FMO DATABASE

FMODB ID: 4JRNN

Calculation Name: 1TBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

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. 2.20220422
Remarks

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	-723091.919307
FMO2-HF: Nuclear repulsion	685000.131731
FMO2-HF: Total energy	-38091.787576
FMO2-MP2: Total energy	-38206.053495

3D Structure Molmil

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.
-1.712	-0.198	-0.009	-0.876	-0.629	0.004

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 : 0.009 / q_NPA : -0.004

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	0.013	0.016	3.868	-2.145	-0.687	-0.008	-0.853	-0.596	0.004
4	A	6	PHE	0	0.003	-0.001	6.200	0.232	0.232	0.000	0.000	0.000	0.000
5	A	7	PHE	0	-0.055	-0.025	8.388	0.110	0.110	0.000	0.000	0.000	0.000
6	A	8	TYR	0	0.086	0.051	6.832	-0.339	-0.339	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.028	-0.007	6.441	0.125	0.125	0.000	0.000	0.000	0.000
8	A	10	GLU	-1	-0.852	-0.938	8.975	-0.274	-0.274	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.010	0.001	11.258	0.036	0.036	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.020	0.013	7.747	0.041	0.041	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.005	-0.009	11.305	0.029	0.029	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.003	0.000	13.665	0.022	0.022	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.006	-0.006	15.002	0.019	0.019	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.053	-0.048	13.066	0.011	0.011	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.014	0.012	16.777	0.010	0.010	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.029	0.015	19.479	0.016	0.016	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.869	-0.930	21.615	-0.119	-0.119	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.183	-0.097	20.568	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	21	GLU	-1	-0.809	-0.928	23.115	-0.101	-0.101	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.013	0.015	25.035	0.004	0.004	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.052	-0.017	20.059	0.002	0.002	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.046	0.010	22.990	0.003	0.003	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.007	-0.045	18.396	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	26	TYR	0	0.012	0.009	15.799	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.861	-0.937	17.237	-0.178	-0.178	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.055	-0.023	15.748	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	29	TYR	0	-0.053	-0.036	9.691	0.016	0.016	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.938	0.960	12.914	0.155	0.155	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.934	0.978	14.001	0.159	0.159	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.034	0.019	9.850	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.013	0.000	8.766	-0.156	-0.156	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.051	-0.016	9.685	-0.084	-0.084	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.946	-0.972	11.184	-0.261	-0.261	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.047	-0.032	7.274	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.007	0.008	5.001	0.087	0.087	0.000	0.000	0.000	0.000
36	A	38	MET	0	-0.016	0.030	4.228	-0.441	-0.385	-0.001	-0.023	-0.033	0.000
37	A	39	SER	0	0.061	0.041	5.899	0.134	0.134	0.000	0.000	0.000	0.000
38	A	40	THR	0	0.062	0.020	8.277	0.078	0.078	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.062	0.035	10.820	0.030	0.030	0.000	0.000	0.000	0.000
40	A	42	THR	0	0.031	0.009	6.058	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.048	0.006	9.454	0.023	0.023	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.062	-0.064	11.243	0.020	0.020	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.905	-0.936	11.562	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.001	0.004	11.280	0.012	0.012	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.887	0.951	13.229	0.126	0.126	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.912	0.945	16.496	0.056	0.056	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.045	0.026	15.015	0.009	0.009	0.000	0.000	0.000	0.000
48	A	50	LEU	0	0.031	0.014	15.386	0.011	0.011	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.053	-0.016	18.516	0.009	0.009	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.018	-0.017	19.338	0.012	0.012	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.932	-0.950	19.089	-0.055	-0.055	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.038	-0.020	21.769	0.000	0.000	0.000	0.000	0.000	0.000
53	A	55	PHE	0	-0.010	-0.038	19.418	0.002	0.002	0.000	0.000	0.000	0.000
54	A	56	VAL	0	0.013	0.000	19.417	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.935	0.968	22.684	0.072	0.072	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.791	-0.896	22.136	-0.114	-0.114	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.855	0.937	25.056	0.081	0.081	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.023	0.019	27.454	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.783	-0.842	29.245	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.915	0.942	30.032	0.056	0.056	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.026	0.007	31.059	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.850	-0.913	25.353	-0.103	-0.103	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.901	0.965	24.067	0.085	0.085	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.834	0.929	23.780	0.086	0.086	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.015	0.018	19.138	0.005	0.005	0.000	0.000	0.000	0.000
66	A	68	TYR	0	-0.048	-0.089	23.313	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.022	0.028	21.130	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.097	-0.011	24.629	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.880	-0.950	26.491	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.989	0.984	23.279	0.072	0.072	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.008	-0.005	22.301	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.886	0.943	22.694	0.076	0.076	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.002	0.009	24.691	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.011	0.007	17.181	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.050	0.013	19.472	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.023	0.030	20.022	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.038	-0.035	21.158	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.003	-0.002	14.940	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.943	0.986	16.596	0.182	0.182	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.024	0.014	18.192	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.061	0.052	16.145	0.000	0.000	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.001	-0.004	12.375	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.864	-0.931	14.778	-0.205	-0.205	0.000	0.000	0.000	0.000
84	A	86	THR	0	-0.015	-0.023	17.451	0.013	0.013	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.005	-0.010	8.263	0.049	0.049	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.866	0.932	13.653	0.257	0.257	0.000	0.000	0.000	0.000
87	A	89	GLN	0	-0.031	-0.014	14.868	0.002	0.002	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.025	-0.004	14.977	0.020	0.020	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.937	0.963	10.085	0.244	0.244	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.970	0.984	14.614	0.174	0.174	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.895	0.938	17.339	0.099	0.099	0.000	0.000	0.000	0.000
92	A	94	HIS	0	0.005	0.008	16.967	0.017	0.017	0.000	0.000	0.000	0.000
93	A	95	HIS	0	-0.005	0.029	12.941	0.017	0.017	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.061	-0.030	17.214	0.011	0.011	0.000	0.000	0.000	0.000

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