FMO DATABASE

FMODB ID: 49L3N

Calculation Name: 3F27-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F27

Chain ID: D

ChEMBL ID:

UniProt ID: Q61473

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469262.071015
FMO2-HF: Nuclear repulsion	437413.003599
FMO2-HF: Total energy	-31849.067417
FMO2-MP2: Total energy	-31940.852574

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(D:68:ILE)

Summations of interaction energy for fragment #1(D:68:ILE)

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.
-13.69	-5.429	10.237	-5.5	-12.998	-0.031

Interaction energy analysis for fragmet #1(D:68:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.018

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	D	70	ARG	1	0.966	0.977	3.152	-3.329	-0.792	0.106	-1.324	-1.319	0.001
4	D	71	PRO	0	0.061	0.048	4.934	0.256	0.256	0.000	0.000	0.000	0.000
5	D	72	MET	0	-0.040	-0.018	7.226	0.124	0.124	0.000	0.000	0.000	0.000
6	D	73	ASN	0	0.047	0.023	10.862	-0.042	-0.042	0.000	0.000	0.000	0.000
7	D	74	ALA	0	0.090	0.030	13.428	0.027	0.027	0.000	0.000	0.000	0.000
8	D	75	PHE	0	-0.003	0.016	17.003	0.015	0.015	0.000	0.000	0.000	0.000
9	D	76	MET	0	-0.025	-0.027	13.242	0.019	0.019	0.000	0.000	0.000	0.000
10	D	77	VAL	0	0.016	0.002	14.184	0.029	0.029	0.000	0.000	0.000	0.000
11	D	78	TRP	0	0.012	0.016	16.128	0.021	0.021	0.000	0.000	0.000	0.000
12	D	79	ALA	0	0.002	-0.007	18.394	0.010	0.010	0.000	0.000	0.000	0.000
13	D	80	LYS	1	0.782	0.883	16.156	-0.068	-0.068	0.000	0.000	0.000	0.000
14	D	81	ASP	-1	-0.814	-0.881	18.168	0.099	0.099	0.000	0.000	0.000	0.000
15	D	82	GLU	-1	-0.743	-0.843	21.506	0.067	0.067	0.000	0.000	0.000	0.000
16	D	83	ARG	1	0.834	0.905	19.746	-0.203	-0.203	0.000	0.000	0.000	0.000
17	D	84	LYS	1	0.925	0.962	21.686	-0.122	-0.122	0.000	0.000	0.000	0.000
18	D	85	ARG	1	0.794	0.856	23.749	-0.064	-0.064	0.000	0.000	0.000	0.000
19	D	86	LEU	0	0.016	-0.012	26.097	-0.003	-0.003	0.000	0.000	0.000	0.000
20	D	87	ALA	0	0.009	0.006	25.575	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	88	GLN	0	0.004	-0.002	26.811	0.005	0.005	0.000	0.000	0.000	0.000
22	D	89	GLN	0	-0.048	-0.008	29.551	-0.011	-0.011	0.000	0.000	0.000	0.000
23	D	90	ASN	0	-0.032	-0.011	30.845	-0.011	-0.011	0.000	0.000	0.000	0.000
24	D	91	PRO	0	0.000	0.001	30.247	0.008	0.008	0.000	0.000	0.000	0.000
25	D	92	ASP	-1	-0.880	-0.930	31.049	0.105	0.105	0.000	0.000	0.000	0.000
26	D	93	LEU	0	-0.026	-0.008	30.385	0.005	0.005	0.000	0.000	0.000	0.000
27	D	94	HIS	0	0.082	0.037	25.791	0.009	0.009	0.000	0.000	0.000	0.000
28	D	95	ASN	0	0.068	0.026	20.517	-0.019	-0.019	0.000	0.000	0.000	0.000
29	D	96	ALA	0	0.001	-0.003	24.273	0.001	0.001	0.000	0.000	0.000	0.000
30	D	97	GLU	-1	-0.756	-0.878	25.879	0.102	0.102	0.000	0.000	0.000	0.000
31	D	98	LEU	0	0.029	0.023	24.549	-0.009	-0.009	0.000	0.000	0.000	0.000
32	D	99	SER	0	-0.010	-0.007	21.746	-0.006	-0.006	0.000	0.000	0.000	0.000
33	D	100	LYS	1	0.802	0.902	24.080	-0.126	-0.126	0.000	0.000	0.000	0.000
34	D	101	MET	0	-0.005	0.008	27.288	-0.015	-0.015	0.000	0.000	0.000	0.000
