FMO DATABASE

FMODB ID: ZV8RN

Calculation Name: 3DS4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DS4

Chain ID: B

ChEMBL ID:

UniProt ID: P12497

Base Structure: X-ray

Registration Date: 2023-09-23

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-470397.594924
FMO2-HF: Nuclear repulsion	440253.890324
FMO2-HF: Total energy	-30143.7046
FMO2-MP2: Total energy	-30228.652709

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:149:SER)

Summations of interaction energy for fragment #1(B:149: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.
-20.537	-10.016	4.558	-6.569	-8.509	0

Interaction energy analysis for fragmet #1(B:149:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.025

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	B	151	LEU	0	-0.033	-0.017	2.217	-10.328	-5.909	3.433	-3.332	-4.519	0.030
4	B	152	ASP	-1	-0.817	-0.902	2.653	-6.019	-2.615	0.911	-1.769	-2.546	-0.019
5	B	153	ILE	0	-0.073	-0.013	4.271	-0.077	0.190	0.000	-0.047	-0.219	0.000
6	B	154	ARG	1	0.846	0.912	5.788	0.792	0.792	0.000	0.000	0.000	0.000
7	B	155	GLN	0	-0.007	-0.001	9.662	-0.053	-0.053	0.000	0.000	0.000	0.000
8	B	156	GLY	0	0.025	0.009	13.100	0.060	0.060	0.000	0.000	0.000	0.000
9	B	157	PRO	0	0.014	-0.011	15.035	0.030	0.030	0.000	0.000	0.000	0.000
10	B	158	LYS	1	0.850	0.903	18.501	0.183	0.183	0.000	0.000	0.000	0.000
11	B	159	GLU	-1	-0.762	-0.821	13.683	-0.663	-0.663	0.000	0.000	0.000	0.000
12	B	160	PRO	0	0.056	0.039	17.906	0.015	0.015	0.000	0.000	0.000	0.000
13	B	161	PHE	0	0.070	0.012	16.864	-0.056	-0.056	0.000	0.000	0.000	0.000
14	B	162	ARG	1	0.959	0.962	17.082	0.202	0.202	0.000	0.000	0.000	0.000
15	B	163	ASP	-1	-0.852	-0.921	16.155	-0.388	-0.388	0.000	0.000	0.000	0.000
16	B	164	TYR	0	-0.057	-0.039	10.471	-0.132	-0.132	0.000	0.000	0.000	0.000
17	B	165	VAL	0	0.016	0.000	12.280	-0.138	-0.138	0.000	0.000	0.000	0.000
18	B	166	ASP	-1	-0.906	-0.947	13.278	-0.477	-0.477	0.000	0.000	0.000	0.000
19	B	167	ARG	1	0.735	0.827	8.952	0.941	0.941	0.000	0.000	0.000	0.000
20	B	168	PHE	0	0.028	0.014	8.633	-0.383	-0.383	0.000	0.000	0.000	0.000
21	B	169	TYR	0	0.030	-0.009	9.181	-0.140	-0.140	0.000	0.000	0.000	0.000
22	B	170	LYS	1	0.876	0.937	9.962	0.771	0.771	0.000	0.000	0.000	0.000
23	B	171	THR	0	0.000	-0.008	3.934	0.210	0.359	0.000	-0.039	-0.110	0.000
24	B	172	LEU	0	0.026	0.021	6.698	-0.028	-0.028	0.000	0.000	0.000	0.000
25	B	173	ARG	1	0.884	0.957	8.326	0.748	0.748	0.000	0.000	0.000	0.000
26	B	174	ALA	0	-0.017	-0.008	7.861	0.160	0.160	0.000	0.000	0.000	0.000
27	B	175	GLU	-1	-0.854	-0.915	3.090	-6.115	-3.833	0.214	-1.382	-1.115	-0.011
28	B	176	GLN	0	-0.032	-0.015	6.557	0.390	0.390	0.000	0.000	0.000	0.000
29	B	177	ALA	0	0.031	0.008	7.842	0.026	0.026	0.000	0.000	0.000	0.000
30	B	178	SER	0	0.051	0.027	9.995	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	179	GLN	0	0.035	-0.007	12.681	-0.024	-0.024	0.000	0.000	0.000	0.000
32	B	180	GLU	-1	-0.929	-0.954	14.857	0.057	0.057	0.000	0.000	0.000	0.000
33	B	181	VAL	0	0.021	0.006	9.478	0.024	0.024	0.000	0.000	0.000	0.000
34	B	182	LYS	1	0.849	0.922	9.555	0.559	0.559	0.000	0.000	0.000	0.000
