FMO DATABASE

FMODB ID: YY592

Calculation Name: 3RD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD4

Chain ID: A

ChEMBL ID:

UniProt ID: C0AZM8

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:

Apendix: None

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500693.500021
FMO2-HF: Nuclear repulsion	469131.396797
FMO2-HF: Total energy	-31562.103223
FMO2-MP2: Total energy	-31653.613529

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:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-0.031	3.327	0.028	-1.574	-1.809	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.021

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	A	4	VAL	0	0.010	-0.011	3.757	-1.212	1.153	-0.008	-1.316	-1.040	0.005
4	A	5	LYS	1	0.920	0.961	4.799	-0.027	0.050	-0.001	-0.004	-0.071	0.000
5	A	6	LEU	0	0.013	0.010	7.576	0.013	0.013	0.000	0.000	0.000	0.000
6	A	7	TYR	0	-0.036	-0.022	7.282	0.128	0.128	0.000	0.000	0.000	0.000
7	A	8	MET	0	0.029	0.028	13.285	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.020	-0.016	16.435	0.031	0.031	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.794	-0.890	18.553	-0.073	-0.073	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.050	-0.018	20.862	0.010	0.010	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.021	0.003	22.347	0.008	0.008	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.793	-0.891	23.063	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.798	0.877	23.369	0.084	0.084	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.820	0.909	23.859	0.019	0.019	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.782	-0.881	24.056	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.080	-0.032	22.522	0.010	0.010	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.018	0.005	25.057	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.003	0.000	24.466	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	ASN	0	0.012	0.007	26.581	0.006	0.006	0.000	0.000	0.000	0.000
20	A	33	GLU	-1	-0.861	-0.924	30.319	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	34	ILE	0	-0.120	-0.078	25.640	0.003	0.003	0.000	0.000	0.000	0.000
22	A	35	THR	0	-0.040	-0.010	21.659	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	36	HIS	0	-0.028	-0.015	23.968	0.009	0.009	0.000	0.000	0.000	0.000
24	A	37	TYR	0	-0.043	-0.025	18.025	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	38	TYR	0	-0.001	-0.010	20.365	0.001	0.001	0.000	0.000	0.000	0.000
26	A	39	GLN	0	0.019	0.014	19.037	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	40	VAL	0	0.044	0.015	18.271	0.003	0.003	0.000	0.000	0.000	0.000
28	A	41	THR	0	-0.040	-0.009	18.537	0.002	0.002	0.000	0.000	0.000	0.000
29	A	42	PHE	0	0.034	0.018	16.272	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	43	ARG	1	0.872	0.910	17.544	0.018	0.018	0.000	0.000	0.000	0.000
31	A	44	LEU	0	-0.059	-0.053	14.066	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	45	THR	0	-0.017	-0.011	18.084	0.007	0.007	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.065	-0.044	17.820	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.916	-0.958	20.443	0.033	0.033	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.876	-0.929	16.040	0.058	0.058	0.000	0.000	0.000	0.000
36	A	49	ARG	1	0.969	0.977	18.822	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	50	LYS	1	0.874	0.953	12.513	-0.077	-0.077	0.000	0.000	0.000	0.000
38	A	51	ASP	-1	-0.752	-0.831	17.971	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	52	LEU	0	-0.038	-0.038	11.769	0.035	0.035	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.005	0.013	15.552	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.037	-0.016	11.991	0.016	0.016	0.000	0.000	0.000	0.000
42	A	55	ASN	0	0.000	0.000	14.448	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	56	ILE	0	-0.034	-0.023	14.492	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	57	ASP	-1	-0.841	-0.919	16.513	-0.255	-0.255	0.000	0.000	0.000	0.000
45	A	58	LYS	1	0.918	0.956	18.626	0.118	0.118	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.005	-0.014	21.534	0.015	0.015	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.030	0.003	17.832	0.021	0.021	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.049	-0.032	20.619	0.011	0.011	0.000	0.000	0.000	0.000
49	A	62	GLN	0	0.016	0.007	22.218	0.010	0.010	0.000	0.000	0.000	0.000
50	A	63	ASN	0	-0.073	-0.021	23.428	0.014	0.014	0.000	0.000	0.000	0.000
51	A	64	ILE	0	-0.023	0.002	19.324	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	65	GLU	-1	-0.825	-0.948	23.872	-0.080	-0.080	0.000	0.000	0.000	0.000
53	A	66	PRO	0	-0.013	-0.018	25.816	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.918	-0.959	26.039	-0.053	-0.053	0.000	0.000	0.000	0.000
55	A	68	MET	0	-0.029	0.039	23.892	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	69	LYS	1	0.850	0.906	22.572	0.080	0.080	0.000	0.000	0.000	0.000
57	A	70	GLY	0	0.043	0.019	20.666	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.744	0.866	16.065	0.280	0.280	0.000	0.000	0.000	0.000
59	A	72	LEU	0	0.004	0.000	12.457	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	73	PHE	0	0.016	0.003	10.906	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	74	MET	0	0.015	0.018	7.963	0.033	0.033	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.007	0.018	3.299	0.884	1.423	0.024	-0.152	-0.410	0.000
63	A	76	GLY	0	-0.028	-0.017	3.739	0.014	0.331	0.010	-0.077	-0.250	0.000
64	A	77	SER	0	0.002	-0.005	4.228	-0.134	-0.074	0.003	-0.025	-0.038	0.000
65	A	78	ARG	1	0.920	0.962	6.558	1.213	1.213	0.000	0.000	0.000	0.000
66	A	79	PHE	0	0.059	0.033	8.268	-0.175	-0.175	0.000	0.000	0.000	0.000
67	A	80	VAL	0	-0.100	-0.060	8.189	-0.096	-0.096	0.000	0.000	0.000	0.000
68	A	81	GLN	0	0.083	0.038	11.178	0.043	0.043	0.000	0.000	0.000	0.000
69	A	82	PHE	0	-0.013	-0.014	14.413	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.886	-0.922	17.210	-0.372	-0.372	0.000	0.000	0.000	0.000
71	A	84	THR	0	0.016	0.002	19.753	0.013	0.013	0.000	0.000	0.000	0.000
72	A	85	ASP	-1	-0.836	-0.897	22.702	-0.197	-0.197	0.000	0.000	0.000	0.000
73	A	86	VAL	0	-0.057	-0.032	25.042	0.015	0.015	0.000	0.000	0.000	0.000
74	A	87	PRO	0	0.006	-0.003	28.137	0.001	0.001	0.000	0.000	0.000	0.000
75	A	88	ILE	0	-0.047	-0.017	30.392	0.001	0.001	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.934	-0.956	31.467	-0.124	-0.124	0.000	0.000	0.000	0.000

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