FMO DATABASE

FMODB ID: 82GRY

Calculation Name: 1D7M-A-Xray372

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: 2023-03-13

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	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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-489185.245871
FMO2-HF: Nuclear repulsion	448652.857327
FMO2-HF: Total energy	-40532.388544
FMO2-MP2: Total energy	-40651.070101

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.
-75.512	-67.887	4.17	-4.802	-6.994	0.049

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 : -0.829 / q_NPA : -0.924

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	0.033	0.028	3.629	-7.536	-5.710	0.062	-0.875	-1.014	0.007
4	A	246	ASN	0	0.011	0.004	2.553	-6.947	-5.909	0.212	-0.429	-0.821	0.001
5	A	247	ARG	1	0.903	0.963	2.553	-76.621	-72.149	3.894	-3.432	-4.934	0.041
6	A	248	LEU	0	-0.004	0.002	4.360	-4.938	-4.649	0.002	-0.066	-0.225	0.000
7	A	249	ALA	0	0.068	0.041	7.732	-3.019	-3.019	0.000	0.000	0.000	0.000
8	A	250	GLY	0	-0.015	-0.006	7.688	-2.889	-2.889	0.000	0.000	0.000	0.000
9	A	251	LEU	0	-0.037	-0.029	6.773	-2.505	-2.505	0.000	0.000	0.000	0.000
10	A	252	GLU	-1	-0.907	-0.959	9.851	22.547	22.547	0.000	0.000	0.000	0.000
11	A	253	ASN	0	-0.026	-0.014	12.366	-2.946	-2.946	0.000	0.000	0.000	0.000
12	A	254	SER	0	-0.069	-0.042	12.211	-1.402	-1.402	0.000	0.000	0.000	0.000
13	A	255	LEU	0	0.071	0.042	13.892	-1.853	-1.853	0.000	0.000	0.000	0.000
14	A	256	GLU	-1	-0.851	-0.904	15.842	14.574	14.574	0.000	0.000	0.000	0.000
15	A	257	SER	0	-0.045	-0.038	17.158	-1.245	-1.245	0.000	0.000	0.000	0.000
16	A	258	GLU	-1	-0.857	-0.906	15.303	19.247	19.247	0.000	0.000	0.000	0.000
17	A	259	LYS	1	0.841	0.904	19.107	-17.365	-17.365	0.000	0.000	0.000	0.000
18	A	260	VAL	0	-0.006	0.000	22.064	-0.844	-0.844	0.000	0.000	0.000	0.000
19	A	261	SER	0	-0.013	-0.019	22.018	-0.759	-0.759	0.000	0.000	0.000	0.000
20	A	262	ARG	1	0.826	0.883	23.838	-12.829	-12.829	0.000	0.000	0.000	0.000
21	A	263	GLU	-1	-0.805	-0.882	25.584	11.400	11.400	0.000	0.000	0.000	0.000
22	A	264	GLN	0	-0.032	-0.010	27.447	-0.569	-0.569	0.000	0.000	0.000	0.000
23	A	265	LEU	0	-0.005	-0.005	26.028	-0.482	-0.482	0.000	0.000	0.000	0.000
24	A	266	ILE	0	-0.025	-0.007	28.894	-0.450	-0.450	0.000	0.000	0.000	0.000
25	A	267	LYS	1	0.978	0.990	31.747	-9.452	-9.452	0.000	0.000	0.000	0.000
26	A	268	GLN	0	0.017	-0.006	31.043	-0.582	-0.582	0.000	0.000	0.000	0.000
27	A	269	LYS	1	0.827	0.908	33.977	-9.493	-9.493	0.000	0.000	0.000	0.000
28	A	270	ASP	-1	-0.805	-0.885	35.729	8.635	8.635	0.000	0.000	0.000	0.000
29	A	271	GLN	0	-0.036	-0.012	36.917	-0.443	-0.443	0.000	0.000	0.000	0.000
30	A	272	LEU	0	0.013	0.006	36.666	-0.227	-0.227	0.000	0.000	0.000	0.000
