FMO DATABASE

FMODB ID: 6Y2LZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-469714.093247
FMO2-HF: Nuclear repulsion	439570.628845
FMO2-HF: Total energy	-30143.464402
FMO2-MP2: Total energy	-30228.419971

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.
-20.718	-11.151	5.707	-6.585	-8.689	-8.673617379884E-19

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 : 0.037 / 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	-0.039	-0.020	2.233	-9.953	-6.297	4.527	-3.388	-4.795	0.030
4	B	152	ASP	-1	-0.854	-0.930	2.622	-7.738	-3.897	1.095	-2.159	-2.777	-0.023
5	B	153	ILE	0	-0.077	-0.017	4.233	0.064	0.313	0.000	-0.042	-0.207	0.000
6	B	154	ARG	1	0.894	0.939	6.179	1.032	1.032	0.000	0.000	0.000	0.000
7	B	155	GLN	0	-0.004	0.015	9.740	-0.052	-0.052	0.000	0.000	0.000	0.000
8	B	156	GLY	0	0.025	0.013	13.191	0.053	0.053	0.000	0.000	0.000	0.000
9	B	157	PRO	0	0.009	-0.017	15.116	0.034	0.034	0.000	0.000	0.000	0.000
10	B	158	LYS	1	0.936	0.953	18.574	0.181	0.181	0.000	0.000	0.000	0.000
11	B	159	GLU	-1	-0.759	-0.840	13.714	-0.650	-0.650	0.000	0.000	0.000	0.000
12	B	160	PRO	0	0.063	0.038	18.009	0.013	0.013	0.000	0.000	0.000	0.000
13	B	161	PHE	0	0.078	0.016	16.849	-0.053	-0.053	0.000	0.000	0.000	0.000
14	B	162	ARG	1	0.946	0.945	16.962	0.176	0.176	0.000	0.000	0.000	0.000
15	B	163	ASP	-1	-0.852	-0.912	15.924	-0.369	-0.369	0.000	0.000	0.000	0.000
16	B	164	TYR	0	-0.062	-0.045	10.584	-0.121	-0.121	0.000	0.000	0.000	0.000
17	B	165	VAL	0	0.016	-0.002	12.165	-0.128	-0.128	0.000	0.000	0.000	0.000
18	B	166	ASP	-1	-0.896	-0.939	13.187	-0.425	-0.425	0.000	0.000	0.000	0.000
19	B	167	ARG	1	0.733	0.839	8.551	1.014	1.014	0.000	0.000	0.000	0.000
20	B	168	PHE	0	0.026	0.010	8.576	-0.368	-0.368	0.000	0.000	0.000	0.000
21	B	169	TYR	0	0.036	-0.016	9.116	-0.099	-0.099	0.000	0.000	0.000	0.000
22	B	170	LYS	1	0.881	0.940	9.912	0.644	0.644	0.000	0.000	0.000	0.000
23	B	171	THR	0	-0.009	-0.006	3.899	-0.188	-0.050	0.000	-0.039	-0.099	0.000
24	B	172	LEU	0	0.032	0.015	6.708	0.064	0.064	0.000	0.000	0.000	0.000
25	B	173	ARG	1	0.868	0.947	8.325	0.635	0.635	0.000	0.000	0.000	0.000
26	B	174	ALA	0	-0.016	-0.008	7.893	0.131	0.131	0.000	0.000	0.000	0.000
27	B	175	GLU	-1	-0.888	-0.931	3.270	-4.691	-3.008	0.085	-0.957	-0.811	-0.007
28	B	176	GLN	0	-0.036	-0.025	6.554	0.227	0.227	0.000	0.000	0.000	0.000
29	B	177	ALA	0	0.040	0.011	7.957	0.015	0.015	0.000	0.000	0.000	0.000
30	B	178	SER	0	0.043	0.029	10.125	-0.023	-0.023	0.000	0.000	0.000	0.000
31	B	179	GLN	0	0.026	-0.009	12.822	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	180	GLU	-1	-0.932	-0.957	15.003	0.079	0.079	0.000	0.000	0.000	0.000
33	B	181	VAL	0	0.024	0.006	9.646	0.020	0.020	0.000	0.000	0.000	0.000
34	B	182	LYS	1	0.886	0.948	9.680	0.367	0.367	0.000	0.000	0.000	0.000
35	B	183	ASN	0	0.064	0.026	11.611	-0.029	-0.029	0.000	0.000	0.000	0.000
36	B	184	TRP	0	0.070	0.055	10.017	0.029	0.029	0.000	0.000	0.000	0.000
