FMO DATABASE

FMODB ID: MN9JZ

Calculation Name: 5D4Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D4Z

Chain ID: B

ChEMBL ID:

UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-676051.912371
FMO2-HF: Nuclear repulsion	635190.775756
FMO2-HF: Total energy	-40861.136615
FMO2-MP2: Total energy	-40978.630612

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(B:92:VAL)

Summations of interaction energy for fragment #1(B:92:VAL)

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.
-20.09	-12.207	2.973	-3.59	-7.265	0.003

Interaction energy analysis for fragmet #1(B:92:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.000

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	B	94	LYS	1	0.919	0.937	2.905	-14.696	-11.287	1.025	-1.696	-2.739	0.011
4	B	95	GLN	0	-0.016	-0.002	2.342	-4.571	-1.731	1.733	-1.444	-3.130	-0.007
5	B	96	ALA	0	0.053	0.030	3.860	0.079	0.612	0.003	-0.209	-0.326	0.000
6	B	97	ALA	0	-0.001	0.003	5.878	0.165	0.165	0.000	0.000	0.000	0.000
7	B	98	ALA	0	0.008	0.010	7.098	-0.072	-0.072	0.000	0.000	0.000	0.000
8	B	99	THR	0	-0.006	-0.001	7.322	0.071	0.071	0.000	0.000	0.000	0.000
9	B	100	LEU	0	0.020	0.013	9.550	0.052	0.052	0.000	0.000	0.000	0.000
10	B	101	ASN	0	-0.026	-0.024	11.319	0.002	0.002	0.000	0.000	0.000	0.000
11	B	102	ALA	0	-0.025	-0.013	12.501	0.005	0.005	0.000	0.000	0.000	0.000
12	B	103	TRP	0	-0.048	-0.041	12.282	-0.010	-0.010	0.000	0.000	0.000	0.000
13	B	104	MET	0	0.069	0.043	15.128	0.031	0.031	0.000	0.000	0.000	0.000
14	B	105	ARG	1	0.862	0.957	17.030	-0.047	-0.047	0.000	0.000	0.000	0.000
15	B	106	LYS	1	0.879	0.952	18.593	0.077	0.077	0.000	0.000	0.000	0.000
16	B	107	ASP	-1	-0.745	-0.879	19.889	-0.105	-0.105	0.000	0.000	0.000	0.000
17	B	108	THR	0	-0.021	-0.013	22.081	0.016	0.016	0.000	0.000	0.000	0.000
18	B	109	GLU	-1	-0.933	-0.966	21.556	-0.044	-0.044	0.000	0.000	0.000	0.000
19	B	110	MET	0	-0.019	-0.004	23.884	0.012	0.012	0.000	0.000	0.000	0.000
20	B	111	THR	0	0.034	0.004	19.138	0.001	0.001	0.000	0.000	0.000	0.000
21	B	112	SER	0	-0.049	-0.038	20.616	0.012	0.012	0.000	0.000	0.000	0.000
22	B	113	GLU	-1	-0.751	-0.866	17.815	0.110	0.110	0.000	0.000	0.000	0.000
23	B	114	LYS	1	0.843	0.920	19.215	-0.081	-0.081	0.000	0.000	0.000	0.000
24	B	115	LYS	1	0.917	0.945	21.762	0.009	0.009	0.000	0.000	0.000	0.000
25	B	116	VAL	0	0.118	0.075	15.404	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	117	ALA	0	-0.041	-0.020	18.059	-0.022	-0.022	0.000	0.000	0.000	0.000
27	B	118	VAL	0	-0.071	-0.040	18.960	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	119	ALA	0	-0.017	-0.001	19.825	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	120	ALA	0	-0.013	-0.004	16.141	-0.014	-0.014	0.000	0.000	0.000	0.000
