FMO DATABASE

FMODB ID: GN8J1

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	OptHSide
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	-489604.071139
FMO2-HF: Nuclear repulsion	449072.209922
FMO2-HF: Total energy	-40531.861217
FMO2-MP2: Total energy	-40650.650371

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.
-68.236	-60.94	3.72	-4.511	-6.507	0.039

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 : -0.853 / q_NPA : -0.947

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	0.036	0.025	3.568	-9.626	-7.331	0.124	-1.093	-1.327	0.009
4	A	246	ASN	0	-0.011	-0.004	2.577	-8.164	-6.719	0.353	-0.672	-1.127	0.000
5	A	247	ARG	1	0.920	0.960	2.405	-64.692	-61.380	3.242	-2.678	-3.876	0.030
6	A	248	LEU	0	0.005	0.008	4.463	-5.447	-5.203	0.001	-0.068	-0.177	0.000
7	A	249	ALA	0	0.062	0.033	7.452	-2.816	-2.816	0.000	0.000	0.000	0.000
8	A	250	GLY	0	-0.016	0.002	7.962	-2.646	-2.646	0.000	0.000	0.000	0.000
9	A	251	LEU	0	-0.018	-0.022	7.573	-3.072	-3.072	0.000	0.000	0.000	0.000
10	A	252	GLU	-1	-0.927	-0.962	10.048	22.112	22.112	0.000	0.000	0.000	0.000
11	A	253	ASN	0	-0.017	-0.006	12.324	-2.743	-2.743	0.000	0.000	0.000	0.000
12	A	254	SER	0	-0.078	-0.054	12.402	-1.227	-1.227	0.000	0.000	0.000	0.000
13	A	255	LEU	0	0.025	0.003	13.996	-1.717	-1.717	0.000	0.000	0.000	0.000
14	A	256	GLU	-1	-0.927	-0.957	15.989	14.099	14.099	0.000	0.000	0.000	0.000
15	A	257	SER	0	-0.040	-0.016	17.625	-1.145	-1.145	0.000	0.000	0.000	0.000
16	A	258	GLU	-1	-0.857	-0.923	15.981	18.183	18.183	0.000	0.000	0.000	0.000
17	A	259	LYS	1	0.945	0.975	19.509	-16.709	-16.709	0.000	0.000	0.000	0.000
18	A	260	VAL	0	0.024	0.017	22.164	-0.861	-0.861	0.000	0.000	0.000	0.000
19	A	261	SER	0	-0.023	-0.022	22.511	-0.721	-0.721	0.000	0.000	0.000	0.000
20	A	262	ARG	1	0.841	0.903	24.183	-12.665	-12.665	0.000	0.000	0.000	0.000
21	A	263	GLU	-1	-0.822	-0.899	25.974	10.997	10.997	0.000	0.000	0.000	0.000
22	A	264	GLN	0	-0.030	-0.013	27.921	-0.435	-0.435	0.000	0.000	0.000	0.000
23	A	265	LEU	0	-0.009	-0.001	26.726	-0.464	-0.464	0.000	0.000	0.000	0.000
24	A	266	ILE	0	-0.010	-0.001	29.067	-0.437	-0.437	0.000	0.000	0.000	0.000
25	A	267	LYS	1	1.007	1.014	32.106	-9.372	-9.372	0.000	0.000	0.000	0.000
26	A	268	GLN	0	-0.021	-0.026	31.084	-0.499	-0.499	0.000	0.000	0.000	0.000
27	A	269	LYS	1	0.822	0.905	34.297	-9.357	-9.357	0.000	0.000	0.000	0.000
28	A	270	ASP	-1	-0.816	-0.894	36.006	8.491	8.491	0.000	0.000	0.000	0.000
29	A	271	GLN	0	-0.045	-0.025	38.061	-0.413	-0.413	0.000	0.000	0.000	0.000
30	A	272	LEU	0	0.005	0.004	37.143	-0.224	-0.224	0.000	0.000	0.000	0.000
31	A	273	ASN	0	-0.007	-0.008	39.807	-0.320	-0.320	0.000	0.000	0.000	0.000
32	A	274	SER	0	0.027	0.021	41.960	-0.195	-0.195	0.000	0.000	0.000	0.000
33	A	275	LEU	0	-0.028	-0.005	43.714	-0.206	-0.206	0.000	0.000	0.000	0.000
34	A	276	LEU	0	-0.007	-0.012	43.134	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	277	ALA	0	0.057	0.043	46.115	-0.165	-0.165	0.000	0.000	0.000	0.000
36	A	278	SER	0	-0.064	-0.040	48.150	-0.195	-0.195	0.000	0.000	0.000	0.000
37	A	279	LEU	0	-0.007	-0.014	47.388	-0.146	-0.146	0.000	0.000	0.000	0.000
38	A	280	GLU	-1	-0.907	-0.953	48.040	6.534	6.534	0.000	0.000	0.000	0.000
39	A	281	SER	0	-0.013	0.001	51.952	-0.150	-0.150	0.000	0.000	0.000	0.000
40	A	282	GLU	-1	-0.903	-0.935	53.895	5.831	5.831	0.000	0.000	0.000	0.000
41	A	283	GLY	0	-0.002	-0.014	54.615	-0.130	-0.130	0.000	0.000	0.000	0.000
42	A	284	ALA	0	0.027	0.022	56.155	-0.109	-0.109	0.000	0.000	0.000	0.000
43	A	285	GLU	-1	-0.833	-0.908	57.989	5.111	5.111	0.000	0.000	0.000	0.000
44	A	286	ARG	1	0.784	0.879	56.047	-5.800	-5.800	0.000	0.000	0.000	0.000
45	A	287	GLU	-1	-0.883	-0.954	59.112	5.265	5.265	0.000	0.000	0.000	0.000
46	A	288	LYS	1	0.789	0.903	61.784	-5.173	-5.173	0.000	0.000	0.000	0.000
47	A	289	ARG	1	0.945	0.966	63.971	-5.029	-5.029	0.000	0.000	0.000	0.000
48	A	290	LEU	0	-0.013	0.006	63.035	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	291	ARG	1	0.909	0.941	65.736	-4.902	-4.902	0.000	0.000	0.000	0.000
50	A	292	GLU	-1	-0.920	-0.971	67.594	4.705	4.705	0.000	0.000	0.000	0.000
