FMO DATABASE

FMODB ID: YV662

Calculation Name: 1TBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TBX

Chain ID: A

ChEMBL ID:

UniProt ID: P20222

Base Structure: X-ray

Registration Date: 2023-09-20

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723165.765479
FMO2-HF: Nuclear repulsion	685072.025946
FMO2-HF: Total energy	-38093.739532
FMO2-MP2: Total energy	-38207.815773

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
0.049000000000001	1.657	-0.007	-0.83	-0.77	0.003

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.005

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	5	PRO	0	0.020	0.014	3.835	-1.063	0.452	-0.006	-0.823	-0.686	0.003
4	A	6	PHE	0	-0.027	-0.016	6.208	0.476	0.476	0.000	0.000	0.000	0.000
5	A	7	PHE	0	-0.005	0.002	8.125	0.354	0.354	0.000	0.000	0.000	0.000
6	A	8	TYR	0	0.074	0.049	6.839	-0.485	-0.485	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.033	-0.008	6.279	0.283	0.283	0.000	0.000	0.000	0.000
8	A	10	GLU	-1	-0.837	-0.920	8.789	-0.519	-0.519	0.000	0.000	0.000	0.000
9	A	11	ALA	0	0.001	-0.003	11.615	0.080	0.080	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.011	-0.006	7.517	0.083	0.083	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.001	-0.007	11.606	0.071	0.071	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.021	-0.005	13.903	0.025	0.025	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.015	-0.003	14.807	0.023	0.023	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.082	-0.091	13.234	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.044	-0.009	16.891	0.029	0.029	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.026	0.007	19.826	0.002	0.002	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.899	-0.939	21.703	-0.054	-0.054	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.041	-0.028	21.300	0.038	0.038	0.000	0.000	0.000	0.000
19	A	21	GLU	-1	-0.772	-0.867	23.405	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.018	0.016	25.277	0.000	0.000	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.059	-0.018	20.034	0.013	0.013	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.033	0.013	23.100	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.003	-0.046	18.457	0.007	0.007	0.000	0.000	0.000	0.000
24	A	26	TYR	0	0.029	0.009	16.325	0.018	0.018	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.820	-0.895	17.750	0.223	0.223	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.010	0.003	16.112	0.008	0.008	0.000	0.000	0.000	0.000
27	A	29	TYR	0	-0.060	-0.039	10.313	-0.093	-0.093	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.854	0.898	13.430	-0.173	-0.173	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.883	0.941	14.614	-0.070	-0.070	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.017	0.011	9.974	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.013	0.001	9.574	0.235	0.235	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.014	-0.002	10.277	0.059	0.059	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.816	-0.866	10.941	-0.083	-0.083	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.042	-0.028	6.705	-0.224	-0.224	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.009	0.007	5.905	0.255	0.255	0.000	0.000	0.000	0.000
36	A	38	MET	0	-0.009	0.013	4.858	1.002	1.095	-0.001	-0.007	-0.084	0.000
37	A	39	SER	0	0.035	0.021	6.396	-0.892	-0.892	0.000	0.000	0.000	0.000
38	A	40	THR	0	0.064	0.014	8.501	-0.118	-0.118	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.035	0.026	10.604	-0.118	-0.118	0.000	0.000	0.000	0.000
40	A	42	THR	0	0.038	0.015	5.885	0.117	0.117	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.003	-0.003	9.159	-0.195	-0.195	0.000	0.000	0.000	0.000
42	A	44	TYR	0	0.010	-0.008	11.502	-0.144	-0.144	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.815	-0.898	12.022	0.085	0.085	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.003	0.013	11.004	-0.098	-0.098	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.815	0.890	13.080	-0.195	-0.195	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.862	0.928	16.273	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.038	0.018	15.298	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	50	LEU	0	0.008	0.000	15.407	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.057	-0.019	18.618	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.034	-0.022	20.447	0.014	0.014	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.899	-0.936	19.309	-0.172	-0.172	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.009	0.005	22.067	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	55	PHE	0	0.003	-0.015	19.983	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.008	-0.006	19.161	0.006	0.006	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.929	0.968	22.387	0.036	0.036	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.742	-0.848	21.872	0.123	0.123	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.807	0.908	24.902	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.044	0.051	27.773	0.013	0.013	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.764	-0.862	29.421	0.022	0.022	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.938	0.961	30.371	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.054	0.028	31.497	0.004	0.004	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.878	-0.916	25.184	0.150	0.150	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.855	0.911	23.896	-0.132	-0.132	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.823	0.906	23.997	-0.062	-0.062	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.021	0.012	19.101	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	68	TYR	0	0.005	-0.031	23.355	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.013	-0.004	21.097	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.038	-0.030	24.769	0.011	0.011	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.856	-0.923	26.333	-0.081	-0.081	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.882	0.932	22.952	0.148	0.148	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.000	0.005	22.428	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.849	0.897	22.707	0.037	0.037	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.028	0.016	24.451	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.006	0.008	17.204	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.054	0.028	19.540	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.025	0.025	20.018	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.063	-0.040	21.087	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.002	0.000	15.272	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.874	0.944	15.674	0.122	0.122	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.028	0.011	17.870	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.025	0.010	16.532	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	84	ILE	0	0.019	0.007	12.102	-0.033	-0.033	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.785	-0.882	14.343	-0.164	-0.164	0.000	0.000	0.000	0.000
84	A	86	THR	0	-0.023	-0.027	16.841	0.026	0.026	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.019	0.008	8.333	0.094	0.094	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.782	0.876	12.970	0.118	0.118	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.029	0.019	14.479	0.044	0.044	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.035	-0.016	15.189	0.025	0.025	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.883	0.940	10.253	0.768	0.768	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.937	0.956	14.528	0.164	0.164	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.911	0.961	17.349	0.221	0.221	0.000	0.000	0.000	0.000
92	A	94	HIS	0	0.027	0.014	16.501	0.041	0.041	0.000	0.000	0.000	0.000
93	A	95	HIS	0	-0.018	0.019	13.131	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.059	-0.028	17.067	0.048	0.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)