FMO DATABASE

FMODB ID: 5J55Z

Calculation Name: 2QYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QYB

Chain ID: A

ChEMBL ID:

UniProt ID: Q74D90

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	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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1462067.561858
FMO2-HF: Nuclear repulsion	1403077.006935
FMO2-HF: Total energy	-58990.554923
FMO2-MP2: Total energy	-59164.341907

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
-9.435	-4.795	2.913	-3.183	-4.369	0.015

Interaction energy analysis for fragmet #1(A:7:SER)

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 : -0.006

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	9	ILE	0	0.075	0.033	2.875	-0.853	1.357	0.401	-1.050	-1.560	0.006
4	A	10	MET	0	-0.028	0.007	2.213	-4.733	-3.385	2.500	-1.671	-2.177	0.008
5	A	11	ASN	0	-0.001	-0.027	3.709	-2.562	-1.480	0.012	-0.462	-0.632	0.001
6	A	12	ARG	1	0.934	0.982	5.693	-1.302	-1.302	0.000	0.000	0.000	0.000
7	A	13	THR	0	-0.025	-0.025	7.221	-0.372	-0.372	0.000	0.000	0.000	0.000
8	A	14	LEU	0	-0.052	-0.032	6.506	-0.272	-0.272	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.871	-0.932	9.462	0.684	0.684	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.075	-0.040	11.422	-0.136	-0.136	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.077	-0.068	12.514	-0.050	-0.050	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.043	0.028	13.311	-0.078	-0.078	0.000	0.000	0.000	0.000
13	A	19	ILE	0	0.013	0.021	15.436	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	20	MET	0	-0.076	-0.038	15.355	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.781	-0.868	17.868	0.349	0.349	0.000	0.000	0.000	0.000
16	A	22	ASP	-1	-0.923	-0.951	19.955	0.267	0.267	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.052	-0.026	21.270	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.020	-0.003	22.967	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	25	ASN	0	0.026	0.024	22.968	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	26	LEU	0	-0.064	-0.026	25.408	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.014	0.005	27.689	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.040	-0.028	28.589	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.892	0.952	29.922	-0.158	-0.158	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.959	-0.958	32.154	0.128	0.128	0.000	0.000	0.000	0.000
25	A	31	PHE	0	0.009	0.001	33.173	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	32	LYS	1	0.964	0.991	35.121	-0.085	-0.085	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.007	0.003	31.865	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	34	ASP	-1	-0.821	-0.901	33.815	0.110	0.110	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.054	-0.041	28.326	0.002	0.002	0.000	0.000	0.000	0.000
30	A	36	ALA	0	0.017	0.017	27.305	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	37	VAL	0	-0.008	-0.010	24.350	0.008	0.008	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.060	0.036	20.373	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.785	0.886	21.599	-0.190	-0.190	0.000	0.000	0.000	0.000
34	A	40	LEU	0	0.006	-0.006	16.397	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.015	0.011	19.820	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	42	ASP	-1	-0.832	-0.909	16.578	0.326	0.326	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.808	-0.911	14.823	0.305	0.305	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.742	0.863	17.052	-0.296	-0.296	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.011	-0.002	20.646	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	46	VAL	0	-0.003	0.006	21.790	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.033	-0.014	21.352	0.034	0.034	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.785	0.875	17.983	-0.291	-0.291	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.000	-0.020	20.541	0.024	0.024	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.868	0.941	15.360	-0.448	-0.448	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.030	-0.004	17.555	0.021	0.021	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.006	-0.015	20.028	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	53	SER	0	0.023	0.018	23.265	0.000	0.000	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.074	0.033	25.863	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	55	LYS	1	0.934	0.962	28.264	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.084	0.019	30.720	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	57	ILE	0	0.014	0.030	24.679	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.017	-0.003	28.021	0.002	0.002	0.000	0.000	0.000	0.000
