FMO DATABASE

FMODB ID: Z6YRN

Calculation Name: 2FDB-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FDB

Chain ID: M

ChEMBL ID:

UniProt ID: P55075

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1519193.26383
FMO2-HF: Nuclear repulsion	1458490.875296
FMO2-HF: Total energy	-60702.388533
FMO2-MP2: Total energy	-60878.848134

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(M:32:PHE)

Summations of interaction energy for fragment #1(M:32:PHE)

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.
-4.874	-1.187	0.302	-1.202	-2.783	0.001

Interaction energy analysis for fragmet #1(M:32:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : 0.029

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	M	34	GLN	0	0.009	-0.002	3.884	-2.151	-0.765	-0.006	-0.573	-0.806	0.002
4	M	35	HIS	0	0.093	0.051	2.975	-1.929	-0.564	0.176	-0.349	-1.191	-0.001
5	M	36	VAL	0	0.007	-0.002	2.818	-0.449	0.392	0.133	-0.276	-0.697	0.000
6	M	37	ARG	1	0.884	0.952	5.259	-0.891	-0.796	-0.001	-0.004	-0.089	0.000
7	M	38	GLU	-1	-0.850	-0.911	7.946	0.432	0.432	0.000	0.000	0.000	0.000
8	M	39	GLN	0	0.028	0.005	7.200	0.017	0.017	0.000	0.000	0.000	0.000
9	M	40	SER	0	-0.069	-0.046	8.947	0.023	0.023	0.000	0.000	0.000	0.000
10	M	41	LEU	0	-0.079	-0.023	11.089	0.022	0.022	0.000	0.000	0.000	0.000
11	M	42	VAL	0	-0.062	-0.034	13.519	0.008	0.008	0.000	0.000	0.000	0.000
12	M	43	THR	0	-0.065	-0.056	13.900	-0.013	-0.013	0.000	0.000	0.000	0.000
13	M	44	ASP	-1	-0.760	-0.848	10.989	-0.258	-0.258	0.000	0.000	0.000	0.000
14	M	45	GLN	0	-0.041	-0.052	13.705	0.031	0.031	0.000	0.000	0.000	0.000
15	M	46	LEU	0	0.016	0.022	11.879	0.005	0.005	0.000	0.000	0.000	0.000
16	M	47	SER	0	-0.009	-0.018	10.935	-0.037	-0.037	0.000	0.000	0.000	0.000
17	M	48	ARG	1	0.930	0.955	13.403	0.221	0.221	0.000	0.000	0.000	0.000
18	M	49	ARG	1	0.758	0.866	14.711	0.113	0.113	0.000	0.000	0.000	0.000
19	M	50	LEU	0	-0.014	0.003	15.736	0.001	0.001	0.000	0.000	0.000	0.000
20	M	51	ILE	0	0.021	-0.001	17.570	0.014	0.014	0.000	0.000	0.000	0.000
21	M	52	ARG	1	0.929	0.970	17.568	0.097	0.097	0.000	0.000	0.000	0.000
22	M	53	THR	0	0.037	0.012	23.257	0.004	0.004	0.000	0.000	0.000	0.000
23	M	54	TYR	0	-0.021	-0.021	23.194	0.001	0.001	0.000	0.000	0.000	0.000
24	M	55	GLN	0	0.024	0.013	28.856	0.004	0.004	0.000	0.000	0.000	0.000
25	M	56	LEU	0	0.008	0.002	26.640	0.001	0.001	0.000	0.000	0.000	0.000
26	M	57	TYR	0	0.021	0.024	30.533	0.003	0.003	0.000	0.000	0.000	0.000
27	M	58	SER	0	0.017	0.006	32.126	0.002	0.002	0.000	0.000	0.000	0.000
28	M	59	ARG	1	0.833	0.909	31.678	-0.010	-0.010	0.000	0.000	0.000	0.000
29	M	60	THR	0	-0.035	-0.023	34.662	0.002	0.002	0.000	0.000	0.000	0.000
30	M	61	SER	0	-0.042	-0.045	37.442	0.000	0.000	0.000	0.000	0.000	0.000
31	M	62	GLY	0	0.035	0.034	37.974	0.000	0.000	0.000	0.000	0.000	0.000
32	M	63	LYS	1	0.808	0.898	38.082	0.012	0.012	0.000	0.000	0.000	0.000