51	A	293	LEU	0	-0.040	-0.026	68.091	-0.090	-0.090	0.000	0.000	0.000	0.000
52	A	294	GLU	-1	-0.868	-0.915	68.127	4.729	4.729	0.000	0.000	0.000	0.000
53	A	295	ALA	0	0.006	0.008	71.551	-0.077	-0.077	0.000	0.000	0.000	0.000
54	A	296	LYS	1	0.840	0.897	73.853	-4.196	-4.196	0.000	0.000	0.000	0.000
55	A	297	LEU	0	-0.001	0.008	73.309	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	298	ASP	-1	-0.803	-0.877	75.785	4.111	4.111	0.000	0.000	0.000	0.000
57	A	299	GLU	-1	-0.845	-0.908	77.413	4.014	4.014	0.000	0.000	0.000	0.000
58	A	300	THR	0	-0.026	-0.032	78.771	-0.066	-0.066	0.000	0.000	0.000	0.000
59	A	301	LEU	0	-0.011	-0.003	77.544	-0.059	-0.059	0.000	0.000	0.000	0.000
60	A	302	LYS	1	0.794	0.888	79.402	-4.142	-4.142	0.000	0.000	0.000	0.000
61	A	303	ASN	0	0.004	-0.012	83.617	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	304	LEU	0	-0.009	0.007	83.258	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	305	GLU	-1	-0.787	-0.876	85.351	3.699	3.699	0.000	0.000	0.000	0.000
64	A	306	LEU	0	-0.018	-0.023	87.128	-0.052	-0.052	0.000	0.000	0.000	0.000
65	A	307	GLU	-1	-0.910	-0.951	89.266	3.510	3.510	0.000	0.000	0.000	0.000
66	A	308	LYS	1	0.772	0.871	87.429	-3.758	-3.758	0.000	0.000	0.000	0.000
67	A	309	LEU	0	-0.012	-0.011	90.428	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	310	ALA	0	0.014	0.012	93.376	-0.049	-0.049	0.000	0.000	0.000	0.000
69	A	311	ARG	1	0.848	0.904	92.300	-3.518	-3.518	0.000	0.000	0.000	0.000
70	A	312	MET	0	-0.015	-0.012	91.944	-0.027	-0.027	0.000	0.000	0.000	0.000
71	A	313	GLU	-1	-0.930	-0.957	96.918	3.187	3.187	0.000	0.000	0.000	0.000
72	A	314	LEU	0	-0.007	-0.016	98.467	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	315	GLU	-1	-0.831	-0.889	97.080	3.348	3.348	0.000	0.000	0.000	0.000
74	A	316	ALA	0	0.003	0.009	101.176	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	317	ARG	1	0.914	0.955	103.097	-3.110	-3.110	0.000	0.000	0.000	0.000
76	A	318	LEU	0	0.028	0.031	103.860	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	319	ALA	0	0.046	0.024	105.280	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	320	LYS	1	0.882	0.935	106.557	-3.098	-3.098	0.000	0.000	0.000	0.000
79	A	321	THR	0	-0.002	-0.020	108.775	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	322	GLU	-1	-0.842	-0.902	108.587	2.965	2.965	0.000	0.000	0.000	0.000
81	A	323	LYS	1	0.853	0.917	111.245	-2.902	-2.902	0.000	0.000	0.000	0.000
82	A	324	ASP	-1	-0.861	-0.923	113.058	2.841	2.841	0.000	0.000	0.000	0.000
83	A	325	ARG	1	0.820	0.910	111.125	-2.937	-2.937	0.000	0.000	0.000	0.000
84	A	326	ALA	0	0.051	0.024	115.305	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	327	ILE	0	-0.016	-0.019	116.662	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	328	LEU	0	-0.026	-0.015	118.326	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	329	GLU	-1	-0.933	-0.960	117.560	2.756	2.756	0.000	0.000	0.000	0.000
88	A	330	LEU	0	-0.018	-0.009	120.157	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	331	LYS	1	0.799	0.869	123.351	-2.596	-2.596	0.000	0.000	0.000	0.000
90	A	332	LEU	0	-0.009	0.007	124.532	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	333	ALA	0	0.003	-0.003	125.803	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	334	GLU	-1	-0.784	-0.879	127.595	2.531	2.531	0.000	0.000	0.000	0.000
93	A	335	ALA	0	0.061	0.033	129.272	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	336	ILE	0	-0.065	-0.036	128.953	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	337	ASP	-1	-0.835	-0.892	131.909	2.423	2.423	0.000	0.000	0.000	0.000
96	A	338	GLU	-1	-0.935	-0.968	133.644	2.433	2.433	0.000	0.000	0.000	0.000
97	A	339	LYS	1	0.772	0.881	135.056	-2.405	-2.405	0.000	0.000	0.000	0.000
98	A	340	SER	0	-0.021	-0.026	135.255	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	341	LYS	1	0.821	0.884	135.158	-2.442	-2.442	0.000	0.000	0.000	0.000
100	A	342	LEU	0	-0.056	0.004	139.456	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	343	GLU	-1	-0.946	-0.957	139.740	2.313	2.313	0.000	0.000	0.000	0.000

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