FMO DATABASE

FMODB ID: 4JYYN

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	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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1461248.956088
FMO2-HF: Nuclear repulsion	1402259.462599
FMO2-HF: Total energy	-58989.493489
FMO2-MP2: Total energy	-59163.347909

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.
-11.946	-7.239	3.137	-3.407	-4.438	0.018

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 : 0.017 / q_NPA : -0.008

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	-0.006	-0.009	3.185	-2.116	0.264	0.373	-1.163	-1.591	0.007
4	A	10	MET	0	-0.015	0.008	2.189	-5.241	-3.908	2.754	-1.820	-2.267	0.010
5	A	11	ASN	0	0.020	-0.013	3.746	-2.846	-1.852	0.010	-0.424	-0.580	0.001
6	A	12	ARG	1	0.966	1.001	5.680	-1.864	-1.864	0.000	0.000	0.000	0.000
7	A	13	THR	0	-0.018	-0.015	7.356	-0.447	-0.447	0.000	0.000	0.000	0.000
8	A	14	LEU	0	-0.051	-0.033	6.483	-0.304	-0.304	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.864	-0.928	9.459	0.759	0.759	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.079	-0.042	11.422	-0.141	-0.141	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.062	-0.058	12.513	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.038	0.031	13.110	-0.079	-0.079	0.000	0.000	0.000	0.000
13	A	19	ILE	0	0.020	0.024	15.621	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	20	MET	0	-0.083	-0.045	15.391	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.808	-0.884	18.358	0.315	0.315	0.000	0.000	0.000	0.000
16	A	22	ASP	-1	-0.927	-0.954	19.944	0.270	0.270	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.042	-0.027	21.390	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.032	0.003	22.895	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	25	ASN	0	0.040	0.030	22.831	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	26	LEU	0	-0.076	-0.034	25.614	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.009	0.007	27.687	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.041	-0.027	28.750	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.912	0.960	30.152	-0.156	-0.156	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.976	-0.961	32.148	0.132	0.132	0.000	0.000	0.000	0.000
25	A	31	PHE	0	0.018	-0.002	32.933	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	32	LYS	1	0.961	0.987	35.121	-0.086	-0.086	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.002	-0.008	31.723	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	34	ASP	-1	-0.822	-0.876	33.756	0.105	0.105	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.067	-0.044	28.123	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	36	ALA	0	0.019	0.021	27.246	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	37	VAL	0	-0.004	-0.009	24.390	0.005	0.005	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.064	0.035	20.381	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.796	0.894	21.611	-0.192	-0.192	0.000	0.000	0.000	0.000
34	A	40	LEU	0	-0.006	-0.014	16.383	0.004	0.004	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.029	0.025	19.747	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	42	ASP	-1	-0.882	-0.934	16.828	0.327	0.327	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.863	-0.970	14.750	0.327	0.327	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.833	0.933	17.222	-0.263	-0.263	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.018	-0.010	20.579	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	46	VAL	0	-0.003	0.002	21.700	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.036	-0.016	21.284	0.036	0.036	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.864	0.925	17.041	-0.292	-0.292	0.000	0.000	0.000	0.000
