FMO DATABASE

FMODB ID: 2294R

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	OptHSide
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	-626393.644193
FMO2-HF: Nuclear repulsion	590359.35983
FMO2-HF: Total energy	-36034.284363
FMO2-MP2: Total energy	-36139.266987

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.
-0.587	0.029	0	-0.276	-0.34	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 : 0.001 / q_NPA : -0.014

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].	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	0.056	0.020	3.852	-0.759	-0.143	-0.276	-0.340	0.001
4	A	3	ASP	-1	-0.878	-0.950	6.397	-0.705	-0.705	0.000	0.000	0.000
5	A	4	ALA	0	-0.007	-0.005	9.038	0.222	0.222	0.000	0.000	0.000
6	A	5	PHE	0	-0.026	-0.022	7.647	0.250	0.250	0.000	0.000	0.000
7	A	6	THR	0	-0.031	-0.004	8.558	0.128	0.128	0.000	0.000	0.000
8	A	7	ASP	-1	-0.830	-0.925	10.327	-0.154	-0.154	0.000	0.000	0.000
9	A	8	VAL	0	-0.048	-0.030	13.495	0.040	0.040	0.000	0.000	0.000
10	A	9	ALA	0	0.010	0.017	12.775	0.055	0.055	0.000	0.000	0.000
11	A	10	LYS	1	0.892	0.938	11.886	0.213	0.213	0.000	0.000	0.000
12	A	11	MET	0	0.004	0.003	15.321	0.055	0.055	0.000	0.000	0.000
13	A	12	LYS	1	0.792	0.889	18.250	0.253	0.253	0.000	0.000	0.000
14	A	13	LYS	1	0.874	0.919	17.849	0.197	0.197	0.000	0.000	0.000
15	A	14	ILE	0	0.046	0.031	17.675	0.024	0.024	0.000	0.000	0.000
16	A	15	LYS	1	0.847	0.926	21.033	0.126	0.126	0.000	0.000	0.000
17	A	16	GLU	-1	-0.871	-0.920	22.067	-0.182	-0.182	0.000	0.000	0.000
18	A	17	GLU	-1	-0.819	-0.883	20.560	-0.124	-0.124	0.000	0.000	0.000
19	A	18	ILE	0	0.006	0.000	24.684	0.012	0.012	0.000	0.000	0.000
20	A	19	LYS	1	0.939	0.973	26.962	0.099	0.099	0.000	0.000	0.000
21	A	20	ALA	0	-0.064	-0.035	27.659	0.006	0.006	0.000	0.000	0.000
22	A	21	HIS	0	0.011	0.011	28.388	-0.001	-0.001	0.000	0.000	0.000
23	A	22	GLU	-1	-0.920	-0.957	30.423	-0.043	-0.043	0.000	0.000	0.000
24	A	23	GLY	0	-0.038	-0.020	33.159	0.001	0.001	0.000	0.000	0.000
25	A	24	GLN	0	-0.063	-0.028	32.368	0.002	0.002	0.000	0.000	0.000
26	A	25	VAL	0	0.020	0.007	32.488	0.001	0.001	0.000	0.000	0.000
27	A	26	VAL	0	-0.007	-0.001	28.194	-0.004	-0.004	0.000	0.000	0.000
28	A	27	GLU	-1	-0.841	-0.904	27.669	0.030	0.030	0.000	0.000	0.000
29	A	28	MET	0	-0.050	-0.027	25.949	-0.005	-0.005	0.000	0.000	0.000
30	A	29	THR	0	-0.024	-0.020	24.345	0.007	0.007	0.000	0.000	0.000
31	A	30	LEU	0	-0.021	-0.009	24.628	-0.004	-0.004	0.000	0.000	0.000
32	A	31	GLU	-1	-0.815	-0.885	18.619	0.149	0.149	0.000	0.000	0.000
33	A	32	ASN	0	0.001	-0.004	21.999	0.001	0.001	0.000	0.000	0.000
34	A	33	GLY	0	0.002	0.016	21.472	0.019	0.019	0.000	0.000	0.000
35	A	34	ARG	1	0.952	0.962	20.381	-0.200	-0.200	0.000	0.000	0.000
36	A	35	LYS	1	0.865	0.937	22.249	-0.090	-0.090	0.000	0.000	0.000
37	A	36	ARG	1	0.883	0.936	18.979	-0.120	-0.120	0.000	0.000	0.000
38	A	37	GLN	0	0.030	0.005	25.960	-0.001	-0.001	0.000	0.000	0.000
39	A	38	LYS	1	0.913	0.948	29.026	-0.041	-0.041	0.000	0.000	0.000
40	A	39	ASN	0	-0.002	-0.007	26.675	0.003	0.003	0.000	0.000	0.000
41	A	40	ARG	1	0.763	0.868	29.656	-0.010	-0.010	0.000	0.000	0.000
42	A	41	LEU	0	0.023	0.005	30.936	-0.003	-0.003	0.000	0.000	0.000
43	A	42	GLY	0	0.009	-0.006	32.675	0.002	0.002	0.000	0.000	0.000
