FMO DATABASE

FMODB ID: 3JR8L

Calculation Name: 3U97-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U97

Chain ID: A

ChEMBL ID:

UniProt ID: Q57DF0

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-486277.080135
FMO2-HF: Nuclear repulsion	456213.570431
FMO2-HF: Total energy	-30063.509704
FMO2-MP2: Total energy	-30151.230942

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:0:THR)

Summations of interaction energy for fragment #1(A:0:THR)

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.
-3.109	0.391	1.233	-1.845	-2.888	0.004

Interaction energy analysis for fragmet #1(A:0:THR)

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 : -0.026

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	2	LYS	1	0.910	0.954	2.289	-2.753	0.699	1.234	-1.844	-2.843	0.004
4	A	3	ILE	0	0.047	0.038	5.373	0.353	0.401	-0.001	-0.001	-0.045	0.000
5	A	4	ILE	0	0.004	0.002	8.806	0.010	0.010	0.000	0.000	0.000	0.000
6	A	5	TRP	0	0.010	-0.022	11.303	0.060	0.060	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.861	-0.919	15.130	-0.297	-0.297	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.786	-0.868	18.004	-0.196	-0.196	0.000	0.000	0.000	0.000
9	A	8	PRO	0	0.042	0.004	19.467	0.018	0.018	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.872	0.940	20.436	0.175	0.175	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.823	0.866	17.080	0.199	0.199	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.004	-0.013	20.326	0.028	0.028	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.064	-0.047	23.635	0.017	0.017	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.027	-0.026	21.799	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	ILE	0	0.031	0.027	21.085	0.012	0.012	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.025	-0.017	24.655	0.011	0.011	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.854	0.931	27.159	0.094	0.094	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.064	-0.037	24.322	0.015	0.015	0.000	0.000	0.000	0.000
19	A	18	GLY	0	0.029	0.035	26.576	0.003	0.003	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.013	-0.003	21.564	0.004	0.004	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.728	-0.836	18.129	-0.184	-0.184	0.000	0.000	0.000	0.000
22	A	21	PHE	0	0.015	-0.016	15.275	0.003	0.003	0.000	0.000	0.000	0.000
23	A	22	ALA	0	-0.032	-0.014	13.753	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.904	-0.943	13.874	-0.107	-0.107	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.104	-0.053	13.491	0.022	0.022	0.000	0.000	0.000	0.000
26	A	25	HIS	0	0.054	0.032	10.131	-0.088	-0.088	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.007	-0.018	4.914	0.069	0.069	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.858	-0.940	10.193	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	28	PHE	0	-0.020	0.003	13.286	0.020	0.020	0.000	0.000	0.000	0.000
30	A	29	PHE	0	-0.006	-0.020	12.201	0.019	0.019	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.033	-0.005	11.693	0.024	0.024	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.042	-0.010	15.507	0.020	0.020	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.036	-0.011	18.004	0.008	0.008	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.864	0.931	19.720	0.028	0.028	0.000	0.000	0.000	0.000
35	A	34	VAL	0	0.014	-0.003	17.309	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.004	0.010	20.590	0.012	0.012	0.000	0.000	0.000	0.000
37	A	36	PRO	0	0.018	0.013	22.231	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	37	THR	0	-0.019	-0.024	23.376	0.005	0.005	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.920	0.952	25.216	0.085	0.085	0.000	0.000	0.000	0.000
40	A	39	ALA	0	0.038	0.021	24.377	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.802	-0.895	19.198	-0.177	-0.177	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.792	0.887	20.359	0.128	0.128	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.037	0.034	16.526	0.022	0.022	0.000	0.000	0.000	0.000
44	A	43	MET	0	-0.033	-0.017	20.250	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.013	0.010	17.826	0.009	0.009	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.008	-0.007	19.838	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.055	0.016	20.879	0.008	0.008	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.900	-0.941	21.862	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	48	PHE	0	-0.014	-0.021	17.937	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	49	ASN	0	-0.004	-0.021	19.754	0.008	0.008	0.000	0.000	0.000	0.000
51	A	50	GLY	0	0.038	0.038	21.168	0.008	0.008	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.051	-0.022	23.942	0.004	0.004	0.000	0.000	0.000	0.000
53	A	52	ILE	0	-0.009	0.003	24.473	0.000	0.000	0.000	0.000	0.000	0.000
54	A	53	ILE	0	0.029	0.026	24.450	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.007	-0.005	19.131	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	55	ALA	0	0.000	-0.003	22.558	0.004	0.004	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.006	0.003	16.654	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	57	ILE	0	-0.024	-0.010	19.976	0.007	0.007	0.000	0.000	0.000	0.000
59	A	58	PHE	0	0.010	-0.014	14.644	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.952	0.979	16.308	0.323	0.323	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.009	0.008	13.238	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	61	VAL	0	0.018	0.008	11.001	0.037	0.037	0.000	0.000	0.000	0.000
63	A	62	GLY	0	0.029	0.009	10.154	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	63	SER	0	0.002	-0.003	6.855	-0.109	-0.109	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.942	-0.961	5.442	-0.222	-0.222	0.000	0.000	0.000	0.000
66	A	65	ALA	0	-0.012	-0.022	6.202	-0.983	-0.983	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.008	0.017	8.562	0.287	0.287	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.002	0.011	11.135	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	68	VAL	0	0.032	0.005	13.481	0.067	0.067	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.060	-0.022	15.936	0.009	0.009	0.000	0.000	0.000	0.000
71	A	70	SER	0	-0.015	-0.021	19.709	0.021	0.021	0.000	0.000	0.000	0.000
72	A	71	MET	0	-0.008	0.022	18.497	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.931	0.976	21.240	0.078	0.078	0.000	0.000	0.000	0.000
74	A	73	SER	0	0.083	0.047	24.518	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	74	ALA	0	-0.023	-0.006	26.598	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	SER	0	-0.016	-0.011	28.641	0.001	0.001	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.002	0.002	31.867	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:THR)