43	A	49	VAL	0	-0.005	-0.017	20.463	0.029	0.029	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.847	0.930	14.966	-0.441	-0.441	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.033	0.001	17.565	0.018	0.018	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.002	-0.022	20.036	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	53	SER	0	0.019	0.017	23.268	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.071	0.032	25.866	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	55	LYS	1	0.929	0.957	28.267	-0.092	-0.092	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.075	0.009	30.722	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	57	ILE	0	0.024	0.034	24.723	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.026	-0.008	28.033	0.002	0.002	0.000	0.000	0.000	0.000
53	A	59	GLY	0	-0.004	0.006	29.567	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.040	-0.032	31.342	0.008	0.008	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.035	-0.018	31.226	0.003	0.003	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.008	-0.004	27.648	0.013	0.013	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.934	0.978	26.217	-0.097	-0.097	0.000	0.000	0.000	0.000
58	A	64	ASP	-1	-0.739	-0.858	22.103	0.237	0.237	0.000	0.000	0.000	0.000
59	A	65	TRP	0	-0.055	-0.035	25.081	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.873	-0.931	26.004	0.144	0.144	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.077	-0.022	26.307	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.835	-0.938	29.328	0.098	0.098	0.000	0.000	0.000	0.000
63	A	69	ILE	0	-0.001	0.011	33.087	0.002	0.002	0.000	0.000	0.000	0.000
64	A	70	GLU	-1	-0.905	-0.947	36.140	0.087	0.087	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.100	-0.047	33.426	0.000	0.000	0.000	0.000	0.000	0.000
66	A	72	TYR	0	0.025	-0.016	35.442	0.000	0.000	0.000	0.000	0.000	0.000
67	A	73	ILE	0	0.018	0.007	28.013	0.002	0.002	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.026	0.010	30.770	0.011	0.011	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.861	-0.922	31.821	0.115	0.115	0.000	0.000	0.000	0.000
70	A	76	ALA	0	-0.023	-0.029	31.384	0.001	0.001	0.000	0.000	0.000	0.000
71	A	77	PHE	0	-0.029	-0.019	24.532	0.005	0.005	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.018	-0.017	29.595	0.005	0.005	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.044	0.001	31.607	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	80	ASN	0	-0.023	-0.021	29.763	0.007	0.007	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.964	0.979	31.706	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.016	0.025	33.504	0.001	0.001	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.059	-0.022	34.429	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.036	-0.020	35.685	0.006	0.006	0.000	0.000	0.000	0.000
79	A	85	VAL	0	0.016	0.016	38.179	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.033	-0.005	40.432	0.004	0.004	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.803	-0.910	42.743	0.071	0.071	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.032	-0.048	40.677	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	89	GLN	0	-0.036	-0.005	43.748	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	90	TYR	0	-0.014	-0.020	46.779	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	91	MET	0	-0.046	0.005	40.407	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	THR	0	0.026	0.004	45.382	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	93	LYS	1	0.958	0.990	39.633	-0.089	-0.089	0.000	0.000	0.000	0.000
88	A	94	PRO	0	0.048	0.019	44.318	0.002	0.002	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.053	0.027	41.866	0.000	0.000	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.023	0.009	38.585	0.000	0.000	0.000	0.000	0.000	0.000
91	A	97	ARG	1	0.903	0.956	41.094	-0.061	-0.061	0.000	0.000	0.000	0.000
92	A	98	GLU	-1	-0.965	-0.976	43.207	0.060	0.060	0.000	0.000	0.000	0.000
93	A	99	LEU	0	-0.028	-0.033	38.917	0.000	0.000	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.005	-0.001	36.171	0.002	0.002	0.000	0.000	0.000	0.000
95	A	101	GLN	0	0.019	0.007	39.716	0.002	0.002	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.947	0.994	41.686	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	103	GLU	-1	-0.862	-0.930	35.449	0.097	0.097	0.000	0.000	0.000	0.000
