FMO DATABASE

FMODB ID: 6NV8Z

Calculation Name: 3B83-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B83

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-638337.243136
FMO2-HF: Nuclear repulsion	602186.019829
FMO2-HF: Total energy	-36151.223307
FMO2-MP2: Total energy	-36258.421894

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:0:MET)

Summations of interaction energy for fragment #1(A:0: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.
-2.521	-0.054	-0.004	-1.04	-1.423	0.001

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.028

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	2	GLN	0	-0.005	-0.005	3.867	1.301	2.824	-0.018	-0.738	-0.767	0.001
4	A	3	PRO	0	0.041	0.014	6.610	-0.157	-0.157	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.018	0.016	8.781	-0.146	-0.146	0.000	0.000	0.000	0.000
6	A	5	PHE	0	0.000	-0.016	12.422	0.105	0.105	0.000	0.000	0.000	0.000
7	A	6	ASN	0	-0.006	-0.015	14.933	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	7	ILE	0	0.037	0.031	15.152	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.851	0.918	19.360	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.036	0.015	23.156	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.016	-0.015	25.915	0.005	0.005	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.023	-0.023	29.528	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	12	ILE	0	0.004	0.025	28.941	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.020	0.002	32.638	0.001	0.001	0.000	0.000	0.000	0.000
15	A	14	LEU	0	0.021	0.013	34.825	0.001	0.001	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.035	0.021	34.636	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	THR	0	-0.039	-0.017	32.217	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.023	0.011	28.425	0.005	0.005	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.013	0.016	27.717	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.031	0.018	21.935	0.009	0.009	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.015	0.010	22.918	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	21	TRP	0	0.015	0.017	16.889	0.027	0.027	0.000	0.000	0.000	0.000
23	A	22	GLN	0	-0.060	-0.027	17.235	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	23	PRO	0	0.035	0.008	15.261	0.025	0.025	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.001	0.003	10.274	0.039	0.039	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.021	-0.008	11.538	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	26	LEU	0	-0.009	0.007	7.808	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.016	-0.010	11.556	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.018	-0.001	9.823	-0.161	-0.161	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.867	-0.919	12.438	-0.536	-0.536	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.025	-0.008	13.205	0.073	0.073	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.038	-0.023	12.731	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	32	LEU	0	0.038	0.022	11.909	0.018	0.018	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.015	-0.004	14.776	0.042	0.042	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.001	0.008	16.271	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	35	PHE	0	-0.022	-0.021	18.527	0.023	0.023	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.111	0.072	21.559	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	37	ARG	1	0.793	0.865	24.215	0.042	0.042	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.890	0.941	21.593	-0.055	-0.055	0.000	0.000	0.000	0.000
40	A	39	ASN	0	-0.050	-0.032	24.698	0.006	0.006	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.797	-0.877	26.120	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	41	PRO	0	-0.003	-0.008	22.198	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	42	SER	0	-0.073	-0.046	22.993	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.817	-0.891	25.600	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.869	-0.900	19.439	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	45	THR	0	-0.009	0.008	22.512	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.025	-0.040	17.004	0.007	0.007	0.000	0.000	0.000	0.000
48	A	47	VAL	0	-0.033	-0.012	19.401	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.815	-0.888	15.827	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.025	-0.005	17.477	0.019	0.019	0.000	0.000	0.000	0.000
51	A	50	THR	0	0.086	0.024	17.228	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	51	SER	0	0.029	0.002	15.952	0.032	0.032	0.000	0.000	0.000	0.000
53	A	52	SER	0	-0.045	-0.023	17.798	0.018	0.018	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.017	0.007	20.495	0.019	0.019	0.000	0.000	0.000	0.000
55	A	54	THR	0	0.010	-0.004	19.918	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	55	SER	0	-0.023	-0.043	21.468	0.020	0.020	0.000	0.000	0.000	0.000
57	A	56	LEU	0	0.016	0.013	21.942	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.026	-0.026	25.627	0.009	0.009	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.014	0.035	24.228	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	59	THR	0	0.010	-0.015	28.447	0.005	0.005	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.027	-0.021	31.463	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.010	0.019	28.501	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.849	-0.928	32.439	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	63	PRO	0	0.046	0.026	33.756	0.003	0.003	0.000	0.000	0.000	0.000
65	A	64	ASN	0	-0.081	-0.030	35.558	0.000	0.000	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.011	0.003	30.369	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.049	-0.035	26.787	0.000	0.000	0.000	0.000	0.000	0.000
68	A	67	TYR	0	-0.015	-0.009	25.519	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.854	-0.926	18.357	0.072	0.072	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.014	0.000	18.870	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.798	0.874	14.509	0.066	0.066	0.000	0.000	0.000	0.000
72	A	71	ILE	0	0.003	-0.002	13.650	-0.039	-0.039	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.000	0.012	8.356	0.094	0.094	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.007	0.015	8.880	-0.072	-0.072	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.834	0.881	8.370	0.356	0.356	0.000	0.000	0.000	0.000
76	A	75	ASN	0	0.025	-0.009	8.516	0.238	0.238	0.000	0.000	0.000	0.000
77	A	76	GLY	0	0.032	0.019	8.792	-0.274	-0.274	0.000	0.000	0.000	0.000
78	A	77	GLN	0	-0.068	-0.040	9.557	0.047	0.047	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.021	0.003	3.651	-1.653	-1.191	0.010	-0.142	-0.330	-0.001
80	A	79	TYR	0	0.038	0.002	5.056	0.513	0.513	0.000	0.000	0.000	0.000
81	A	80	SER	0	-0.053	-0.002	4.069	-0.888	-0.741	-0.001	-0.053	-0.093	0.000
82	A	81	PRO	0	0.014	0.006	3.962	-0.801	-0.466	0.005	-0.107	-0.233	0.001
83	A	82	PRO	0	0.000	0.001	6.521	-0.139	-0.139	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.024	-0.008	10.214	0.096	0.096	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.002	-0.027	12.890	-0.063	-0.063	0.000	0.000	0.000	0.000
86	A	85	THR	0	-0.051	-0.021	16.456	0.017	0.017	0.000	0.000	0.000	0.000
87	A	86	THR	0	-0.005	-0.006	20.068	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.014	-0.001	23.453	0.004	0.004	0.000	0.000	0.000	0.000
89	A	88	THR	0	0.034	0.015	27.033	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	89	THR	0	-0.017	-0.014	30.456	0.002	0.002	0.000	0.000	0.000	0.000
91	A	90	GLY	0	-0.006	-0.008	32.957	0.002	0.002	0.000	0.000	0.000	0.000
92	A	91	SER	0	0.032	0.010	36.475	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	92	LEU	0	-0.040	-0.033	39.238	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.919	-0.945	42.273	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	94	HIS	0	-0.057	-0.024	45.318	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)