FMO DATABASE

FMODB ID: LJM59

Calculation Name: 3ZDM-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZDM

Chain ID: A

ChEMBL ID:

UniProt ID: Q12285

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	71
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-361785.983712
FMO2-HF: Nuclear repulsion	335423.029745
FMO2-HF: Total energy	-26362.953966
FMO2-MP2: Total energy	-26439.519722

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(A:1:ACE )

Summations of interaction energy for fragment #1(A:1:ACE )

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.
-3.711	-1.479	1.398	-2.101	-1.529	-0.013

Interaction energy analysis for fragmet #1(A:1:ACE )

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 : -0.034

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	A	3	ALA	0	-0.028	0.008	3.817	0.299	1.717	-0.004	-0.677	-0.737	-0.002
4	A	4	SER	0	0.029	0.031	6.022	0.070	0.070	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.914	0.938	9.032	0.348	0.348	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.806	-0.909	10.896	-0.190	-0.190	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.867	-0.942	8.900	-0.564	-0.564	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.024	-0.015	6.329	0.109	0.109	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.019	0.014	10.262	0.059	0.059	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.037	0.017	13.759	0.024	0.024	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.026	-0.022	8.922	0.032	0.032	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.039	-0.010	12.778	0.023	0.023	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.021	0.011	15.183	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.009	-0.003	15.805	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.057	-0.020	16.177	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.014	-0.012	18.028	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.021	-0.010	20.758	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.018	0.012	20.447	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.007	0.007	21.468	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.007	0.003	24.417	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.937	-0.954	24.238	0.040	0.040	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.820	0.905	22.752	-0.088	-0.088	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.895	0.952	28.045	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.938	-0.968	24.813	0.099	0.099	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.035	-0.017	26.440	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.009	-0.003	29.660	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.884	-0.956	31.838	0.034	0.034	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.853	-0.915	33.190	0.037	0.037	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.054	-0.036	30.014	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.009	-0.013	28.446	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.884	-0.932	28.914	0.029	0.029	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.072	-0.041	28.152	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.013	-0.012	23.079	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.035	0.030	24.869	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.029	0.024	26.642	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.021	-0.003	22.709	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.037	-0.028	21.419	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.817	-0.892	22.566	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.072	-0.042	23.909	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.045	-0.015	17.555	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.009	-0.017	19.786	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.928	-0.958	21.303	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.091	-0.037	20.123	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.102	-0.071	14.599	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.002	0.024	18.673	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.081	-0.037	16.243	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.865	-0.937	21.208	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.937	0.949	22.198	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.931	-0.974	22.460	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.056	-0.027	21.444	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.019	0.013	16.941	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.028	0.001	17.552	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.019	-0.005	18.679	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.023	-0.017	14.206	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.014	0.002	12.314	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.003	0.003	14.511	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.912	0.956	15.029	0.154	0.154	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.012	-0.016	14.557	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.944	-0.955	12.608	-0.379	-0.379	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.060	0.038	8.410	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.892	0.945	9.573	0.021	0.021	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.002	-0.001	10.375	0.034	0.034	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.033	0.017	5.923	0.325	0.325	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.032	0.025	5.527	-0.264	-0.264	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.043	-0.023	6.313	0.268	0.268	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.016	-0.017	7.756	0.136	0.136	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.809	-0.881	2.440	-4.397	-3.671	1.402	-1.416	-0.712	-0.011
68	A	68	ILE	0	-0.065	-0.026	4.379	0.499	0.587	0.000	-0.008	-0.080	0.000
69	A	69	LEU	0	-0.096	-0.052	6.712	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.036	-0.007	6.567	0.125	0.125	0.000	0.000	0.000	0.000
71	A	71	NME	0	-0.034	-0.011	7.636	-0.216	-0.216	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ACE )