FMO DATABASE

FMODB ID: LJMJ9

Calculation Name: 3MGJ-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MGJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q58875

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-723652.005129
FMO2-HF: Nuclear repulsion	683990.230642
FMO2-HF: Total energy	-39661.774487
FMO2-MP2: Total energy	-39776.815069

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:1:MET )

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

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.
-21.653	-14.622	19.88	-11.034	-15.881	-0.083

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.017

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	3	MET	0	0.010	0.003	3.642	-2.716	-0.254	0.005	-1.178	-1.290	0.002
4	A	4	ARG	1	0.877	0.947	5.912	0.464	0.464	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.889	-0.951	9.557	-0.303	-0.303	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.023	0.012	12.191	0.041	0.041	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.925	-0.985	15.007	-0.101	-0.101	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.043	-0.003	17.981	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.982	0.973	20.850	0.019	0.019	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.028	0.019	24.442	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.011	0.006	27.699	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.012	0.008	22.647	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.028	-0.026	25.560	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.965	-0.981	27.793	0.032	0.032	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.030	0.038	25.963	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.044	-0.039	25.582	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.033	0.014	21.518	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.034	0.017	19.140	0.008	0.008	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.015	-0.011	19.012	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.996	1.009	19.721	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.041	0.019	15.527	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.036	-0.032	14.844	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.877	-0.933	14.679	0.269	0.269	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.913	0.977	15.884	-0.152	-0.152	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.002	-0.011	9.958	0.021	0.021	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.014	0.000	11.125	0.069	0.069	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.920	-0.940	12.296	0.312	0.312	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.114	-0.041	11.594	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.073	-0.038	9.420	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.038	-0.018	6.467	0.158	0.158	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.897	-0.950	6.687	1.217	1.217	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.030	-0.024	7.803	-0.262	-0.262	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.953	0.975	9.410	0.093	0.093	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.032	-0.015	11.000	-0.082	-0.082	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.067	-0.027	10.919	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.904	-0.959	14.606	-0.160	-0.160	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.028	-0.035	18.292	0.020	0.020	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.903	-0.927	21.343	-0.074	-0.074	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.027	-0.014	24.728	0.008	0.008	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.052	0.042	28.028	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.950	0.972	31.004	0.021	0.021	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.869	0.904	34.342	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	LYS	1	1.039	1.028	33.744	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.015	-0.016	34.325	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.979	-0.978	32.983	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.006	-0.001	28.931	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.055	-0.033	26.166	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.000	-0.002	21.152	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.010	-0.001	18.965	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.925	1.002	15.731	0.153	0.153	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.011	-0.010	12.274	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.010	0.017	6.707	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.018	0.007	8.154	0.191	0.191	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.000	-0.003	2.559	-1.233	-0.798	1.749	-0.413	-1.771	-0.001
55	A	55	GLY	0	0.042	-0.001	3.881	0.645	1.040	0.002	-0.098	-0.299	0.000
56	A	56	ARG	1	0.929	0.961	2.465	-4.232	-3.341	4.367	-2.383	-2.875	-0.027
57	A	57	ASP	-1	-0.865	-0.959	2.629	1.437	2.947	1.934	-1.349	-2.096	-0.013
58	A	58	GLU	-1	-0.903	-0.948	4.179	-0.729	-0.626	0.001	-0.015	-0.089	0.000
59	A	59	ARG	1	0.949	0.984	7.127	-0.724	-0.724	0.000	0.000	0.000	0.000
60	A	60	HIS	1	0.807	0.900	6.891	-0.576	-0.576	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.040	0.035	5.543	-0.067	-0.067	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.805	-0.907	8.279	0.148	0.148	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.978	-0.992	11.259	0.269	0.269	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.045	-0.026	8.651	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.025	-0.001	11.252	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	66	ASN	0	0.002	0.002	13.846	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.907	-0.957	15.918	0.140	0.140	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.062	-0.035	13.430	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.922	0.976	17.414	-0.072	-0.072	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.933	-0.970	19.583	0.074	0.074	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.063	-0.034	19.434	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.006	-0.019	21.646	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.023	0.005	23.242	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.990	-0.981	25.483	0.059	0.059	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.111	-0.062	24.900	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.033	0.016	27.589	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.942	-0.975	29.704	0.013	0.013	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.145	-0.069	22.967	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.875	-0.924	24.825	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.938	-0.987	17.062	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.010	-0.001	19.528	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.895	-0.959	15.052	-0.059	-0.059	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.034	-0.019	15.368	0.010	0.010	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.073	-0.040	14.687	-0.043	-0.043	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.075	0.050	12.249	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.067	-0.035	14.607	0.040	0.040	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.957	-0.991	12.108	-0.742	-0.742	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.891	0.939	13.650	0.185	0.185	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.895	-0.936	8.048	-0.738	-0.738	0.000	0.000	0.000	0.000
90	A	90	MET	0	0.027	0.015	8.138	-0.124	-0.124	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.016	-0.021	3.105	-0.882	-0.217	0.043	-0.255	-0.453	0.001
92	A	92	LEU	0	0.002	0.003	2.286	-1.376	0.396	1.936	-0.978	-2.731	-0.002
93	A	93	PRO	0	-0.029	-0.009	1.868	-6.775	-9.805	9.800	-3.646	-3.124	-0.038
94	A	94	GLU	-1	-0.902	-0.958	3.281	-6.423	-4.772	0.043	-0.714	-0.980	-0.005
95	A	95	GLY	0	-0.030	-0.017	5.444	0.251	0.251	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.025	-0.019	4.612	0.108	0.285	0.000	-0.005	-0.173	0.000
97	A	97	TYR	0	-0.075	-0.033	6.227	0.173	0.173	0.000	0.000	0.000	0.000
98	A	98	NME	0	0.045	0.040	4.929	0.420	0.420	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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