FMO DATABASE

FMODB ID: YY422

Calculation Name: 3MGJ-A-Xray372

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: 2023-06-19

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	OptH
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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-722077.413731
FMO2-HF: Nuclear repulsion	682434.786419
FMO2-HF: Total energy	-39642.627312
FMO2-MP2: Total energy	-39757.560377

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.
-21.586	-14.86	20.117	-10.953	-15.891	-0.081

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 : -0.037 / q_NPA : -0.018

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	3.621	-2.830	-0.298	0.001	-1.211	-1.322	0.002
4	A	4	ARG	1	0.874	0.947	5.954	0.527	0.527	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.886	-0.949	9.580	-0.349	-0.349	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.022	0.012	12.149	0.042	0.042	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.922	-0.984	15.026	-0.120	-0.120	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.047	-0.005	17.976	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.986	0.974	20.862	0.031	0.031	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.024	0.018	24.461	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.011	0.006	27.713	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.015	0.009	22.463	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.029	-0.027	25.455	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.967	-0.981	27.617	0.026	0.026	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.027	0.037	25.952	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.041	-0.036	25.541	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.032	0.013	21.495	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.032	0.017	19.046	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.013	-0.010	18.991	0.014	0.014	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.996	1.009	19.791	-0.061	-0.061	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.040	0.019	15.489	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.033	-0.031	14.811	0.013	0.013	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.878	-0.933	14.743	0.261	0.261	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.912	0.976	15.921	-0.137	-0.137	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.001	-0.010	10.025	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.019	-0.003	11.168	0.069	0.069	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.917	-0.940	12.298	0.308	0.308	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.115	-0.041	11.592	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.073	-0.039	9.383	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.035	-0.016	6.498	0.161	0.161	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.900	-0.951	6.756	1.214	1.214	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.029	-0.024	7.787	-0.272	-0.272	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.952	0.975	9.299	0.122	0.122	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.031	-0.015	10.879	-0.083	-0.083	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.068	-0.028	10.833	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.902	-0.959	14.501	-0.174	-0.174	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.029	-0.036	18.177	0.019	0.019	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.903	-0.927	21.212	-0.083	-0.083	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.028	-0.014	24.592	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.054	0.042	27.884	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.950	0.972	30.846	0.026	0.026	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.869	0.905	34.198	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	LYS	1	1.038	1.027	33.573	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.015	-0.017	34.138	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.979	-0.977	32.802	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.003	0.001	28.730	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.056	-0.034	25.998	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.000	-0.003	21.002	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.010	0.000	18.788	0.002	0.002	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.923	1.002	15.560	0.173	0.173	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.012	-0.010	12.262	0.018	0.018	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.011	0.017	6.585	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.018	0.006	8.097	0.193	0.193	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.001	-0.003	2.531	-1.297	-0.860	1.846	-0.423	-1.861	-0.001
55	A	55	GLY	0	0.038	-0.001	3.791	0.726	1.136	0.001	-0.102	-0.310	0.000
56	A	56	ARG	1	0.929	0.960	2.498	-4.041	-3.238	4.402	-2.277	-2.927	-0.025
57	A	57	ASP	-1	-0.864	-0.958	2.597	1.235	2.680	2.103	-1.388	-2.160	-0.013
58	A	58	GLU	-1	-0.904	-0.947	4.148	-0.737	-0.630	0.000	-0.016	-0.092	0.000
59	A	59	ARG	1	0.953	0.985	7.102	-0.679	-0.679	0.000	0.000	0.000	0.000
60	A	60	HIS	1	0.804	0.899	6.882	-0.533	-0.533	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.042	0.036	5.545	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.806	-0.907	8.280	0.102	0.102	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.980	-0.993	11.251	0.248	0.248	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.039	-0.023	8.701	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.025	-0.001	11.187	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	66	ASN	0	0.000	0.000	13.771	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.907	-0.957	15.965	0.126	0.126	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.064	-0.036	13.377	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.924	0.977	17.344	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.933	-0.970	19.520	0.059	0.059	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.060	-0.032	19.374	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.010	-0.021	21.589	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.019	0.006	23.195	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.992	-0.981	25.415	0.051	0.051	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.109	-0.062	24.843	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.031	0.015	27.549	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.940	-0.974	29.683	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.146	-0.069	22.947	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.878	-0.925	24.807	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.936	-0.987	17.029	-0.038	-0.038	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.012	-0.001	19.526	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.894	-0.959	15.033	-0.097	-0.097	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.033	-0.018	15.296	0.015	0.015	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.075	-0.040	14.727	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.077	0.051	12.183	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.068	-0.036	14.458	0.042	0.042	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.956	-0.991	12.120	-0.757	-0.757	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.890	0.939	13.539	0.196	0.196	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.895	-0.936	8.022	-0.769	-0.769	0.000	0.000	0.000	0.000
90	A	90	MET	0	0.026	0.015	8.199	-0.108	-0.108	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.016	-0.021	3.072	-0.962	-0.269	0.048	-0.269	-0.472	0.001
92	A	92	LEU	0	0.001	0.003	2.311	-1.266	0.525	1.854	-0.951	-2.694	-0.003
93	A	93	PRO	0	-0.030	-0.009	1.869	-6.579	-9.698	9.821	-3.617	-3.085	-0.037
94	A	94	GLU	-1	-0.903	-0.958	3.290	-6.273	-4.646	0.041	-0.699	-0.968	-0.005
95	A	95	GLY	0	-0.035	-0.018	5.418	0.156	0.156	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.031	-0.019	4.881	0.328	0.328	0.000	0.000	0.000	0.000
97	A	97	TYR	0	-0.017	0.010	6.163	0.290	0.290	0.000	0.000	0.000	0.000

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