33	M	64	HIS	0	0.013	0.009	33.798	0.000	0.000	0.000	0.000	0.000	0.000
34	M	65	VAL	0	-0.077	-0.036	31.529	0.002	0.002	0.000	0.000	0.000	0.000
35	M	66	GLN	0	0.033	0.008	33.805	-0.005	-0.005	0.000	0.000	0.000	0.000
36	M	67	VAL	0	-0.056	-0.047	32.272	0.004	0.004	0.000	0.000	0.000	0.000
37	M	68	LEU	0	0.061	0.047	35.700	-0.002	-0.002	0.000	0.000	0.000	0.000
38	M	69	ALA	0	0.094	0.043	38.810	0.001	0.001	0.000	0.000	0.000	0.000
39	M	70	ASN	0	-0.004	0.001	40.603	0.000	0.000	0.000	0.000	0.000	0.000
40	M	71	LYS	1	0.940	0.971	37.457	0.021	0.021	0.000	0.000	0.000	0.000
41	M	72	ARG	1	0.766	0.886	36.824	0.006	0.006	0.000	0.000	0.000	0.000
42	M	73	ILE	0	0.035	0.019	32.574	0.000	0.000	0.000	0.000	0.000	0.000
43	M	74	ASN	0	-0.050	-0.022	36.592	0.003	0.003	0.000	0.000	0.000	0.000
44	M	75	ALA	0	0.042	0.019	35.556	-0.002	-0.002	0.000	0.000	0.000	0.000
45	M	76	MET	0	-0.016	-0.010	37.290	0.001	0.001	0.000	0.000	0.000	0.000
46	M	77	ALA	0	0.045	0.058	37.917	0.000	0.000	0.000	0.000	0.000	0.000
47	M	78	GLU	-1	-0.721	-0.864	39.171	-0.017	-0.017	0.000	0.000	0.000	0.000
48	M	79	ASP	-1	-0.825	-0.894	37.170	-0.035	-0.035	0.000	0.000	0.000	0.000
49	M	80	GLY	0	0.024	0.013	37.579	0.000	0.000	0.000	0.000	0.000	0.000
50	M	81	ASP	-1	-0.841	-0.903	38.810	-0.028	-0.028	0.000	0.000	0.000	0.000
51	M	82	PRO	0	0.028	0.013	37.627	-0.002	-0.002	0.000	0.000	0.000	0.000
52	M	83	PHE	0	0.051	0.015	36.446	-0.002	-0.002	0.000	0.000	0.000	0.000
53	M	84	ALA	0	-0.034	-0.019	34.995	0.001	0.001	0.000	0.000	0.000	0.000
54	M	85	LYS	1	0.813	0.910	32.629	0.038	0.038	0.000	0.000	0.000	0.000
55	M	86	LEU	0	-0.049	-0.024	28.519	0.001	0.001	0.000	0.000	0.000	0.000
56	M	87	ILE	0	0.049	0.019	25.236	-0.004	-0.004	0.000	0.000	0.000	0.000
57	M	88	VAL	0	-0.052	-0.033	21.373	0.006	0.006	0.000	0.000	0.000	0.000
58	M	89	GLU	-1	-0.772	-0.862	19.697	-0.088	-0.088	0.000	0.000	0.000	0.000
59	M	90	THR	0	0.014	0.004	14.945	0.006	0.006	0.000	0.000	0.000	0.000
60	M	91	ASP	-1	-0.800	-0.861	16.864	-0.061	-0.061	0.000	0.000	0.000	0.000
61	M	92	THR	0	0.010	-0.001	11.622	-0.025	-0.025	0.000	0.000	0.000	0.000
62	M	93	PHE	0	0.050	0.024	6.267	-0.014	-0.014	0.000	0.000	0.000	0.000
63	M	94	GLY	0	0.031	0.011	10.489	0.025	0.025	0.000	0.000	0.000	0.000
64	M	95	SER	0	-0.005	-0.009	12.265	0.011	0.011	0.000	0.000	0.000	0.000
65	M	96	ARG	1	0.833	0.920	14.222	-0.032	-0.032	0.000	0.000	0.000	0.000
66	M	97	VAL	0	0.023	0.008	16.509	-0.016	-0.016	0.000	0.000	0.000	0.000
67	M	98	ARG	1	0.751	0.863	19.246	0.063	0.063	0.000	0.000	0.000	0.000
68	M	99	VAL	0	0.021	0.000	22.597	-0.005	-0.005	0.000	0.000	0.000	0.000
69	M	100	ARG	1	0.866	0.926	25.740	0.057	0.057	0.000	0.000	0.000	0.000
70	M	101	GLY	0	0.029	0.026	28.590	-0.002	-0.002	0.000	0.000	0.000	0.000
71	M	102	ALA	0	-0.026	-0.024	31.620	-0.001	-0.001	0.000	0.000	0.000	0.000
72	M	103	GLU	-1	-0.860	-0.929	32.483	-0.042	-0.042	0.000	0.000	0.000	0.000
