FMO DATABASE

FMODB ID: GN141

Calculation Name: 1M1E-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M1E

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NSA3

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	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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-341717.274897
FMO2-HF: Nuclear repulsion	313278.558879
FMO2-HF: Total energy	-28438.716018
FMO2-MP2: Total energy	-28519.2601

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(B:9:LYS)

Summations of interaction energy for fragment #1(B:9:LYS)

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.
-110.966	-106.988	20.891	-11.498	-13.372	-0.104

Interaction energy analysis for fragmet #1(B:9:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.907 / q_NPA : 0.949

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	B	11	PRO	0	0.030	-0.002	3.796	-5.343	-2.159	-0.029	-1.716	-1.439	0.008
4	B	12	GLU	-1	-0.905	-0.942	6.382	-28.401	-28.401	0.000	0.000	0.000	0.000
5	B	13	GLU	-1	-0.824	-0.902	2.399	-73.228	-68.969	4.745	-4.575	-4.429	-0.047
6	B	14	MET	0	-0.068	-0.032	3.123	-11.186	-10.065	1.821	-0.635	-2.307	-0.009
7	B	15	TYR	0	0.018	0.012	4.779	2.850	2.919	-0.001	-0.004	-0.065	0.000
8	B	16	ILE	0	0.026	0.016	7.281	1.984	1.984	0.000	0.000	0.000	0.000
9	B	17	GLN	0	0.028	0.017	1.794	-26.521	-31.176	14.355	-4.568	-5.132	-0.056
10	B	18	GLN	0	-0.011	-0.009	6.418	0.906	0.906	0.000	0.000	0.000	0.000
11	B	19	LYS	1	0.975	1.005	8.656	21.930	21.930	0.000	0.000	0.000	0.000
12	B	20	VAL	0	0.003	0.003	9.260	1.997	1.997	0.000	0.000	0.000	0.000
13	B	21	ARG	1	0.916	0.954	6.773	35.525	35.525	0.000	0.000	0.000	0.000
14	B	22	VAL	0	-0.007	-0.005	11.621	1.834	1.834	0.000	0.000	0.000	0.000
15	B	23	LEU	0	-0.013	0.000	14.332	1.320	1.320	0.000	0.000	0.000	0.000
16	B	24	LEU	0	0.004	-0.001	12.370	1.227	1.227	0.000	0.000	0.000	0.000
17	B	25	MET	0	-0.032	0.010	15.810	0.911	0.911	0.000	0.000	0.000	0.000
18	B	26	LEU	0	0.017	-0.001	17.608	0.901	0.901	0.000	0.000	0.000	0.000
19	B	27	ARG	1	0.839	0.876	19.053	15.676	15.676	0.000	0.000	0.000	0.000
20	B	28	LYS	1	0.864	0.942	19.388	15.793	15.793	0.000	0.000	0.000	0.000
21	B	29	MET	0	-0.064	-0.017	20.218	0.515	0.515	0.000	0.000	0.000	0.000
22	B	30	GLY	0	0.025	0.022	23.750	0.521	0.521	0.000	0.000	0.000	0.000
23	B	31	SER	0	-0.047	-0.005	23.647	0.517	0.517	0.000	0.000	0.000	0.000
24	B	32	ASN	0	-0.025	-0.022	24.021	-0.505	-0.505	0.000	0.000	0.000	0.000
25	B	33	LEU	0	-0.011	0.001	18.890	-0.300	-0.300	0.000	0.000	0.000	0.000
26	B	34	THR	0	-0.013	-0.043	22.034	0.527	0.527	0.000	0.000	0.000	0.000
27	B	35	ALA	0	0.044	0.006	22.758	-0.410	-0.410	0.000	0.000	0.000	0.000
28	B	36	SER	0	0.026	0.010	21.003	-0.153	-0.153	0.000	0.000	0.000	0.000
29	B	37	GLU	-1	-0.857	-0.903	18.284	-16.248	-16.248	0.000	0.000	0.000	0.000
30	B	38	GLU	-1	-0.759	-0.844	17.955	-15.451	-15.451	0.000	0.000	0.000	0.000