53	A	59	GLY	0	-0.001	0.010	29.556	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.041	-0.035	31.328	0.007	0.007	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.013	-0.006	31.229	0.002	0.002	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.013	0.004	27.636	0.012	0.012	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.939	0.979	26.201	-0.106	-0.106	0.000	0.000	0.000	0.000
58	A	64	ASP	-1	-0.737	-0.848	22.228	0.252	0.252	0.000	0.000	0.000	0.000
59	A	65	TRP	0	-0.041	-0.031	25.158	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.874	-0.930	26.074	0.143	0.143	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.073	-0.023	26.410	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.863	-0.943	29.395	0.094	0.094	0.000	0.000	0.000	0.000
63	A	69	ILE	0	0.014	0.007	33.153	0.003	0.003	0.000	0.000	0.000	0.000
64	A	70	GLU	-1	-0.878	-0.936	36.206	0.083	0.083	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.080	-0.027	33.470	0.001	0.001	0.000	0.000	0.000	0.000
66	A	72	TYR	0	0.034	-0.012	35.507	0.000	0.000	0.000	0.000	0.000	0.000
67	A	73	ILE	0	0.024	0.012	27.912	0.001	0.001	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.025	0.006	30.808	0.009	0.009	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.814	-0.898	31.883	0.104	0.104	0.000	0.000	0.000	0.000
70	A	76	ALA	0	-0.019	-0.010	31.442	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	77	PHE	0	-0.024	-0.019	24.591	0.003	0.003	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.019	-0.014	29.595	0.003	0.003	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.041	-0.013	31.607	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	80	ASN	0	-0.028	-0.023	29.618	0.006	0.006	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.888	0.945	31.706	-0.104	-0.104	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.004	0.010	33.471	0.002	0.002	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.032	-0.006	34.429	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.037	-0.023	35.685	0.007	0.007	0.000	0.000	0.000	0.000
79	A	85	VAL	0	0.022	0.022	38.179	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.018	-0.010	40.421	0.005	0.005	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.774	-0.885	42.733	0.071	0.071	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.025	-0.044	40.731	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	89	GLN	0	-0.061	-0.028	43.737	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	90	TYR	0	-0.004	-0.014	46.750	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	91	MET	0	-0.045	0.009	40.456	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	THR	0	0.034	0.006	45.355	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	93	LYS	1	0.904	0.960	39.608	-0.087	-0.087	0.000	0.000	0.000	0.000
88	A	94	PRO	0	0.054	0.024	44.396	0.002	0.002	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.048	0.023	42.380	0.000	0.000	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.030	0.009	38.595	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	ARG	1	0.876	0.954	41.079	-0.061	-0.061	0.000	0.000	0.000	0.000
92	A	98	GLU	-1	-0.919	-0.962	43.193	0.065	0.065	0.000	0.000	0.000	0.000
93	A	99	LEU	0	-0.044	-0.039	38.797	0.001	0.001	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.005	-0.001	36.152	0.002	0.002	0.000	0.000	0.000	0.000
95	A	101	GLN	0	0.021	0.011	39.696	0.002	0.002	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.930	0.985	41.619	-0.069	-0.069	0.000	0.000	0.000	0.000
97	A	103	GLU	-1	-0.876	-0.941	35.227	0.110	0.110	0.000	0.000	0.000	0.000
