FMO DATABASE

FMODB ID: 1N67Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-353108.961471
FMO2-HF: Nuclear repulsion	326528.634001
FMO2-HF: Total energy	-26580.32747
FMO2-MP2: Total energy	-26651.473305

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.
-2.212	0.785	4.514	-2.705	-4.804	-0.021

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 : -0.065 / q_NPA : -0.041

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	-0.794	-0.887	3.813	-1.248	-0.018	-0.012	-0.630	-0.587	0.000
4	A	4	GLY	0	-0.042	-0.028	6.209	0.221	0.221	0.000	0.000	0.000	0.000
5	A	5	TYR	0	-0.080	-0.045	9.199	0.018	0.018	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.051	0.050	9.861	0.024	0.024	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.029	-0.035	11.196	0.105	0.105	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.790	-0.885	13.762	-0.253	-0.253	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.060	-0.046	16.417	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.961	-0.976	17.465	-0.152	-0.152	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.039	-0.031	17.020	-0.030	-0.030	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.013	0.031	18.072	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.065	0.038	15.481	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.010	0.002	15.133	0.032	0.032	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.019	0.015	17.834	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.106	-0.054	14.740	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.001	-0.004	20.904	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.039	-0.001	21.658	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.108	0.050	17.596	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.022	-0.007	16.953	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.009	0.007	17.519	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	CYS	0	0.009	0.003	13.712	0.010	0.010	0.000	0.000	0.000	0.000
23	A	23	HIS	0	0.088	0.067	12.462	-0.074	-0.074	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.006	0.046	12.877	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.007	0.010	13.168	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.079	-0.055	7.276	0.123	0.123	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.003	-0.028	9.094	-0.073	-0.073	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.951	-0.971	10.644	-0.150	-0.150	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.776	0.893	8.998	0.357	0.357	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.864	0.906	7.093	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.043	0.036	4.987	-0.162	-0.162	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.877	-0.917	5.537	1.380	1.380	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.098	-0.075	7.315	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.033	0.006	8.938	-0.156	-0.156	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.064	-0.027	11.545	0.073	0.073	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.826	-0.911	16.239	-0.197	-0.197	0.000	0.000	0.000	0.000
37	A	38	TRP	0	-0.060	-0.053	18.146	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	TRP	0	-0.062	-0.026	21.210	0.010	0.010	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.047	0.059	17.442	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	41	PRO	0	-0.041	-0.036	19.206	0.016	0.016	0.000	0.000	0.000	0.000
41	A	42	TYR	0	-0.024	-0.022	16.993	0.019	0.019	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.016	0.015	21.637	0.008	0.008	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.005	-0.002	21.199	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.016	-0.029	16.461	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	TRP	0	0.012	0.015	9.384	-0.081	-0.081	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.908	-0.952	6.421	0.024	0.024	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.829	-0.914	2.538	2.020	2.327	1.319	-0.426	-1.200	0.002
48	A	51	LEU	0	-0.057	-0.034	2.451	-1.675	-1.884	2.165	-0.209	-1.746	-0.012
49	A	52	PRO	0	-0.011	-0.013	2.682	-2.599	-1.000	1.039	-1.419	-1.219	-0.011
50	A	53	THR	0	0.076	0.031	3.938	-0.254	-0.184	0.003	-0.021	-0.052	0.000
51	A	54	PRO	0	-0.118	-0.055	5.543	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.043	-0.022	7.408	0.105	0.105	0.000	0.000	0.000	0.000
53	A	56	PRO	0	0.034	0.025	8.104	-0.148	-0.148	0.000	0.000	0.000	0.000
54	A	57	ILE	0	0.050	0.033	8.031	0.040	0.040	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.782	0.895	11.124	0.375	0.375	0.000	0.000	0.000	0.000
56	A	59	GLY	0	0.071	0.041	14.122	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	60	SER	0	-0.041	-0.029	15.906	0.043	0.043	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.022	0.011	19.336	0.009	0.009	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.908	0.930	22.311	0.133	0.133	0.000	0.000	0.000	0.000
60	A	64	ARG	1	0.952	0.979	20.102	0.198	0.198	0.000	0.000	0.000	0.000

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