30	B	121	GLY	0	-0.003	0.009	18.217	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	122	ILE	0	-0.060	-0.029	15.252	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.046	0.022	18.465	0.014	0.014	0.000	0.000	0.000	0.000
33	B	124	PRO	0	0.056	-0.008	18.177	0.004	0.004	0.000	0.000	0.000	0.000
34	B	125	ALA	0	-0.034	-0.013	19.018	0.014	0.014	0.000	0.000	0.000	0.000
35	B	126	THR	0	0.009	-0.012	14.521	0.036	0.036	0.000	0.000	0.000	0.000
36	B	127	VAL	0	0.048	0.040	13.503	0.020	0.020	0.000	0.000	0.000	0.000
37	B	128	ASN	0	-0.048	-0.027	13.350	0.061	0.061	0.000	0.000	0.000	0.000
38	B	129	ARG	1	0.982	0.998	13.354	-0.083	-0.083	0.000	0.000	0.000	0.000
39	B	130	ILE	0	0.013	0.007	8.144	0.117	0.117	0.000	0.000	0.000	0.000
40	B	131	MET	0	-0.028	-0.017	9.583	0.116	0.116	0.000	0.000	0.000	0.000
41	B	132	LYS	1	0.782	0.883	11.163	-0.311	-0.311	0.000	0.000	0.000	0.000
42	B	133	ALA	0	-0.029	-0.016	6.882	0.187	0.187	0.000	0.000	0.000	0.000
43	B	134	GLU	-1	-0.865	-0.903	8.765	0.737	0.737	0.000	0.000	0.000	0.000
44	B	135	VAL	0	-0.047	-0.032	10.170	-0.007	-0.007	0.000	0.000	0.000	0.000
45	B	136	SER	0	-0.038	-0.047	4.868	-0.175	-0.175	0.000	0.000	0.000	0.000
46	B	137	THR	0	-0.001	0.004	6.020	-0.047	-0.047	0.000	0.000	0.000	0.000
47	B	138	THR	0	0.041	0.022	6.614	-0.185	-0.185	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.105	0.029	6.898	-0.024	-0.024	0.000	0.000	0.000	0.000
49	B	140	GLY	0	0.012	0.024	8.824	0.028	0.028	0.000	0.000	0.000	0.000
50	B	141	VAL	0	0.013	-0.004	10.874	0.014	0.014	0.000	0.000	0.000	0.000
51	B	142	LEU	0	-0.012	-0.001	5.472	0.032	0.032	0.000	0.000	0.000	0.000
52	B	143	SER	0	-0.014	-0.009	9.437	0.050	0.050	0.000	0.000	0.000	0.000
53	B	144	SER	0	-0.008	-0.017	12.378	0.016	0.016	0.000	0.000	0.000	0.000
54	B	145	LEU	0	-0.027	-0.007	10.398	0.045	0.045	0.000	0.000	0.000	0.000
55	B	146	ALA	0	0.032	0.011	11.505	0.030	0.030	0.000	0.000	0.000	0.000
56	B	147	ARG	1	0.821	0.894	13.411	0.369	0.369	0.000	0.000	0.000	0.000
57	B	148	ALA	0	-0.034	0.000	16.638	0.025	0.025	0.000	0.000	0.000	0.000
58	B	149	PHE	0	0.013	0.001	15.245	0.024	0.024	0.000	0.000	0.000	0.000
59	B	150	GLY	0	-0.049	-0.011	18.109	0.009	0.009	0.000	0.000	0.000	0.000
60	B	151	HIS	1	0.766	0.859	13.945	0.303	0.303	0.000	0.000	0.000	0.000
61	B	152	GLU	-1	-0.781	-0.875	13.333	-0.352	-0.352	0.000	0.000	0.000	0.000
62	B	153	ALA	0	0.000	-0.026	8.972	-0.043	-0.043	0.000	0.000	0.000	0.000
63	B	154	TYR	0	0.038	0.002	7.446	-0.166	-0.166	0.000	0.000	0.000	0.000
64	B	155	GLU	-1	-0.769	-0.857	7.724	-0.564	-0.564	0.000	0.000	0.000	0.000
65	B	156	MET	0	-0.050	-0.013	7.536	0.030	0.030	0.000	0.000	0.000	0.000
66	B	157	ILE	0	-0.087	-0.039	2.798	-1.013	-0.127	0.213	-0.228	-0.870	-0.001
67	B	158	ILE	0	0.016	0.029	4.660	-0.456	-0.241	-0.001	-0.013	-0.200	0.000
68	B	159	PRO	0	-0.019	-0.011	5.179	0.094	0.094	0.000	0.000	0.000	0.000
