FMO DATABASE

FMODB ID: 4J8NN

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	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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-592647.999013
FMO2-HF: Nuclear repulsion	557183.882526
FMO2-HF: Total energy	-35464.116487
FMO2-MP2: Total energy	-35563.848507

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.
-3.699	-0.552	0.176	-1.754	-1.57	-0.003

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 : 0.022 / q_NPA : 0.008

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	0.016	0.011	3.587	0.226	2.442	-0.009	-1.209	-0.999	0.002
4	A	3	ILE	0	0.039	0.018	5.662	0.301	0.369	-0.001	-0.003	-0.063	0.000
5	A	4	ARG	1	0.772	0.876	7.029	1.505	1.505	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.736	0.815	10.622	0.468	0.468	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.020	-0.009	14.271	0.000	0.000	0.000	0.000	0.000	0.000
8	A	7	VAL	0	0.005	0.002	16.965	0.006	0.006	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.016	-0.015	19.991	0.006	0.006	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.803	-0.868	23.193	-0.159	-0.159	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.049	-0.027	25.342	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.050	0.035	28.254	0.008	0.008	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.897	0.931	31.192	0.154	0.154	0.000	0.000	0.000	0.000
14	A	13	PRO	0	0.045	0.024	33.248	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	ILE	0	-0.045	-0.012	36.307	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.888	0.939	38.643	0.100	0.100	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.025	0.009	36.546	0.001	0.001	0.000	0.000	0.000	0.000
18	A	17	THR	0	-0.022	-0.032	30.697	0.009	0.009	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.051	-0.049	33.835	0.000	0.000	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.089	0.018	30.593	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.011	0.013	29.439	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.825	-0.866	29.330	-0.198	-0.198	0.000	0.000	0.000	0.000
23	A	22	LEU	0	0.014	0.013	26.511	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	23	ALA	0	0.021	0.009	25.128	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.854	-0.911	24.366	-0.274	-0.274	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.766	0.857	24.838	0.193	0.193	0.000	0.000	0.000	0.000
27	A	26	ILE	0	0.088	0.025	20.340	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.118	-0.073	20.255	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.791	0.882	20.599	0.286	0.286	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.015	0.009	17.484	0.000	0.000	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.901	-0.959	13.740	-0.721	-0.721	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.026	-0.009	11.984	-0.075	-0.075	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.033	-0.012	12.661	-0.068	-0.068	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.922	-0.944	11.463	-1.142	-1.142	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.028	-0.016	16.141	0.081	0.081	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.000	-0.002	18.766	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	36	ASN	0	-0.072	-0.033	21.568	0.040	0.040	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.032	0.022	24.475	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.027	-0.016	27.196	0.015	0.015	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.027	-0.015	29.991	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.047	-0.034	30.575	0.001	0.001	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.908	-0.936	33.365	-0.115	-0.115	0.000	0.000	0.000	0.000
43	A	42	MET	0	-0.025	-0.022	36.130	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.847	-0.870	38.703	-0.095	-0.095	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.048	-0.046	41.574	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.985	-0.996	41.260	-0.090	-0.090	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.031	-0.038	36.997	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	47	MET	0	-0.040	-0.021	34.249	0.002	0.002	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.072	0.055	32.669	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.034	-0.036	28.996	0.001	0.001	0.000	0.000	0.000	0.000
51	A	50	MET	0	0.065	0.049	25.511	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.039	-0.024	22.355	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	52	ILE	0	0.004	-0.004	19.878	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	53	ILE	0	0.002	-0.003	16.427	0.007	0.007	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.831	-0.915	14.931	-0.516	-0.516	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.052	0.029	12.792	0.061	0.061	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.074	-0.058	6.765	-0.328	-0.328	0.000	0.000	0.000	0.000
58	A	57	SER	0	-0.058	-0.031	6.659	0.100	0.100	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.000	0.020	8.330	0.269	0.269	0.000	0.000	0.000	0.000
60	A	59	ASN	0	-0.005	-0.020	12.038	0.033	0.033	0.000	0.000	0.000	0.000
61	A	60	PHE	0	0.036	0.013	13.561	0.097	0.097	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.866	-0.938	16.067	-0.318	-0.318	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.888	-0.918	17.042	-0.463	-0.463	0.000	0.000	0.000	0.000
64	A	63	ILE	0	0.013	0.006	16.080	0.043	0.043	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.815	0.896	19.742	0.277	0.277	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.843	0.919	20.211	0.383	0.383	0.000	0.000	0.000	0.000
67	A	66	MET	0	0.043	0.038	22.712	0.023	0.023	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.017	-0.020	22.723	0.026	0.026	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.839	-0.902	25.522	-0.203	-0.203	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.961	-0.989	26.152	-0.238	-0.238	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.855	-0.885	27.851	-0.202	-0.202	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.056	-0.024	30.274	0.009	0.009	0.000	0.000	0.000	0.000
73	A	72	CYS	0	-0.092	-0.046	28.233	0.010	0.010	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.011	-0.002	28.706	0.000	0.000	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.031	-0.013	22.204	0.001	0.001	0.000	0.000	0.000	0.000
76	A	75	HIS	0	-0.117	-0.059	26.471	0.018	0.018	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.044	-0.052	25.734	0.013	0.013	0.000	0.000	0.000	0.000
78	A	77	ILE	0	-0.027	-0.027	18.908	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.844	-0.893	21.386	-0.184	-0.184	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.871	-0.935	17.458	-0.258	-0.258	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.013	-0.004	13.456	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.003	0.017	11.313	0.052	0.052	0.000	0.000	0.000	0.000
83	A	82	SER	0	0.019	0.005	7.951	-0.319	-0.319	0.000	0.000	0.000	0.000
84	A	83	GLY	0	0.021	0.014	5.356	0.423	0.423	0.000	0.000	0.000	0.000
85	A	84	ASN	0	0.004	-0.024	3.051	-2.365	-1.502	0.186	-0.542	-0.508	-0.005
86	A	85	ARG	1	0.909	0.968	5.633	-0.158	-0.158	0.000	0.000	0.000	0.000
87	A	86	ILE	0	0.103	0.061	9.460	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.096	-0.062	11.978	0.125	0.125	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.776	-0.854	14.475	-0.319	-0.319	0.000	0.000	0.000	0.000
90	A	89	GLY	0	-0.021	0.003	18.040	0.048	0.048	0.000	0.000	0.000	0.000

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