FMO DATABASE

FMODB ID: N1R2Q

Calculation Name: 1MVF-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MVF

Chain ID: D

ChEMBL ID:

UniProt ID: P0AE72

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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-171431.019682
FMO2-HF: Nuclear repulsion	154658.206174
FMO2-HF: Total energy	-16772.813508
FMO2-MP2: Total energy	-16821.975643

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(D:4:SER)

Summations of interaction energy for fragment #1(D:4: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.
-2.641	-1.055	-0.021	-0.812	-0.754	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.003

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	D	6	VAL	0	0.057	0.049	3.860	0.346	1.899	-0.020	-0.810	-0.723	0.003
4	D	7	LYS	1	0.826	0.900	6.123	-0.544	-0.544	0.000	0.000	0.000	0.000
5	D	8	ARG	1	0.951	0.966	9.066	-0.340	-0.340	0.000	0.000	0.000	0.000
6	D	9	TRP	0	0.042	0.034	12.498	0.088	0.088	0.000	0.000	0.000	0.000
7	D	10	GLY	0	0.037	0.019	13.889	-0.053	-0.053	0.000	0.000	0.000	0.000
8	D	11	ASN	0	-0.009	-0.011	17.338	-0.040	-0.040	0.000	0.000	0.000	0.000
9	D	12	SER	0	0.018	0.011	16.177	-0.044	-0.044	0.000	0.000	0.000	0.000
10	D	13	PRO	0	-0.017	-0.014	12.258	0.069	0.069	0.000	0.000	0.000	0.000
11	D	14	ALA	0	0.043	0.028	10.494	0.010	0.010	0.000	0.000	0.000	0.000
12	D	15	VAL	0	0.024	-0.004	4.795	-0.109	-0.076	-0.001	-0.002	-0.031	0.000
13	D	16	ARG	1	0.940	0.977	5.775	-2.685	-2.685	0.000	0.000	0.000	0.000
14	D	17	ILE	0	0.077	0.043	5.553	0.955	0.955	0.000	0.000	0.000	0.000
15	D	18	PRO	0	-0.016	0.001	5.329	-0.161	-0.161	0.000	0.000	0.000	0.000
16	D	19	ALA	0	0.068	0.017	7.823	-0.325	-0.325	0.000	0.000	0.000	0.000
17	D	20	THR	0	0.037	0.019	9.332	-0.020	-0.020	0.000	0.000	0.000	0.000
18	D	21	LEU	0	-0.001	-0.002	6.843	-0.102	-0.102	0.000	0.000	0.000	0.000
19	D	22	MET	0	-0.011	0.008	10.677	-0.093	-0.093	0.000	0.000	0.000	0.000
20	D	23	GLN	0	0.008	-0.006	13.173	-0.066	-0.066	0.000	0.000	0.000	0.000
21	D	24	ALA	0	-0.036	-0.012	13.246	-0.064	-0.064	0.000	0.000	0.000	0.000
22	D	25	LEU	0	-0.032	-0.022	12.410	-0.066	-0.066	0.000	0.000	0.000	0.000
23	D	26	ASN	0	-0.086	-0.040	15.975	-0.040	-0.040	0.000	0.000	0.000	0.000
24	D	27	LEU	0	0.003	0.021	14.081	-0.016	-0.016	0.000	0.000	0.000	0.000
25	D	28	ASN	0	-0.085	-0.058	17.052	0.058	0.058	0.000	0.000	0.000	0.000
26	D	29	ILE	0	-0.058	-0.048	15.722	0.044	0.044	0.000	0.000	0.000	0.000
27	D	30	ASP	-1	-0.926	-0.969	18.389	0.293	0.293	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.821	-0.884	18.762	0.249	0.249	0.000	0.000	0.000	0.000
29	D	32	GLU	-1	-0.919	-0.966	18.554	0.198	0.198	0.000	0.000	0.000	0.000
30	D	33	VAL	0	-0.074	-0.042	14.836	0.003	0.003	0.000	0.000	0.000	0.000
31	D	34	LYS	1	0.790	0.880	17.835	-0.091	-0.091	0.000	0.000	0.000	0.000
32	D	35	ILE	0	-0.032	-0.030	13.578	0.014	0.014	0.000	0.000	0.000	0.000
33	D	36	ASP	-1	-0.853	-0.917	15.192	-0.102	-0.102	0.000	0.000	0.000	0.000
34	D	37	LEU	0	-0.095	-0.048	14.731	-0.043	-0.043	0.000	0.000	0.000	0.000
35	D	38	VAL	0	0.057	0.035	15.750	0.013	0.013	0.000	0.000	0.000	0.000
36	D	39	ASP	-1	-0.843	-0.909	15.957	-0.317	-0.317	0.000	0.000	0.000	0.000
37	D	40	GLY	0	-0.020	-0.008	16.030	-0.043	-0.043	0.000	0.000	0.000	0.000
38	D	41	LYS	1	0.791	0.879	11.853	0.284	0.284	0.000	0.000	0.000	0.000
39	D	42	LEU	0	-0.016	-0.010	9.356	0.066	0.066	0.000	0.000	0.000	0.000
40	D	43	ILE	0	-0.022	-0.007	10.636	-0.017	-0.017	0.000	0.000	0.000	0.000
41	D	44	ILE	0	0.010	-0.014	9.515	0.032	0.032	0.000	0.000	0.000	0.000
42	D	45	GLU	-1	-0.848	-0.901	13.054	0.066	0.066	0.000	0.000	0.000	0.000
43	D	46	PRO	0	0.057	0.035	15.816	-0.013	-0.013	0.000	0.000	0.000	0.000
44	D	47	VAL	0	-0.043	-0.001	18.543	-0.035	-0.035	0.000	0.000	0.000	0.000

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