FMO DATABASE

FMODB ID: N3RKQ

Calculation Name: 1TR8-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TR8

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0K9

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:

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	94
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-546615.477557
FMO2-HF: Nuclear repulsion	508795.603295
FMO2-HF: Total energy	-37819.874262
FMO2-MP2: Total energy	-37926.371037

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:24:ACE )

Summations of interaction energy for fragment #1(A:24: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.
1.552	2.844	0.119	-0.543	-0.868	0

Interaction energy analysis for fragmet #1(A:24:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.006

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].
3	A	26	MET	0	-0.018	0.005	3.369	1.315	2.406	0.093	-0.462	-0.722
4	A	27	LYS	1	0.955	0.991	5.513	0.289	0.289	0.000	0.000	0.000
5	A	28	ASP	-1	-0.831	-0.914	9.291	-0.059	-0.059	0.000	0.000	0.000
6	A	29	LEU	0	-0.042	-0.028	11.862	-0.024	-0.024	0.000	0.000	0.000
7	A	30	ARG	1	0.943	0.960	14.624	0.110	0.110	0.000	0.000	0.000
8	A	31	GLY	0	0.001	-0.003	17.881	0.000	0.000	0.000	0.000	0.000
9	A	32	VAL	0	0.004	0.009	17.365	0.003	0.003	0.000	0.000	0.000
10	A	33	GLU	-1	-0.867	-0.930	20.512	0.001	0.001	0.000	0.000	0.000
11	A	34	GLU	-1	-0.967	-0.999	22.741	0.042	0.042	0.000	0.000	0.000
12	A	35	VAL	0	-0.043	-0.009	17.979	-0.003	-0.003	0.000	0.000	0.000
13	A	36	VAL	0	0.011	0.001	21.287	0.004	0.004	0.000	0.000	0.000
14	A	37	ILE	0	-0.035	-0.020	19.216	0.001	0.001	0.000	0.000	0.000
15	A	38	LYS	1	0.979	0.996	22.881	-0.044	-0.044	0.000	0.000	0.000
16	A	39	LEU	0	-0.011	-0.004	24.277	0.006	0.006	0.000	0.000	0.000
17	A	40	LYS	1	0.999	0.994	27.552	-0.063	-0.063	0.000	0.000	0.000
18	A	41	ARG	1	0.850	0.897	30.893	-0.061	-0.061	0.000	0.000	0.000
19	A	42	LYS	1	0.918	0.964	26.677	-0.099	-0.099	0.000	0.000	0.000
20	A	43	GLU	-1	-0.862	-0.912	27.068	0.053	0.053	0.000	0.000	0.000
21	A	44	ILE	0	-0.019	-0.005	22.655	0.000	0.000	0.000	0.000	0.000
22	A	45	ILE	0	0.002	-0.004	24.130	-0.001	-0.001	0.000	0.000	0.000
23	A	46	ILE	0	-0.030	-0.022	19.001	0.003	0.003	0.000	0.000	0.000
24	A	47	LYS	1	0.975	0.973	22.451	-0.052	-0.052	0.000	0.000	0.000
25	A	48	ASN	0	-0.034	-0.003	22.190	0.000	0.000	0.000	0.000	0.000
26	A	49	PRO	0	-0.025	-0.005	17.483	0.004	0.004	0.000	0.000	0.000
27	A	50	LYS	1	0.901	0.958	12.273	-0.013	-0.013	0.000	0.000	0.000
28	A	51	VAL	0	-0.009	-0.023	13.199	0.038	0.038	0.000	0.000	0.000
29	A	52	ASN	0	0.011	0.012	7.861	-0.125	-0.125	0.000	0.000	0.000
30	A	53	VAL	0	-0.028	-0.017	9.325	0.098	0.098	0.000	0.000	0.000
31	A	54	MET	0	0.020	0.012	3.428	-0.024	0.177	0.026	-0.081	-0.146
32	A	55	GLU	-1	-0.895	-0.958	7.642	0.005	0.005	0.000	0.000	0.000
33	A	56	PHE	0	-0.007	-0.011	6.882	-0.134	-0.134	0.000	0.000	0.000
34	A	57	MET	0	-0.018	-0.013	8.973	0.055	0.055	0.000	0.000	0.000
35	A	58	GLY	0	0.038	0.030	12.354	0.026	0.026	0.000	0.000	0.000
36	A	59	GLN	0	0.008	0.014	12.200	-0.006	-0.006	0.000	0.000	0.000
37	A	60	LYS	1	0.909	0.958	11.104	0.080	0.080	0.000	0.000	0.000
38	A	61	THR	0	-0.009	-0.003	8.065	0.090	0.090	0.000	0.000	0.000
39	A	62	TYR	0	0.017	-0.009	9.571	-0.067	-0.067	0.000	0.000	0.000
40	A	63	GLN	0	-0.012	-0.001	7.646	0.008	0.008	0.000	0.000	0.000
41	A	64	VAL	0	0.032	0.012	10.794	-0.070	-0.070	0.000	0.000	0.000
42	A	65	THR	0	-0.012	0.000	13.321	0.032	0.032	0.000	0.000	0.000
