FMO DATABASE

FMODB ID: 145MZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-488871.137194
FMO2-HF: Nuclear repulsion	448340.777785
FMO2-HF: Total energy	-40530.359409
FMO2-MP2: Total energy	-40649.141341

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	-66.907	8.46	-2.397	-7.155	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 : -0.877 / 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	0.040	0.030	3.280	-7.890	-8.228	0.080	1.810	-1.552	0.008
4	A	246	ASN	0	0.000	-0.004	2.554	-8.452	-7.009	0.353	-0.665	-1.130	-0.001
5	A	247	ARG	1	0.924	0.963	2.260	-62.879	-63.240	8.019	-3.415	-4.243	0.032
6	A	248	LEU	0	-0.015	-0.001	4.054	-7.429	-7.080	0.008	-0.127	-0.230	0.001
7	A	249	ALA	0	0.069	0.038	6.785	-3.239	-3.239	0.000	0.000	0.000	0.000
8	A	250	GLY	0	-0.030	-0.006	7.904	-2.941	-2.941	0.000	0.000	0.000	0.000
9	A	251	LEU	0	0.004	-0.014	7.879	-3.390	-3.390	0.000	0.000	0.000	0.000
10	A	252	GLU	-1	-0.938	-0.965	9.869	22.665	22.665	0.000	0.000	0.000	0.000
11	A	253	ASN	0	-0.006	0.001	11.988	-2.866	-2.866	0.000	0.000	0.000	0.000
12	A	254	SER	0	-0.023	-0.013	12.587	-1.401	-1.401	0.000	0.000	0.000	0.000
13	A	255	LEU	0	-0.020	-0.018	13.868	-1.633	-1.633	0.000	0.000	0.000	0.000
14	A	256	GLU	-1	-0.902	-0.944	15.850	14.471	14.471	0.000	0.000	0.000	0.000
15	A	257	SER	0	-0.052	-0.016	17.671	-1.324	-1.324	0.000	0.000	0.000	0.000
16	A	258	GLU	-1	-0.894	-0.966	17.246	17.232	17.232	0.000	0.000	0.000	0.000
17	A	259	LYS	1	0.924	0.961	19.989	-15.925	-15.925	0.000	0.000	0.000	0.000
18	A	260	VAL	0	0.048	0.033	22.015	-0.850	-0.850	0.000	0.000	0.000	0.000
19	A	261	SER	0	0.000	-0.005	22.709	-0.792	-0.792	0.000	0.000	0.000	0.000
20	A	262	ARG	1	0.940	0.967	24.173	-12.921	-12.921	0.000	0.000	0.000	0.000
21	A	263	GLU	-1	-0.919	-0.958	25.977	10.873	10.873	0.000	0.000	0.000	0.000
22	A	264	GLN	0	-0.047	-0.025	27.573	-0.445	-0.445	0.000	0.000	0.000	0.000
23	A	265	LEU	0	0.002	-0.013	26.874	-0.469	-0.469	0.000	0.000	0.000	0.000
24	A	266	ILE	0	-0.022	-0.004	29.100	-0.386	-0.386	0.000	0.000	0.000	0.000
25	A	267	LYS	1	0.980	1.005	32.107	-9.484	-9.484	0.000	0.000	0.000	0.000
26	A	268	GLN	0	-0.021	-0.010	31.173	-0.550	-0.550	0.000	0.000	0.000	0.000
27	A	269	LYS	1	0.900	0.962	34.314	-9.443	-9.443	0.000	0.000	0.000	0.000
28	A	270	ASP	-1	-0.871	-0.936	36.101	8.509	8.509	0.000	0.000	0.000	0.000
29	A	271	GLN	0	-0.038	-0.029	38.080	-0.452	-0.452	0.000	0.000	0.000	0.000
30	A	272	LEU	0	0.003	0.001	37.519	-0.219	-0.219	0.000	0.000	0.000	0.000
31	A	273	ASN	0	-0.021	-0.014	39.665	-0.351	-0.351	0.000	0.000	0.000	0.000
32	A	274	SER	0	-0.002	0.010	42.055	-0.242	-0.242	0.000	0.000	0.000	0.000
33	A	275	LEU	0	0.005	0.004	43.436	-0.200	-0.200	0.000	0.000	0.000	0.000
34	A	276	LEU	0	-0.025	-0.020	43.537	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	277	ALA	0	0.052	0.043	46.263	-0.164	-0.164	0.000	0.000	0.000	0.000
36	A	278	SER	0	-0.053	-0.029	48.320	-0.207	-0.207	0.000	0.000	0.000	0.000
37	A	279	LEU	0	0.005	-0.009	47.819	-0.140	-0.140	0.000	0.000	0.000	0.000
38	A	280	GLU	-1	-0.934	-0.967	48.167	6.551	6.551	0.000	0.000	0.000	0.000
39	A	281	SER	0	-0.045	-0.009	52.116	-0.180	-0.180	0.000	0.000	0.000	0.000
40	A	282	GLU	-1	-0.907	-0.963	54.034	5.864	5.864	0.000	0.000	0.000	0.000
41	A	283	GLY	0	-0.016	-0.020	54.785	-0.128	-0.128	0.000	0.000	0.000	0.000
42	A	284	ALA	0	0.019	0.016	56.334	-0.110	-0.110	0.000	0.000	0.000	0.000
43	A	285	GLU	-1	-0.928	-0.967	58.158	5.248	5.248	0.000	0.000	0.000	0.000
44	A	286	ARG	1	0.862	0.929	56.053	-5.789	-5.789	0.000	0.000	0.000	0.000
45	A	287	GLU	-1	-0.892	-0.955	59.454	5.259	5.259	0.000	0.000	0.000	0.000
46	A	288	LYS	1	0.936	0.990	62.006	-5.094	-5.094	0.000	0.000	0.000	0.000
47	A	289	ARG	1	0.937	0.957	64.136	-5.042	-5.042	0.000	0.000	0.000	0.000
48	A	290	LEU	0	-0.018	0.005	62.854	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	291	ARG	1	0.998	0.998	65.956	-4.916	-4.916	0.000	0.000	0.000	0.000
