FMO DATABASE

FMODB ID: 2J27R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1513321.401621
FMO2-HF: Nuclear repulsion	1452620.253468
FMO2-HF: Total energy	-60701.148154
FMO2-MP2: Total energy	-60877.672206

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.
-6.326	-2.21	0.766	-1.648	-3.234	-0.002

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 : 0.072 / q_NPA : 0.023

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	0.003	-0.005	3.826	-2.622	-1.146	-0.009	-0.610	-0.857	0.003
4	M	35	HIS	0	0.081	0.042	2.584	-2.861	-1.049	0.728	-0.773	-1.767	-0.005
5	M	36	VAL	0	0.036	0.016	3.043	-0.634	0.194	0.047	-0.265	-0.610	0.000
6	M	37	ARG	1	0.882	0.942	5.405	-0.959	-0.959	0.000	0.000	0.000	0.000
7	M	38	GLU	-1	-0.847	-0.912	7.683	0.750	0.750	0.000	0.000	0.000	0.000
8	M	39	GLN	0	0.006	-0.012	6.603	-0.055	-0.055	0.000	0.000	0.000	0.000
9	M	40	SER	0	-0.071	-0.038	8.679	-0.011	-0.011	0.000	0.000	0.000	0.000
10	M	41	LEU	0	-0.075	-0.020	10.952	0.012	0.012	0.000	0.000	0.000	0.000
11	M	42	VAL	0	-0.069	-0.036	13.576	0.003	0.003	0.000	0.000	0.000	0.000
12	M	43	THR	0	-0.083	-0.071	13.974	-0.014	-0.014	0.000	0.000	0.000	0.000
13	M	44	ASP	-1	-0.779	-0.871	10.640	-0.310	-0.310	0.000	0.000	0.000	0.000
14	M	45	GLN	0	-0.106	-0.077	13.505	0.004	0.004	0.000	0.000	0.000	0.000
15	M	46	LEU	0	0.013	0.014	11.884	0.012	0.012	0.000	0.000	0.000	0.000
16	M	47	SER	0	-0.006	0.013	10.722	-0.060	-0.060	0.000	0.000	0.000	0.000
17	M	48	ARG	1	0.952	0.978	13.227	0.262	0.262	0.000	0.000	0.000	0.000
18	M	49	ARG	1	0.945	0.975	14.878	0.122	0.122	0.000	0.000	0.000	0.000
19	M	50	LEU	0	-0.028	-0.005	15.412	0.011	0.011	0.000	0.000	0.000	0.000
20	M	51	ILE	0	0.054	0.013	17.821	0.014	0.014	0.000	0.000	0.000	0.000
21	M	52	ARG	1	0.914	0.966	18.012	0.125	0.125	0.000	0.000	0.000	0.000
22	M	53	THR	0	0.023	0.000	22.876	0.007	0.007	0.000	0.000	0.000	0.000
23	M	54	TYR	0	-0.009	-0.018	22.782	0.001	0.001	0.000	0.000	0.000	0.000
24	M	55	GLN	0	0.014	0.024	28.391	0.006	0.006	0.000	0.000	0.000	0.000
25	M	56	LEU	0	0.012	0.009	26.458	-0.001	-0.001	0.000	0.000	0.000	0.000
26	M	57	TYR	0	0.020	0.020	30.198	0.003	0.003	0.000	0.000	0.000	0.000
27	M	58	SER	0	0.028	0.005	31.785	0.002	0.002	0.000	0.000	0.000	0.000
28	M	59	ARG	1	0.904	0.951	32.700	0.001	0.001	0.000	0.000	0.000	0.000
29	M	60	THR	0	-0.051	0.013	34.805	0.002	0.002	0.000	0.000	0.000	0.000
30	M	61	SER	0	-0.049	-0.041	37.269	0.000	0.000	0.000	0.000	0.000	0.000
31	M	62	GLY	0	0.001	0.025	37.653	0.000	0.000	0.000	0.000	0.000	0.000
32	M	63	LYS	1	0.836	0.919	38.082	0.017	0.017	0.000	0.000	0.000	0.000
33	M	64	HIS	0	0.028	0.006	33.547	-0.002	-0.002	0.000	0.000	0.000	0.000
34	M	65	VAL	0	-0.073	-0.032	31.239	0.003	0.003	0.000	0.000	0.000	0.000
35	M	66	GLN	0	0.027	0.013	33.871	-0.005	-0.005	0.000	0.000	0.000	0.000