35	D	102	LEU	0	0.016	0.035	21.801	-0.010	-0.010	0.000	0.000	0.000	0.000
36	D	103	GLY	0	0.010	0.002	24.435	-0.012	-0.012	0.000	0.000	0.000	0.000
37	D	104	LYS	1	0.924	0.953	25.266	-0.082	-0.082	0.000	0.000	0.000	0.000
38	D	105	SER	0	0.029	-0.004	27.584	-0.008	-0.008	0.000	0.000	0.000	0.000
39	D	106	TRP	0	0.036	0.019	20.583	-0.009	-0.009	0.000	0.000	0.000	0.000
40	D	107	LYS	1	0.915	0.947	25.647	-0.038	-0.038	0.000	0.000	0.000	0.000
41	D	108	ALA	0	-0.032	-0.010	27.920	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	109	LEU	0	0.007	0.029	25.845	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	110	THR	0	0.030	0.002	28.357	-0.004	-0.004	0.000	0.000	0.000	0.000
44	D	111	LEU	0	-0.007	-0.017	25.833	-0.002	-0.002	0.000	0.000	0.000	0.000
45	D	112	ALA	0	0.017	-0.001	26.480	-0.006	-0.006	0.000	0.000	0.000	0.000
46	D	113	GLU	-1	-0.809	-0.886	27.836	-0.005	-0.005	0.000	0.000	0.000	0.000
47	D	114	LYS	1	0.800	0.889	23.057	0.000	0.000	0.000	0.000	0.000	0.000
48	D	115	ARG	1	0.890	0.936	22.474	0.062	0.062	0.000	0.000	0.000	0.000
49	D	116	PRO	0	0.036	0.023	22.085	-0.014	-0.014	0.000	0.000	0.000	0.000
50	D	117	PHE	0	0.054	0.019	19.379	-0.010	-0.010	0.000	0.000	0.000	0.000
51	D	118	VAL	0	-0.036	-0.023	17.794	-0.012	-0.012	0.000	0.000	0.000	0.000
52	D	119	GLU	-1	-0.803	-0.895	17.556	-0.121	-0.121	0.000	0.000	0.000	0.000
53	D	120	GLU	-1	-0.882	-0.913	16.350	-0.109	-0.109	0.000	0.000	0.000	0.000
54	D	121	ALA	0	-0.010	-0.010	13.635	-0.034	-0.034	0.000	0.000	0.000	0.000
55	D	122	GLU	-1	-0.800	-0.863	12.779	-0.358	-0.358	0.000	0.000	0.000	0.000
56	D	123	ARG	1	0.847	0.918	13.796	0.095	0.095	0.000	0.000	0.000	0.000
57	D	124	LEU	0	0.002	-0.003	10.428	-0.055	-0.055	0.000	0.000	0.000	0.000
58	D	125	ARG	1	0.731	0.823	9.274	0.249	0.249	0.000	0.000	0.000	0.000
59	D	126	VAL	0	0.008	-0.012	9.490	-0.138	-0.138	0.000	0.000	0.000	0.000
60	D	127	GLN	0	-0.019	-0.015	9.292	0.018	0.018	0.000	0.000	0.000	0.000
61	D	128	HIS	0	-0.018	-0.017	2.365	-0.830	-0.434	1.707	-0.585	-1.518	-0.001
62	D	129	MET	0	-0.034	-0.015	5.727	-0.409	-0.409	0.000	0.000	0.000	0.000
63	D	130	GLN	0	-0.005	0.008	7.962	-0.022	-0.022	0.000	0.000	0.000	0.000
64	D	131	ASP	-1	-0.854	-0.904	5.996	-1.058	-1.058	0.000	0.000	0.000	0.000
65	D	132	HIS	0	-0.087	-0.048	2.337	-6.303	-2.770	3.371	-2.100	-4.804	-0.028
66	D	133	PRO	0	0.066	0.036	4.325	0.110	0.184	-0.001	-0.004	-0.069	0.000
67	D	134	ASN	0	-0.017	-0.008	5.654	0.134	0.134	0.000	0.000	0.000	0.000
68	D	135	TYR	0	-0.042	-0.029	2.356	-2.166	-0.536	5.055	-1.478	-5.207	-0.003
69	D	136	LYS	1	0.932	0.974	4.632	0.467	0.558	-0.001	-0.009	-0.081	0.000
70	D	137	TYR	0	0.035	0.004	5.778	0.093	0.093	0.000	0.000	0.000	0.000
71	D	138	ARG	1	0.943	0.962	6.590	0.351	0.351	0.000	0.000	0.000	0.000
72	D	139	PRO	0	0.016	0.012	8.322	0.128	0.128	0.000	0.000	0.000	0.000
73	D	140	ARG	1	0.919	0.962	7.989	-0.336	-0.336	0.000	0.000	0.000	0.000
74	D	141	ARG	1	1.045	1.037	13.007	-0.109	-0.109	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(D:68:ILE)