FMO DATABASE

FMODB ID: NN26Q

Calculation Name: 3TRB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TRB

Chain ID: A

ChEMBL ID:

UniProt ID: Q83BL4

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptH
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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-596848.364901
FMO2-HF: Nuclear repulsion	561049.638896
FMO2-HF: Total energy	-35798.726005
FMO2-MP2: Total energy	-35903.511169

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:6:MET)

Summations of interaction energy for fragment #1(A:6:MET)

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.
-15.683	-15.884	10.252	-3.849	-6.198	0.005

Interaction energy analysis for fragmet #1(A:6:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.003

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	8	PRO	0	-0.002	-0.018	2.582	-4.259	-1.673	0.842	-1.545	-1.883	-0.011
4	A	9	ILE	0	0.003	0.014	3.604	-0.580	-0.182	0.006	-0.041	-0.362	0.000
5	A	10	HIS	0	0.031	0.041	6.113	0.291	0.291	0.000	0.000	0.000	0.000
6	A	11	PRO	0	0.066	0.023	9.729	-0.089	-0.089	0.000	0.000	0.000	0.000
7	A	12	GLY	0	0.040	0.014	11.725	-0.082	-0.082	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.836	-0.902	8.924	-0.232	-0.232	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.019	0.010	8.104	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	15	LEU	0	-0.036	-0.013	12.099	-0.035	-0.035	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.001	-0.012	15.234	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.943	-0.968	12.204	-0.277	-0.277	0.000	0.000	0.000	0.000
13	A	18	GLU	-1	-0.937	-0.964	14.785	-0.183	-0.183	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.082	-0.043	17.098	0.006	0.006	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.019	-0.008	19.133	0.003	0.003	0.000	0.000	0.000	0.000
16	A	21	PHE	0	-0.004	-0.002	18.485	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	22	LEU	0	-0.037	-0.006	20.452	0.006	0.006	0.000	0.000	0.000	0.000
18	A	23	ASP	-1	-0.924	-0.962	23.210	-0.058	-0.058	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.869	0.935	23.537	0.077	0.077	0.000	0.000	0.000	0.000
20	A	25	MET	0	0.005	0.030	23.572	0.017	0.017	0.000	0.000	0.000	0.000
21	A	26	SER	0	0.013	-0.016	23.664	0.008	0.008	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.077	0.014	23.722	0.002	0.002	0.000	0.000	0.000	0.000
23	A	28	ASN	0	-0.010	-0.020	24.919	0.007	0.007	0.000	0.000	0.000	0.000
24	A	29	GLN	0	0.024	0.032	27.435	0.002	0.002	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.100	0.062	21.516	0.002	0.002	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.010	-0.004	25.957	0.005	0.005	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.935	0.959	27.394	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	33	HIS	0	0.003	0.016	27.243	0.003	0.003	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.028	-0.008	23.071	0.003	0.003	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.019	0.003	27.650	0.006	0.006	0.000	0.000	0.000	0.000
31	A	36	ILE	0	-0.061	-0.028	24.267	0.009	0.009	0.000	0.000	0.000	0.000
32	A	37	PRO	0	0.013	-0.004	27.969	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	38	THR	0	0.085	0.016	26.914	0.005	0.005	0.000	0.000	0.000	0.000
34	A	39	ASN	0	-0.010	-0.006	25.610	0.002	0.002	0.000	0.000	0.000	0.000
35	A	40	ARG	1	0.951	0.987	23.033	-0.089	-0.089	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.062	0.038	21.687	0.013	0.013	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.023	0.006	20.721	0.002	0.002	0.000	0.000	0.000	0.000
38	A	43	ALA	0	-0.037	-0.018	20.525	0.004	0.004	0.000	0.000	0.000	0.000
39	A	44	ILE	0	-0.032	-0.008	16.439	0.013	0.013	0.000	0.000	0.000	0.000
40	A	45	LEU	0	0.016	0.006	16.086	0.017	0.017	0.000	0.000	0.000	0.000
41	A	46	ASN	0	-0.032	-0.012	16.193	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.037	0.020	14.369	0.007	0.007	0.000	0.000	0.000	0.000
43	A	48	ALA	0	-0.041	-0.012	15.145	0.018	0.018	0.000	0.000	0.000	0.000
44	A	49	ARG	1	0.835	0.895	17.651	-0.158	-0.158	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.041	0.025	15.985	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.003	0.005	15.061	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	52	THR	0	0.004	0.002	17.737	0.019	0.019	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.105	0.034	20.502	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.883	-0.929	21.932	0.080	0.080	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.007	-0.016	20.368	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.015	0.016	18.891	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.012	0.006	20.266	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.809	0.905	23.553	-0.083	-0.083	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.010	0.000	18.093	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.017	0.011	20.767	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.932	0.965	21.628	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	62	PHE	0	-0.054	-0.032	22.797	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.016	-0.007	19.802	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	64	GLY	0	0.003	0.025	21.536	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	65	THR	0	-0.002	-0.004	17.350	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	66	THR	0	0.020	0.012	17.269	0.007	0.007	0.000	0.000	0.000	0.000
62	A	67	PRO	0	0.007	-0.002	18.148	0.010	0.010	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.836	-0.950	16.413	0.146	0.146	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.015	0.001	11.388	0.088	0.088	0.000	0.000	0.000	0.000
65	A	70	TRP	0	0.041	0.005	12.877	0.099	0.099	0.000	0.000	0.000	0.000
66	A	71	LEU	0	-0.013	-0.014	13.866	0.063	0.063	0.000	0.000	0.000	0.000
67	A	72	ASN	0	0.072	0.040	10.918	0.097	0.097	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.046	-0.005	8.704	0.325	0.325	0.000	0.000	0.000	0.000
69	A	74	GLN	0	-0.026	-0.027	9.398	0.176	0.176	0.000	0.000	0.000	0.000
70	A	75	ASP	-1	-0.850	-0.914	11.313	0.674	0.674	0.000	0.000	0.000	0.000
71	A	76	ALA	0	-0.044	-0.021	5.711	0.209	0.249	-0.001	-0.003	-0.035	0.000
72	A	77	TYR	0	-0.054	-0.028	7.049	0.275	0.275	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.791	-0.909	8.038	0.395	0.395	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.005	0.000	8.790	-0.115	-0.115	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.920	0.962	2.032	-10.759	-13.984	9.405	-2.260	-3.918	0.016
76	A	81	MET	0	-0.025	-0.014	7.534	-0.333	-0.333	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.010	-0.002	10.238	-0.095	-0.095	0.000	0.000	0.000	0.000
78	A	83	LEU	0	0.010	-0.001	7.960	-0.088	-0.088	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.902	0.952	8.027	-0.466	-0.466	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.940	0.981	11.221	-0.277	-0.277	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.024	-0.026	14.616	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.046	0.041	12.998	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.947	0.958	13.514	-0.243	-0.243	0.000	0.000	0.000	0.000
84	A	89	LYS	1	0.893	0.961	16.040	-0.176	-0.176	0.000	0.000	0.000	0.000
85	A	90	ILE	0	0.084	0.030	15.876	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.929	-0.958	15.523	0.193	0.193	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.848	0.929	18.572	-0.169	-0.169	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.956	-0.981	21.643	0.158	0.158	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.025	-0.008	20.813	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	95	THR	0	0.002	-0.002	22.778	0.000	0.000	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.006	0.018	22.195	0.006	0.006	0.000	0.000	0.000	0.000
92	A	97	TYR	0	0.001	-0.001	23.808	-0.016	-0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:MET)