FMO DATABASE

FMODB ID: VR3L1

Calculation Name: 3ZDM-A-Xray372

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: 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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-358511.821416
FMO2-HF: Nuclear repulsion	332319.439807
FMO2-HF: Total energy	-26192.381609
FMO2-MP2: Total energy	-26268.449231

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:2:SER)

Summations of interaction energy for fragment #1(A: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.
-36.499	-44.07	30.701	-13.135	-9.996	-0.118

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.096 / q_NPA : -0.086

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	4	SER	0	-0.010	-0.033	3.815	1.865	3.079	-0.012	-0.538	-0.665	0.002
4	A	5	LYS	1	0.862	0.896	6.492	-0.076	-0.076	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.762	-0.871	9.509	0.003	0.003	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.806	-0.869	6.492	-2.729	-2.729	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.027	-0.014	6.188	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.008	0.006	9.664	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.035	0.017	12.440	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.024	-0.019	8.220	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.034	-0.006	12.585	0.034	0.034	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.021	0.009	14.990	0.004	0.004	0.000	0.000	0.000	0.000
13	A	14	ASN	0	0.000	-0.006	15.186	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.053	-0.020	16.053	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.021	-0.011	17.819	0.018	0.018	0.000	0.000	0.000	0.000
16	A	17	SER	0	0.013	-0.021	20.236	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.045	-0.003	20.253	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.018	0.008	21.821	0.010	0.010	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.012	-0.003	24.356	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.888	-0.927	23.006	-0.241	-0.241	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.786	0.904	22.773	0.242	0.242	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.850	0.934	27.942	0.094	0.094	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.935	-0.969	24.831	-0.145	-0.145	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.041	-0.020	26.950	0.011	0.011	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.042	-0.034	29.921	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.848	-0.943	31.964	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.810	-0.887	33.171	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.025	-0.012	30.367	0.005	0.005	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.006	-0.009	28.394	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.881	-0.936	28.739	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.093	-0.049	28.712	0.007	0.007	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.006	-0.008	23.117	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.023	0.025	24.646	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.038	0.026	26.170	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.015	0.001	22.880	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.031	-0.017	20.936	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.813	-0.874	21.855	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	39	CYS	0	-0.068	-0.037	23.488	0.006	0.006	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.037	-0.014	17.128	0.018	0.018	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.020	-0.037	18.712	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.932	-0.957	20.003	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.092	-0.038	19.275	0.010	0.010	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.089	-0.065	13.365	0.054	0.054	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.002	0.023	16.483	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.087	-0.038	14.532	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.865	-0.935	18.953	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.925	0.928	20.320	0.077	0.077	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.930	-0.973	20.998	-0.200	-0.200	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.059	-0.028	18.952	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.014	0.011	15.769	-0.081	-0.081	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.027	0.001	15.743	-0.094	-0.094	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.016	-0.003	16.647	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.028	-0.020	11.995	-0.090	-0.090	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.001	0.009	11.079	-0.189	-0.189	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.019	0.010	12.617	-0.103	-0.103	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.941	0.978	11.702	0.743	0.743	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.012	-0.015	11.760	-0.156	-0.156	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.949	-0.957	8.798	-1.178	-1.178	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.057	0.034	6.418	-0.267	-0.267	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.852	0.920	7.071	0.325	0.325	0.000	0.000	0.000	0.000
61	A	62	GLY	0	-0.001	-0.002	8.741	-0.185	-0.185	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.013	-0.001	2.374	2.849	4.358	0.725	-0.889	-1.345	0.000
63	A	64	HIS	0	0.034	0.025	4.387	-2.782	-2.620	-0.001	-0.026	-0.135	0.000
64	A	65	LEU	0	-0.041	-0.020	5.498	0.437	0.437	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.011	-0.016	5.409	0.492	0.492	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.780	-0.858	1.675	-37.991	-48.541	29.990	-11.643	-7.797	-0.120
67	A	68	ILE	0	-0.052	-0.020	4.416	1.932	2.026	-0.001	-0.039	-0.054	0.000
68	A	69	LEU	0	-0.067	-0.032	8.084	0.586	0.586	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.110	-0.042	6.953	0.725	0.725	0.000	0.000	0.000	0.000

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