FMO DATABASE

FMODB ID: R82N8

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	OptAll
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	-473489.851715
FMO2-HF: Nuclear repulsion	443346.030777
FMO2-HF: Total energy	-30143.820938
FMO2-MP2: Total energy	-30228.784912

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.
-31.847	-24.223	12.233	-9.498	-10.356	-0.032

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 : 0.036 / q_NPA : 0.019

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	-0.017	-0.005	2.226	-10.003	-5.020	3.288	-3.605	-4.665	0.034
4	B	152	ASP	-1	-0.839	-0.905	3.107	-3.998	-1.755	0.100	-0.984	-1.358	-0.005
5	B	153	ILE	0	-0.074	-0.018	4.405	-0.016	0.247	-0.001	-0.050	-0.212	0.000
6	B	154	ARG	1	0.825	0.906	6.342	0.874	0.874	0.000	0.000	0.000	0.000
7	B	155	GLN	0	-0.007	-0.004	9.886	-0.068	-0.068	0.000	0.000	0.000	0.000
8	B	156	GLY	0	0.021	0.009	13.414	0.055	0.055	0.000	0.000	0.000	0.000
9	B	157	PRO	0	0.006	-0.012	15.466	0.028	0.028	0.000	0.000	0.000	0.000
10	B	158	LYS	1	0.815	0.872	18.779	0.208	0.208	0.000	0.000	0.000	0.000
11	B	159	GLU	-1	-0.765	-0.827	14.177	-0.655	-0.655	0.000	0.000	0.000	0.000
12	B	160	PRO	0	0.065	0.036	18.536	0.010	0.010	0.000	0.000	0.000	0.000
13	B	161	PHE	0	0.054	-0.001	16.756	-0.054	-0.054	0.000	0.000	0.000	0.000
14	B	162	ARG	1	0.924	0.962	17.131	0.257	0.257	0.000	0.000	0.000	0.000
15	B	163	ASP	-1	-0.866	-0.927	16.221	-0.426	-0.426	0.000	0.000	0.000	0.000
16	B	164	TYR	0	-0.044	-0.035	10.704	-0.136	-0.136	0.000	0.000	0.000	0.000
17	B	165	VAL	0	0.027	0.018	12.274	-0.154	-0.154	0.000	0.000	0.000	0.000
18	B	166	ASP	-1	-0.868	-0.940	13.351	-0.532	-0.532	0.000	0.000	0.000	0.000
19	B	167	ARG	1	0.725	0.814	9.323	0.907	0.907	0.000	0.000	0.000	0.000
20	B	168	PHE	0	0.021	0.006	8.534	-0.386	-0.386	0.000	0.000	0.000	0.000
21	B	169	TYR	0	0.046	-0.009	8.857	-0.255	-0.255	0.000	0.000	0.000	0.000
22	B	170	LYS	1	0.882	0.961	9.919	0.824	0.824	0.000	0.000	0.000	0.000
23	B	171	THR	0	0.008	-0.004	3.867	0.243	0.437	0.004	-0.048	-0.149	0.000
24	B	172	LEU	0	0.013	0.016	6.413	-0.157	-0.157	0.000	0.000	0.000	0.000
25	B	173	ARG	1	0.857	0.934	7.966	0.888	0.888	0.000	0.000	0.000	0.000
26	B	174	ALA	0	0.001	-0.005	7.091	0.150	0.150	0.000	0.000	0.000	0.000
27	B	175	GLU	-1	-0.790	-0.878	1.862	-20.507	-20.566	8.842	-4.811	-3.972	-0.061
28	B	176	GLN	0	-0.037	-0.018	5.547	0.756	0.756	0.000	0.000	0.000	0.000
29	B	177	ALA	0	0.008	0.006	7.270	0.180	0.180	0.000	0.000	0.000	0.000
30	B	178	SER	0	0.005	-0.017	9.044	-0.040	-0.040	0.000	0.000	0.000	0.000
31	B	179	GLN	0	0.025	-0.011	11.711	-0.072	-0.072	0.000	0.000	0.000	0.000
32	B	180	GLU	-1	-0.842	-0.897	13.837	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	181	VAL	0	0.011	0.006	8.850	0.018	0.018	0.000	0.000	0.000	0.000
34	B	182	LYS	1	0.830	0.909	8.339	0.901	0.901	0.000	0.000	0.000	0.000
35	B	183	ASN	0	0.046	0.030	10.597	-0.061	-0.061	0.000	0.000	0.000	0.000
36	B	184	TRP	0	0.090	0.065	9.287	0.030	0.030	0.000	0.000	0.000	0.000
