FMO DATABASE

FMODB ID: M3Q7Z

Calculation Name: 4DJG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DJG

Chain ID: A

ChEMBL ID:

UniProt ID: O48791

Base Structure: X-ray

Registration Date: 2023-06-20

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-220633.074954
FMO2-HF: Nuclear repulsion	201471.743111
FMO2-HF: Total energy	-19161.331843
FMO2-MP2: Total energy	-19217.613659

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:103:LEU)

Summations of interaction energy for fragment #1(A:103:LEU)

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.
-11.467	-2.52	10.841	-5.336	-14.453	-0.003

Interaction energy analysis for fragmet #1(A:103:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.004

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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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	105	LYS	1	0.921	0.973	3.724	-4.922	-3.016	-0.006	-0.834	-1.065	0.001
4	A	106	HIS	0	0.037	0.016	2.102	-0.759	0.430	3.208	-1.535	-2.861	0.004
5	A	107	VAL	0	0.033	0.017	3.648	-1.111	-0.360	0.018	-0.267	-0.503	-0.002
6	A	108	LEU	0	0.027	0.015	4.917	0.018	0.148	-0.001	-0.005	-0.124	0.000
7	A	109	LEU	0	0.056	0.035	2.616	-1.074	0.032	0.488	-0.276	-1.319	0.000
8	A	110	LYS	1	0.818	0.901	2.204	-1.069	1.087	3.508	-1.838	-3.827	0.001
9	A	111	LYS	1	0.843	0.892	3.168	0.866	0.417	0.078	0.721	-0.349	0.001
10	A	112	LEU	0	0.025	0.028	6.279	0.087	0.087	0.000	0.000	0.000	0.000
11	A	113	ARG	1	0.949	0.962	2.820	-0.438	0.423	0.100	-0.229	-0.733	0.002
12	A	114	ASP	-1	-0.791	-0.874	6.276	-0.381	-0.381	0.000	0.000	0.000	0.000
13	A	115	ALA	0	-0.047	-0.023	7.987	0.041	0.041	0.000	0.000	0.000	0.000
14	A	116	LEU	0	0.017	0.012	8.822	0.042	0.042	0.000	0.000	0.000	0.000
15	A	117	GLU	-1	-0.774	-0.884	8.907	-0.302	-0.302	0.000	0.000	0.000	0.000
16	A	118	SER	0	-0.042	-0.009	11.472	0.043	0.043	0.000	0.000	0.000	0.000
17	A	119	LEU	0	-0.043	-0.014	13.811	0.028	0.028	0.000	0.000	0.000	0.000
18	A	120	ARG	1	0.829	0.883	12.375	0.316	0.316	0.000	0.000	0.000	0.000
19	A	121	GLY	0	-0.035	-0.013	15.793	0.019	0.019	0.000	0.000	0.000	0.000
20	A	122	ARG	1	0.822	0.892	16.011	0.197	0.197	0.000	0.000	0.000	0.000
21	A	123	VAL	0	-0.013	0.015	18.635	0.009	0.009	0.000	0.000	0.000	0.000
22	A	124	ALA	0	-0.004	-0.011	21.365	0.000	0.000	0.000	0.000	0.000	0.000
23	A	125	GLY	0	0.020	0.007	23.678	0.000	0.000	0.000	0.000	0.000	0.000
24	A	126	ARG	1	0.902	0.920	22.088	0.147	0.147	0.000	0.000	0.000	0.000
25	A	127	ASN	0	-0.014	-0.013	21.648	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	128	LYS	1	0.854	0.933	18.595	0.155	0.155	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.835	-0.922	17.734	-0.173	-0.173	0.000	0.000	0.000	0.000
28	A	130	ASP	-1	-0.793	-0.870	17.524	-0.200	-0.200	0.000	0.000	0.000	0.000
29	A	131	VAL	0	-0.042	-0.019	14.034	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	132	GLU	-1	-0.818	-0.902	13.244	-0.261	-0.261	0.000	0.000	0.000	0.000
31	A	133	GLU	-1	-0.875	-0.930	12.992	-0.317	-0.317	0.000	0.000	0.000	0.000
32	A	134	ALA	0	-0.038	-0.022	12.411	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	135	ILE	0	-0.049	-0.026	8.260	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	136	ALA	0	0.060	0.036	8.278	-0.140	-0.140	0.000	0.000	0.000	0.000
35	A	137	MET	0	-0.013	-0.002	9.633	-0.085	-0.085	0.000	0.000	0.000	0.000
36	A	138	VAL	0	-0.025	-0.023	5.062	-0.102	-0.102	0.000	0.000	0.000	0.000
37	A	139	GLU	-1	-0.959	-0.984	4.840	-1.229	-1.229	0.000	0.000	0.000	0.000
38	A	140	ALA	0	0.017	0.012	5.907	-0.187	-0.187	0.000	0.000	0.000	0.000
39	A	141	LEU	0	-0.030	-0.009	6.715	0.055	0.055	0.000	0.000	0.000	0.000
40	A	142	ALA	0	-0.018	-0.019	2.255	-0.935	-0.888	2.458	-0.782	-1.723	-0.004
41	A	143	VAL	0	0.021	0.026	3.170	-0.021	0.349	0.009	0.121	-0.499	-0.003
42	A	144	GLN	0	-0.031	-0.023	5.862	0.387	0.387	0.000	0.000	0.000	0.000
43	A	145	LEU	0	-0.056	-0.012	3.427	-0.160	0.194	0.015	-0.071	-0.299	0.000
44	A	146	THR	0	-0.145	-0.108	2.505	-0.097	0.429	0.966	-0.341	-1.151	-0.003
45	A	147	GLN	0	-0.024	0.008	5.432	0.292	0.292	0.000	0.000	0.000	0.000
46	A	148	ARG	1	0.806	0.875	9.034	-0.774	-0.774	0.000	0.000	0.000	0.000
47	A	149	GLU	-1	-0.912	-0.963	11.668	0.157	0.157	0.000	0.000	0.000	0.000
48	A	150	GLY	0	-0.032	-0.021	15.396	0.040	0.040	0.000	0.000	0.000	0.000
49	A	151	GLU	-1	-0.846	-0.877	10.875	0.543	0.543	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:103:LEU)