FMO DATABASE

FMODB ID: ZY5LN

Calculation Name: 4D3G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3G

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G229

Base Structure: X-ray

Registration Date: 2023-06-19

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-480336.29189
FMO2-HF: Nuclear repulsion	449002.348821
FMO2-HF: Total energy	-31333.943069
FMO2-MP2: Total energy	-31422.316645

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:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-30.36	-20.108	10.426	-8.814	-11.861	-0.073

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.014

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	LYS	1	0.830	0.899	3.751	-3.676	-0.447	-0.018	-1.610	-1.601	0.009
4	A	3	MET	0	0.000	0.006	6.787	0.176	0.176	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.013	0.009	9.791	-0.124	-0.124	0.000	0.000	0.000	0.000
6	A	5	ILE	0	-0.008	-0.006	13.362	0.005	0.005	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.028	0.006	16.360	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.035	-0.020	19.357	0.007	0.007	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.005	-0.001	22.802	0.006	0.006	0.000	0.000	0.000	0.000
10	A	9	GLN	0	0.089	0.036	25.190	0.002	0.002	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.786	-0.875	28.620	-0.049	-0.049	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.039	-0.014	30.052	0.004	0.004	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.724	-0.850	28.327	0.007	0.007	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.034	-0.019	26.228	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	GLN	0	-0.084	-0.064	26.318	0.008	0.008	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.794	-0.893	27.803	0.035	0.035	0.000	0.000	0.000	0.000
17	A	16	LEU	0	0.008	0.019	21.126	0.014	0.014	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.039	-0.035	22.952	0.018	0.018	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.853	-0.907	23.536	0.114	0.114	0.000	0.000	0.000	0.000
20	A	19	GLN	0	0.010	-0.005	22.944	0.022	0.022	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.000	0.006	17.632	0.021	0.021	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.006	0.007	18.995	0.038	0.038	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.781	0.882	20.651	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.034	-0.013	17.640	0.013	0.013	0.000	0.000	0.000	0.000
25	A	24	ASN	0	-0.062	-0.021	15.709	0.030	0.030	0.000	0.000	0.000	0.000
26	A	25	PHE	0	0.047	0.017	12.109	0.069	0.069	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.954	0.983	13.755	-0.231	-0.231	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.026	0.015	14.454	0.017	0.017	0.000	0.000	0.000	0.000
29	A	28	THR	0	-0.085	-0.057	16.700	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	29	LYS	1	0.936	0.984	18.256	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.007	0.006	18.754	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.002	-0.008	22.376	0.005	0.005	0.000	0.000	0.000	0.000
33	A	32	THR	0	-0.013	-0.023	25.916	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	33	THR	0	0.022	0.032	27.909	0.003	0.003	0.000	0.000	0.000	0.000
35	A	41	ASN	0	-0.052	-0.053	27.830	0.007	0.007	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.042	-0.049	25.155	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	43	THR	0	0.013	0.017	19.993	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.025	-0.014	18.788	0.006	0.006	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.001	0.002	14.444	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.061	-0.041	13.492	0.052	0.052	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.073	0.048	9.163	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.037	-0.013	9.113	0.053	0.053	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.017	-0.038	4.334	0.707	0.768	-0.001	-0.018	-0.041	0.000
44	A	50	ASP	-1	-0.811	-0.905	2.474	-8.951	-5.062	1.905	-2.595	-3.198	-0.029
45	A	51	ASP	-1	-0.888	-0.915	4.657	0.512	0.704	-0.001	-0.016	-0.174	0.000
46	A	52	ARG	1	0.819	0.886	7.319	-0.195	-0.195	0.000	0.000	0.000	0.000
47	A	53	VAL	0	0.001	-0.004	8.440	0.049	0.049	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.868	-0.941	11.068	0.046	0.046	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.864	-0.904	13.347	0.305	0.305	0.000	0.000	0.000	0.000
50	A	56	ILE	0	0.003	-0.002	13.263	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.009	-0.009	14.646	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.017	-0.008	17.235	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	59	VAL	0	0.007	0.006	18.768	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.014	-0.009	17.802	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.026	-0.003	21.396	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	62	GLN	0	-0.026	-0.001	22.447	0.002	0.002	0.000	0.000	0.000	0.000
57	A	63	THR	0	-0.081	-0.032	23.932	0.001	0.001	0.000	0.000	0.000	0.000
58	A	64	CYS	0	-0.135	-0.077	25.374	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	65	GLY	0	0.055	0.023	25.913	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	66	ASN	0	-0.019	-0.026	27.936	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.849	0.952	29.606	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	93	VAL	0	0.032	0.009	34.546	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	94	GLY	0	0.018	0.019	31.160	0.005	0.005	0.000	0.000	0.000	0.000
64	A	95	GLY	0	-0.021	-0.015	28.332	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	96	ALA	0	0.005	0.001	23.123	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	97	THR	0	-0.047	-0.022	21.733	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	98	VAL	0	-0.002	-0.001	16.336	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	99	PHE	0	-0.016	0.011	15.688	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.024	0.006	9.763	0.033	0.033	0.000	0.000	0.000	0.000
70	A	101	MET	0	-0.040	-0.023	10.579	-0.057	-0.057	0.000	0.000	0.000	0.000
71	A	102	PRO	0	0.031	0.012	6.731	0.330	0.330	0.000	0.000	0.000	0.000
72	A	103	VAL	0	-0.012	-0.008	3.053	-0.699	-0.069	0.055	-0.156	-0.529	0.001
73	A	104	ASP	-1	-0.882	-0.929	2.791	-7.074	-5.572	1.818	-1.001	-2.320	-0.010
74	A	105	ALA	0	-0.048	-0.037	1.968	-13.991	-13.902	6.646	-3.319	-3.416	-0.042
75	A	106	PHE	0	0.000	0.006	3.390	1.408	2.001	0.023	-0.097	-0.519	-0.002
76	A	107	HIS	0	0.002	-0.003	4.603	0.650	0.717	-0.001	-0.002	-0.063	0.000
77	A	108	GLN	0	-0.021	-0.017	8.086	0.208	0.208	0.000	0.000	0.000	0.000
78	A	109	PHE	0	0.024	0.026	11.142	0.065	0.065	0.000	0.000	0.000	0.000

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