FMO DATABASE

FMODB ID: Z2QNN

Calculation Name: 1D7M-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D7M

Chain ID: A

ChEMBL ID:

UniProt ID: Q54HG2

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-488772.679037
FMO2-HF: Nuclear repulsion	448243.140737
FMO2-HF: Total energy	-40529.538301
FMO2-MP2: Total energy	-40648.328879

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:243:GLU )

Summations of interaction energy for fragment #1(A:243:GLU )

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.
-67.397	-66.358	8.481	-2.411	-7.107	0.04

Interaction energy analysis for fragmet #1(A:243:GLU )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.875 / q_NPA : -0.971

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	245	ALA	0	0.042	0.031	3.280	-8.589	-8.939	0.094	1.791	-1.534	0.008
4	A	246	ASN	0	0.001	-0.004	2.554	-8.494	-7.066	0.354	-0.661	-1.121	-0.001
5	A	247	ARG	1	0.924	0.963	2.260	-62.618	-63.004	8.024	-3.415	-4.222	0.032
6	A	248	LEU	0	-0.016	-0.001	4.054	-7.800	-7.453	0.009	-0.126	-0.230	0.001
7	A	249	ALA	0	0.072	0.039	6.785	-3.453	-3.453	0.000	0.000	0.000	0.000
8	A	250	GLY	0	-0.031	-0.007	7.904	-2.966	-2.966	0.000	0.000	0.000	0.000
9	A	251	LEU	0	0.003	-0.015	7.879	-3.437	-3.437	0.000	0.000	0.000	0.000
10	A	252	GLU	-1	-0.936	-0.964	9.869	22.568	22.568	0.000	0.000	0.000	0.000
11	A	253	ASN	0	-0.005	0.001	11.988	-2.924	-2.924	0.000	0.000	0.000	0.000
12	A	254	SER	0	-0.024	-0.014	12.589	-1.411	-1.411	0.000	0.000	0.000	0.000
13	A	255	LEU	0	-0.020	-0.018	13.867	-1.674	-1.674	0.000	0.000	0.000	0.000
14	A	256	GLU	-1	-0.900	-0.943	15.850	14.432	14.432	0.000	0.000	0.000	0.000
15	A	257	SER	0	-0.053	-0.017	17.671	-1.354	-1.354	0.000	0.000	0.000	0.000
16	A	258	GLU	-1	-0.894	-0.966	17.246	17.218	17.218	0.000	0.000	0.000	0.000
17	A	259	LYS	1	0.924	0.961	19.989	-15.953	-15.953	0.000	0.000	0.000	0.000
18	A	260	VAL	0	0.051	0.034	22.015	-0.874	-0.874	0.000	0.000	0.000	0.000
19	A	261	SER	0	-0.002	-0.006	22.703	-0.808	-0.808	0.000	0.000	0.000	0.000
20	A	262	ARG	1	0.941	0.967	24.174	-12.933	-12.933	0.000	0.000	0.000	0.000
21	A	263	GLU	-1	-0.919	-0.958	25.977	10.856	10.856	0.000	0.000	0.000	0.000
22	A	264	GLN	0	-0.048	-0.026	27.573	-0.459	-0.459	0.000	0.000	0.000	0.000
23	A	265	LEU	0	0.002	-0.013	26.875	-0.478	-0.478	0.000	0.000	0.000	0.000
24	A	266	ILE	0	-0.023	-0.004	29.100	-0.396	-0.396	0.000	0.000	0.000	0.000
25	A	267	LYS	1	0.982	1.006	32.107	-9.496	-9.496	0.000	0.000	0.000	0.000
26	A	268	GLN	0	-0.024	-0.011	31.173	-0.559	-0.559	0.000	0.000	0.000	0.000
27	A	269	LYS	1	0.902	0.963	34.315	-9.449	-9.449	0.000	0.000	0.000	0.000
28	A	270	ASP	-1	-0.871	-0.936	36.101	8.500	8.500	0.000	0.000	0.000	0.000
29	A	271	GLN	0	-0.037	-0.028	38.080	-0.460	-0.460	0.000	0.000	0.000	0.000
30	A	272	LEU	0	0.002	0.000	37.519	-0.224	-0.224	0.000	0.000	0.000	0.000
