FMO DATABASE

FMODB ID: MVNRZ

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	OptH
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	-140443.023976
FMO2-HF: Nuclear repulsion	122480.261265
FMO2-HF: Total energy	-17962.762711
FMO2-MP2: Total energy	-18014.02123

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.
-4.904	-1.124	0.066	-2.038	-1.808	0.008

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 : 0.036 / q_NPA : 0.029

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	4	17	ASN	0	-0.002	-0.001	3.367	-5.924	-2.840	0.006	-1.848	-1.242	0.008
4	4	18	THR	0	-0.069	-0.057	2.841	1.425	1.993	0.061	-0.147	-0.482	0.000
5	4	19	GLY	0	0.035	0.017	4.101	-1.312	-1.184	-0.001	-0.043	-0.084	0.000
6	4	20	SER	0	-0.018	0.012	6.717	0.135	0.135	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.029	0.003	8.150	0.039	0.039	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.043	-0.001	10.558	0.077	0.077	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.017	0.000	10.218	0.002	0.002	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.005	-0.006	9.026	-0.128	-0.128	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.030	0.022	11.456	-0.023	-0.023	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.015	0.000	13.748	-0.039	-0.039	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.011	-0.002	13.190	0.052	0.052	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.050	0.001	9.014	0.096	0.096	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.006	-0.018	11.801	0.039	0.039	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.038	-0.010	14.348	-0.037	-0.037	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.013	0.010	9.007	-0.154	-0.154	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.055	-0.036	7.180	0.079	0.079	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.016	0.030	10.989	-0.131	-0.131	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.031	-0.018	11.577	0.112	0.112	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.885	-0.932	10.686	0.755	0.755	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.056	-0.032	13.806	-0.032	-0.032	0.000	0.000	0.000	0.000
23	4	37	GLN	0	0.009	-0.002	13.472	-0.011	-0.011	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.008	-0.002	17.801	-0.010	-0.010	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.022	0.003	20.762	-0.007	-0.007	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.010	0.003	12.252	0.017	0.017	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.920	-0.997	13.045	0.021	0.021	0.000	0.000	0.000	0.000
28	4	67	TRP	0	0.010	-0.019	14.714	-0.062	-0.062	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.109	0.067	16.437	-0.001	-0.001	0.000	0.000	0.000	0.000
30	4	69	SER	0	-0.035	0.014	14.011	0.001	0.001	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.974	0.979	16.092	0.083	0.083	0.000	0.000	0.000	0.000
32	4	71	LEU	0	0.003	0.002	19.053	0.005	0.005	0.000	0.000	0.000	0.000
33	4	72	ALA	0	-0.039	-0.007	18.842	0.010	0.010	0.000	0.000	0.000	0.000
34	4	73	SER	0	0.010	-0.009	19.239	-0.005	-0.005	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.109	-0.038	21.589	0.014	0.014	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.012	0.016	24.437	0.015	0.015	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.008	0.002	26.305	-0.003	-0.003	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.013	-0.007	27.792	-0.008	-0.008	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.046	-0.015	30.226	-0.001	-0.001	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.049	-0.001	33.695	-0.001	-0.001	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.021	-0.003	37.067	0.002	0.002	0.000	0.000	0.000	0.000
42	4	81	GLY	0	-0.007	0.007	38.901	0.004	0.004	0.000	0.000	0.000	0.000
43	4	82	ALA	0	0.019	0.002	42.211	0.001	0.001	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.044	-0.015	40.024	0.001	0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.009	0.013	43.698	0.002	0.002	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.012	0.007	43.442	-0.002	-0.002	0.000	0.000	0.000	0.000

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