73	M	104	THR	0	-0.046	-0.024	35.054	0.001	0.001	0.000	0.000	0.000	0.000
74	M	105	GLY	0	0.055	0.045	32.007	0.001	0.001	0.000	0.000	0.000	0.000
75	M	106	LEU	0	-0.066	-0.022	31.739	0.000	0.000	0.000	0.000	0.000	0.000
76	M	107	TYR	0	0.051	0.015	24.943	0.000	0.000	0.000	0.000	0.000	0.000
77	M	108	ILE	0	0.017	-0.001	28.346	0.005	0.005	0.000	0.000	0.000	0.000
78	M	109	CYS	0	-0.055	-0.017	27.688	-0.001	-0.001	0.000	0.000	0.000	0.000
79	M	110	MET	0	-0.019	0.012	28.689	0.003	0.003	0.000	0.000	0.000	0.000
80	M	111	ASN	0	0.044	0.022	30.105	0.004	0.004	0.000	0.000	0.000	0.000
81	M	112	LYS	1	1.088	1.033	32.380	-0.022	-0.022	0.000	0.000	0.000	0.000
82	M	113	LYS	1	0.910	0.954	33.326	-0.023	-0.023	0.000	0.000	0.000	0.000
83	M	114	GLY	0	0.047	0.039	32.424	0.001	0.001	0.000	0.000	0.000	0.000
84	M	115	LYS	1	0.893	0.952	33.509	-0.007	-0.007	0.000	0.000	0.000	0.000
85	M	116	LEU	0	0.069	0.039	30.622	0.000	0.000	0.000	0.000	0.000	0.000
86	M	117	ILE	0	-0.054	-0.032	32.887	0.000	0.000	0.000	0.000	0.000	0.000
87	M	118	ALA	0	0.072	0.040	32.497	-0.001	-0.001	0.000	0.000	0.000	0.000
88	M	119	LYS	1	0.825	0.918	28.837	0.011	0.011	0.000	0.000	0.000	0.000
89	M	120	SER	0	0.082	0.044	31.683	-0.002	-0.002	0.000	0.000	0.000	0.000
90	M	121	ASN	0	0.039	0.017	28.382	-0.007	-0.007	0.000	0.000	0.000	0.000
91	M	122	GLY	0	0.067	0.004	26.701	0.006	0.006	0.000	0.000	0.000	0.000
92	M	123	LYS	1	0.928	0.977	19.886	0.056	0.056	0.000	0.000	0.000	0.000
93	M	124	GLY	0	0.040	0.020	23.033	0.001	0.001	0.000	0.000	0.000	0.000
94	M	125	LYS	1	1.000	0.984	19.023	-0.060	-0.060	0.000	0.000	0.000	0.000
95	M	126	ASP	-1	-0.812	-0.899	23.047	0.005	0.005	0.000	0.000	0.000	0.000
96	M	127	CYS	0	-0.077	-0.027	24.731	0.000	0.000	0.000	0.000	0.000	0.000
97	M	128	VAL	0	0.005	0.019	18.857	-0.006	-0.006	0.000	0.000	0.000	0.000
98	M	129	PHE	0	-0.041	-0.027	21.303	0.012	0.012	0.000	0.000	0.000	0.000
99	M	130	THR	0	0.041	0.035	16.985	-0.012	-0.012	0.000	0.000	0.000	0.000
100	M	131	GLU	-1	-0.863	-0.921	18.864	-0.032	-0.032	0.000	0.000	0.000	0.000
101	M	132	ILE	0	0.007	-0.004	18.575	0.000	0.000	0.000	0.000	0.000	0.000
102	M	133	VAL	0	0.011	0.006	19.914	-0.003	-0.003	0.000	0.000	0.000	0.000
103	M	134	LEU	0	-0.037	-0.018	21.315	0.008	0.008	0.000	0.000	0.000	0.000
104	M	135	GLU	-1	-0.723	-0.858	23.982	0.037	0.037	0.000	0.000	0.000	0.000
105	M	136	ASN	0	-0.087	-0.048	25.035	-0.010	-0.010	0.000	0.000	0.000	0.000
106	M	137	ASN	0	-0.004	-0.014	25.319	-0.009	-0.009	0.000	0.000	0.000	0.000
107	M	138	TYR	0	-0.022	-0.010	26.113	-0.006	-0.006	0.000	0.000	0.000	0.000
108	M	139	THR	0	-0.019	-0.004	23.411	0.000	0.000	0.000	0.000	0.000	0.000
109	M	140	ALA	0	0.019	0.005	24.108	0.002	0.002	0.000	0.000	0.000	0.000
110	M	141	LEU	0	0.020	0.005	22.658	-0.003	-0.003	0.000	0.000	0.000	0.000
111	M	142	GLN	0	0.034	0.039	20.857	0.000	0.000	0.000	0.000	0.000	0.000
