.100	-0.044	12.264	0.052	0.052	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.788	-0.887	14.644	0.034	0.034	0.000	0.000	0.000	0.000
90	A	89	GLY	0	-0.009	-0.002	18.141	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)