FMO DATABASE

FMODB ID: N3R4Q

Calculation Name: 2PTU-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTU

Chain ID: A

ChEMBL ID:

UniProt ID: Q07763

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-813867.862483
FMO2-HF: Nuclear repulsion	772555.137654
FMO2-HF: Total energy	-41312.724829
FMO2-MP2: Total energy	-41435.372996

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:4:ACE )

Summations of interaction energy for fragment #1(A:4:ACE )

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.
-0.632	-2.003	10.585	-5.852	-3.36	-0.027

Interaction energy analysis for fragmet #1(A:4:ACE )

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 : -0.053

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

Sort

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	6	SER	0	-0.001	-0.005	3.595	0.337	1.863	-0.003	-0.811	-0.712	-0.002
4	A	7	SER	0	-0.067	-0.033	4.993	0.579	0.659	0.000	-0.006	-0.073	0.000
5	A	8	GLU	-1	-0.883	-0.943	7.476	-0.114	-0.114	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.933	-0.942	10.941	0.276	0.276	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.015	0.012	14.078	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.003	0.002	16.621	0.021	0.021	0.000	0.000	0.000	0.000
9	A	12	GLY	0	-0.008	-0.015	20.054	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.023	0.003	22.847	0.002	0.002	0.000	0.000	0.000	0.000
11	A	14	SER	0	0.020	0.008	26.267	0.003	0.003	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.022	-0.009	27.493	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.922	0.954	27.268	-0.056	-0.056	0.000	0.000	0.000	0.000
14	A	17	PRO	0	-0.023	0.011	24.779	0.008	0.008	0.000	0.000	0.000	0.000
15	A	18	VAL	0	0.010	0.008	19.105	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.030	-0.038	18.327	0.002	0.002	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.005	0.011	13.221	0.000	0.000	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.957	0.978	14.907	0.058	0.058	0.000	0.000	0.000	0.000
19	A	22	PRO	0	0.047	0.047	10.983	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	23	SER	0	0.000	-0.014	11.951	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	24	ASN	0	-0.046	-0.039	11.957	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.019	0.028	10.342	-0.110	-0.110	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.061	-0.039	12.775	0.001	0.001	0.000	0.000	0.000	0.000
24	A	27	THR	0	0.030	0.012	14.362	0.004	0.004	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.936	0.956	17.024	0.123	0.123	0.000	0.000	0.000	0.000
26	A	29	ASP	-1	-0.893	-0.937	18.441	-0.132	-0.132	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.042	-0.016	14.089	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	31	SER	0	0.001	0.021	14.426	0.017	0.017	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.012	-0.012	12.912	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	33	GLN	0	-0.005	-0.005	11.383	0.031	0.031	0.000	0.000	0.000	0.000
31	A	34	TRP	0	-0.004	0.013	11.100	0.080	0.080	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.830	0.903	10.013	-0.485	-0.485	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.931	0.983	11.578	-0.217	-0.217	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.057	-0.035	10.422	0.000	0.000	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.929	-0.957	13.075	0.192	0.192	0.000	0.000	0.000	0.000
36	A	39	GLN	0	0.005	-0.018	16.234	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	40	GLY	0	-0.028	0.003	17.383	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.000	0.003	18.508	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.007	0.004	15.935	0.064	0.064	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.882	0.944	14.499	-0.176	-0.176	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.968	0.989	8.029	-1.179	-1.179	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.054	0.030	14.127	-0.047	-0.047	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.915	-0.964	14.893	0.243	0.243	0.000	0.000	0.000	0.000
44	A	47	ILE	0	-0.034	-0.021	14.850	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.013	0.003	16.211	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	49	ASN	0	-0.003	0.000	15.779	0.038	0.038	0.000	0.000	0.000	0.000
47	A	50	TRP	0	0.026	0.014	16.695	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	51	TYR	0	0.027	0.004	14.144	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.017	-0.017	19.561	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	53	ASP	-1	-0.922	-0.941	23.206	0.017	0.017	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.028	-0.008	23.457	0.003	0.003	0.000	0.000	0.000	0.000