112	M	143	ASN	0	-0.036	-0.046	22.546	0.000	0.000	0.000	0.000	0.000	0.000
113	M	144	ALA	0	0.071	0.029	19.692	0.008	0.008	0.000	0.000	0.000	0.000
114	M	145	LYS	1	0.820	0.917	21.483	-0.012	-0.012	0.000	0.000	0.000	0.000
115	M	146	TYR	0	-0.022	-0.034	24.173	0.006	0.006	0.000	0.000	0.000	0.000
116	M	147	GLU	-1	-0.725	-0.841	19.587	0.060	0.060	0.000	0.000	0.000	0.000
117	M	148	GLY	0	0.043	0.035	23.795	0.005	0.005	0.000	0.000	0.000	0.000
118	M	149	TRP	0	-0.104	-0.054	26.939	-0.006	-0.006	0.000	0.000	0.000	0.000
119	M	150	TYR	0	0.020	-0.004	24.112	-0.002	-0.002	0.000	0.000	0.000	0.000
120	M	151	MET	0	-0.033	-0.007	26.794	-0.002	-0.002	0.000	0.000	0.000	0.000
121	M	152	ALA	0	0.027	0.008	29.569	0.001	0.001	0.000	0.000	0.000	0.000
122	M	153	PHE	0	-0.033	-0.020	32.072	-0.001	-0.001	0.000	0.000	0.000	0.000
123	M	154	THR	0	-0.002	0.000	36.255	0.000	0.000	0.000	0.000	0.000	0.000
124	M	155	ARG	1	0.929	0.962	39.578	-0.001	-0.001	0.000	0.000	0.000	0.000
125	M	156	LYS	1	0.986	0.987	41.695	-0.005	-0.005	0.000	0.000	0.000	0.000
126	M	157	GLY	0	0.099	0.052	39.336	-0.001	-0.001	0.000	0.000	0.000	0.000
127	M	158	ARG	1	0.956	0.984	39.375	-0.003	-0.003	0.000	0.000	0.000	0.000
128	M	159	PRO	0	0.033	0.017	36.234	0.002	0.002	0.000	0.000	0.000	0.000
129	M	160	ARG	1	0.804	0.886	35.663	-0.016	-0.016	0.000	0.000	0.000	0.000
130	M	161	LYS	1	0.884	0.934	35.139	-0.012	-0.012	0.000	0.000	0.000	0.000
131	M	162	GLY	0	0.108	0.048	31.971	0.002	0.002	0.000	0.000	0.000	0.000
132	M	163	SER	0	-0.007	-0.003	32.569	0.003	0.003	0.000	0.000	0.000	0.000
133	M	164	LYS	1	0.882	0.940	34.576	-0.031	-0.031	0.000	0.000	0.000	0.000
134	M	165	THR	0	-0.050	-0.022	31.192	-0.002	-0.002	0.000	0.000	0.000	0.000
135	M	166	ARG	1	0.970	0.966	30.612	-0.036	-0.036	0.000	0.000	0.000	0.000
136	M	167	GLN	0	0.048	0.018	23.471	-0.005	-0.005	0.000	0.000	0.000	0.000
137	M	168	HIS	0	0.111	0.061	28.586	-0.006	-0.006	0.000	0.000	0.000	0.000
138	M	169	GLN	0	-0.027	0.002	31.393	-0.001	-0.001	0.000	0.000	0.000	0.000
139	M	170	ARG	1	1.049	1.012	32.579	-0.014	-0.014	0.000	0.000	0.000	0.000
140	M	171	GLU	-1	-0.797	-0.872	33.814	0.013	0.013	0.000	0.000	0.000	0.000
141	M	172	VAL	0	-0.043	-0.020	28.699	-0.003	-0.003	0.000	0.000	0.000	0.000
142	M	173	HIS	0	0.001	0.025	28.973	-0.005	-0.005	0.000	0.000	0.000	0.000
143	M	174	PHE	0	-0.048	-0.030	28.141	-0.002	-0.002	0.000	0.000	0.000	0.000
144	M	175	MET	0	0.028	0.020	28.609	0.002	0.002	0.000	0.000	0.000	0.000
145	M	176	LYS	1	0.806	0.889	21.423	0.040	0.040	0.000	0.000	0.000	0.000
146	M	177	ARG	1	0.859	0.919	27.685	0.028	0.028	0.000	0.000	0.000	0.000
147	M	178	LEU	0	0.076	0.031	27.962	-0.001	-0.001	0.000	0.000	0.000	0.000
148	M	179	PRO	0	-0.003	-0.001	29.598	0.005	0.005	0.000	0.000	0.000	0.000
149	M	180	ARG	1	0.942	0.983	32.839	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(M:32:PHE)