FMO DATABASE

FMODB ID: 3JRQL

Calculation Name: 3FMY-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n5-methylglutamine

ligand 3-letter code: MEQ

PDB ID: 3FMY

Chain ID: A

ChEMBL ID:

UniProt ID: Q46864

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:

Apendix: None

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-391901.607041
FMO2-HF: Nuclear repulsion	366628.220688
FMO2-HF: Total energy	-25273.386353
FMO2-MP2: Total energy	-25349.602339

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:66:ALA)

Summations of interaction energy for fragment #1(A:66:ALA)

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.
0.415	2.975	0.602	-1.319	-1.844	0.003

Interaction energy analysis for fragmet #1(A:66:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.023

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	68	THR	0	0.020	0.001	3.477	-0.439	1.738	0.029	-1.081	-1.126	0.004
4	A	69	VAL	0	-0.030	-0.022	5.683	0.289	0.289	0.000	0.000	0.000	0.000
5	A	70	ALA	0	0.044	0.040	9.196	0.062	0.062	0.000	0.000	0.000	0.000
6	A	71	PRO	0	0.055	0.023	12.213	0.051	0.051	0.000	0.000	0.000	0.000
7	A	72	GLU	-1	-0.827	-0.928	14.362	-0.367	-0.367	0.000	0.000	0.000	0.000
8	A	73	PHE	0	-0.020	-0.017	13.660	0.030	0.030	0.000	0.000	0.000	0.000
9	A	74	ILE	0	-0.021	-0.004	11.126	0.039	0.039	0.000	0.000	0.000	0.000
10	A	75	VAL	0	0.009	0.009	15.234	0.045	0.045	0.000	0.000	0.000	0.000
11	A	76	LYS	1	0.809	0.910	17.604	0.367	0.367	0.000	0.000	0.000	0.000
12	A	77	VAL	0	-0.011	-0.005	16.331	0.024	0.024	0.000	0.000	0.000	0.000
13	A	78	ARG	1	0.769	0.834	18.536	0.150	0.150	0.000	0.000	0.000	0.000
14	A	79	LYS	1	0.909	0.955	20.044	0.176	0.176	0.000	0.000	0.000	0.000
15	A	80	LYS	1	0.834	0.916	21.038	0.225	0.225	0.000	0.000	0.000	0.000
16	A	81	LEU	0	-0.013	0.000	19.370	0.011	0.011	0.000	0.000	0.000	0.000
17	A	82	SER	0	-0.030	-0.010	23.499	0.014	0.014	0.000	0.000	0.000	0.000
18	A	83	LEU	0	0.004	0.028	20.607	0.011	0.011	0.000	0.000	0.000	0.000
19	A	84	THR	0	0.010	-0.036	23.643	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	85	GLN	0	-0.016	-0.032	20.212	0.015	0.015	0.000	0.000	0.000	0.000
21	A	86	LYS	1	0.846	0.929	20.574	0.002	0.002	0.000	0.000	0.000	0.000
22	A	87	GLU	-1	-0.697	-0.805	22.021	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	88	ALA	0	0.019	0.015	18.357	0.006	0.006	0.000	0.000	0.000	0.000
24	A	89	SER	0	-0.032	-0.042	17.494	0.004	0.004	0.000	0.000	0.000	0.000
25	A	90	GLU	-1	-0.866	-0.906	18.522	0.032	0.032	0.000	0.000	0.000	0.000
26	A	91	ILE	0	-0.009	0.002	19.381	0.013	0.013	0.000	0.000	0.000	0.000
27	A	92	PHE	0	-0.017	-0.011	14.673	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	93	GLY	0	0.044	0.037	14.539	0.027	0.027	0.000	0.000	0.000	0.000
29	A	94	GLY	0	0.027	0.001	14.415	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	95	GLY	0	0.012	0.009	15.032	0.001	0.001	0.000	0.000	0.000	0.000
31	A	96	VAL	0	0.049	0.001	18.657	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	97	ASN	0	0.027	0.016	20.207	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	98	ALA	0	-0.031	-0.002	14.830	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	99	PHE	0	0.073	0.021	15.237	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	100	SER	0	-0.030	-0.016	16.817	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	101	ARG	1	0.907	0.960	13.783	-0.060	-0.060	0.000	0.000	0.000	0.000
37	A	102	TYR	0	-0.016	-0.003	11.485	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	103	GLU	-1	-0.739	-0.838	13.523	-0.214	-0.214	0.000	0.000	0.000	0.000
39	A	104	LYS	1	0.861	0.930	16.106	0.091	0.091	0.000	0.000	0.000	0.000
40	A	105	GLY	0	0.030	0.022	12.532	0.000	0.000	0.000	0.000	0.000	0.000
41	A	106	ASN	0	-0.057	-0.035	12.506	0.016	0.016	0.000	0.000	0.000	0.000
42	A	107	ALA	0	-0.042	-0.028	11.250	0.068	0.068	0.000	0.000	0.000	0.000
43	A	108	MEQ	0	0.026	0.023	2.789	-0.655	-0.430	0.569	-0.204	-0.589	-0.001
44	A	109	PRO	0	0.011	0.004	7.623	0.123	0.123	0.000	0.000	0.000	0.000
45	A	110	HIS	0	0.080	0.051	6.559	0.022	0.022	0.000	0.000	0.000	0.000
46	A	111	PRO	0	0.049	0.002	3.573	-0.362	-0.204	0.004	-0.034	-0.129	0.000
47	A	112	SER	0	0.017	0.005	5.961	-0.174	-0.174	0.000	0.000	0.000	0.000
48	A	113	THR	0	0.021	0.021	9.780	-0.052	-0.052	0.000	0.000	0.000	0.000
49	A	114	ILE	0	-0.011	0.000	5.163	-0.037	-0.037	0.000	0.000	0.000	0.000
50	A	115	LYS	1	0.830	0.896	5.898	0.265	0.265	0.000	0.000	0.000	0.000
51	A	116	LEU	0	0.050	0.034	10.946	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	117	LEU	0	0.036	0.020	12.345	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	118	ARG	1	0.828	0.885	8.996	0.755	0.755	0.000	0.000	0.000	0.000
54	A	119	VAL	0	0.019	0.020	14.263	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	120	LEU	0	0.064	0.026	16.941	0.007	0.007	0.000	0.000	0.000	0.000
56	A	121	ASP	-1	-0.860	-0.922	17.233	-0.305	-0.305	0.000	0.000	0.000	0.000
57	A	122	LYS	1	0.764	0.880	16.837	0.344	0.344	0.000	0.000	0.000	0.000
58	A	123	HIS	0	0.054	0.049	20.068	0.017	0.017	0.000	0.000	0.000	0.000
59	A	124	PRO	0	0.012	0.008	22.257	0.008	0.008	0.000	0.000	0.000	0.000
60	A	125	GLU	-1	-0.835	-0.928	23.253	-0.092	-0.092	0.000	0.000	0.000	0.000
61	A	126	LEU	0	0.051	0.024	21.230	0.009	0.009	0.000	0.000	0.000	0.000
62	A	127	LEU	0	-0.025	-0.014	22.103	0.011	0.011	0.000	0.000	0.000	0.000
63	A	128	ASN	0	-0.084	-0.063	23.615	0.015	0.015	0.000	0.000	0.000	0.000
64	A	129	GLU	-1	-0.936	-0.953	23.972	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	130	ILE	0	-0.071	-0.032	19.318	0.009	0.009	0.000	0.000	0.000	0.000
66	A	131	ARG	1	0.830	0.914	22.987	0.042	0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:66:ALA)