36	M	67	VAL	0	-0.061	-0.041	32.435	0.004	0.004	0.000	0.000	0.000	0.000
37	M	68	LEU	0	0.030	0.015	35.725	-0.002	-0.002	0.000	0.000	0.000	0.000
38	M	69	ALA	0	0.117	0.054	38.886	0.000	0.000	0.000	0.000	0.000	0.000
39	M	70	ASN	0	-0.009	0.005	40.929	0.000	0.000	0.000	0.000	0.000	0.000
40	M	71	LYS	1	0.941	0.960	36.989	0.023	0.023	0.000	0.000	0.000	0.000
41	M	72	ARG	1	0.810	0.945	37.107	0.009	0.009	0.000	0.000	0.000	0.000
42	M	73	ILE	0	0.053	0.013	32.973	-0.001	-0.001	0.000	0.000	0.000	0.000
43	M	74	ASN	0	-0.038	-0.035	36.802	0.002	0.002	0.000	0.000	0.000	0.000
44	M	75	ALA	0	0.053	0.025	35.465	-0.002	-0.002	0.000	0.000	0.000	0.000
45	M	76	MET	0	-0.036	-0.037	37.152	0.001	0.001	0.000	0.000	0.000	0.000
46	M	77	ALA	0	0.050	0.057	37.569	0.000	0.000	0.000	0.000	0.000	0.000
47	M	78	GLU	-1	-0.774	-0.884	38.913	-0.023	-0.023	0.000	0.000	0.000	0.000
48	M	79	ASP	-1	-0.811	-0.919	36.671	-0.044	-0.044	0.000	0.000	0.000	0.000
49	M	80	GLY	0	-0.010	-0.029	36.961	0.000	0.000	0.000	0.000	0.000	0.000
50	M	81	ASP	-1	-0.863	-0.912	38.164	-0.032	-0.032	0.000	0.000	0.000	0.000
51	M	82	PRO	0	0.046	0.013	37.206	-0.002	-0.002	0.000	0.000	0.000	0.000
52	M	83	PHE	0	0.025	0.010	36.241	-0.002	-0.002	0.000	0.000	0.000	0.000
53	M	84	ALA	0	-0.036	-0.032	34.617	0.002	0.002	0.000	0.000	0.000	0.000
54	M	85	LYS	1	0.827	0.935	32.283	0.045	0.045	0.000	0.000	0.000	0.000
55	M	86	LEU	0	-0.034	-0.022	28.153	0.002	0.002	0.000	0.000	0.000	0.000
56	M	87	ILE	0	0.018	0.001	25.011	-0.005	-0.005	0.000	0.000	0.000	0.000
57	M	88	VAL	0	-0.047	-0.034	21.018	0.006	0.006	0.000	0.000	0.000	0.000
58	M	89	GLU	-1	-0.912	-0.949	19.570	-0.115	-0.115	0.000	0.000	0.000	0.000
59	M	90	THR	0	-0.037	-0.024	15.119	0.006	0.006	0.000	0.000	0.000	0.000
60	M	91	ASP	-1	-0.856	-0.907	16.546	-0.066	-0.066	0.000	0.000	0.000	0.000
61	M	92	THR	0	0.064	0.021	11.449	-0.028	-0.028	0.000	0.000	0.000	0.000
62	M	93	PHE	0	0.027	0.017	6.412	-0.005	-0.005	0.000	0.000	0.000	0.000
63	M	94	GLY	0	0.032	0.007	10.395	0.039	0.039	0.000	0.000	0.000	0.000
64	M	95	SER	0	-0.008	-0.005	12.189	0.012	0.012	0.000	0.000	0.000	0.000
65	M	96	ARG	1	0.965	1.014	14.137	-0.004	-0.004	0.000	0.000	0.000	0.000
66	M	97	VAL	0	0.020	0.011	16.455	-0.020	-0.020	0.000	0.000	0.000	0.000
67	M	98	ARG	1	0.775	0.861	19.191	0.065	0.065	0.000	0.000	0.000	0.000
68	M	99	VAL	0	0.020	0.006	22.579	-0.007	-0.007	0.000	0.000	0.000	0.000
69	M	100	ARG	1	0.909	0.950	25.606	0.066	0.066	0.000	0.000	0.000	0.000
70	M	101	GLY	0	0.027	0.021	28.260	-0.003	-0.003	0.000	0.000	0.000	0.000
71	M	102	ALA	0	-0.028	-0.027	31.054	0.000	0.000	0.000	0.000	0.000	0.000
72	M	103	GLU	-1	-0.866	-0.919	32.046	-0.045	-0.045	0.000	0.000	0.000	0.000
73	M	104	THR	0	-0.027	-0.011	35.108	0.000	0.000	0.000	0.000	0.000	0.000
74	M	105	GLY	0	0.046	0.030	32.024	0.001	0.001	0.000	0.000	0.000	0.000