31	A	273	ASN	0	-0.021	-0.014	39.665	-0.356	-0.356	0.000	0.000	0.000	0.000
32	A	274	SER	0	-0.002	0.010	42.055	-0.250	-0.250	0.000	0.000	0.000	0.000
33	A	275	LEU	0	0.004	0.003	43.436	-0.205	-0.205	0.000	0.000	0.000	0.000
34	A	276	LEU	0	-0.023	-0.019	43.537	-0.164	-0.164	0.000	0.000	0.000	0.000
35	A	277	ALA	0	0.052	0.043	46.263	-0.169	-0.169	0.000	0.000	0.000	0.000
36	A	278	SER	0	-0.052	-0.028	48.320	-0.212	-0.212	0.000	0.000	0.000	0.000
37	A	279	LEU	0	0.002	-0.010	47.818	-0.143	-0.143	0.000	0.000	0.000	0.000
38	A	280	GLU	-1	-0.933	-0.966	48.167	6.548	6.548	0.000	0.000	0.000	0.000
39	A	281	SER	0	-0.045	-0.009	52.116	-0.185	-0.185	0.000	0.000	0.000	0.000
40	A	282	GLU	-1	-0.908	-0.964	54.034	5.861	5.861	0.000	0.000	0.000	0.000
41	A	283	GLY	0	-0.015	-0.020	54.786	-0.130	-0.130	0.000	0.000	0.000	0.000
42	A	284	ALA	0	0.019	0.016	56.333	-0.114	-0.114	0.000	0.000	0.000	0.000
43	A	285	GLU	-1	-0.926	-0.966	58.158	5.245	5.245	0.000	0.000	0.000	0.000
44	A	286	ARG	1	0.860	0.929	56.053	-5.791	-5.791	0.000	0.000	0.000	0.000
45	A	287	GLU	-1	-0.891	-0.955	59.454	5.257	5.257	0.000	0.000	0.000	0.000
46	A	288	LYS	1	0.936	0.990	62.006	-5.097	-5.097	0.000	0.000	0.000	0.000
47	A	289	ARG	1	0.938	0.957	64.136	-5.045	-5.045	0.000	0.000	0.000	0.000
48	A	290	LEU	0	-0.018	0.005	62.854	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	291	ARG	1	0.998	0.998	65.956	-4.918	-4.918	0.000	0.000	0.000	0.000
50	A	292	GLU	-1	-0.974	-0.993	67.831	4.651	4.651	0.000	0.000	0.000	0.000
51	A	293	LEU	0	-0.031	-0.022	69.306	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	294	GLU	-1	-0.938	-0.962	68.108	4.743	4.743	0.000	0.000	0.000	0.000
53	A	295	ALA	0	-0.004	0.005	71.822	-0.077	-0.077	0.000	0.000	0.000	0.000
54	A	296	LYS	1	0.852	0.919	74.078	-4.211	-4.211	0.000	0.000	0.000	0.000
55	A	297	LEU	0	-0.014	-0.010	73.719	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	298	ASP	-1	-0.902	-0.946	76.051	4.137	4.137	0.000	0.000	0.000	0.000
57	A	299	GLU	-1	-0.882	-0.940	77.706	4.013	4.013	0.000	0.000	0.000	0.000
58	A	300	THR	0	-0.013	-0.012	79.260	-0.071	-0.071	0.000	0.000	0.000	0.000
59	A	301	LEU	0	0.001	-0.001	77.981	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	302	LYS	1	0.912	0.967	80.990	-4.093	-4.093	0.000	0.000	0.000	0.000
61	A	303	ASN	0	0.000	-0.016	83.859	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	304	LEU	0	-0.013	0.008	83.659	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	305	GLU	-1	-0.913	-0.961	85.701	3.701	3.701	0.000	0.000	0.000	0.000
64	A	306	LEU	0	0.000	-0.013	87.458	-0.055	-0.055	0.000	0.000	0.000	0.000
65	A	307	GLU	-1	-0.919	-0.958	89.557	3.528	3.528	0.000	0.000	0.000	0.000
66	A	308	LYS	1	0.897	0.952	88.278	-3.734	-3.734	0.000	0.000	0.000	0.000