31	A	273	ASN	0	-0.023	-0.017	38.830	-0.304	-0.304	0.000	0.000	0.000	0.000
32	A	274	SER	0	0.008	0.007	41.811	-0.202	-0.202	0.000	0.000	0.000	0.000
33	A	275	LEU	0	-0.038	-0.001	43.340	-0.200	-0.200	0.000	0.000	0.000	0.000
34	A	276	LEU	0	-0.010	-0.005	42.852	-0.162	-0.162	0.000	0.000	0.000	0.000
35	A	277	ALA	0	0.082	0.044	45.837	-0.179	-0.179	0.000	0.000	0.000	0.000
36	A	278	SER	0	-0.068	-0.041	47.871	-0.204	-0.204	0.000	0.000	0.000	0.000
37	A	279	LEU	0	0.001	-0.007	47.039	-0.157	-0.157	0.000	0.000	0.000	0.000
38	A	280	GLU	-1	-0.915	-0.961	47.555	6.641	6.641	0.000	0.000	0.000	0.000
39	A	281	SER	0	-0.017	-0.005	51.590	-0.155	-0.155	0.000	0.000	0.000	0.000
40	A	282	GLU	-1	-0.883	-0.922	53.478	5.888	5.888	0.000	0.000	0.000	0.000
41	A	283	GLY	0	-0.011	-0.009	54.230	-0.125	-0.125	0.000	0.000	0.000	0.000
42	A	284	ALA	0	0.003	0.002	55.765	-0.119	-0.119	0.000	0.000	0.000	0.000
43	A	285	GLU	-1	-0.829	-0.904	57.717	5.129	5.129	0.000	0.000	0.000	0.000
44	A	286	ARG	1	0.778	0.880	55.687	-5.869	-5.869	0.000	0.000	0.000	0.000
45	A	287	GLU	-1	-0.876	-0.955	58.579	5.332	5.332	0.000	0.000	0.000	0.000
46	A	288	LYS	1	0.781	0.894	61.375	-5.195	-5.195	0.000	0.000	0.000	0.000
47	A	289	ARG	1	0.970	0.981	63.514	-5.073	-5.073	0.000	0.000	0.000	0.000
48	A	290	LEU	0	-0.037	-0.010	62.853	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	291	ARG	1	0.889	0.924	65.328	-4.966	-4.966	0.000	0.000	0.000	0.000
50	A	292	GLU	-1	-0.914	-0.962	67.405	4.770	4.770	0.000	0.000	0.000	0.000
51	A	293	LEU	0	-0.045	-0.025	67.331	-0.093	-0.093	0.000	0.000	0.000	0.000
52	A	294	GLU	-1	-0.838	-0.911	67.209	4.783	4.783	0.000	0.000	0.000	0.000
53	A	295	ALA	0	0.000	0.008	71.048	-0.077	-0.077	0.000	0.000	0.000	0.000
54	A	296	LYS	1	0.857	0.913	73.525	-4.211	-4.211	0.000	0.000	0.000	0.000
55	A	297	LEU	0	-0.004	0.020	72.563	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	298	ASP	-1	-0.799	-0.883	75.168	4.140	4.140	0.000	0.000	0.000	0.000
57	A	299	GLU	-1	-0.842	-0.903	76.944	4.037	4.037	0.000	0.000	0.000	0.000
58	A	300	THR	0	-0.016	-0.032	78.329	-0.074	-0.074	0.000	0.000	0.000	0.000
59	A	301	LEU	0	-0.013	-0.009	77.180	-0.058	-0.058	0.000	0.000	0.000	0.000
60	A	302	LYS	1	0.779	0.874	78.824	-4.176	-4.176	0.000	0.000	0.000	0.000
61	A	303	ASN	0	-0.020	-0.019	83.170	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	304	LEU	0	0.015	0.013	82.607	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	305	GLU	-1	-0.791	-0.871	84.852	3.723	3.723	0.000	0.000	0.000	0.000
64	A	306	LEU	0	-0.008	-0.013	86.636	-0.054	-0.054	0.000	0.000	0.000	0.000
65	A	307	GLU	-1	-0.916	-0.951	88.738	3.535	3.535	0.000	0.000	0.000	0.000
66	A	308	LYS	1	0.765	0.864	87.220	-3.772	-3.772	0.000	0.000	0.000	0.000
