FMO DATABASE

FMODB ID: R5GJ8

Calculation Name: 1T07-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T07

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HU36

Base Structure: X-ray

Registration Date: 2023-06-20

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	81
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-575501.23798
FMO2-HF: Nuclear repulsion	539930.924097
FMO2-HF: Total energy	-35570.313883
FMO2-MP2: Total energy	-35669.625925

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.
0.317	2.214	-0.011	-1.086	-0.801	0.005

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 : 0.070 / q_NPA : 0.039

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	1	MET	0	0.016	0.006	3.869	-0.185	1.712	-0.011	-1.086	-0.801	0.005
4	A	2	SER	0	-0.014	-0.031	7.081	0.007	0.007	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.848	0.927	10.239	0.356	0.356	0.000	0.000	0.000	0.000
6	A	4	THR	0	-0.077	-0.049	11.610	-0.056	-0.056	0.000	0.000	0.000	0.000
7	A	5	VAL	0	0.016	0.008	14.381	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	6	MET	0	0.020	0.031	17.190	0.022	0.022	0.000	0.000	0.000	0.000
9	A	7	CYM	-1	-0.847	-0.751	18.553	-0.068	-0.068	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.822	0.867	20.377	0.069	0.069	0.000	0.000	0.000	0.000
11	A	9	LYS	1	0.826	0.917	22.330	0.024	0.024	0.000	0.000	0.000	0.000
12	A	10	TYR	0	0.011	-0.031	19.346	0.009	0.009	0.000	0.000	0.000	0.000
13	A	11	HIS	0	-0.022	-0.001	21.658	0.021	0.021	0.000	0.000	0.000	0.000
14	A	12	GLU	-1	-0.833	-0.920	16.795	0.158	0.158	0.000	0.000	0.000	0.000
15	A	13	GLU	-1	-0.857	-0.919	14.201	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.034	-0.021	13.176	0.035	0.035	0.000	0.000	0.000	0.000
17	A	15	PRO	0	-0.017	-0.020	10.008	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.059	0.042	12.703	0.048	0.048	0.000	0.000	0.000	0.000
19	A	17	LEU	0	-0.005	0.002	15.491	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.865	-0.920	15.241	-0.541	-0.541	0.000	0.000	0.000	0.000
21	A	19	ARG	1	0.912	0.951	17.786	0.380	0.380	0.000	0.000	0.000	0.000
22	A	20	PRO	0	0.043	0.017	21.650	0.002	0.002	0.000	0.000	0.000	0.000
23	A	21	PRO	0	-0.034	0.008	24.301	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	22	TYR	0	0.017	-0.005	25.590	0.005	0.005	0.000	0.000	0.000	0.000
25	A	23	PRO	0	-0.001	0.001	28.922	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	24	GLY	0	0.046	0.017	31.068	0.008	0.008	0.000	0.000	0.000	0.000
27	A	25	ALA	0	0.060	0.019	31.063	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	26	LYS	1	0.853	0.914	30.878	0.061	0.061	0.000	0.000	0.000	0.000
29	A	27	GLY	0	0.041	0.024	28.020	0.000	0.000	0.000	0.000	0.000	0.000
30	A	28	GLU	-1	-0.946	-0.986	26.413	-0.126	-0.126	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.812	-0.868	26.349	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	30	ILE	0	0.005	0.002	23.501	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	31	TYR	0	-0.040	-0.019	20.147	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	32	ASN	0	-0.058	-0.029	21.401	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	33	ASN	0	-0.008	0.000	22.336	0.009	0.009	0.000	0.000	0.000	0.000
36	A	34	VAL	0	-0.004	0.002	21.652	0.019	0.019	0.000	0.000	0.000	0.000
37	A	35	SER	0	-0.045	-0.143	16.441	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.796	0.874	12.267	0.529	0.529	0.000	0.000	0.000	0.000