98	A	104	GLY	0	-0.043	-0.019	38.820	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	ILE	0	-0.062	-0.040	35.636	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	LYS	1	0.900	0.978	39.437	-0.086	-0.086	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.011	0.015	39.395	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	108	PHE	0	-0.054	-0.041	35.045	0.004	0.004	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.040	0.023	34.215	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	110	HIS	0	0.005	0.012	31.222	0.017	0.017	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.041	0.014	29.571	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	112	PRO	0	0.032	0.022	27.848	0.016	0.016	0.000	0.000	0.000	0.000
107	A	113	ILE	0	-0.024	0.006	21.838	0.000	0.000	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.037	0.017	24.079	0.011	0.011	0.000	0.000	0.000	0.000
109	A	115	ARG	1	0.892	0.951	22.933	-0.217	-0.217	0.000	0.000	0.000	0.000
110	A	116	LYS	1	0.979	0.965	24.948	-0.138	-0.138	0.000	0.000	0.000	0.000
111	A	117	GLY	0	-0.013	-0.004	28.195	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.843	-0.896	22.970	0.220	0.220	0.000	0.000	0.000	0.000
113	A	119	PRO	0	0.026	0.008	25.099	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	120	PRO	0	-0.010	0.007	24.552	0.019	0.019	0.000	0.000	0.000	0.000
115	A	121	PHE	0	0.009	-0.001	19.684	0.000	0.000	0.000	0.000	0.000	0.000
116	A	122	GLY	0	0.030	0.002	20.883	0.033	0.033	0.000	0.000	0.000	0.000
117	A	123	ILE	0	-0.074	-0.016	23.047	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	124	LEU	0	0.030	0.031	25.058	0.017	0.017	0.000	0.000	0.000	0.000
119	A	125	SER	0	-0.031	-0.031	26.725	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	126	VAL	0	-0.019	-0.014	28.867	0.008	0.008	0.000	0.000	0.000	0.000
121	A	127	PHE	0	0.029	-0.004	29.993	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	128	SER	0	0.055	0.030	34.270	0.001	0.001	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.783	0.885	33.180	-0.122	-0.122	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.063	-0.045	38.495	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	131	ILE	0	-0.070	-0.047	40.654	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	132	VAL	0	0.046	0.029	41.595	0.004	0.004	0.000	0.000	0.000	0.000
127	A	133	GLY	0	-0.023	-0.024	43.588	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	134	LEU	0	-0.037	-0.016	37.255	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	135	PHE	0	-0.007	0.005	34.865	0.003	0.003	0.000	0.000	0.000	0.000
130	A	136	ASN	0	0.030	0.025	39.780	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.804	-0.935	40.053	0.094	0.094	0.000	0.000	0.000	0.000
132	A	138	PRO	0	-0.043	-0.022	39.325	0.005	0.005	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.008	0.004	33.871	0.006	0.006	0.000	0.000	0.000	0.000
134	A	140	LEU	0	0.024	0.005	35.393	0.010	0.010	0.000	0.000	0.000	0.000
135	A	141	ASN	0	0.037	0.023	34.704	0.008	0.008	0.000	0.000	0.000	0.000
136	A	142	LEU	0	-0.023	0.010	31.843	0.008	0.008	0.000	0.000	0.000	0.000
137	A	143	LEU	0	-0.008	-0.012	30.847	0.013	0.013	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.872	-0.938	29.652	0.149	0.149	0.000	0.000	0.000	0.000
139	A	145	SER	0	-0.077	-0.036	29.370	0.008	0.008	0.000	0.000	0.000	0.000
140	A	146	LEU	0	-0.018	-0.013	25.104	0.014	0.014	0.000	0.000	0.000	0.000
141	A	147	ALA	0	0.029	0.009	25.387	0.023	0.023	0.000	0.000	0.000	0.000
142	A	148	GLY	0	0.032	0.014	24.521	0.021	0.021	0.000	0.000	0.000	0.000
143	A	149	GLN	0	-0.052	-0.033	23.813	0.023	0.023	0.000	0.000	0.000	0.000
144	A	150	LEU	0	0.006	0.012	20.701	0.030	0.030	0.000	0.000	0.000	0.000
145	A	151	ALA	0	0.011	-0.001	19.754	0.041	0.041	0.000	0.000	0.000	0.000
146	A	152	GLN	0	-0.046	-0.022	19.232	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	153	ALA	0	0.048	0.023	17.203	0.023	0.023	0.000	0.000	0.000	0.000
148	A	154	VAL	0	0.052	0.022	15.244	0.071	0.071	0.000	0.000	0.000	0.000
149	A	155	LYS	1	0.795	0.918	14.479	-0.184	-0.184	0.000	0.000	0.000	0.000
150	A	156	ILE	0	-0.073	-0.012	13.486	0.008	0.008	0.000	0.000	0.000	0.000
151	A	157	VAL	0	-0.078	-0.073	9.117	0.073	0.073	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)