50	A	292	GLU	-1	-0.974	-0.993	67.831	4.654	4.654	0.000	0.000	0.000	0.000
51	A	293	LEU	0	-0.031	-0.022	69.306	-0.089	-0.089	0.000	0.000	0.000	0.000
52	A	294	GLU	-1	-0.938	-0.961	68.108	4.744	4.744	0.000	0.000	0.000	0.000
53	A	295	ALA	0	-0.004	0.004	71.822	-0.075	-0.075	0.000	0.000	0.000	0.000
54	A	296	LYS	1	0.852	0.919	74.078	-4.209	-4.209	0.000	0.000	0.000	0.000
55	A	297	LEU	0	-0.013	-0.009	73.719	-0.077	-0.077	0.000	0.000	0.000	0.000
56	A	298	ASP	-1	-0.903	-0.946	76.051	4.138	4.138	0.000	0.000	0.000	0.000
57	A	299	GLU	-1	-0.882	-0.940	77.706	4.015	4.015	0.000	0.000	0.000	0.000
58	A	300	THR	0	-0.013	-0.012	79.267	-0.070	-0.070	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	0.914	0.968	80.989	-4.091	-4.091	0.000	0.000	0.000	0.000
61	A	303	ASN	0	-0.002	-0.017	83.859	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	304	LEU	0	-0.012	0.008	83.661	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	305	GLU	-1	-0.914	-0.962	85.701	3.702	3.702	0.000	0.000	0.000	0.000
64	A	306	LEU	0	0.000	-0.014	87.458	-0.053	-0.053	0.000	0.000	0.000	0.000
65	A	307	GLU	-1	-0.918	-0.957	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	-3.733	-3.733	0.000	0.000	0.000	0.000
67	A	309	LEU	0	-0.013	-0.005	90.751	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	310	ALA	0	0.017	0.014	93.716	-0.049	-0.049	0.000	0.000	0.000	0.000
69	A	311	ARG	1	0.885	0.942	92.232	-3.525	-3.525	0.000	0.000	0.000	0.000
70	A	312	MET	0	-0.045	-0.026	92.443	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	313	GLU	-1	-0.931	-0.953	97.266	3.203	3.203	0.000	0.000	0.000	0.000
72	A	314	LEU	0	-0.007	-0.021	98.841	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	315	GLU	-1	-0.855	-0.922	97.674	3.333	3.333	0.000	0.000	0.000	0.000
74	A	316	ALA	0	0.000	0.009	101.512	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	317	ARG	1	0.906	0.943	103.457	-3.117	-3.117	0.000	0.000	0.000	0.000
76	A	318	LEU	0	0.026	0.021	104.171	-0.041	-0.041	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	0.858	0.921	107.397	-3.083	-3.083	0.000	0.000	0.000	0.000
79	A	321	THR	0	0.026	0.014	109.385	-0.036	-0.036	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	0.932	0.973	111.595	-2.928	-2.928	0.000	0.000	0.000	0.000
82	A	324	ASP	-1	-0.913	-0.961	113.418	2.842	2.842	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	0.033	0.016	115.668	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	327	ILE	0	-0.016	-0.015	117.327	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	328	LEU	0	-0.019	-0.014	118.713	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	329	GLU	-1	-0.937	-0.960	118.014	2.746	2.746	0.000	0.000	0.000	0.000
88	A	330	LEU	0	-0.010	-0.007	120.704	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	331	LYS	1	0.871	0.930	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	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	333	ALA	0	0.000	-0.005	126.131	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	334	GLU	-1	-0.860	-0.936	127.941	2.528	2.528	0.000	0.000	0.000	0.000
93	A	335	ALA	0	0.045	0.029	129.610	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	336	ILE	0	-0.095	-0.048	129.219	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	337	ASP	-1	-0.892	-0.953	132.227	2.439	2.439	0.000	0.000	0.000	0.000
96	A	338	GLU	-1	-0.957	-0.987	133.354	2.445	2.445	0.000	0.000	0.000	0.000
97	A	339	LYS	1	0.869	0.951	135.382	-2.430	-2.430	0.000	0.000	0.000	0.000
98	A	340	SER	0	0.007	-0.009	135.565	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	341	LYS	1	0.913	0.950	137.187	-2.403	-2.403	0.000	0.000	0.000	0.000
100	A	342	LEU	0	-0.063	-0.010	139.790	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	343	GLU	-1	-1.026	-1.000	139.805	2.321	2.321	0.000	0.000	0.000	0.000

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