44	A	43	LYS	1	0.939	0.989	33.463	0.021	0.021	0.000	0.000	0.000
45	A	44	LEU	0	-0.010	-0.005	29.387	0.002	0.002	0.000	0.000	0.000
46	A	45	ILE	0	-0.055	-0.029	33.257	-0.003	-0.003	0.000	0.000	0.000
47	A	46	GLU	-1	-0.837	-0.894	34.712	-0.034	-0.034	0.000	0.000	0.000
48	A	47	VAL	0	0.007	0.004	29.882	-0.001	-0.001	0.000	0.000	0.000
49	A	48	TYR	0	-0.036	-0.030	31.592	-0.001	-0.001	0.000	0.000	0.000
50	A	49	PRO	0	-0.014	-0.011	30.030	-0.006	-0.006	0.000	0.000	0.000
51	A	50	SER	0	-0.048	-0.036	28.301	-0.008	-0.008	0.000	0.000	0.000
52	A	51	LEU	0	-0.020	-0.010	28.146	0.000	0.000	0.000	0.000	0.000
53	A	52	PHE	0	0.033	0.023	25.394	-0.003	-0.003	0.000	0.000	0.000
54	A	53	ILE	0	0.017	0.007	30.718	0.005	0.005	0.000	0.000	0.000
55	A	54	VAL	0	0.008	0.008	30.318	-0.003	-0.003	0.000	0.000	0.000
56	A	55	GLU	-1	-0.944	-0.965	33.656	-0.010	-0.010	0.000	0.000	0.000
57	A	56	PHE	0	0.032	-0.014	30.747	0.000	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.053	0.019	36.771	0.000	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.787	-0.893	39.488	-0.002	-0.002	0.000	0.000	0.000
60	A	59	VAL	0	0.007	0.032	35.753	-0.002	-0.002	0.000	0.000	0.000
61	A	60	GLU	-1	-0.938	-0.979	38.943	0.001	0.001	0.000	0.000	0.000
62	A	61	GLY	0	-0.017	-0.012	38.645	0.000	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.851	-0.926	35.345	0.019	0.019	0.000	0.000	0.000
64	A	63	LYS	1	0.760	0.889	38.236	0.000	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.086	-0.055	38.217	0.004	0.004	0.000	0.000	0.000
66	A	65	VAL	0	-0.036	-0.019	42.074	-0.002	-0.002	0.000	0.000	0.000
67	A	66	ASN	0	-0.042	-0.018	40.941	-0.002	-0.002	0.000	0.000	0.000
68	A	67	VAL	0	0.047	0.032	41.131	0.001	0.001	0.000	0.000	0.000
69	A	68	TYR	0	-0.067	-0.018	35.223	0.000	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.047	0.021	37.072	-0.001	-0.001	0.000	0.000	0.000
71	A	70	GLU	-1	-0.823	-0.881	31.310	0.009	0.009	0.000	0.000	0.000
72	A	71	SER	0	-0.014	0.000	32.322	-0.003	-0.003	0.000	0.000	0.000
73	A	72	PHE	0	-0.006	-0.007	26.782	0.005	0.005	0.000	0.000	0.000
74	A	73	THR	0	-0.006	-0.029	25.399	-0.009	-0.009	0.000	0.000	0.000
75	A	74	TYR	0	0.044	-0.016	22.729	-0.002	-0.002	0.000	0.000	0.000
76	A	75	SER	0	0.010	0.000	20.828	-0.013	-0.013	0.000	0.000	0.000
77	A	76	ASP	-1	-0.788	-0.833	20.544	-0.013	-0.013	0.000	0.000	0.000
78	A	77	ILE	0	0.016	0.013	19.861	0.011	0.011	0.000	0.000	0.000
79	A	78	LEU	0	-0.019	-0.009	15.328	0.002	0.002	0.000	0.000	0.000
80	A	79	THR	0	-0.079	-0.064	15.976	-0.001	-0.001	0.000	0.000	0.000
81	A	80	GLU	-1	-0.909	-0.942	14.064	0.028	0.028	0.000	0.000	0.000
82	A	81	LYS	1	0.897	0.953	18.361	0.016	0.016	0.000	0.000	0.000
83	A	82	ASN	0	-0.054	-0.044	21.694	0.007	0.007	0.000	0.000	0.000
84	A	83	LEU	0	0.005	0.005	18.847	-0.009	-0.009	0.000	0.000	0.000
85	A	84	ILE	0	-0.007	-0.018	21.846	0.003	0.003	0.000	0.000	0.000
86	A	85	HIS	0	0.005	0.009	22.397	-0.010	-0.010	0.000	0.000	0.000
87	A	86	TYR	0	-0.001	-0.020	22.123	0.008	0.008	0.000	0.000	0.000
88	A	87	LEU	0	-0.048	-0.008	26.986	-0.001	-0.001	0.000	0.000	0.000
89	A	88	ASP	-1	-0.933	-0.972	29.697	-0.039	-0.039	0.000	0.000	0.000

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