37	B	185	MET	0	-0.042	-0.013	6.149	-0.027	-0.027	0.000	0.000	0.000	0.000
38	B	186	THR	0	-0.079	-0.051	10.997	-0.031	-0.031	0.000	0.000	0.000	0.000
39	B	187	GLU	-1	-0.890	-0.942	13.402	0.007	0.007	0.000	0.000	0.000	0.000
40	B	188	THR	0	-0.078	-0.039	12.987	0.040	0.040	0.000	0.000	0.000	0.000
41	B	189	LEU	0	-0.040	-0.019	6.043	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	190	LEU	0	0.012	0.017	10.677	-0.081	-0.081	0.000	0.000	0.000	0.000
43	B	191	VAL	0	0.057	0.033	12.246	-0.067	-0.067	0.000	0.000	0.000	0.000
44	B	192	GLN	0	-0.117	-0.063	11.715	-0.094	-0.094	0.000	0.000	0.000	0.000
45	B	193	ASN	0	-0.006	-0.017	7.018	0.136	0.136	0.000	0.000	0.000	0.000
46	B	194	ALA	0	0.026	0.032	11.439	-0.135	-0.135	0.000	0.000	0.000	0.000
47	B	195	ASN	0	-0.030	-0.016	14.688	0.060	0.060	0.000	0.000	0.000	0.000
48	B	196	PRO	0	0.025	-0.013	16.934	0.024	0.024	0.000	0.000	0.000	0.000
49	B	197	ASP	-1	-0.911	-0.947	19.893	-0.097	-0.097	0.000	0.000	0.000	0.000
50	B	198	CYS	0	0.000	0.009	18.717	0.005	0.005	0.000	0.000	0.000	0.000
51	B	199	LYS	1	0.889	0.952	15.000	-0.026	-0.026	0.000	0.000	0.000	0.000
52	B	200	THR	0	-0.018	-0.011	19.368	0.026	0.026	0.000	0.000	0.000	0.000
53	B	201	ILE	0	0.003	0.006	23.037	0.012	0.012	0.000	0.000	0.000	0.000
54	B	202	LEU	0	0.006	-0.019	17.682	0.010	0.010	0.000	0.000	0.000	0.000
55	B	203	LYS	1	0.882	0.938	17.755	-0.067	-0.067	0.000	0.000	0.000	0.000
56	B	204	ALA	0	-0.023	-0.003	22.344	0.010	0.010	0.000	0.000	0.000	0.000
57	B	205	LEU	0	-0.042	-0.008	22.309	0.000	0.000	0.000	0.000	0.000	0.000
58	B	206	GLY	0	0.018	0.031	24.053	0.002	0.002	0.000	0.000	0.000	0.000
59	B	207	PRO	0	-0.057	-0.058	21.383	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	208	GLY	0	0.032	0.020	21.120	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	209	ALA	0	0.004	0.026	21.227	-0.009	-0.009	0.000	0.000	0.000	0.000
62	B	210	THR	0	0.069	0.031	19.914	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	211	SER	0	0.059	0.005	17.005	-0.009	-0.009	0.000	0.000	0.000	0.000
64	B	212	GLU	-1	-0.955	-0.969	19.046	-0.154	-0.154	0.000	0.000	0.000	0.000
65	B	213	GLU	-1	-0.870	-0.936	22.478	-0.044	-0.044	0.000	0.000	0.000	0.000
66	B	214	MET	0	-0.069	-0.028	17.067	-0.016	-0.016	0.000	0.000	0.000	0.000
67	B	215	MET	0	-0.014	0.009	18.562	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	216	THR	0	-0.051	-0.021	22.075	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	217	ALA	0	-0.024	-0.006	24.149	0.002	0.002	0.000	0.000	0.000	0.000
70	B	218	CYS	0	0.002	-0.006	21.385	0.005	0.005	0.000	0.000	0.000	0.000
71	B	219	GLN	0	-0.014	0.009	22.343	-0.026	-0.026	0.000	0.000	0.000	0.000
72	B	220	GLY	0	0.001	0.008	23.362	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	221	VAL	0	0.001	0.003	23.194	0.010	0.010	0.000	0.000	0.000	0.000
74	B	222	GLY	0	-0.045	-0.018	24.070	-0.016	-0.016	0.000	0.000	0.000	0.000
75	B	223	GLY	0	-0.036	-0.008	25.767	-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)