FMO DATABASE

FMODB ID: 39QML

Calculation Name: 3FBI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FBI

Chain ID: A

ChEMBL ID:

UniProt ID: P38633

Base Structure: X-ray

Registration Date: 2023-06-21

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-273405.74951
FMO2-HF: Nuclear repulsion	249816.534021
FMO2-HF: Total energy	-23589.215489
FMO2-MP2: Total energy	-23658.195681

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:12:SER)

Summations of interaction energy for fragment #1(A:12: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.
-3.258	-0.121	0.103	-1.463	-1.777	-0.003

Interaction energy analysis for fragmet #1(A:12:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.021

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

Sort

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	14	TYR	0	-0.015	-0.003	3.092	-1.256	1.017	0.039	-1.062	-1.250	0.001
4	A	15	PRO	0	0.014	0.018	3.212	-3.493	-2.629	0.064	-0.401	-0.527	-0.004
5	A	16	PRO	0	0.010	0.006	5.301	0.540	0.540	0.000	0.000	0.000	0.000
6	A	17	PRO	0	0.015	-0.006	6.980	0.144	0.144	0.000	0.000	0.000	0.000
7	A	18	PRO	0	0.036	0.019	10.694	0.010	0.010	0.000	0.000	0.000	0.000
8	A	19	PRO	0	0.039	0.016	13.094	0.080	0.080	0.000	0.000	0.000	0.000
9	A	20	TYR	0	0.012	-0.004	14.831	0.054	0.054	0.000	0.000	0.000	0.000
10	A	21	VAL	0	0.029	0.015	14.455	0.059	0.059	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.934	0.980	17.037	0.361	0.361	0.000	0.000	0.000	0.000
12	A	23	PHE	0	0.017	0.003	18.457	0.038	0.038	0.000	0.000	0.000	0.000
13	A	24	PHE	0	0.001	0.013	20.075	0.028	0.028	0.000	0.000	0.000	0.000
14	A	25	THR	0	0.001	0.002	22.142	0.014	0.014	0.000	0.000	0.000	0.000
15	A	26	GLN	0	0.061	0.015	23.903	0.001	0.001	0.000	0.000	0.000	0.000
16	A	27	SER	0	0.069	0.045	26.993	0.007	0.007	0.000	0.000	0.000	0.000
17	A	28	ASN	0	-0.073	-0.043	24.944	0.020	0.020	0.000	0.000	0.000	0.000
18	A	29	LEU	0	0.021	0.002	24.532	0.002	0.002	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.912	-0.963	28.640	-0.105	-0.105	0.000	0.000	0.000	0.000
20	A	31	LYS	1	0.858	0.930	30.674	0.126	0.126	0.000	0.000	0.000	0.000
21	A	32	LEU	0	-0.030	0.001	28.201	0.003	0.003	0.000	0.000	0.000	0.000
22	A	33	PRO	0	-0.002	0.002	31.940	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	34	LYS	1	1.046	1.018	35.194	0.083	0.083	0.000	0.000	0.000	0.000
24	A	35	TYR	0	-0.091	-0.065	31.307	0.007	0.007	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.898	0.950	29.194	0.171	0.171	0.000	0.000	0.000	0.000
26	A	37	GLU	-1	-0.922	-0.962	35.365	-0.091	-0.091	0.000	0.000	0.000	0.000
27	A	38	LYS	1	0.926	0.962	37.765	0.104	0.104	0.000	0.000	0.000	0.000
28	A	39	LYS	1	0.789	0.876	32.034	0.162	0.162	0.000	0.000	0.000	0.000
29	A	40	ALA	0	-0.025	0.002	37.460	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	41	ALA	0	-0.042	-0.008	39.859	0.005	0.005	0.000	0.000	0.000	0.000
31	A	57	GLU	-1	-0.993	-1.010	24.567	-0.281	-0.281	0.000	0.000	0.000	0.000
32	A	58	GLU	-1	-0.852	-0.930	28.811	-0.146	-0.146	0.000	0.000	0.000	0.000
33	A	59	ILE	0	-0.033	-0.005	25.008	0.005	0.005	0.000	0.000	0.000	0.000
34	A	60	THR	0	-0.052	-0.025	28.412	0.011	0.011	0.000	0.000	0.000	0.000
35	A	61	CYS	0	-0.060	-0.023	28.888	0.006	0.006	0.000	0.000	0.000	0.000
36	A	62	ALA	0	0.024	-0.007	25.355	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	63	LEU	0	0.025	-0.005	25.473	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	64	ASP	-1	-0.692	-0.798	27.695	-0.174	-0.174	0.000	0.000	0.000	0.000
39	A	65	TYR	0	0.014	0.004	22.264	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	66	LEU	0	-0.055	-0.010	23.389	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	67	ILE	0	-0.008	-0.026	25.702	0.022	0.022	0.000	0.000	0.000	0.000
42	A	68	PRO	0	-0.008	0.002	25.356	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	69	PRO	0	0.031	0.028	23.479	0.015	0.015	0.000	0.000	0.000	0.000
44	A	70	PRO	0	0.016	-0.003	26.619	0.005	0.005	0.000	0.000	0.000	0.000
45	A	71	MET	0	0.011	0.008	28.698	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	72	PRO	0	-0.001	0.008	27.258	0.014	0.014	0.000	0.000	0.000	0.000
47	A	73	LYS	1	0.953	0.969	30.422	0.148	0.148	0.000	0.000	0.000	0.000
48	A	74	ASN	0	0.017	0.009	29.155	0.010	0.010	0.000	0.000	0.000	0.000
49	A	75	GLN	0	0.061	0.012	31.049	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	76	GLN	0	0.026	0.021	28.712	0.003	0.003	0.000	0.000	0.000	0.000
51	A	77	TYR	0	0.012	0.009	24.414	0.000	0.000	0.000	0.000	0.000	0.000
52	A	78	ARG	1	0.866	0.942	26.986	0.125	0.125	0.000	0.000	0.000	0.000
53	A	79	ALA	0	0.015	0.006	26.538	0.003	0.003	0.000	0.000	0.000	0.000
54	A	80	PHE	0	0.009	0.001	25.424	0.012	0.012	0.000	0.000	0.000	0.000
55	A	81	GLY	0	0.012	0.002	28.597	0.016	0.016	0.000	0.000	0.000	0.000
56	A	82	SER	0	-0.044	-0.014	26.558	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	83	ILE	0	0.005	0.005	21.467	0.010	0.010	0.000	0.000	0.000	0.000
58	A	84	TRP	0	0.028	0.022	22.677	-0.016	-0.016	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:12:SER)