FMO DATABASE

FMODB ID: 4311N

Calculation Name: 3ZDM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZDM

Chain ID: B

ChEMBL ID:

UniProt ID: Q12285

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	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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-223272.442772
FMO2-HF: Nuclear repulsion	203955.829967
FMO2-HF: Total energy	-19316.612805
FMO2-MP2: Total energy	-19372.008501

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:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
-3.026	-1.844	-0.009	-0.47	-0.703	0.002

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.035

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

Sort

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	B	4	SER	0	-0.025	-0.053	3.828	2.032	3.214	-0.009	-0.470	-0.703	0.002
4	B	5	LYS	1	0.963	0.953	6.129	0.589	0.589	0.000	0.000	0.000	0.000
5	B	6	GLU	-1	-0.876	-0.921	9.097	-0.688	-0.688	0.000	0.000	0.000	0.000
6	B	7	GLU	-1	-0.806	-0.864	5.812	-4.788	-4.788	0.000	0.000	0.000	0.000
7	B	8	ILE	0	-0.054	-0.029	6.225	0.300	0.300	0.000	0.000	0.000	0.000
8	B	9	ALA	0	-0.005	-0.002	9.808	0.100	0.100	0.000	0.000	0.000	0.000
9	B	10	ALA	0	0.060	0.025	12.462	0.071	0.071	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.009	-0.020	8.865	0.084	0.084	0.000	0.000	0.000	0.000
11	B	12	ILE	0	-0.053	-0.008	13.072	0.088	0.088	0.000	0.000	0.000	0.000
12	B	13	VAL	0	0.034	0.012	15.277	0.025	0.025	0.000	0.000	0.000	0.000
13	B	14	ASN	0	-0.003	0.010	15.834	0.037	0.037	0.000	0.000	0.000	0.000
14	B	15	TYR	0	0.001	0.009	16.426	0.033	0.033	0.000	0.000	0.000	0.000
15	B	16	PHE	0	0.030	-0.005	18.222	0.020	0.020	0.000	0.000	0.000	0.000
16	B	17	SER	0	0.018	-0.002	20.812	0.002	0.002	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.055	-0.019	20.931	0.011	0.011	0.000	0.000	0.000	0.000
18	B	19	ILE	0	-0.002	0.000	22.061	0.009	0.009	0.000	0.000	0.000	0.000
19	B	20	VAL	0	-0.010	-0.012	24.574	0.004	0.004	0.000	0.000	0.000	0.000
20	B	21	GLU	-1	-0.969	-0.983	24.673	-0.093	-0.093	0.000	0.000	0.000	0.000
21	B	22	LYS	1	0.850	0.940	23.698	0.006	0.006	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.821	0.902	28.602	0.021	0.021	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.916	-0.965	25.553	0.053	0.053	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.071	-0.023	26.900	0.012	0.012	0.000	0.000	0.000	0.000
25	B	26	SER	0	-0.061	-0.054	30.256	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	27	GLU	-1	-0.816	-0.913	32.059	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.795	-0.869	33.225	0.009	0.009	0.000	0.000	0.000	0.000
28	B	29	GLY	0	-0.021	-0.013	30.554	0.000	0.000	0.000	0.000	0.000	0.000
29	B	30	ALA	0	0.011	-0.013	28.592	0.000	0.000	0.000	0.000	0.000	0.000
30	B	31	ASP	-1	-0.905	-0.944	28.888	-0.029	-0.029	0.000	0.000	0.000	0.000
31	B	32	SER	0	-0.078	-0.043	28.968	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	33	LEU	0	-0.007	-0.010	23.334	0.000	0.000	0.000	0.000	0.000	0.000
33	B	34	ASN	0	-0.003	0.010	24.712	-0.021	-0.021	0.000	0.000	0.000	0.000
34	B	35	VAL	0	0.046	0.031	26.044	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	36	ALA	0	-0.023	-0.009	22.772	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	37	MET	0	-0.015	-0.001	20.957	-0.012	-0.012	0.000	0.000	0.000	0.000
37	B	38	ASP	-1	-0.805	-0.873	21.393	-0.134	-0.134	0.000	0.000	0.000	0.000
38	B	39	CYS	0	-0.062	-0.030	23.045	-0.010	-0.010	0.000	0.000	0.000	0.000
39	B	40	ILE	0	-0.069	-0.033	16.885	0.002	0.002	0.000	0.000	0.000	0.000
40	B	41	SER	0	0.002	-0.029	18.110	-0.031	-0.031	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.929	-0.948	19.128	-0.146	-0.146	0.000	0.000	0.000	0.000
42	B	43	ALA	0	-0.080	-0.035	18.493	-0.012	-0.012	0.000	0.000	0.000	0.000
43	B	44	PHE	0	-0.116	-0.078	13.048	0.034	0.034	0.000	0.000	0.000	0.000
44	B	45	GLY	0	-0.023	0.011	15.397	-0.082	-0.082	0.000	0.000	0.000	0.000
45	B	46	PHE	0	-0.022	-0.009	14.700	-0.045	-0.045	0.000	0.000	0.000	0.000
46	B	47	GLU	-1	-0.902	-0.958	18.511	-0.198	-0.198	0.000	0.000	0.000	0.000
47	B	48	ARG	1	0.861	0.895	20.042	0.081	0.081	0.000	0.000	0.000	0.000
48	B	49	GLU	-1	-0.947	-0.983	20.769	-0.210	-0.210	0.000	0.000	0.000	0.000
49	B	50	ALA	0	-0.065	-0.023	18.351	-0.013	-0.013	0.000	0.000	0.000	0.000
50	B	51	VAL	0	-0.062	-0.008	15.710	-0.096	-0.096	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)