52	A	55	PRO	0	-0.041	-0.026	20.386	0.007	0.007	0.000	0.000	0.000	0.000
53	A	56	SER	0	0.031	-0.002	20.715	0.003	0.003	0.000	0.000	0.000	0.000
54	A	57	TRP	0	-0.023	-0.013	19.284	0.017	0.017	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.003	-0.002	19.067	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	59	ASN	0	-0.037	-0.013	21.763	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	60	VAL	0	0.066	0.017	24.777	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	61	SER	0	0.023	0.011	26.990	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	62	PHE	0	-0.043	-0.025	19.710	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.007	0.014	23.621	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.877	-0.934	25.666	0.055	0.055	0.000	0.000	0.000	0.000
62	A	65	ILE	0	-0.084	-0.031	22.667	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	66	TYR	0	0.035	0.006	18.661	0.009	0.009	0.000	0.000	0.000	0.000
64	A	67	GLY	0	-0.037	-0.003	21.114	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	68	PHE	0	0.000	-0.003	16.093	0.011	0.011	0.000	0.000	0.000	0.000
66	A	69	ASP	-1	-0.822	-0.879	19.397	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.016	-0.022	19.317	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	71	GLY	0	-0.023	-0.005	20.379	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	72	ASP	-1	-0.904	-0.975	17.826	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	73	PHE	0	-0.009	-0.027	13.616	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.013	0.006	15.287	0.033	0.033	0.000	0.000	0.000	0.000
72	A	75	LEU	0	-0.016	0.021	15.049	0.000	0.000	0.000	0.000	0.000	0.000
73	A	76	SER	0	-0.042	-0.027	17.018	0.004	0.004	0.000	0.000	0.000	0.000
74	A	77	ILE	0	0.034	0.021	18.143	0.003	0.003	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.874	0.904	21.696	-0.075	-0.075	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.017	-0.015	25.397	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.003	0.020	23.118	0.005	0.005	0.000	0.000	0.000	0.000
78	A	81	LYS	1	1.012	0.995	24.095	-0.110	-0.110	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.073	0.038	23.399	0.014	0.014	0.000	0.000	0.000	0.000
80	A	83	GLN	0	-0.053	-0.025	22.424	0.013	0.013	0.000	0.000	0.000	0.000
81	A	84	ASP	-1	-0.835	-0.907	20.012	0.171	0.171	0.000	0.000	0.000	0.000
82	A	85	SER	0	0.011	0.023	18.089	0.023	0.023	0.000	0.000	0.000	0.000
83	A	86	GLY	0	-0.050	-0.029	15.577	0.005	0.005	0.000	0.000	0.000	0.000
84	A	87	HIS	0	0.005	0.019	6.655	-0.185	-0.185	0.000	0.000	0.000	0.000
85	A	88	TYR	0	-0.035	-0.062	10.681	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.063	-0.038	4.642	0.135	0.176	0.000	-0.009	-0.031	0.000
87	A	90	LEU	0	0.031	0.020	7.565	-0.142	-0.142	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.869	-0.934	6.402	0.818	0.818	0.000	0.000	0.000	0.000
89	A	92	ILE	0	0.036	0.023	8.230	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	93	THR	0	-0.039	-0.009	9.147	-0.140	-0.140	0.000	0.000	0.000	0.000
91	A	94	ASN	0	0.078	0.033	11.273	0.051	0.051	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.051	0.016	14.041	0.005	0.005	0.000	0.000	0.000	0.000
93	A	96	GLY	0	-0.051	-0.013	15.500	0.017	0.017	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.014	0.010	13.345	0.009	0.009	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.878	0.936	9.705	0.455	0.455	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.034	0.013	5.198	0.054	0.054	0.000	0.000	0.000	0.000
97	A	100	CYS	0	-0.001	0.006	5.516	-0.579	-0.579	0.000	0.000	0.000	0.000
98	A	101	ASN	0	-0.041	0.000	2.113	0.268	-3.007	10.097	-4.595	-2.226	-0.024
99	A	102	LYS	1	0.926	0.960	3.796	-0.212	-0.277	0.014	-0.094	0.146	0.000
100	A	103	ASN	0	-0.036	-0.031	2.401	-0.429	-0.107	0.477	-0.337	-0.464	-0.001
101	A	104	PHE	0	0.046	0.022	6.182	-0.239	-0.239	0.000	0.000	0.000	0.000
102	A	105	GLN	0	-0.012	-0.019	9.912	0.160	0.160	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.016	-0.001	12.562	-0.058	-0.058	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.032	-0.020	15.843	0.009	0.009	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.025	-0.017	19.014	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.033	-0.025	22.314	0.002	0.002	0.000	0.000	0.000	0.000
107	A	110	ASP	-2	-1.831	-1.925	25.501	0.151	0.151	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE )