FMO DATABASE

FMODB ID: 1719Z

Calculation Name: 3ADG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ADG

Chain ID: A

ChEMBL ID:

UniProt ID: O04492

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-437189.235965
FMO2-HF: Nuclear repulsion	409324.517408
FMO2-HF: Total energy	-27864.718557
FMO2-MP2: Total energy	-27948.775258

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:13:SER)

Summations of interaction energy for fragment #1(A:13: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.
0.564	4.976	5.643	-3.81	-6.245	-0.001

Interaction energy analysis for fragmet #1(A:13:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.012

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	15	VAL	0	0.010	0.000	3.731	-0.304	1.625	-0.030	-0.884	-1.015	0.004
4	A	16	PHE	0	0.053	0.040	2.130	-1.873	-1.786	4.296	-1.816	-2.566	-0.012
5	A	17	LYS	1	0.886	0.926	5.685	0.678	0.678	0.000	0.000	0.000	0.000
6	A	18	SER	0	0.032	0.016	8.267	0.029	0.029	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.995	1.003	7.368	0.811	0.811	0.000	0.000	0.000	0.000
8	A	20	LEU	0	0.023	0.024	9.949	0.095	0.095	0.000	0.000	0.000	0.000
9	A	21	GLN	0	0.031	0.007	11.777	0.044	0.044	0.000	0.000	0.000	0.000
10	A	22	GLU	-1	-0.952	-0.978	13.544	-0.472	-0.472	0.000	0.000	0.000	0.000
11	A	23	TYR	0	0.016	0.007	14.466	0.034	0.034	0.000	0.000	0.000	0.000
12	A	24	ALA	0	0.017	0.000	15.911	0.018	0.018	0.000	0.000	0.000	0.000
13	A	25	GLN	0	-0.028	-0.008	17.889	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.906	0.959	19.163	0.084	0.084	0.000	0.000	0.000	0.000
15	A	27	TYR	0	-0.024	-0.021	19.172	0.003	0.003	0.000	0.000	0.000	0.000
16	A	28	LYS	1	0.893	0.961	22.204	0.083	0.083	0.000	0.000	0.000	0.000
17	A	29	LEU	0	0.022	0.026	19.400	0.014	0.014	0.000	0.000	0.000	0.000
18	A	30	PRO	0	-0.015	-0.016	21.068	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	31	THR	0	-0.008	-0.006	16.206	0.021	0.021	0.000	0.000	0.000	0.000
20	A	32	PRO	0	-0.037	-0.003	13.592	0.026	0.026	0.000	0.000	0.000	0.000
21	A	33	VAL	0	0.006	0.015	15.629	-0.064	-0.064	0.000	0.000	0.000	0.000
22	A	34	TYR	0	-0.014	-0.023	9.602	0.075	0.075	0.000	0.000	0.000	0.000
23	A	35	GLU	-1	-0.780	-0.868	14.286	0.230	0.230	0.000	0.000	0.000	0.000
24	A	36	ILE	0	-0.061	-0.042	12.312	0.105	0.105	0.000	0.000	0.000	0.000
25	A	37	VAL	0	0.065	0.038	14.354	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	38	LYS	1	0.896	0.943	14.764	-0.069	-0.069	0.000	0.000	0.000	0.000
27	A	39	GLU	-1	-0.904	-0.942	16.848	0.378	0.378	0.000	0.000	0.000	0.000
28	A	40	GLY	0	0.045	0.016	18.196	0.018	0.018	0.000	0.000	0.000	0.000
29	A	41	PRO	0	0.007	-0.007	20.556	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	42	SER	0	0.043	0.017	20.463	0.015	0.015	0.000	0.000	0.000	0.000
31	A	43	HIS	0	0.012	0.010	19.796	0.006	0.006	0.000	0.000	0.000	0.000
32	A	44	LYS	1	0.860	0.922	17.842	-0.172	-0.172	0.000	0.000	0.000	0.000
33	A	45	SER	0	-0.022	0.000	16.424	0.015	0.015	0.000	0.000	0.000	0.000
34	A	46	LEU	0	-0.007	0.006	13.515	0.041	0.041	0.000	0.000	0.000	0.000
35	A	47	PHE	0	-0.039	-0.032	10.635	-0.139	-0.139	0.000	0.000	0.000	0.000
36	A	48	GLN	0	-0.032	-0.009	11.100	0.130	0.130	0.000	0.000	0.000	0.000
37	A	49	SER	0	-0.054	-0.041	9.892	-0.161	-0.161	0.000	0.000	0.000	0.000
38	A	50	THR	0	0.026	0.007	11.919	0.150	0.150	0.000	0.000	0.000	0.000
39	A	51	VAL	0	-0.038	-0.007	11.528	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	52	ILE	0	-0.011	-0.012	13.580	0.019	0.019	0.000	0.000	0.000	0.000
41	A	53	LEU	0	0.005	-0.018	15.407	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	54	ASP	-1	-0.886	-0.944	18.102	0.127	0.127	0.000	0.000	0.000	0.000
43	A	55	GLY	0	0.017	0.015	21.640	0.006	0.006	0.000	0.000	0.000	0.000
44	A	56	VAL	0	-0.025	0.002	18.546	0.018	0.018	0.000	0.000	0.000	0.000
45	A	57	ARG	1	0.824	0.893	17.375	-0.324	-0.324	0.000	0.000	0.000	0.000
46	A	58	TYR	0	0.041	0.016	13.167	0.038	0.038	0.000	0.000	0.000	0.000
47	A	59	ASN	0	0.023	0.019	13.195	0.022	0.022	0.000	0.000	0.000	0.000
48	A	60	SER	0	0.015	0.004	8.336	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	61	LEU	0	0.027	0.013	8.362	-0.314	-0.314	0.000	0.000	0.000	0.000
50	A	62	PRO	0	0.053	0.029	10.323	0.042	0.042	0.000	0.000	0.000	0.000
51	A	63	GLY	0	0.012	-0.004	11.070	0.152	0.152	0.000	0.000	0.000	0.000
52	A	64	PHE	0	0.040	0.030	5.487	0.120	0.120	0.000	0.000	0.000	0.000
53	A	65	PHE	0	0.053	0.011	9.053	-0.224	-0.224	0.000	0.000	0.000	0.000
54	A	66	ASN	0	-0.031	-0.020	7.023	-0.408	-0.408	0.000	0.000	0.000	0.000
55	A	67	ARG	1	0.983	0.986	8.565	0.484	0.484	0.000	0.000	0.000	0.000
56	A	68	LYS	1	0.937	0.970	5.569	1.485	1.485	0.000	0.000	0.000	0.000
57	A	69	ALA	0	0.014	0.011	3.641	-0.469	-0.279	0.002	-0.050	-0.142	0.000
58	A	70	ALA	0	0.047	0.037	4.441	1.864	1.939	-0.001	-0.012	-0.062	0.000
59	A	71	GLU	-1	-0.787	-0.897	7.238	0.143	0.143	0.000	0.000	0.000	0.000
60	A	72	GLN	0	-0.003	-0.005	2.576	-1.141	0.620	1.378	-1.015	-2.124	0.007
61	A	73	SER	0	0.025	0.035	4.506	-0.064	0.260	-0.001	-0.032	-0.292	0.000
62	A	74	ALA	0	0.053	0.015	5.330	-0.782	-0.736	-0.001	-0.001	-0.044	0.000
63	A	75	ALA	0	-0.028	-0.016	6.831	-0.301	-0.301	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.879	-0.933	5.161	2.882	2.882	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.035	-0.018	7.131	-0.468	-0.468	0.000	0.000	0.000	0.000
66	A	78	ALA	0	0.025	0.013	10.433	-0.224	-0.224	0.000	0.000	0.000	0.000
67	A	79	LEU	0	-0.053	-0.036	7.838	-0.175	-0.175	0.000	0.000	0.000	0.000
68	A	80	ARG	1	0.824	0.908	8.362	-1.244	-1.244	0.000	0.000	0.000	0.000
69	A	81	GLU	-1	-0.861	-0.917	12.603	0.388	0.388	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.027	-0.021	14.109	-0.066	-0.066	0.000	0.000	0.000	0.000
71	A	83	ALA	0	-0.056	-0.015	15.307	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	84	LYS	1	0.826	0.929	16.400	-0.531	-0.531	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:SER)