FMO DATABASE

FMODB ID: KGM13

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	OptHSide
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	-357700.621828
FMO2-HF: Nuclear repulsion	332290.285284
FMO2-HF: Total energy	-25410.336545
FMO2-MP2: Total energy	-25482.506502

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.
-1.729	0.404	2.849	-2.016	-2.967	0.01

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 : 0.031 / q_NPA : -0.005

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	A	14	PRO	0	-0.005	0.016	2.919	-0.665	0.716	0.134	-0.676	-0.840	0.003
4	A	15	ILE	0	-0.010	0.001	3.556	-1.072	-0.590	0.020	-0.204	-0.299	-0.001
5	A	16	LEU	0	0.005	0.007	5.695	0.457	0.457	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.009	-0.016	9.096	-0.033	-0.033	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.759	-0.841	11.608	-0.265	-0.265	0.000	0.000	0.000	0.000
8	A	19	LEU	0	0.015	0.012	14.914	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	20	LYS	1	0.859	0.905	17.888	0.290	0.290	0.000	0.000	0.000	0.000
10	A	21	ASN	0	-0.068	-0.048	21.043	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	22	GLY	0	0.022	0.016	20.787	0.018	0.018	0.000	0.000	0.000	0.000
12	A	23	GLU	-1	-0.780	-0.837	19.146	-0.268	-0.268	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.035	-0.022	14.116	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	25	PHE	0	-0.008	-0.010	13.679	0.046	0.046	0.000	0.000	0.000	0.000
15	A	26	ASN	0	-0.024	-0.009	9.666	-0.220	-0.220	0.000	0.000	0.000	0.000
16	A	27	GLY	0	0.105	0.053	9.295	0.180	0.180	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.095	-0.045	7.431	-0.416	-0.416	0.000	0.000	0.000	0.000
18	A	29	LEU	0	-0.002	-0.012	5.883	0.326	0.326	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.806	-0.892	8.105	-0.084	-0.084	0.000	0.000	0.000	0.000
20	A	31	ASN	0	-0.026	-0.031	11.145	0.159	0.159	0.000	0.000	0.000	0.000
21	A	32	CYS	0	0.008	0.008	9.887	-0.157	-0.157	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.733	-0.827	11.912	-0.220	-0.220	0.000	0.000	0.000	0.000
23	A	34	ASN	0	0.002	-0.018	14.020	-0.062	-0.062	0.000	0.000	0.000	0.000
24	A	35	TYR	0	-0.057	-0.019	15.979	0.019	0.019	0.000	0.000	0.000	0.000
25	A	36	MET	0	-0.018	-0.018	9.859	0.005	0.005	0.000	0.000	0.000	0.000
26	A	37	ASN	0	-0.097	-0.063	14.239	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	38	LEU	0	0.007	-0.002	10.349	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	39	THR	0	-0.002	-0.001	12.868	0.061	0.061	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.015	0.005	9.301	-0.133	-0.133	0.000	0.000	0.000	0.000
30	A	41	ARG	1	0.834	0.876	11.552	0.370	0.370	0.000	0.000	0.000	0.000
31	A	42	GLU	-1	-0.849	-0.897	12.256	-0.292	-0.292	0.000	0.000	0.000	0.000
32	A	43	VAL	0	-0.044	-0.020	12.855	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	44	ILE	0	-0.026	-0.015	13.727	0.078	0.078	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.858	0.907	14.971	0.196	0.196	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.039	-0.022	16.755	0.048	0.048	0.000	0.000	0.000	0.000
36	A	47	MET	0	0.022	0.012	18.951	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	48	PRO	0	0.000	-0.018	22.047	0.000	0.000	0.000	0.000	0.000	0.000
38	A	49	ASP	-1	-0.908	-0.958	23.375	-0.153	-0.153	0.000	0.000	0.000	0.000
39	A	50	GLY	0	-0.020	0.002	22.847	0.012	0.012	0.000	0.000	0.000	0.000
40	A	51	ASP	-1	-0.890	-0.924	23.123	-0.140	-0.140	0.000	0.000	0.000	0.000
41	A	52	LYS	1	0.877	0.922	17.329	0.214	0.214	0.000	0.000	0.000	0.000
42	A	53	PHE	0	-0.013	0.006	20.273	0.021	0.021	0.000	0.000	0.000	0.000
43	A	54	PHE	0	0.013	-0.015	17.782	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	55	ARG	1	0.836	0.888	17.509	0.176	0.176	0.000	0.000	0.000	0.000
45	A	56	LEU	0	0.023	0.023	17.661	0.026	0.026	0.000	0.000	0.000	0.000
46	A	57	PRO	0	0.015	0.014	17.056	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.808	-0.910	16.175	-0.279	-0.279	0.000	0.000	0.000	0.000
48	A	59	CYS	0	-0.063	-0.006	15.588	0.042	0.042	0.000	0.000	0.000	0.000
49	A	60	TYR	0	0.045	0.029	15.560	-0.044	-0.044	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.003	-0.005	13.675	0.034	0.034	0.000	0.000	0.000	0.000
51	A	62	ARG	1	0.943	0.971	16.525	0.215	0.215	0.000	0.000	0.000	0.000
52	A	63	GLY	0	0.108	0.062	16.373	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	64	ASN	0	-0.020	-0.025	17.360	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	65	ASN	0	-0.016	-0.008	19.482	0.036	0.036	0.000	0.000	0.000	0.000
55	A	66	ILE	0	-0.003	0.017	13.360	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	67	LYS	1	0.818	0.908	16.637	0.326	0.326	0.000	0.000	0.000	0.000
57	A	68	TYR	0	-0.066	-0.076	12.450	0.014	0.014	0.000	0.000	0.000	0.000
58	A	69	LEU	0	0.025	0.021	6.783	0.003	0.003	0.000	0.000	0.000	0.000
59	A	70	ARG	1	0.901	0.955	8.169	0.557	0.557	0.000	0.000	0.000	0.000
60	A	71	ILE	0	0.047	0.031	2.225	-0.885	-0.615	2.695	-1.136	-1.828	0.008

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