FMO DATABASE

FMODB ID: 3Q5LL

Calculation Name: 5B3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B3D

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1J7

Base Structure: X-ray

Registration Date: 2023-06-20

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734469.391747
FMO2-HF: Nuclear repulsion	688227.556305
FMO2-HF: Total energy	-46241.835442
FMO2-MP2: Total energy	-46377.406619

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-8.314	-3.531	0.578	-2.097	-3.265	0

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.019

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	4	LEU	0	-0.007	-0.007	3.390	-3.052	-0.546	0.018	-1.103	-1.421	0.005
4	A	5	SER	0	0.013	-0.005	2.611	-0.446	0.326	0.532	-0.360	-0.944	-0.002
5	A	6	GLU	-1	-0.903	-0.945	2.992	-5.387	-3.882	0.028	-0.634	-0.900	-0.003
6	A	7	ILE	0	-0.033	-0.019	5.646	0.684	0.684	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.005	-0.010	7.860	0.187	0.187	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.860	-0.923	7.894	-0.401	-0.401	0.000	0.000	0.000	0.000
9	A	10	GLN	0	-0.062	-0.039	9.407	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.014	-0.008	11.855	0.091	0.091	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.003	0.005	12.779	0.060	0.060	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.007	0.005	13.887	0.044	0.044	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.017	0.011	16.152	0.028	0.028	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.022	-0.019	16.823	0.026	0.026	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.029	-0.013	18.071	0.028	0.028	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.899	-0.947	20.174	-0.129	-0.129	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.032	-0.032	21.487	0.013	0.013	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.862	0.942	23.620	0.073	0.073	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.001	0.009	25.042	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.025	-0.015	26.299	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.007	-0.006	27.346	0.004	0.004	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.811	-0.893	29.491	-0.050	-0.050	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.034	-0.021	31.327	0.005	0.005	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.950	-0.980	32.464	-0.042	-0.042	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.043	0.021	33.945	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.041	-0.005	34.913	0.002	0.002	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.071	-0.047	36.860	0.004	0.004	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.013	-0.003	36.984	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.074	-0.034	39.190	0.002	0.002	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.003	-0.015	41.736	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.009	0.021	45.409	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.071	-0.039	41.470	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.028	0.011	44.424	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.032	-0.015	41.729	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.031	0.030	42.024	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.023	0.010	40.636	0.000	0.000	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.005	-0.035	42.429	0.002	0.002	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.069	0.047	42.097	0.001	0.001	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.033	0.042	44.274	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.924	0.958	44.247	0.027	0.027	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.018	0.021	46.522	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.046	-0.031	46.865	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.887	-0.964	49.183	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.926	-0.953	51.915	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.926	0.966	51.355	0.019	0.019	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.037	-0.029	53.175	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.003	0.005	55.423	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.010	-0.003	57.067	0.001	0.001	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.038	-0.027	56.050	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.022	0.025	59.706	0.001	0.001	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.017	-0.003	61.445	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.033	-0.019	62.387	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.913	-0.958	63.132	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.016	0.009	65.124	0.000	0.000	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.013	-0.024	67.144	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.802	-0.864	67.863	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.032	-0.024	67.203	0.001	0.001	0.000	0.000	0.000	0.000
58	A	59	GLN	0	-0.011	-0.009	71.264	0.000	0.000	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.848	0.912	71.783	0.009	0.009	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.870	0.929	70.120	0.009	0.009	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.056	-0.026	75.339	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.945	-0.960	77.698	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.063	-0.031	77.349	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.034	-0.020	80.945	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.006	0.026	82.836	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.024	-0.021	84.613	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.975	0.993	85.134	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	SER	0	0.015	-0.020	85.296	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.070	0.023	86.360	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.024	-0.033	84.020	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.802	-0.944	81.494	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.843	-0.898	77.805	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.001	-0.010	77.819	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.016	-0.018	76.784	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.931	-0.954	75.525	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.896	0.939	73.510	0.008	0.008	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.026	-0.018	70.869	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	GLN	0	0.004	-0.007	70.538	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.035	0.017	69.454	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.030	-0.011	67.747	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.047	-0.034	66.726	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.858	-0.909	66.202	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.928	0.959	63.253	0.011	0.011	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.030	-0.015	61.914	0.000	0.000	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.012	0.001	61.218	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.037	0.018	57.020	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.017	-0.015	57.168	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.891	0.958	56.751	0.010	0.010	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.837	-0.920	56.492	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.025	-0.006	51.629	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.027	-0.024	52.094	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.004	0.002	51.793	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	HIS	0	0.028	0.023	47.483	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	ASN	0	0.010	-0.020	47.690	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.006	0.011	46.839	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	TRP	0	0.039	0.015	46.619	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.072	-0.033	43.458	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.046	-0.024	42.315	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.888	-0.946	41.876	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.036	0.025	40.383	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	102	GLN	0	-0.084	-0.055	37.713	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.010	0.010	37.032	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.930	-0.952	36.598	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.936	0.956	33.483	0.033	0.033	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.006	0.009	32.468	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.029	0.000	32.255	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.039	-0.018	30.908	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.010	-0.007	28.348	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.014	-0.004	27.402	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.931	-0.978	27.352	-0.022	-0.022	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.093	-0.035	22.727	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.021	-0.009	22.710	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.917	0.992	23.719	0.016	0.016	0.000	0.000	0.000	0.000
114	A	115	PRO	0	-0.033	-0.020	20.972	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)