31	B	39	GLU	-1	-0.866	-0.923	19.076	-14.947	-14.947	0.000	0.000	0.000	0.000
32	B	40	PHE	0	-0.028	-0.017	11.269	-0.832	-0.832	0.000	0.000	0.000	0.000
33	B	41	LEU	0	-0.005	-0.021	13.804	-1.515	-1.515	0.000	0.000	0.000	0.000
34	B	42	ARG	1	0.854	0.935	15.018	13.819	13.819	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.022	-0.009	14.152	-0.240	-0.240	0.000	0.000	0.000	0.000
36	B	44	TYR	0	-0.014	-0.011	10.006	-1.055	-1.055	0.000	0.000	0.000	0.000
37	B	45	ALA	0	0.098	0.049	11.249	-1.511	-1.511	0.000	0.000	0.000	0.000
38	B	46	GLY	0	-0.005	0.015	10.641	-0.051	-0.051	0.000	0.000	0.000	0.000
39	B	47	VAL	0	0.015	-0.001	6.025	-1.442	-1.442	0.000	0.000	0.000	0.000
40	B	48	VAL	0	0.013	0.009	8.181	-0.592	-0.592	0.000	0.000	0.000	0.000
41	B	49	ASN	0	-0.012	-0.023	11.323	1.284	1.284	0.000	0.000	0.000	0.000
42	B	50	SER	0	-0.055	-0.015	7.072	-1.502	-1.502	0.000	0.000	0.000	0.000
43	B	51	GLN	0	-0.052	-0.049	7.134	1.363	1.363	0.000	0.000	0.000	0.000
44	B	52	LEU	0	-0.047	-0.017	9.891	1.369	1.369	0.000	0.000	0.000	0.000
45	B	53	SER	0	-0.033	-0.008	12.142	2.201	2.201	0.000	0.000	0.000	0.000
46	B	54	GLN	0	0.019	0.028	7.507	-1.049	-1.049	0.000	0.000	0.000	0.000
47	B	55	LEU	0	0.044	0.012	12.573	1.126	1.126	0.000	0.000	0.000	0.000
48	B	56	PRO	0	-0.061	-0.006	12.355	-0.865	-0.865	0.000	0.000	0.000	0.000
49	B	57	PRO	0	0.043	0.007	14.888	0.684	0.684	0.000	0.000	0.000	0.000
50	B	58	HIS	0	-0.037	-0.040	16.393	-0.331	-0.331	0.000	0.000	0.000	0.000
51	B	59	SER	0	0.027	-0.016	18.704	0.748	0.748	0.000	0.000	0.000	0.000
52	B	60	ILE	0	-0.052	-0.040	21.694	-0.244	-0.244	0.000	0.000	0.000	0.000
53	B	61	ASP	-1	-0.842	-0.903	24.865	-10.002	-10.002	0.000	0.000	0.000	0.000
54	B	62	GLN	0	-0.066	-0.032	27.957	-0.336	-0.336	0.000	0.000	0.000	0.000
55	B	63	GLY	0	0.022	0.013	30.426	-0.033	-0.033	0.000	0.000	0.000	0.000
56	B	64	ALA	0	-0.058	-0.020	32.107	0.162	0.162	0.000	0.000	0.000	0.000
57	B	65	GLU	-1	-0.937	-0.973	34.668	-8.576	-8.576	0.000	0.000	0.000	0.000
58	B	66	ASP	-1	-0.926	-0.952	37.069	-7.612	-7.612	0.000	0.000	0.000	0.000
59	B	67	VAL	0	-0.048	-0.032	40.880	0.016	0.016	0.000	0.000	0.000	0.000
60	B	68	VAL	0	-0.020	-0.005	43.244	0.146	0.146	0.000	0.000	0.000	0.000
61	B	69	MET	0	0.000	-0.002	46.747	0.021	0.021	0.000	0.000	0.000	0.000
62	B	70	ALA	0	0.020	0.010	49.878	0.085	0.085	0.000	0.000	0.000	0.000
63	B	71	PHE	0	0.032	0.004	52.386	0.080	0.080	0.000	0.000	0.000	0.000
64	B	72	SER	0	-0.019	-0.007	55.740	0.096	0.096	0.000	0.000	0.000	0.000
65	B	73	ARG	1	0.827	0.893	55.273	5.556	5.556	0.000	0.000	0.000	0.000
66	B	74	SER	0	0.029	0.028	60.562	0.017	0.017	0.000	0.000	0.000	0.000
67	B	75	GLU	-1	-0.926	-0.953	62.872	-4.862	-4.862	0.000	0.000	0.000	0.000
68	B	76	THR	0	-0.053	-0.033	65.556	-0.046	-0.046	0.000	0.000	0.000	0.000
69	B	77	GLU	-1	-0.962	-0.989	67.594	-4.596	-4.596	0.000	0.000	0.000	0.000
70	B	78	ASP	-1	-0.981	-0.969	67.990	-4.688	-4.688	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:LYS)