43	A	66	GLY	0	0.070	0.022	15.702	-0.031	-0.031	0.000	0.000	0.000
44	A	67	LYS	1	0.913	0.959	19.410	-0.075	-0.075	0.000	0.000	0.000
45	A	68	ALA	0	0.042	0.024	22.038	-0.007	-0.007	0.000	0.000	0.000
46	A	69	ARG	1	0.903	0.954	23.794	-0.060	-0.060	0.000	0.000	0.000
47	A	70	GLU	-1	-0.850	-0.909	26.746	0.092	0.092	0.000	0.000	0.000
48	A	71	ARG	1	0.872	0.929	29.044	-0.049	-0.049	0.000	0.000	0.000
49	A	72	SER	0	-0.007	-0.007	31.223	0.004	0.004	0.000	0.000	0.000
50	A	73	LEU	0	0.001	-0.008	31.952	-0.003	-0.003	0.000	0.000	0.000
51	A	74	GLU	-1	-0.897	-0.949	35.066	0.044	0.044	0.000	0.000	0.000
52	A	75	ALA	0	-0.036	-0.012	38.584	-0.001	-0.001	0.000	0.000	0.000
53	A	76	GLU	-1	-0.937	-0.960	40.701	0.024	0.024	0.000	0.000	0.000
54	A	77	MET	0	-0.045	-0.030	42.869	0.000	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.944	-0.960	46.272	0.018	0.018	0.000	0.000	0.000
56	A	79	ILE	0	-0.025	-0.014	47.425	0.001	0.001	0.000	0.000	0.000
57	A	80	PRO	0	0.001	0.004	51.299	-0.001	-0.001	0.000	0.000	0.000
58	A	81	GLU	-1	-0.819	-0.899	55.028	0.020	0.020	0.000	0.000	0.000
59	A	82	ASP	-1	-0.870	-0.938	56.964	0.018	0.018	0.000	0.000	0.000
60	A	83	ASP	-1	-0.910	-0.957	53.857	0.023	0.023	0.000	0.000	0.000
61	A	84	ILE	0	-0.037	-0.030	52.111	0.001	0.001	0.000	0.000	0.000
62	A	85	GLU	-1	-0.948	-0.989	54.434	0.019	0.019	0.000	0.000	0.000
63	A	86	LEU	0	-0.025	-0.001	56.832	0.000	0.000	0.000	0.000	0.000
64	A	87	VAL	0	0.021	-0.002	51.316	0.001	0.001	0.000	0.000	0.000
65	A	88	MET	0	-0.051	0.006	54.379	0.001	0.001	0.000	0.000	0.000
66	A	89	ASN	0	-0.036	-0.024	55.778	0.001	0.001	0.000	0.000	0.000
67	A	90	GLN	0	-0.062	-0.020	56.831	0.000	0.000	0.000	0.000	0.000
68	A	91	THR	0	-0.066	-0.039	52.671	0.001	0.001	0.000	0.000	0.000
69	A	92	GLY	0	-0.007	0.003	54.834	0.001	0.001	0.000	0.000	0.000
70	A	93	ALA	0	-0.037	0.003	51.153	0.000	0.000	0.000	0.000	0.000
71	A	94	SER	0	0.047	0.017	50.139	-0.001	-0.001	0.000	0.000	0.000
72	A	95	ARG	1	0.963	0.936	51.932	-0.021	-0.021	0.000	0.000	0.000
73	A	96	GLU	-1	-0.980	-0.979	46.347	0.033	0.033	0.000	0.000	0.000
74	A	97	ASP	-1	-0.836	-0.923	46.952	0.036	0.036	0.000	0.000	0.000
75	A	98	ALA	0	-0.001	0.009	47.665	0.001	0.001	0.000	0.000	0.000
76	A	99	THR	0	-0.002	-0.009	47.630	0.000	0.000	0.000	0.000	0.000
77	A	100	ARG	1	0.909	0.951	41.556	-0.038	-0.038	0.000	0.000	0.000
78	A	101	ALA	0	-0.059	-0.032	44.267	0.002	0.002	0.000	0.000	0.000
79	A	102	LEU	0	0.072	0.026	45.553	0.001	0.001	0.000	0.000	0.000
80	A	103	GLN	0	-0.039	-0.015	42.998	0.000	0.000	0.000	0.000	0.000
81	A	104	GLU	-1	-0.927	-0.949	39.213	0.051	0.051	0.000	0.000	0.000
82	A	105	THR	0	-0.083	-0.046	41.727	0.002	0.002	0.000	0.000	0.000
83	A	106	GLY	0	-0.027	-0.006	43.962	-0.001	-0.001	0.000	0.000	0.000
84	A	107	GLY	0	0.011	-0.004	44.994	-0.002	-0.002	0.000	0.000	0.000
85	A	108	ASP	-1	-0.897	-0.931	47.613	0.029	0.029	0.000	0.000	0.000
86	A	109	LEU	0	0.070	0.018	49.286	0.001	0.001	0.000	0.000	0.000
87	A	110	ALA	0	-0.010	0.000	51.338	0.000	0.000	0.000	0.000	0.000
88	A	111	GLU	-1	-0.922	-0.976	45.720	0.037	0.037	0.000	0.000	0.000
89	A	112	ALA	0	-0.040	-0.014	47.797	0.002	0.002	0.000	0.000	0.000
90	A	113	ILE	0	-0.013	-0.020	48.819	0.001	0.001	0.000	0.000	0.000
91	A	114	MET	0	-0.058	-0.027	49.343	0.000	0.000	0.000	0.000	0.000
92	A	115	ARG	1	0.880	0.963	40.436	-0.043	-0.043	0.000	0.000	0.000
93	A	116	LEU	0	-0.062	-0.024	46.695	0.002	0.002	0.000	0.000	0.000
94	A	117	NME	0	0.001	0.012	49.190	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:ACE )