37	B	185	MET	0	-0.048	-0.018	5.562	-0.080	-0.080	0.000	0.000	0.000	0.000
38	B	186	THR	0	-0.058	-0.054	10.464	-0.034	-0.034	0.000	0.000	0.000	0.000
39	B	187	GLU	-1	-0.888	-0.940	12.986	-0.064	-0.064	0.000	0.000	0.000	0.000
40	B	188	THR	0	-0.090	-0.052	12.959	0.057	0.057	0.000	0.000	0.000	0.000
41	B	189	LEU	0	-0.021	-0.004	5.826	0.012	0.012	0.000	0.000	0.000	0.000
42	B	190	LEU	0	0.015	0.012	10.491	-0.069	-0.069	0.000	0.000	0.000	0.000
43	B	191	VAL	0	0.040	0.023	12.207	-0.039	-0.039	0.000	0.000	0.000	0.000
44	B	192	GLN	0	-0.014	-0.010	11.389	-0.078	-0.078	0.000	0.000	0.000	0.000
45	B	193	ASN	0	-0.022	-0.018	6.988	0.168	0.168	0.000	0.000	0.000	0.000
46	B	194	ALA	0	0.036	0.037	11.518	-0.124	-0.124	0.000	0.000	0.000	0.000
47	B	195	ASN	0	-0.009	-0.007	14.963	0.067	0.067	0.000	0.000	0.000	0.000
48	B	196	PRO	0	0.033	-0.005	17.383	0.017	0.017	0.000	0.000	0.000	0.000
49	B	197	ASP	-1	-0.838	-0.881	20.485	-0.136	-0.136	0.000	0.000	0.000	0.000
50	B	198	CYS	0	0.005	0.032	19.091	0.004	0.004	0.000	0.000	0.000	0.000
51	B	199	LYS	1	0.832	0.910	14.785	0.036	0.036	0.000	0.000	0.000	0.000
52	B	200	THR	0	-0.033	-0.028	19.607	0.028	0.028	0.000	0.000	0.000	0.000
53	B	201	ILE	0	0.013	0.009	23.284	0.014	0.014	0.000	0.000	0.000	0.000
54	B	202	LEU	0	-0.005	-0.016	17.352	0.009	0.009	0.000	0.000	0.000	0.000
55	B	203	LYS	1	0.893	0.940	18.477	-0.024	-0.024	0.000	0.000	0.000	0.000
56	B	204	ALA	0	-0.029	-0.005	22.391	0.012	0.012	0.000	0.000	0.000	0.000
57	B	205	LEU	0	-0.032	0.001	22.056	0.002	0.002	0.000	0.000	0.000	0.000
58	B	206	GLY	0	0.022	0.028	23.470	0.005	0.005	0.000	0.000	0.000	0.000
59	B	207	PRO	0	-0.080	-0.070	20.826	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	208	GLY	0	0.041	0.023	20.621	0.004	0.004	0.000	0.000	0.000	0.000
61	B	209	ALA	0	-0.017	0.019	21.218	-0.011	-0.011	0.000	0.000	0.000	0.000
62	B	210	THR	0	0.014	-0.030	19.257	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	211	SER	0	0.026	-0.020	16.417	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	212	GLU	-1	-0.852	-0.904	18.395	-0.280	-0.280	0.000	0.000	0.000	0.000
65	B	213	GLU	-1	-0.822	-0.862	21.935	-0.101	-0.101	0.000	0.000	0.000	0.000
66	B	214	MET	0	-0.053	-0.015	16.574	-0.011	-0.011	0.000	0.000	0.000	0.000
67	B	215	MET	0	-0.013	-0.002	18.551	0.000	0.000	0.000	0.000	0.000	0.000
68	B	216	THR	0	-0.083	-0.056	21.617	0.006	0.006	0.000	0.000	0.000	0.000
69	B	217	ALA	0	-0.024	-0.005	24.071	0.007	0.007	0.000	0.000	0.000	0.000
70	B	218	CYS	0	-0.008	-0.003	21.282	0.012	0.012	0.000	0.000	0.000	0.000
71	B	219	GLN	0	-0.010	-0.012	22.197	-0.029	-0.029	0.000	0.000	0.000	0.000
72	B	220	GLY	0	0.025	0.023	23.199	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	221	VAL	0	-0.037	-0.017	22.978	0.015	0.015	0.000	0.000	0.000	0.000
74	B	222	GLY	0	-0.020	-0.009	23.789	-0.019	-0.019	0.000	0.000	0.000	0.000
75	B	223	GLY	0	-0.036	-0.011	25.846	0.002	0.002	0.000	0.000	0.000	0.000

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