75	M	106	LEU	0	-0.083	-0.043	31.796	0.001	0.001	0.000	0.000	0.000	0.000
76	M	107	TYR	0	0.058	0.016	25.106	0.000	0.000	0.000	0.000	0.000	0.000
77	M	108	ILE	0	-0.002	0.005	28.453	0.006	0.006	0.000	0.000	0.000	0.000
78	M	109	CYS	0	-0.073	-0.058	27.743	-0.001	-0.001	0.000	0.000	0.000	0.000
79	M	110	MET	0	-0.008	0.028	28.726	0.003	0.003	0.000	0.000	0.000	0.000
80	M	111	ASN	0	0.036	0.019	29.984	0.004	0.004	0.000	0.000	0.000	0.000
81	M	112	LYS	1	1.073	1.018	32.267	-0.024	-0.024	0.000	0.000	0.000	0.000
82	M	113	LYS	1	0.886	0.953	33.255	-0.021	-0.021	0.000	0.000	0.000	0.000
83	M	114	GLY	0	0.051	0.029	32.246	0.000	0.000	0.000	0.000	0.000	0.000
84	M	115	LYS	1	0.886	0.945	33.328	-0.006	-0.006	0.000	0.000	0.000	0.000
85	M	116	LEU	0	0.055	0.032	30.610	0.000	0.000	0.000	0.000	0.000	0.000
86	M	117	ILE	0	-0.077	-0.060	32.700	0.000	0.000	0.000	0.000	0.000	0.000
87	M	118	ALA	0	0.084	0.045	32.480	-0.001	-0.001	0.000	0.000	0.000	0.000
88	M	119	LYS	1	0.830	0.904	29.648	0.007	0.007	0.000	0.000	0.000	0.000
89	M	120	SER	0	0.070	0.034	31.811	-0.002	-0.002	0.000	0.000	0.000	0.000
90	M	121	ASN	0	0.061	0.030	28.740	-0.009	-0.009	0.000	0.000	0.000	0.000
91	M	122	GLY	0	0.037	0.006	27.026	0.006	0.006	0.000	0.000	0.000	0.000
92	M	123	LYS	1	0.996	1.014	20.399	0.037	0.037	0.000	0.000	0.000	0.000
93	M	124	GLY	0	0.021	0.004	23.584	0.001	0.001	0.000	0.000	0.000	0.000
94	M	125	LYS	1	1.024	1.006	19.611	-0.077	-0.077	0.000	0.000	0.000	0.000
95	M	126	ASP	-1	-0.856	-0.920	23.033	0.004	0.004	0.000	0.000	0.000	0.000
96	M	127	CYS	0	-0.033	0.008	25.015	-0.001	-0.001	0.000	0.000	0.000	0.000
97	M	128	VAL	0	-0.007	0.017	18.656	-0.008	-0.008	0.000	0.000	0.000	0.000
98	M	129	PHE	0	-0.041	-0.027	21.189	0.014	0.014	0.000	0.000	0.000	0.000
99	M	130	THR	0	0.037	0.020	16.832	-0.013	-0.013	0.000	0.000	0.000	0.000
100	M	131	GLU	-1	-0.885	-0.931	18.396	-0.059	-0.059	0.000	0.000	0.000	0.000
101	M	132	ILE	0	0.003	0.000	18.303	-0.002	-0.002	0.000	0.000	0.000	0.000
102	M	133	VAL	0	-0.007	-0.009	19.136	-0.005	-0.005	0.000	0.000	0.000	0.000
103	M	134	LEU	0	-0.027	-0.025	21.602	0.006	0.006	0.000	0.000	0.000	0.000
104	M	135	GLU	-1	-0.788	-0.889	23.697	0.033	0.033	0.000	0.000	0.000	0.000
105	M	136	ASN	0	-0.083	-0.032	25.309	-0.006	-0.006	0.000	0.000	0.000	0.000
106	M	137	ASN	0	0.007	-0.013	25.345	-0.006	-0.006	0.000	0.000	0.000	0.000
107	M	138	TYR	0	-0.026	-0.009	26.429	-0.006	-0.006	0.000	0.000	0.000	0.000
108	M	139	THR	0	0.006	0.002	23.597	-0.001	-0.001	0.000	0.000	0.000	0.000
109	M	140	ALA	0	0.007	0.006	23.836	0.004	0.004	0.000	0.000	0.000	0.000
110	M	141	LEU	0	0.003	-0.001	22.583	-0.004	-0.004	0.000	0.000	0.000	0.000
111	M	142	GLN	0	0.022	0.016	20.646	0.000	0.000	0.000	0.000	0.000	0.000
112	M	143	ASN	0	-0.050	-0.035	22.210	0.001	0.001	0.000	0.000	0.000	0.000
