FMO DATABASE

FMODB ID: 66KZZ

Calculation Name: 3FB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FB9

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626723.405406
FMO2-HF: Nuclear repulsion	590688.766546
FMO2-HF: Total energy	-36034.638861
FMO2-MP2: Total energy	-36139.598104

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:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-0.375	0.504	-0.002	-0.395	-0.482	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.015

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	SER	0	0.002	-0.015	3.849	-0.825	0.054	-0.002	-0.395	-0.482	0.001
4	A	3	ASP	-1	-0.794	-0.903	6.260	-0.409	-0.409	0.000	0.000	0.000	0.000
5	A	4	ALA	0	-0.030	0.003	9.294	0.184	0.184	0.000	0.000	0.000	0.000
6	A	5	PHE	0	-0.012	-0.012	7.489	0.165	0.165	0.000	0.000	0.000	0.000
7	A	6	THR	0	-0.028	-0.021	8.322	0.195	0.195	0.000	0.000	0.000	0.000
8	A	7	ASP	-1	-0.812	-0.923	10.054	0.148	0.148	0.000	0.000	0.000	0.000
9	A	8	VAL	0	-0.025	-0.013	13.376	0.002	0.002	0.000	0.000	0.000	0.000
10	A	9	ALA	0	-0.003	0.010	12.629	0.011	0.011	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.855	0.932	12.027	-0.137	-0.137	0.000	0.000	0.000	0.000
12	A	11	MET	0	0.002	0.010	15.385	0.010	0.010	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.783	0.871	18.052	0.143	0.143	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.881	0.925	17.540	0.118	0.118	0.000	0.000	0.000	0.000
15	A	14	ILE	0	0.056	0.028	17.873	0.008	0.008	0.000	0.000	0.000	0.000
16	A	15	LYS	1	0.823	0.917	21.068	0.020	0.020	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.867	-0.916	21.562	-0.115	-0.115	0.000	0.000	0.000	0.000
18	A	17	GLU	-1	-0.824	-0.876	20.631	-0.057	-0.057	0.000	0.000	0.000	0.000
19	A	18	ILE	0	0.011	0.003	24.680	0.004	0.004	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.933	0.964	26.935	0.045	0.045	0.000	0.000	0.000	0.000
21	A	20	ALA	0	-0.069	-0.032	27.518	0.001	0.001	0.000	0.000	0.000	0.000
22	A	21	HIS	0	0.003	0.003	28.570	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.860	-0.936	30.580	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	23	GLY	0	-0.044	-0.015	33.264	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	24	GLN	0	-0.049	-0.019	32.350	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	25	VAL	0	0.002	-0.004	33.043	0.003	0.003	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.006	0.009	28.514	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.855	-0.911	28.075	0.045	0.045	0.000	0.000	0.000	0.000
29	A	28	MET	0	-0.043	-0.020	26.236	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	THR	0	-0.021	-0.023	24.954	0.002	0.002	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.015	-0.003	25.174	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.736	-0.833	19.124	0.229	0.229	0.000	0.000	0.000	0.000
33	A	32	ASN	0	-0.100	-0.061	22.473	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.037	0.020	22.220	0.017	0.017	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.960	0.977	19.743	-0.170	-0.170	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.870	0.944	22.240	-0.101	-0.101	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.871	0.915	19.359	-0.179	-0.179	0.000	0.000	0.000	0.000
38	A	37	GLN	0	0.029	-0.003	26.312	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.921	0.951	29.649	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	39	ASN	0	-0.006	0.000	26.904	0.009	0.009	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.771	0.870	30.168	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.006	-0.005	31.527	0.000	0.000	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.033	-0.007	33.109	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.845	0.933	33.598	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.000	-0.001	29.245	0.004	0.004	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.047	-0.017	33.235	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.833	-0.885	34.609	0.003	0.003	0.000	0.000	0.000	0.000
48	A	47	VAL	0	-0.020	-0.005	29.668	0.004	0.004	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.042	-0.038	31.326	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	49	PRO	0	-0.028	-0.021	29.747	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.036	-0.025	28.038	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.015	-0.008	27.755	0.006	0.006	0.000	0.000	0.000	0.000
53	A	52	PHE	0	0.042	0.027	25.366	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	53	ILE	0	0.003	-0.006	30.646	0.007	0.007	0.000	0.000	0.000	0.000
55	A	54	VAL	0	-0.009	-0.005	30.502	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.844	-0.912	33.855	0.013	0.013	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.019	-0.006	31.005	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.048	0.012	37.081	0.000	0.000	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.824	-0.919	39.852	0.011	0.011	0.000	0.000	0.000	0.000
60	A	59	VAL	0	0.009	0.032	35.926	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.895	-0.963	39.230	0.010	0.010	0.000	0.000	0.000	0.000
62	A	61	GLY	0	-0.011	-0.005	38.655	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.872	-0.933	36.052	0.036	0.036	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.777	0.910	38.879	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.074	-0.053	39.028	0.002	0.002	0.000	0.000	0.000	0.000
66	A	65	VAL	0	-0.034	-0.020	42.897	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.048	-0.019	41.744	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	67	VAL	0	0.024	0.023	41.656	0.002	0.002	0.000	0.000	0.000	0.000
69	A	68	TYR	0	-0.066	-0.019	35.705	0.002	0.002	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.027	0.010	37.416	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.798	-0.865	31.810	0.055	0.055	0.000	0.000	0.000	0.000
72	A	71	SER	0	-0.013	-0.005	32.233	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	72	PHE	0	-0.006	0.001	26.858	0.007	0.007	0.000	0.000	0.000	0.000
74	A	73	THR	0	-0.002	-0.031	25.488	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	74	TYR	0	0.046	-0.016	22.519	0.003	0.003	0.000	0.000	0.000	0.000
76	A	75	SER	0	0.025	0.007	20.925	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.811	-0.840	20.925	0.092	0.092	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.029	0.024	19.914	0.012	0.012	0.000	0.000	0.000	0.000
79	A	78	LEU	0	-0.025	-0.006	15.724	0.010	0.010	0.000	0.000	0.000	0.000
80	A	79	THR	0	-0.068	-0.052	16.225	0.026	0.026	0.000	0.000	0.000	0.000
81	A	80	GLU	-1	-0.915	-0.961	14.266	0.290	0.290	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.861	0.937	18.716	-0.090	-0.090	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.047	-0.043	21.986	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.024	-0.003	19.438	0.001	0.001	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.009	-0.012	22.325	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	85	HIS	0	0.012	0.017	22.761	0.001	0.001	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.016	-0.039	22.052	0.007	0.007	0.000	0.000	0.000	0.000
88	A	87	LEU	0	-0.043	-0.012	27.227	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	88	ASP	-1	-0.941	-0.972	29.928	-0.028	-0.028	0.000	0.000	0.000	0.000

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