69	B	160	VAL	0	0.050	0.016	7.080	0.116	0.116	0.000	0.000	0.000	0.000
70	B	161	GLY	0	-0.023	-0.007	9.573	0.023	0.023	0.000	0.000	0.000	0.000
71	B	162	ALA	0	-0.023	-0.009	11.349	0.015	0.015	0.000	0.000	0.000	0.000
72	B	163	PRO	0	0.023	0.020	10.847	0.041	0.041	0.000	0.000	0.000	0.000
73	B	164	GLY	0	-0.013	-0.017	12.164	-0.068	-0.068	0.000	0.000	0.000	0.000
74	B	165	ILE	0	-0.051	-0.022	11.579	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	166	ILE	0	-0.013	-0.007	15.522	0.033	0.033	0.000	0.000	0.000	0.000
76	B	167	ASP	-1	-0.919	-0.953	19.091	-0.171	-0.171	0.000	0.000	0.000	0.000
77	B	168	TYR	0	-0.038	-0.026	20.065	0.006	0.006	0.000	0.000	0.000	0.000
78	B	169	ASP	-1	-0.830	-0.916	22.550	-0.147	-0.147	0.000	0.000	0.000	0.000
79	B	170	HIS	0	0.073	0.014	18.490	0.008	0.008	0.000	0.000	0.000	0.000
80	B	171	ARG	1	0.969	0.990	23.640	0.111	0.111	0.000	0.000	0.000	0.000
81	B	172	MET	0	-0.055	-0.021	26.787	0.008	0.008	0.000	0.000	0.000	0.000
82	B	173	TYR	0	0.018	0.010	23.738	0.009	0.009	0.000	0.000	0.000	0.000
83	B	174	ALA	0	-0.017	-0.026	25.137	0.002	0.002	0.000	0.000	0.000	0.000
84	B	175	ALA	0	-0.069	-0.026	26.939	0.005	0.005	0.000	0.000	0.000	0.000
85	B	176	LEU	0	-0.029	-0.005	29.809	0.008	0.008	0.000	0.000	0.000	0.000
86	B	177	PRO	0	0.047	0.027	31.144	-0.006	-0.006	0.000	0.000	0.000	0.000
87	B	178	GLN	0	0.075	0.024	30.765	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	179	GLU	-1	-0.910	-0.950	31.514	-0.092	-0.092	0.000	0.000	0.000	0.000
89	B	180	GLU	-1	-0.815	-0.922	32.633	-0.098	-0.098	0.000	0.000	0.000	0.000
90	B	181	LYS	1	0.792	0.923	26.860	0.132	0.132	0.000	0.000	0.000	0.000
91	B	182	ASN	0	0.048	0.014	28.519	-0.008	-0.008	0.000	0.000	0.000	0.000
92	B	183	LYS	1	0.885	0.953	30.127	0.097	0.097	0.000	0.000	0.000	0.000
93	B	184	ILE	0	0.029	0.018	25.436	0.001	0.001	0.000	0.000	0.000	0.000
94	B	185	THR	0	0.001	0.006	25.342	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	186	SER	0	-0.018	-0.022	26.666	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	187	PHE	0	-0.044	-0.018	28.166	0.003	0.003	0.000	0.000	0.000	0.000
97	B	188	ILE	0	0.005	0.002	22.202	0.003	0.003	0.000	0.000	0.000	0.000
98	B	189	ASN	0	0.006	-0.018	23.702	-0.006	-0.006	0.000	0.000	0.000	0.000
99	B	190	PHE	0	-0.011	0.017	25.773	0.005	0.005	0.000	0.000	0.000	0.000
100	B	191	VAL	0	0.010	0.001	25.493	0.006	0.006	0.000	0.000	0.000	0.000
101	B	192	PHE	0	-0.042	-0.032	19.894	0.001	0.001	0.000	0.000	0.000	0.000
102	B	193	GLU	-1	-0.900	-0.968	24.674	-0.128	-0.128	0.000	0.000	0.000	0.000
103	B	194	GLN	0	-0.061	0.000	27.162	0.010	0.010	0.000	0.000	0.000	0.000
104	B	195	ASN	0	-0.077	-0.038	24.547	0.014	0.014	0.000	0.000	0.000	0.000
105	B	196	LYS	1	0.910	0.974	25.350	0.107	0.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:92:VAL)