113	M	144	ALA	0	0.069	0.032	19.977	0.009	0.009	0.000	0.000	0.000	0.000
114	M	145	LYS	1	0.870	0.953	21.466	-0.022	-0.022	0.000	0.000	0.000	0.000
115	M	146	TYR	0	-0.025	-0.038	24.131	0.009	0.009	0.000	0.000	0.000	0.000
116	M	147	GLU	-1	-0.774	-0.894	19.921	0.067	0.067	0.000	0.000	0.000	0.000
117	M	148	GLY	0	0.022	0.032	23.957	0.001	0.001	0.000	0.000	0.000	0.000
118	M	149	TRP	0	-0.102	-0.046	26.951	-0.007	-0.007	0.000	0.000	0.000	0.000
119	M	150	TYR	0	0.045	0.014	23.994	-0.002	-0.002	0.000	0.000	0.000	0.000
120	M	151	MET	0	-0.060	-0.010	26.801	-0.001	-0.001	0.000	0.000	0.000	0.000
121	M	152	ALA	0	0.027	0.006	29.408	0.000	0.000	0.000	0.000	0.000	0.000
122	M	153	PHE	0	-0.021	-0.017	31.894	-0.001	-0.001	0.000	0.000	0.000	0.000
123	M	154	THR	0	-0.014	-0.002	35.939	0.001	0.001	0.000	0.000	0.000	0.000
124	M	155	ARG	1	1.018	0.973	39.247	0.003	0.003	0.000	0.000	0.000	0.000
125	M	156	LYS	1	0.942	0.958	41.287	-0.002	-0.002	0.000	0.000	0.000	0.000
126	M	157	GLY	0	0.093	0.049	39.030	-0.001	-0.001	0.000	0.000	0.000	0.000
127	M	158	ARG	1	0.911	0.960	39.404	-0.001	-0.001	0.000	0.000	0.000	0.000
128	M	159	PRO	0	0.034	0.019	36.328	0.001	0.001	0.000	0.000	0.000	0.000
129	M	160	ARG	1	0.878	0.962	35.402	-0.012	-0.012	0.000	0.000	0.000	0.000
130	M	161	LYS	1	0.916	0.948	34.807	-0.011	-0.011	0.000	0.000	0.000	0.000
131	M	162	GLY	0	0.130	0.054	31.861	0.001	0.001	0.000	0.000	0.000	0.000
132	M	163	SER	0	-0.005	0.015	32.289	0.002	0.002	0.000	0.000	0.000	0.000
133	M	164	LYS	1	0.894	0.949	34.349	-0.028	-0.028	0.000	0.000	0.000	0.000
134	M	165	THR	0	-0.032	-0.042	31.045	-0.001	-0.001	0.000	0.000	0.000	0.000
135	M	166	ARG	1	0.954	0.972	30.554	-0.033	-0.033	0.000	0.000	0.000	0.000
136	M	167	GLN	0	0.087	0.034	23.716	-0.005	-0.005	0.000	0.000	0.000	0.000
137	M	168	HIS	0	0.086	0.042	28.763	-0.008	-0.008	0.000	0.000	0.000	0.000
138	M	169	GLN	0	-0.007	0.013	31.522	-0.004	-0.004	0.000	0.000	0.000	0.000
139	M	170	ARG	1	1.040	1.002	32.488	-0.006	-0.006	0.000	0.000	0.000	0.000
140	M	171	GLU	-1	-0.906	-0.960	33.790	0.008	0.008	0.000	0.000	0.000	0.000
141	M	172	VAL	0	-0.039	-0.019	28.805	-0.003	-0.003	0.000	0.000	0.000	0.000
142	M	173	HIS	0	-0.017	0.027	28.913	-0.005	-0.005	0.000	0.000	0.000	0.000
143	M	174	PHE	0	-0.028	-0.025	27.821	-0.001	-0.001	0.000	0.000	0.000	0.000
144	M	175	MET	0	0.052	0.037	28.260	0.001	0.001	0.000	0.000	0.000	0.000
145	M	176	LYS	1	0.819	0.901	21.330	0.070	0.070	0.000	0.000	0.000	0.000
146	M	177	ARG	1	0.871	0.923	27.520	0.039	0.039	0.000	0.000	0.000	0.000
147	M	178	LEU	0	0.075	0.033	28.252	-0.001	-0.001	0.000	0.000	0.000	0.000
148	M	179	PRO	0	-0.004	0.008	29.378	0.006	0.006	0.000	0.000	0.000	0.000
149	M	180	ARG	1	0.967	1.012	32.566	0.036	0.036	0.000	0.000	0.000	0.000

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