FMO DATABASE

FMODB ID: 89N5Y

Calculation Name: 1DQ7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DQ7

Chain ID: A

ChEMBL ID:

UniProt ID: P60277

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-353122.626677
FMO2-HF: Nuclear repulsion	326541.552488
FMO2-HF: Total energy	-26581.074189
FMO2-MP2: Total energy	-26652.134717

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-25.581	-24.883	17.936	-10.074	-8.559	-0.086

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.028

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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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	3	ASP	-1	-0.847	-0.909	3.860	-4.743	-2.887	-0.012	-1.089	-0.754	0.004
4	A	4	GLY	0	-0.034	-0.026	6.856	0.578	0.578	0.000	0.000	0.000	0.000
5	A	5	TYR	0	-0.082	-0.065	9.662	0.046	0.046	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.043	0.036	9.810	0.085	0.085	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.026	-0.027	11.557	0.068	0.068	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.811	-0.906	13.511	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.002	-0.008	15.520	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.861	-0.922	16.877	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.056	-0.036	16.271	-0.051	-0.051	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.009	0.024	17.545	-0.032	-0.032	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.054	0.025	15.694	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.014	-0.003	14.635	0.065	0.065	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.042	0.027	17.725	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.093	-0.031	14.892	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.025	-0.027	20.850	0.026	0.026	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.045	0.012	21.815	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.075	0.030	17.541	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.005	0.006	16.983	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.011	-0.003	17.615	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.005	0.005	13.967	0.020	0.020	0.000	0.000	0.000	0.000
23	A	23	HIS	0	0.067	0.046	12.390	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.009	0.021	12.912	0.017	0.017	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.010	0.009	13.003	0.051	0.051	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.070	-0.033	7.443	0.422	0.422	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.019	0.018	8.908	0.105	0.105	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.934	-0.980	10.670	0.318	0.318	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.804	0.914	9.378	0.109	0.109	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.794	0.884	7.757	-0.317	-0.317	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.068	0.040	4.673	0.536	0.594	-0.001	-0.006	-0.050	0.000
32	A	32	ASP	-1	-0.953	-0.958	5.485	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.091	-0.094	7.402	0.376	0.376	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.031	0.000	9.022	-0.217	-0.217	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.063	-0.029	11.703	0.127	0.127	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.795	-0.877	16.625	-0.531	-0.531	0.000	0.000	0.000	0.000
37	A	38	TRP	0	-0.038	-0.045	18.478	0.040	0.040	0.000	0.000	0.000	0.000
38	A	39	TRP	0	-0.027	-0.018	21.299	0.046	0.046	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.045	0.053	17.662	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	PRO	0	-0.036	-0.028	19.843	0.041	0.041	0.000	0.000	0.000	0.000
41	A	42	TYR	0	-0.036	-0.025	16.884	0.051	0.051	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.015	0.008	21.662	0.026	0.026	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.012	-0.010	21.282	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.009	-0.019	17.002	0.032	0.032	0.000	0.000	0.000	0.000
45	A	47	TRP	0	-0.001	-0.004	10.186	0.043	0.043	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.840	-0.876	6.963	-1.639	-1.639	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.833	-0.933	1.812	-16.463	-20.205	12.332	-5.279	-3.311	-0.057
48	A	51	LEU	0	-0.030	-0.014	2.364	-0.457	0.262	3.089	-1.664	-2.145	-0.019
49	A	52	PRO	0	0.013	0.003	2.626	-1.297	0.112	2.407	-1.897	-1.919	-0.014
50	A	53	THR	0	0.057	0.023	3.051	-2.202	-1.809	0.122	-0.128	-0.387	0.000
51	A	54	PRO	0	-0.119	-0.053	4.634	-0.680	-0.675	-0.001	-0.011	0.007	0.000
52	A	55	VAL	0	-0.041	-0.012	6.832	-0.269	-0.269	0.000	0.000	0.000	0.000
53	A	56	PRO	0	-0.005	0.001	7.743	-0.228	-0.228	0.000	0.000	0.000	0.000
54	A	57	ILE	0	0.064	0.045	7.810	0.002	0.002	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.791	0.888	10.513	0.412	0.412	0.000	0.000	0.000	0.000
56	A	59	GLY	0	0.073	0.055	14.081	-0.063	-0.063	0.000	0.000	0.000	0.000
57	A	60	SER	0	-0.012	-0.016	15.055	0.026	0.026	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.015	0.013	18.568	0.033	0.033	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.902	0.940	21.647	0.101	0.101	0.000	0.000	0.000	0.000
60	A	64	ARG	1	0.833	0.900	19.401	0.029	0.029	0.000	0.000	0.000	0.000

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