FMO DATABASE

FMODB ID: 726YK

Calculation Name: 1FMD-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FMD

Chain ID: 4

ChEMBL ID:

UniProt ID: P15072

Base Structure: X-ray

Registration Date: 2023-06-22

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140337.294472
FMO2-HF: Nuclear repulsion	122374.112278
FMO2-HF: Total energy	-17963.182194
FMO2-MP2: Total energy	-18014.377826

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15: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.
-4.464	-1.118	0.056	-1.787	-1.613	0.006

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.016

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	4	17	ASN	0	-0.032	-0.016	3.482	-4.686	-2.029	-0.003	-1.596	-1.057	0.006
4	4	18	THR	0	-0.015	-0.028	2.856	0.557	1.136	0.060	-0.156	-0.483	0.000
5	4	19	GLY	0	0.025	0.014	4.170	-1.332	-1.222	-0.001	-0.035	-0.073	0.000
6	4	20	SER	0	-0.019	0.013	6.766	0.116	0.116	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.026	-0.001	8.133	0.057	0.057	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.030	0.001	10.550	0.084	0.084	0.000	0.000	0.000	0.000
9	4	23	ASN	0	-0.016	-0.009	10.030	0.010	0.010	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.009	-0.024	9.175	-0.221	-0.221	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.037	0.027	11.379	-0.036	-0.036	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.011	-0.002	13.691	-0.052	-0.052	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.016	0.000	13.101	0.076	0.076	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.051	0.002	8.819	0.057	0.057	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.001	-0.007	11.684	0.060	0.060	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.036	-0.013	14.329	-0.053	-0.053	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.036	0.007	9.198	-0.125	-0.125	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.034	-0.027	7.208	0.163	0.163	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.042	0.044	10.882	-0.161	-0.161	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.034	-0.018	11.437	0.164	0.164	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.897	-0.936	10.448	0.859	0.859	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.050	-0.034	13.790	-0.047	-0.047	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.014	-0.013	13.630	-0.031	-0.031	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.013	0.000	17.695	-0.011	-0.011	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.005	0.010	20.793	-0.009	-0.009	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.038	0.015	12.268	0.018	0.018	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.821	-0.933	13.128	-0.017	-0.017	0.000	0.000	0.000	0.000
28	4	67	TRP	0	-0.003	-0.029	14.778	-0.077	-0.077	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.084	0.057	16.473	0.001	0.001	0.000	0.000	0.000	0.000
30	4	69	SER	0	-0.031	0.013	14.022	0.004	0.004	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.872	0.917	16.110	0.118	0.118	0.000	0.000	0.000	0.000
32	4	71	LEU	0	0.015	0.005	19.073	0.008	0.008	0.000	0.000	0.000	0.000
33	4	72	ALA	0	-0.036	-0.007	18.809	0.012	0.012	0.000	0.000	0.000	0.000
34	4	73	SER	0	0.001	-0.004	18.965	-0.002	-0.002	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.106	-0.039	21.598	0.018	0.018	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.012	0.015	24.442	0.017	0.017	0.000	0.000	0.000	0.000
37	4	76	PHE	0	0.017	-0.004	26.314	-0.001	-0.001	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.004	-0.013	27.700	-0.010	-0.010	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.040	0.001	30.226	0.000	0.000	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.042	0.002	33.694	-0.001	-0.001	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.034	-0.012	36.999	0.003	0.003	0.000	0.000	0.000	0.000
42	4	81	GLY	0	-0.007	0.010	38.905	0.005	0.005	0.000	0.000	0.000	0.000
43	4	82	ALA	0	0.016	-0.002	42.213	0.002	0.002	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.030	-0.005	40.025	0.001	0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.029	0.021	43.691	0.003	0.003	0.000	0.000	0.000	0.000
46	4	85	ALA	0	-0.021	-0.007	44.186	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)