39	A	37	LYS	1	0.920	0.968	15.410	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	38	ALA	0	0.032	0.017	17.226	0.016	0.016	0.000	0.000	0.000	0.000
41	A	39	TRP	0	0.054	0.012	20.436	0.017	0.017	0.000	0.000	0.000	0.000
42	A	40	ASP	-1	-0.882	-0.953	17.289	-0.232	-0.232	0.000	0.000	0.000	0.000
43	A	41	GLU	-1	-0.868	-0.929	19.788	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	42	TRP	0	-0.002	0.010	22.519	0.013	0.013	0.000	0.000	0.000	0.000
45	A	43	GLN	0	-0.008	-0.005	23.652	0.012	0.012	0.000	0.000	0.000	0.000
46	A	44	LYS	1	0.812	0.904	20.133	0.078	0.078	0.000	0.000	0.000	0.000
47	A	45	HIS	0	0.022	0.007	25.881	0.006	0.006	0.000	0.000	0.000	0.000
48	A	46	GLN	0	0.020	0.005	28.433	0.010	0.010	0.000	0.000	0.000	0.000
49	A	47	THR	0	-0.042	-0.037	28.192	0.001	0.001	0.000	0.000	0.000	0.000
50	A	48	MET	0	-0.019	-0.004	29.159	0.006	0.006	0.000	0.000	0.000	0.000
51	A	49	LEU	0	-0.011	-0.008	31.870	0.004	0.004	0.000	0.000	0.000	0.000
52	A	50	ILE	0	-0.020	-0.017	32.737	0.003	0.003	0.000	0.000	0.000	0.000
53	A	51	ASN	0	0.001	-0.001	32.558	0.002	0.002	0.000	0.000	0.000	0.000
54	A	52	GLU	-1	-0.890	-0.947	35.705	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	53	ARG	1	0.859	0.930	37.688	0.029	0.029	0.000	0.000	0.000	0.000
56	A	54	ARG	1	0.813	0.916	38.983	0.030	0.030	0.000	0.000	0.000	0.000
57	A	55	LEU	0	-0.027	0.022	36.458	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	56	ASN	0	0.037	0.006	39.374	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	57	MET	0	0.057	0.021	33.738	0.003	0.003	0.000	0.000	0.000	0.000
60	A	58	MET	0	0.000	0.008	39.041	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	59	ASN	0	-0.029	-0.016	42.506	0.002	0.002	0.000	0.000	0.000	0.000
62	A	60	ALA	0	0.005	-0.001	42.188	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	61	GLU	-1	-0.783	-0.888	42.489	-0.032	-0.032	0.000	0.000	0.000	0.000
64	A	62	ASP	-1	-0.788	-0.881	39.864	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	63	ARG	1	0.852	0.912	37.816	0.058	0.058	0.000	0.000	0.000	0.000
66	A	64	LYS	1	0.807	0.906	37.664	0.029	0.029	0.000	0.000	0.000	0.000
67	A	65	PHE	0	0.017	0.002	36.602	0.001	0.001	0.000	0.000	0.000	0.000
68	A	66	LEU	0	0.045	0.007	33.408	0.002	0.002	0.000	0.000	0.000	0.000
69	A	67	GLN	0	-0.052	-0.019	33.280	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	68	GLN	0	-0.017	-0.023	34.524	0.001	0.001	0.000	0.000	0.000	0.000
71	A	69	GLU	-1	-0.805	-0.856	33.163	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	70	MET	0	0.003	0.014	29.070	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	71	ASP	-1	-0.816	-0.897	29.922	-0.053	-0.053	0.000	0.000	0.000	0.000
74	A	72	LYS	1	0.862	0.918	31.303	0.019	0.019	0.000	0.000	0.000	0.000
75	A	73	PHE	0	-0.038	-0.014	24.514	0.006	0.006	0.000	0.000	0.000	0.000
76	A	74	LEU	0	-0.024	-0.014	24.604	0.000	0.000	0.000	0.000	0.000	0.000
77	A	75	SER	0	-0.019	-0.028	27.396	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	76	GLY	0	0.036	0.017	26.877	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	77	GLU	-1	-0.905	-0.909	27.897	0.007	0.007	0.000	0.000	0.000	0.000
80	A	78	ASP	-1	-0.915	-0.950	28.797	0.048	0.048	0.000	0.000	0.000	0.000
81	A	79	TYR	0	-0.131	-0.094	28.978	-0.004	-0.004	0.000	0.000	0.000	0.000

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