98	A	104	GLY	0	-0.042	-0.024	38.829	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	ILE	0	-0.064	-0.031	35.677	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	LYS	1	0.936	0.991	39.446	-0.079	-0.079	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.034	0.031	39.532	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	108	PHE	0	-0.048	-0.040	34.967	0.003	0.003	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.043	0.022	34.200	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	110	HIS	0	0.010	0.010	31.183	0.017	0.017	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.038	0.014	29.290	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	112	PRO	0	0.030	0.016	27.847	0.016	0.016	0.000	0.000	0.000	0.000
107	A	113	ILE	0	-0.013	0.005	21.855	0.001	0.001	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.045	0.019	24.079	0.014	0.014	0.000	0.000	0.000	0.000
109	A	115	ARG	1	0.894	0.963	22.578	-0.268	-0.268	0.000	0.000	0.000	0.000
110	A	116	LYS	1	0.974	0.960	24.948	-0.173	-0.173	0.000	0.000	0.000	0.000
111	A	117	GLY	0	-0.010	-0.001	28.288	0.000	0.000	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.908	-0.946	23.127	0.272	0.272	0.000	0.000	0.000	0.000
113	A	119	PRO	0	0.004	0.001	25.046	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	120	PRO	0	-0.011	0.001	24.552	0.023	0.023	0.000	0.000	0.000	0.000
115	A	121	PHE	0	0.005	0.006	19.473	0.000	0.000	0.000	0.000	0.000	0.000
116	A	122	GLY	0	0.033	-0.003	20.883	0.032	0.032	0.000	0.000	0.000	0.000
117	A	123	ILE	0	-0.076	-0.012	23.047	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	124	LEU	0	0.033	0.032	25.058	0.015	0.015	0.000	0.000	0.000	0.000
119	A	125	SER	0	-0.027	-0.026	26.737	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	126	VAL	0	-0.022	-0.010	28.877	0.006	0.006	0.000	0.000	0.000	0.000
121	A	127	PHE	0	0.022	-0.009	30.136	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	128	SER	0	0.057	0.048	34.278	0.000	0.000	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.816	0.895	33.191	-0.113	-0.113	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.068	-0.059	38.326	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	131	ILE	0	-0.044	-0.041	40.765	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	132	VAL	0	0.003	0.006	41.601	0.004	0.004	0.000	0.000	0.000	0.000
127	A	133	GLY	0	-0.033	-0.025	43.613	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	134	LEU	0	-0.055	-0.017	37.202	0.000	0.000	0.000	0.000	0.000	0.000
129	A	135	PHE	0	-0.004	0.008	34.947	0.004	0.004	0.000	0.000	0.000	0.000
130	A	136	ASN	0	0.039	0.027	39.787	0.001	0.001	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.814	-0.938	40.059	0.103	0.103	0.000	0.000	0.000	0.000
132	A	138	PRO	0	-0.043	-0.017	39.330	0.005	0.005	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.000	-0.005	34.166	0.007	0.007	0.000	0.000	0.000	0.000
134	A	140	LEU	0	0.027	0.003	35.397	0.010	0.010	0.000	0.000	0.000	0.000
135	A	141	ASN	0	0.040	0.029	34.704	0.009	0.009	0.000	0.000	0.000	0.000
136	A	142	LEU	0	-0.038	-0.004	32.002	0.010	0.010	0.000	0.000	0.000	0.000
137	A	143	LEU	0	-0.006	-0.011	30.840	0.014	0.014	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.892	-0.943	29.658	0.166	0.166	0.000	0.000	0.000	0.000
139	A	145	SER	0	-0.061	-0.025	29.370	0.012	0.012	0.000	0.000	0.000	0.000
140	A	146	LEU	0	-0.019	-0.014	25.054	0.018	0.018	0.000	0.000	0.000	0.000
141	A	147	ALA	0	0.024	0.009	25.391	0.026	0.026	0.000	0.000	0.000	0.000
142	A	148	GLY	0	0.029	0.011	24.521	0.025	0.025	0.000	0.000	0.000	0.000
143	A	149	GLN	0	-0.051	-0.032	23.812	0.035	0.035	0.000	0.000	0.000	0.000
144	A	150	LEU	0	0.011	0.015	20.640	0.037	0.037	0.000	0.000	0.000	0.000
145	A	151	ALA	0	0.009	-0.003	19.754	0.049	0.049	0.000	0.000	0.000	0.000
146	A	152	GLN	0	-0.067	-0.041	19.561	0.000	0.000	0.000	0.000	0.000	0.000
147	A	153	ALA	0	0.043	0.015	17.147	0.036	0.036	0.000	0.000	0.000	0.000
148	A	154	VAL	0	0.030	0.011	15.243	0.085	0.085	0.000	0.000	0.000	0.000
149	A	155	LYS	1	0.906	0.944	14.479	-0.258	-0.258	0.000	0.000	0.000	0.000
150	A	156	ILE	0	-0.075	-0.002	13.314	0.023	0.023	0.000	0.000	0.000	0.000
151	A	157	VAL	0	-0.037	-0.011	9.124	0.142	0.142	0.000	0.000	0.000	0.000

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