FMO DATABASE

FMODB ID: 4J8MN

Calculation Name: 4EMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMH

Chain ID: A

ChEMBL ID:

UniProt ID: O14352

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356619.891412
FMO2-HF: Nuclear repulsion	331209.422811
FMO2-HF: Total energy	-25410.468601
FMO2-MP2: Total energy	-25482.644644

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-2.499	0.096	1.95	-2.193	-2.353	-0.004

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.001

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	14	PRO	0	-0.001	0.006	3.185	-1.026	0.360	0.040	-0.602	-0.824	0.001
4	A	15	ILE	0	-0.024	-0.009	3.485	-1.287	-0.604	0.043	-0.300	-0.426	-0.002
5	A	16	LEU	0	0.005	0.007	5.767	0.327	0.327	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.003	-0.013	9.204	-0.081	-0.081	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.761	-0.840	11.666	-0.127	-0.127	0.000	0.000	0.000	0.000
8	A	19	LEU	0	0.020	0.012	15.026	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	20	LYS	1	0.847	0.899	17.990	0.245	0.245	0.000	0.000	0.000	0.000
10	A	21	ASN	0	-0.050	-0.034	21.123	0.001	0.001	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.012	0.010	20.967	0.014	0.014	0.000	0.000	0.000	0.000
12	A	23	GLU	-1	-0.784	-0.840	19.339	-0.149	-0.149	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.045	-0.029	14.581	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	25	PHE	0	0.015	0.008	13.840	0.035	0.035	0.000	0.000	0.000	0.000
15	A	26	ASN	0	-0.025	-0.023	9.300	-0.124	-0.124	0.000	0.000	0.000	0.000
16	A	27	GLY	0	0.097	0.054	9.220	0.129	0.129	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.076	-0.026	7.371	-0.217	-0.217	0.000	0.000	0.000	0.000
18	A	29	LEU	0	0.003	0.000	6.194	0.162	0.162	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.782	-0.870	8.256	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	31	ASN	0	-0.052	-0.045	11.238	0.085	0.085	0.000	0.000	0.000	0.000
21	A	32	CYS	0	-0.004	-0.003	10.353	-0.099	-0.099	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.743	-0.834	12.437	-0.304	-0.304	0.000	0.000	0.000	0.000
23	A	34	ASN	0	-0.003	-0.017	14.468	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	35	TYR	0	-0.065	-0.028	16.699	0.024	0.024	0.000	0.000	0.000	0.000
25	A	36	MET	0	-0.003	-0.005	9.923	0.022	0.022	0.000	0.000	0.000	0.000
26	A	37	ASN	0	-0.082	-0.051	14.115	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	38	LEU	0	0.006	0.002	9.917	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.002	-0.006	12.540	0.075	0.075	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.002	0.012	9.320	-0.125	-0.125	0.000	0.000	0.000	0.000
30	A	41	ARG	1	0.810	0.850	11.694	0.238	0.238	0.000	0.000	0.000	0.000
31	A	42	GLU	-1	-0.823	-0.878	12.232	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	43	VAL	0	-0.042	-0.001	12.735	0.004	0.004	0.000	0.000	0.000	0.000
33	A	44	ILE	0	-0.020	-0.008	13.745	0.045	0.045	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.858	0.897	14.901	0.095	0.095	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.049	-0.015	17.046	0.037	0.037	0.000	0.000	0.000	0.000
36	A	47	MET	0	0.023	0.019	19.349	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	48	PRO	0	0.005	-0.014	22.375	0.004	0.004	0.000	0.000	0.000	0.000
38	A	49	ASP	-1	-0.896	-0.946	23.745	-0.064	-0.064	0.000	0.000	0.000	0.000
39	A	50	GLY	0	-0.018	-0.004	22.704	0.009	0.009	0.000	0.000	0.000	0.000
40	A	51	ASP	-1	-0.877	-0.930	22.911	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	52	LYS	1	0.830	0.896	17.661	0.050	0.050	0.000	0.000	0.000	0.000
42	A	53	PHE	0	0.015	0.022	20.474	0.009	0.009	0.000	0.000	0.000	0.000
43	A	54	PHE	0	0.025	-0.013	17.831	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	55	ARG	1	0.820	0.871	17.320	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	56	LEU	0	0.031	0.022	17.614	0.006	0.006	0.000	0.000	0.000	0.000
46	A	57	PRO	0	-0.010	-0.002	17.073	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.806	-0.893	16.339	-0.187	-0.187	0.000	0.000	0.000	0.000
48	A	59	CYS	0	-0.061	-0.026	15.462	0.027	0.027	0.000	0.000	0.000	0.000
49	A	60	TYR	0	0.036	0.030	15.353	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	61	ILE	0	0.000	-0.003	13.417	0.031	0.031	0.000	0.000	0.000	0.000
51	A	62	ARG	1	0.916	0.960	16.116	0.206	0.206	0.000	0.000	0.000	0.000
52	A	63	GLY	0	0.104	0.051	15.936	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	64	ASN	0	-0.029	-0.023	16.831	0.005	0.005	0.000	0.000	0.000	0.000
54	A	65	ASN	0	0.014	0.004	19.091	0.025	0.025	0.000	0.000	0.000	0.000
55	A	66	ILE	0	0.007	0.025	12.677	0.016	0.016	0.000	0.000	0.000	0.000
56	A	67	LYS	1	0.812	0.901	16.461	0.194	0.194	0.000	0.000	0.000	0.000
57	A	68	TYR	0	-0.064	-0.074	12.806	0.014	0.014	0.000	0.000	0.000	0.000
58	A	69	LEU	0	0.023	0.016	6.123	0.014	0.014	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.901	0.954	7.875	0.304	0.304	0.000	0.000	0.000	0.000
60	A	71	ILE	0	0.054	0.037	2.354	-0.777	-0.251	1.867	-1.291	-1.103	-0.003

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)