FMO DATABASE

FMODB ID: GNGM1

Calculation Name: 3M91-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M91

Chain ID: B

ChEMBL ID:

UniProt ID: P9WQN5

Base Structure: X-ray

Registration Date: 2023-06-20

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	31
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-100344.670355
FMO2-HF: Nuclear repulsion	87980.070282
FMO2-HF: Total energy	-12364.600073
FMO2-MP2: Total energy	-12400.81036

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(B:21:SER)

Summations of interaction energy for fragment #1(B:21: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.
-15.251	-13.102	5.239	-3.599	-3.789	0.034

Interaction energy analysis for fragmet #1(B:21:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.031

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	B	23	ALA	0	0.095	0.046	3.881	1.182	3.619	-0.019	-1.396	-1.022	0.006
4	B	24	ALA	0	0.048	0.022	6.900	0.499	0.499	0.000	0.000	0.000	0.000
5	B	25	GLY	0	-0.039	-0.022	4.061	-0.144	-0.053	-0.001	-0.015	-0.075	0.000
6	B	26	GLN	0	-0.141	-0.073	4.827	0.698	0.698	0.000	0.000	0.000	0.000
7	B	27	GLU	-1	-0.758	-0.863	5.956	0.379	0.379	0.000	0.000	0.000	0.000
8	B	28	ARG	1	0.944	0.976	6.739	-1.726	-1.726	0.000	0.000	0.000	0.000
9	B	29	ARG	1	0.846	0.905	1.958	-18.733	-19.112	5.259	-2.188	-2.692	0.028
10	B	30	GLU	-1	-0.801	-0.890	9.334	0.572	0.572	0.000	0.000	0.000	0.000
11	B	31	LYS	1	0.834	0.916	11.455	-0.662	-0.662	0.000	0.000	0.000	0.000
12	B	32	LEU	0	-0.004	0.004	11.401	-0.019	-0.019	0.000	0.000	0.000	0.000
13	B	33	THR	0	-0.062	-0.022	12.650	-0.004	-0.004	0.000	0.000	0.000	0.000
14	B	34	GLU	-1	-0.893	-0.942	14.958	0.350	0.350	0.000	0.000	0.000	0.000
15	B	35	GLU	-1	-0.927	-0.980	17.315	0.578	0.578	0.000	0.000	0.000	0.000
16	B	36	THR	0	-0.103	-0.063	17.104	-0.029	-0.029	0.000	0.000	0.000	0.000
17	B	37	ASP	-1	-0.904	-0.967	18.419	0.485	0.485	0.000	0.000	0.000	0.000
18	B	38	ASP	-1	-0.914	-0.951	20.923	0.285	0.285	0.000	0.000	0.000	0.000
19	B	39	LEU	0	-0.073	-0.030	22.657	-0.027	-0.027	0.000	0.000	0.000	0.000
20	B	40	LEU	0	-0.081	-0.043	21.483	-0.018	-0.018	0.000	0.000	0.000	0.000
21	B	41	ASP	-1	-0.874	-0.931	24.942	0.241	0.241	0.000	0.000	0.000	0.000
22	B	42	GLU	-1	-0.980	-0.984	27.008	0.230	0.230	0.000	0.000	0.000	0.000
23	B	43	ILE	0	-0.076	-0.044	26.159	-0.016	-0.016	0.000	0.000	0.000	0.000
24	B	44	ASP	-1	-0.903	-0.963	29.202	0.230	0.230	0.000	0.000	0.000	0.000
25	B	45	ASP	-1	-0.925	-0.954	31.092	0.168	0.168	0.000	0.000	0.000	0.000
26	B	46	VAL	0	-0.058	-0.032	32.663	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	47	LEU	0	-0.092	-0.051	31.660	-0.012	-0.012	0.000	0.000	0.000	0.000
28	B	48	GLU	-1	-0.996	-0.989	35.174	0.135	0.135	0.000	0.000	0.000	0.000
29	B	49	GLU	-1	-0.963	-0.976	37.113	0.141	0.141	0.000	0.000	0.000	0.000
30	B	50	ASN	0	-0.105	-0.041	38.429	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	51	ALA	0	-0.127	-0.061	40.017	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:21:SER)