FMO DATABASE

FMODB ID: 2N8GR

Calculation Name: 3FIF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FIF

Chain ID: A

ChEMBL ID:

UniProt ID: P65294

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-279984.881553
FMO2-HF: Nuclear repulsion	257308.700342
FMO2-HF: Total energy	-22676.181211
FMO2-MP2: Total energy	-22740.30781

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-9.201	-1.984	3.046	-4.032	-6.232	-0.007

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.023

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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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	5	TYR	0	-0.047	-0.059	2.855	1.658	3.583	0.283	-0.847	-1.361	-0.001
4	A	6	VAL	0	-0.021	-0.010	6.294	-0.717	-0.717	0.000	0.000	0.000	0.000
5	A	7	MET	0	-0.017	-0.003	9.847	0.275	0.275	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.002	-0.002	12.800	-0.100	-0.100	0.000	0.000	0.000	0.000
7	A	9	THR	0	0.007	-0.025	15.791	0.013	0.013	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.834	0.925	19.163	-0.140	-0.140	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.840	-0.868	22.296	0.050	0.050	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.037	-0.015	21.673	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.840	0.895	19.793	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	14	MET	0	-0.004	-0.004	14.331	0.075	0.075	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.014	0.003	14.008	-0.061	-0.061	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.017	0.015	11.153	0.096	0.096	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.098	-0.071	8.244	0.112	0.112	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.922	-0.937	8.240	-2.113	-2.113	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.051	0.021	5.764	0.206	0.206	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.826	0.912	5.379	-1.550	-1.550	0.000	0.000	0.000	0.000
19	A	21	PRO	0	-0.022	-0.012	6.678	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.916	-0.947	10.308	0.093	0.093	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.029	-0.018	13.015	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.752	-0.835	15.665	0.088	0.088	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.870	-0.940	18.794	0.235	0.235	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.948	-0.967	21.446	0.087	0.087	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.125	-0.094	21.725	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	28	GLY	0	-0.055	-0.015	22.287	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.050	-0.028	20.334	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.007	-0.007	14.222	0.025	0.025	0.000	0.000	0.000	0.000
29	A	31	SER	0	0.002	-0.015	14.958	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	32	TYR	0	-0.035	-0.035	12.068	0.059	0.059	0.000	0.000	0.000	0.000
31	A	33	HIS	0	0.104	0.063	11.173	0.098	0.098	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.829	-0.908	12.075	-0.487	-0.487	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.030	0.003	10.993	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.116	-0.050	14.701	-0.059	-0.059	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.025	0.022	15.331	0.040	0.040	0.000	0.000	0.000	0.000
36	A	38	ASN	0	-0.075	-0.039	16.307	0.072	0.072	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.017	0.017	16.327	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	40	MET	0	-0.058	-0.029	16.603	0.045	0.045	0.000	0.000	0.000	0.000
39	A	41	GLN	0	0.012	-0.003	17.146	0.012	0.012	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.035	-0.008	17.210	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	43	ASN	0	0.002	-0.007	19.672	0.014	0.014	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.879	0.926	18.804	-0.228	-0.228	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.858	-0.926	20.264	0.153	0.153	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.897	-0.948	21.866	0.075	0.075	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.028	-0.023	15.571	0.001	0.001	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.056	-0.033	18.069	0.015	0.015	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.052	-0.036	14.133	0.054	0.054	0.000	0.000	0.000	0.000
48	A	50	ILE	0	0.032	0.023	9.307	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.034	-0.018	8.184	0.145	0.145	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.795	-0.874	3.109	2.278	4.050	0.419	-0.939	-1.253	0.001
51	A	53	ARG	1	0.817	0.905	4.349	-0.914	-0.673	0.001	-0.062	-0.180	0.000
52	A	54	LEU	0	-0.008	-0.010	2.562	-2.190	-0.739	1.341	-1.255	-1.537	-0.010
53	A	55	GLU	-1	-0.872	-0.921	2.416	-6.168	-4.507	1.002	-0.901	-1.762	0.003
54	A	56	HIS	0	-0.021	-0.018	4.288	0.102	0.269	0.000	-0.028	-0.139	0.000
55	A	57	HIS	0	-0.086	-0.040	6.225	-0.252	-0.252	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)