FMO DATABASE

FMODB ID: GNMY1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-171625.850144
FMO2-HF: Nuclear repulsion	154853.373624
FMO2-HF: Total energy	-16772.47652
FMO2-MP2: Total energy	-16821.68362

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.
1.06	4.389	-0.031	-1.894	-1.405	0.008

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 : 0.055 / q_NPA : 0.026

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	0.060	0.059	3.801	-1.355	1.930	-0.030	-1.889	-1.367	0.008
4	D	7	LYS	1	0.851	0.909	6.394	2.133	2.133	0.000	0.000	0.000	0.000
5	D	8	ARG	1	0.981	0.989	8.931	0.679	0.679	0.000	0.000	0.000	0.000
6	D	9	TRP	0	0.032	0.017	12.469	-0.001	-0.001	0.000	0.000	0.000	0.000
7	D	10	GLY	0	0.008	0.002	13.925	0.053	0.053	0.000	0.000	0.000	0.000
8	D	11	ASN	0	0.024	0.004	17.462	-0.064	-0.064	0.000	0.000	0.000	0.000
9	D	12	SER	0	-0.010	-0.005	16.165	0.017	0.017	0.000	0.000	0.000	0.000
10	D	13	PRO	0	-0.014	0.001	12.143	-0.040	-0.040	0.000	0.000	0.000	0.000
11	D	14	ALA	0	0.052	0.028	10.256	0.122	0.122	0.000	0.000	0.000	0.000
12	D	15	VAL	0	0.028	0.005	4.317	-0.552	-0.508	-0.001	-0.005	-0.038	0.000
13	D	16	ARG	1	0.934	0.974	5.939	-0.300	-0.300	0.000	0.000	0.000	0.000
14	D	17	ILE	0	0.065	0.032	5.430	0.916	0.916	0.000	0.000	0.000	0.000
15	D	18	PRO	0	-0.016	0.000	5.219	-0.474	-0.474	0.000	0.000	0.000	0.000
16	D	19	ALA	0	0.099	0.026	7.799	-0.287	-0.287	0.000	0.000	0.000	0.000
17	D	20	THR	0	0.030	0.012	9.634	-0.035	-0.035	0.000	0.000	0.000	0.000
18	D	21	LEU	0	0.008	0.004	6.438	-0.083	-0.083	0.000	0.000	0.000	0.000
19	D	22	MET	0	-0.017	0.008	10.571	-0.192	-0.192	0.000	0.000	0.000	0.000
20	D	23	GLN	0	-0.008	-0.008	13.118	-0.093	-0.093	0.000	0.000	0.000	0.000
21	D	24	ALA	0	-0.048	-0.013	13.039	-0.110	-0.110	0.000	0.000	0.000	0.000
22	D	25	LEU	0	-0.037	-0.016	12.710	-0.108	-0.108	0.000	0.000	0.000	0.000
23	D	26	ASN	0	-0.057	-0.019	16.064	-0.075	-0.075	0.000	0.000	0.000	0.000
24	D	27	LEU	0	-0.008	-0.010	13.126	-0.043	-0.043	0.000	0.000	0.000	0.000
25	D	28	ASN	0	-0.096	-0.058	16.912	0.053	0.053	0.000	0.000	0.000	0.000
26	D	29	ILE	0	-0.045	-0.033	15.500	0.011	0.011	0.000	0.000	0.000	0.000
27	D	30	ASP	-1	-0.915	-0.964	18.049	0.254	0.254	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.839	-0.889	18.208	0.418	0.418	0.000	0.000	0.000	0.000
29	D	32	GLU	-1	-0.940	-0.968	18.168	0.212	0.212	0.000	0.000	0.000	0.000
30	D	33	VAL	0	-0.053	-0.045	14.424	0.045	0.045	0.000	0.000	0.000	0.000
31	D	34	LYS	1	0.810	0.892	17.278	-0.324	-0.324	0.000	0.000	0.000	0.000
32	D	35	ILE	0	-0.025	-0.026	13.109	0.043	0.043	0.000	0.000	0.000	0.000
33	D	36	ASP	-1	-0.852	-0.920	14.925	0.004	0.004	0.000	0.000	0.000	0.000
34	D	37	LEU	0	-0.095	-0.043	14.791	-0.014	-0.014	0.000	0.000	0.000	0.000
35	D	38	VAL	0	0.046	0.020	15.884	0.001	0.001	0.000	0.000	0.000	0.000
36	D	39	ASP	-1	-0.916	-0.960	16.100	0.051	0.051	0.000	0.000	0.000	0.000
37	D	40	GLY	0	-0.049	-0.022	16.011	-0.020	-0.020	0.000	0.000	0.000	0.000
38	D	41	LYS	1	0.904	0.950	11.696	-0.204	-0.204	0.000	0.000	0.000	0.000
39	D	42	LEU	0	-0.010	0.004	8.939	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	43	ILE	0	-0.026	-0.018	10.829	0.136	0.136	0.000	0.000	0.000	0.000
41	D	44	ILE	0	0.009	-0.005	9.110	-0.063	-0.063	0.000	0.000	0.000	0.000
42	D	45	GLU	-1	-0.874	-0.920	12.830	0.438	0.438	0.000	0.000	0.000	0.000
43	D	46	PRO	0	0.048	0.025	15.751	-0.057	-0.057	0.000	0.000	0.000	0.000
44	D	47	VAL	0	-0.032	0.005	18.120	-0.031	-0.031	0.000	0.000	0.000	0.000

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