35	B	183	ASN	0	0.055	0.025	11.464	-0.031	-0.031	0.000	0.000	0.000	0.000
36	B	184	TRP	0	0.076	0.059	9.647	0.038	0.038	0.000	0.000	0.000	0.000
37	B	185	MET	0	-0.040	-0.017	6.018	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	186	THR	0	-0.075	-0.055	10.935	-0.029	-0.029	0.000	0.000	0.000	0.000
39	B	187	GLU	-1	-0.901	-0.944	13.346	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	188	THR	0	-0.072	-0.039	13.003	0.047	0.047	0.000	0.000	0.000	0.000
41	B	189	LEU	0	-0.036	-0.014	6.001	-0.008	-0.008	0.000	0.000	0.000	0.000
42	B	190	LEU	0	0.020	0.018	10.649	-0.073	-0.073	0.000	0.000	0.000	0.000
43	B	191	VAL	0	0.049	0.027	12.220	-0.062	-0.062	0.000	0.000	0.000	0.000
44	B	192	GLN	0	-0.042	-0.021	11.549	-0.106	-0.106	0.000	0.000	0.000	0.000
45	B	193	ASN	0	-0.029	-0.021	6.950	0.151	0.151	0.000	0.000	0.000	0.000
46	B	194	ALA	0	0.027	0.037	11.445	-0.136	-0.136	0.000	0.000	0.000	0.000
47	B	195	ASN	0	-0.008	-0.004	14.704	0.068	0.068	0.000	0.000	0.000	0.000
48	B	196	PRO	0	0.034	-0.006	16.961	0.021	0.021	0.000	0.000	0.000	0.000
49	B	197	ASP	-1	-0.870	-0.920	19.913	-0.098	-0.098	0.000	0.000	0.000	0.000
50	B	198	CYS	0	0.000	0.014	18.657	0.003	0.003	0.000	0.000	0.000	0.000
51	B	199	LYS	1	0.842	0.915	14.716	-0.060	-0.060	0.000	0.000	0.000	0.000
52	B	200	THR	0	-0.026	-0.019	19.372	0.025	0.025	0.000	0.000	0.000	0.000
53	B	201	ILE	0	0.001	0.005	23.040	0.011	0.011	0.000	0.000	0.000	0.000
54	B	202	LEU	0	0.010	-0.014	17.592	0.009	0.009	0.000	0.000	0.000	0.000
55	B	203	LYS	1	0.894	0.942	18.076	-0.088	-0.088	0.000	0.000	0.000	0.000
56	B	204	ALA	0	-0.027	-0.005	22.332	0.010	0.010	0.000	0.000	0.000	0.000
57	B	205	LEU	0	-0.038	-0.006	22.192	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	206	GLY	0	0.019	0.031	24.021	0.001	0.001	0.000	0.000	0.000	0.000
59	B	207	PRO	0	-0.051	-0.054	21.352	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	208	GLY	0	0.026	0.016	21.074	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	209	ALA	0	-0.020	0.015	21.198	-0.012	-0.012	0.000	0.000	0.000	0.000
62	B	210	THR	0	0.031	-0.018	19.856	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	211	SER	0	0.051	-0.003	16.886	-0.013	-0.013	0.000	0.000	0.000	0.000
64	B	212	GLU	-1	-0.911	-0.950	19.000	-0.188	-0.188	0.000	0.000	0.000	0.000
65	B	213	GLU	-1	-0.833	-0.888	22.478	-0.056	-0.056	0.000	0.000	0.000	0.000
66	B	214	MET	0	-0.076	-0.029	17.059	-0.014	-0.014	0.000	0.000	0.000	0.000
67	B	215	MET	0	-0.010	0.008	18.667	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	216	THR	0	-0.055	-0.022	22.075	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	217	ALA	0	-0.027	-0.007	24.092	0.003	0.003	0.000	0.000	0.000	0.000
70	B	218	CYS	0	-0.006	-0.008	21.391	0.009	0.009	0.000	0.000	0.000	0.000
71	B	219	GLN	0	-0.011	0.003	22.438	-0.027	-0.027	0.000	0.000	0.000	0.000
72	B	220	GLY	0	0.006	0.010	23.457	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	221	VAL	0	-0.009	-0.003	23.054	0.012	0.012	0.000	0.000	0.000	0.000
74	B	222	GLY	0	-0.038	-0.016	23.963	-0.016	-0.016	0.000	0.000	0.000	0.000
75	B	223	GLY	0	-0.031	-0.004	25.665	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:149:SER)