67	A	309	LEU	0	-0.003	-0.015	89.938	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	310	ALA	0	0.009	0.013	92.845	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	311	ARG	1	0.820	0.878	91.893	-3.544	-3.544	0.000	0.000	0.000	0.000
70	A	312	MET	0	0.006	0.002	91.506	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	313	GLU	-1	-0.904	-0.945	96.431	3.196	3.196	0.000	0.000	0.000	0.000
72	A	314	LEU	0	-0.014	-0.014	97.747	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	315	GLU	-1	-0.829	-0.883	96.327	3.376	3.376	0.000	0.000	0.000	0.000
74	A	316	ALA	0	0.000	0.005	100.594	-0.042	-0.042	0.000	0.000	0.000	0.000
75	A	317	ARG	1	0.874	0.935	102.492	-3.121	-3.121	0.000	0.000	0.000	0.000
76	A	318	LEU	0	0.029	0.036	103.376	-0.046	-0.046	0.000	0.000	0.000	0.000
77	A	319	ALA	0	0.038	0.017	104.483	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	320	LYS	1	0.907	0.951	105.589	-3.126	-3.126	0.000	0.000	0.000	0.000
79	A	321	THR	0	0.009	-0.018	108.225	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	322	GLU	-1	-0.836	-0.893	107.774	2.987	2.987	0.000	0.000	0.000	0.000
81	A	323	LYS	1	0.801	0.898	110.631	-2.922	-2.922	0.000	0.000	0.000	0.000
82	A	324	ASP	-1	-0.806	-0.908	112.480	2.854	2.854	0.000	0.000	0.000	0.000
83	A	325	ARG	1	0.783	0.889	110.527	-2.954	-2.954	0.000	0.000	0.000	0.000
84	A	326	ALA	0	0.085	0.045	115.017	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	327	ILE	0	-0.035	-0.021	116.094	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	328	LEU	0	-0.022	-0.011	117.737	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	329	GLU	-1	-0.908	-0.959	116.917	2.779	2.779	0.000	0.000	0.000	0.000
88	A	330	LEU	0	-0.017	-0.013	119.789	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	331	LYS	1	0.795	0.869	122.859	-2.618	-2.618	0.000	0.000	0.000	0.000
90	A	332	LEU	0	-0.021	0.002	123.892	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	333	ALA	0	-0.002	-0.012	125.226	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	334	GLU	-1	-0.789	-0.871	127.000	2.550	2.550	0.000	0.000	0.000	0.000
93	A	335	ALA	0	0.048	0.027	128.739	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	336	ILE	0	-0.033	-0.023	128.290	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	337	ASP	-1	-0.820	-0.862	131.379	2.437	2.437	0.000	0.000	0.000	0.000
96	A	338	GLU	-1	-0.935	-0.968	133.059	2.440	2.440	0.000	0.000	0.000	0.000
97	A	339	LYS	1	0.749	0.856	134.479	-2.418	-2.418	0.000	0.000	0.000	0.000
98	A	340	SER	0	-0.017	-0.032	134.760	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	341	LYS	1	0.781	0.863	134.496	-2.458	-2.458	0.000	0.000	0.000	0.000
100	A	342	LEU	0	-0.052	-0.004	139.019	-0.019	-0.019	0.000	0.000	0.000	0.000
101	A	343	GLU	-1	-0.909	-0.927	139.282	2.327	2.327	0.000	0.000	0.000	0.000

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