FMO DATABASE

FMODB ID: VQY21

Calculation Name: 2FM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FM8

Chain ID: A

ChEMBL ID:

UniProt ID: P0CL52

Base Structure: X-ray

Registration Date: 2023-09-23

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1134419.031195
FMO2-HF: Nuclear repulsion	1081603.692318
FMO2-HF: Total energy	-52815.338877
FMO2-MP2: Total energy	-52965.503492

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-15.853	-8.031	3.247	-3.569	-7.498	0.003

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / 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	A	3	HIS	0	-0.033	-0.012	3.354	-4.776	-1.311	0.018	-1.803	-1.680	0.007
4	A	4	LEU	0	-0.035	-0.007	2.871	-1.067	0.051	0.173	-0.318	-0.972	0.000
5	A	5	ASP	-1	-0.816	-0.911	4.863	-0.190	-0.141	-0.001	-0.008	-0.039	0.000
6	A	6	ILE	0	0.012	-0.006	8.131	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.040	0.024	9.314	-0.071	-0.071	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.881	-0.945	11.396	0.495	0.495	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.040	-0.008	6.786	-0.061	-0.061	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.016	-0.016	11.003	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.919	0.964	13.594	-0.456	-0.456	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.012	0.013	13.279	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.008	-0.002	12.865	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.000	-0.010	14.820	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.963	-0.968	18.072	0.292	0.292	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.030	-0.017	15.709	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.064	-0.031	17.913	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.038	0.000	20.327	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.072	-0.040	21.668	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.836	-0.906	23.498	0.171	0.171	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.004	-0.012	23.433	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.089	-0.054	24.469	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.021	-0.015	25.073	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.056	-0.007	19.877	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.014	0.010	22.915	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.035	-0.022	21.616	0.020	0.020	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.030	-0.013	16.044	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.865	-0.955	15.187	0.275	0.275	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.053	-0.021	16.199	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.024	-0.005	11.649	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.003	0.003	14.152	-0.067	-0.067	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.083	-0.047	15.078	0.033	0.033	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.031	0.031	13.503	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.016	-0.008	16.985	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.017	-0.004	17.377	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.839	-0.908	21.184	0.138	0.138	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.040	-0.029	22.475	0.008	0.008	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.033	-0.015	26.312	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.030	-0.017	29.219	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.014	0.002	25.286	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.002	0.004	24.485	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.027	-0.011	22.971	0.008	0.008	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.031	0.001	17.168	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.065	-0.016	17.343	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.041	0.009	11.611	0.039	0.039	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.017	-0.024	12.095	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.036	0.031	6.360	0.167	0.167	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.898	0.937	8.312	0.035	0.035	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.900	-0.952	7.995	-0.936	-0.936	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.894	-0.935	2.800	-5.329	-4.881	0.094	-0.126	-0.416	-0.001
51	A	51	ASP	-1	-0.959	-0.956	3.475	-1.197	-0.013	0.036	-0.506	-0.713	-0.004
52	A	52	VAL	0	0.000	-0.014	4.884	-0.303	-0.179	0.000	-0.022	-0.101	0.000
53	A	53	TRP	0	-0.040	-0.027	7.206	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.026	0.020	10.815	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	55	TRP	0	-0.053	-0.043	13.616	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.079	0.048	17.022	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.020	0.002	20.742	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.002	-0.019	23.839	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.040	0.032	26.415	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.014	0.020	29.695	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.890	-0.936	32.372	0.037	0.037	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.043	-0.034	29.060	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.011	0.000	28.872	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.032	0.019	31.597	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.036	-0.008	33.448	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.038	0.010	28.811	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.082	-0.047	32.504	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.067	-0.034	35.640	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.963	0.990	32.646	-0.050	-0.050	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.026	0.027	31.042	0.005	0.005	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.029	-0.015	30.653	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.828	-0.880	30.994	0.066	0.066	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.021	0.025	26.425	0.007	0.007	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.004	-0.018	26.201	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	MET	0	-0.045	-0.015	26.763	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	THR	0	0.031	0.003	24.434	0.004	0.004	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.060	-0.024	21.432	0.011	0.011	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.098	-0.063	22.187	0.006	0.006	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.966	-0.956	23.193	0.110	0.110	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.022	0.004	19.956	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	CYS	0	-0.057	-0.036	15.734	0.020	0.020	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.002	-0.012	15.195	0.027	0.027	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.042	0.028	10.956	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.010	0.017	10.185	0.152	0.152	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.956	0.961	5.146	-1.211	-1.211	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.045	-0.022	11.286	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.010	0.007	14.012	-0.039	-0.039	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.007	-0.005	15.693	-0.029	-0.029	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.009	0.024	16.096	0.030	0.030	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.034	-0.024	15.059	-0.039	-0.039	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.031	0.006	18.579	0.012	0.012	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.074	-0.044	21.229	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.884	-0.951	22.038	0.025	0.025	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.067	-0.032	21.217	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.059	-0.036	24.515	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.015	0.024	27.719	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.871	-0.931	26.730	0.071	0.071	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.053	0.017	24.973	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.075	-0.044	19.724	0.009	0.009	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.032	0.029	19.283	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.939	0.955	15.538	-0.066	-0.066	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.031	0.012	13.096	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.017	0.012	8.258	0.036	0.036	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.011	-0.003	6.843	-0.074	-0.074	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.004	0.005	6.672	0.658	0.658	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.051	-0.013	2.223	-0.936	-0.658	2.198	-0.515	-1.962	0.003
107	A	107	ASP	-1	-0.892	-0.934	3.639	-0.584	-0.411	-0.001	-0.005	-0.167	0.000
108	A	108	PHE	0	-0.129	-0.077	6.297	-0.105	-0.105	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.020	-0.017	2.524	-0.810	0.093	0.731	-0.263	-1.372	-0.002
110	A	110	SER	0	-0.057	-0.030	4.969	0.098	0.178	-0.001	-0.003	-0.076	0.000
111	A	111	ASP	-1	-0.809	-0.895	6.338	0.557	0.557	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.076	0.028	9.632	0.019	0.019	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.921	-0.954	12.163	0.269	0.269	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.917	0.961	9.112	-0.315	-0.315	0.000	0.000	0.000	0.000
115	A	115	PHE	0	0.025	0.003	8.459	0.014	0.014	0.000	0.000	0.000	0.000
116	A	116	SER	0	0.042	0.021	10.380	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.051	-0.007	13.069	-0.050	-0.050	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.020	-0.010	10.755	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.007	-0.010	12.848	-0.036	-0.036	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.027	-0.025	14.997	-0.058	-0.058	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.014	0.011	16.613	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.037	-0.026	15.595	-0.025	-0.025	0.000	0.000	0.000	0.000
123	A	123	TYR	0	0.021	0.013	17.577	-0.028	-0.028	0.000	0.000	0.000	0.000
124	A	124	ASN	0	0.027	0.015	20.598	-0.025	-0.025	0.000	0.000	0.000	0.000
125	A	125	TYR	0	-0.025	-0.020	18.162	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.015	0.002	21.423	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.923	-0.966	22.970	0.118	0.118	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.025	-0.011	25.229	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.018	-0.011	22.390	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.032	-0.020	26.401	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.921	0.958	28.204	-0.110	-0.110	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.014	-0.034	29.482	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.103	-0.049	27.883	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	134	MET	0	-0.028	-0.009	31.779	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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