67	A	309	LEU	0	-0.014	-0.005	90.751	-0.050	-0.050	0.000	0.000	0.000	0.000
68	A	310	ALA	0	0.018	0.015	93.716	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	311	ARG	1	0.883	0.942	92.232	-3.526	-3.526	0.000	0.000	0.000	0.000
70	A	312	MET	0	-0.044	-0.026	92.442	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	313	GLU	-1	-0.932	-0.953	97.266	3.202	3.202	0.000	0.000	0.000	0.000
72	A	314	LEU	0	-0.005	-0.021	98.841	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	315	GLU	-1	-0.855	-0.922	97.674	3.332	3.332	0.000	0.000	0.000	0.000
74	A	316	ALA	0	-0.001	0.009	101.512	-0.042	-0.042	0.000	0.000	0.000	0.000
75	A	317	ARG	1	0.907	0.943	103.457	-3.118	-3.118	0.000	0.000	0.000	0.000
76	A	318	LEU	0	0.025	0.021	104.172	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	319	ALA	0	0.055	0.032	105.620	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	320	LYS	1	0.856	0.921	107.397	-3.084	-3.084	0.000	0.000	0.000	0.000
79	A	321	THR	0	0.027	0.014	109.385	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	322	GLU	-1	-0.929	-0.972	108.534	2.998	2.998	0.000	0.000	0.000	0.000
81	A	323	LYS	1	0.931	0.973	111.595	-2.928	-2.928	0.000	0.000	0.000	0.000
82	A	324	ASP	-1	-0.912	-0.960	113.418	2.841	2.841	0.000	0.000	0.000	0.000
83	A	325	ARG	1	0.904	0.961	112.185	-2.923	-2.923	0.000	0.000	0.000	0.000
84	A	326	ALA	0	0.030	0.015	115.668	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	327	ILE	0	-0.017	-0.015	117.329	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	328	LEU	0	-0.018	-0.014	118.713	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	329	GLU	-1	-0.938	-0.961	118.014	2.746	2.746	0.000	0.000	0.000	0.000
88	A	330	LEU	0	-0.012	-0.008	120.704	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	331	LYS	1	0.869	0.929	123.702	-2.600	-2.600	0.000	0.000	0.000	0.000
90	A	332	LEU	0	-0.019	0.002	124.818	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	333	ALA	0	-0.003	-0.006	126.131	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	334	GLU	-1	-0.863	-0.937	127.941	2.529	2.529	0.000	0.000	0.000	0.000
93	A	335	ALA	0	0.041	0.027	129.609	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	336	ILE	0	-0.099	-0.050	129.221	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	337	ASP	-1	-0.896	-0.955	132.227	2.439	2.439	0.000	0.000	0.000	0.000
96	A	338	GLU	-1	-0.963	-0.991	133.354	2.446	2.446	0.000	0.000	0.000	0.000
97	A	339	LYS	1	0.851	0.940	135.383	-2.429	-2.429	0.000	0.000	0.000	0.000
98	A	340	SER	0	-0.004	-0.016	135.561	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	341	LYS	1	0.917	0.957	137.187	-2.400	-2.400	0.000	0.000	0.000	0.000
100	A	342	LEU	0	-0.089	-0.021	139.793	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	343	GLU	-2	-1.944	-1.961	139.805	4.620	4.620	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:243:GLU )