FMO DATABASE

FMODB ID: YVR12

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	OptAll
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	-1466883.699529
FMO2-HF: Nuclear repulsion	1407892.748894
FMO2-HF: Total energy	-58990.950634
FMO2-MP2: Total energy	-59164.754236

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.
-6.5	-2.137	0.601	-1.98	-2.983	0.007

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 : 0.023 / q_NPA : 0.005

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	0.082	0.034	3.374	-1.170	0.905	0.105	-0.949	-1.231	0.005
4	A	10	MET	0	-0.017	0.011	2.593	-2.113	-1.010	0.475	-0.515	-1.063	0.000
5	A	11	ASN	0	-0.021	-0.027	3.587	-2.314	-1.129	0.021	-0.516	-0.689	0.002
6	A	12	ARG	1	0.902	0.936	6.014	-1.111	-1.111	0.000	0.000	0.000	0.000
7	A	13	THR	0	-0.035	-0.029	7.515	-0.283	-0.283	0.000	0.000	0.000	0.000
8	A	14	LEU	0	-0.036	-0.018	7.060	-0.210	-0.210	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.879	-0.943	9.979	0.696	0.696	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.040	-0.023	11.824	-0.118	-0.118	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.084	-0.070	12.697	-0.040	-0.040	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.032	0.018	13.736	-0.074	-0.074	0.000	0.000	0.000	0.000
13	A	19	ILE	0	-0.016	-0.002	15.461	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	20	MET	0	-0.064	-0.030	15.370	-0.057	-0.057	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.737	-0.840	18.116	0.338	0.338	0.000	0.000	0.000	0.000
16	A	22	ASP	-1	-0.864	-0.935	20.162	0.247	0.247	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.046	-0.017	21.315	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.041	-0.009	23.220	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	25	ASN	0	-0.034	-0.013	22.734	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	26	LEU	0	-0.046	-0.025	25.293	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.008	0.010	27.789	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.002	-0.018	29.051	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.859	0.947	30.091	-0.144	-0.144	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.952	-0.960	32.196	0.121	0.121	0.000	0.000	0.000	0.000
25	A	31	PHE	0	0.015	0.008	33.651	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	32	LYS	1	0.958	0.990	35.196	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.005	0.001	31.918	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	34	ASP	-1	-0.768	-0.870	34.147	0.107	0.107	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.059	-0.032	28.376	0.001	0.001	0.000	0.000	0.000	0.000
30	A	36	ALA	0	0.009	0.016	27.511	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.004	-0.010	24.402	0.008	0.008	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.026	0.027	20.306	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.799	0.883	21.643	-0.185	-0.185	0.000	0.000	0.000	0.000
34	A	40	LEU	0	0.014	-0.008	16.643	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.011	0.001	20.112	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	42	ASP	-1	-0.820	-0.894	16.952	0.356	0.356	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.840	-0.923	15.434	0.323	0.323	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.762	0.872	17.744	-0.324	-0.324	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.005	0.005	21.408	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	46	VAL	0	-0.014	-0.004	22.435	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.016	-0.006	21.994	0.031	0.031	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.787	0.869	18.936	-0.299	-0.299	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.003	-0.015	20.733	0.018	0.018	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.864	0.941	15.719	-0.441	-0.441	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.018	-0.005	17.665	0.019	0.019	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.016	-0.027	19.992	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	53	SER	0	0.042	0.026	23.316	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.042	0.024	26.066	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	55	LYS	1	0.929	0.955	28.640	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.087	0.021	30.682	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	57	ILE	0	0.006	0.025	24.759	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.016	-0.002	28.048	0.003	0.003	0.000	0.000	0.000	0.000
53	A	59	GLY	0	0.011	0.015	29.836	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.057	-0.050	31.709	0.007	0.007	0.000	0.000	0.000	0.000
55	A	61	ALA	0	0.007	0.002	31.707	0.003	0.003	0.000	0.000	0.000	0.000
56	A	62	GLY	0	-0.017	0.001	27.894	0.010	0.010	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.966	0.998	26.433	-0.113	-0.113	0.000	0.000	0.000	0.000
58	A	64	ASP	-1	-0.729	-0.845	22.714	0.261	0.261	0.000	0.000	0.000	0.000
59	A	65	TRP	0	-0.034	-0.020	25.538	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.892	-0.939	26.636	0.155	0.155	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.051	-0.026	27.110	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.855	-0.921	30.021	0.100	0.100	0.000	0.000	0.000	0.000
63	A	69	ILE	0	0.006	0.007	33.837	0.003	0.003	0.000	0.000	0.000	0.000
64	A	70	GLU	-1	-0.875	-0.937	36.610	0.087	0.087	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.087	-0.043	33.906	0.000	0.000	0.000	0.000	0.000	0.000
66	A	72	TYR	0	0.026	-0.015	35.607	0.001	0.001	0.000	0.000	0.000	0.000
67	A	73	ILE	0	0.012	0.012	28.132	0.001	0.001	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.039	0.023	31.014	0.009	0.009	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.787	-0.891	32.098	0.106	0.106	0.000	0.000	0.000	0.000
70	A	76	ALA	0	-0.027	-0.009	31.856	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	77	PHE	0	-0.021	-0.009	24.856	0.003	0.003	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.022	-0.021	29.942	0.001	0.001	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.040	-0.012	32.048	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	80	ASN	0	0.001	-0.006	29.594	0.006	0.006	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.856	0.919	31.802	-0.103	-0.103	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.024	0.010	33.555	0.005	0.005	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.051	-0.011	34.473	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.037	-0.030	35.684	0.007	0.007	0.000	0.000	0.000	0.000
79	A	85	VAL	0	0.006	0.011	38.174	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.019	-0.008	40.553	0.004	0.004	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.790	-0.878	42.594	0.071	0.071	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.031	-0.040	40.866	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	89	GLN	0	-0.029	-0.014	43.756	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	90	TYR	0	0.001	0.001	47.009	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	91	MET	0	-0.050	-0.001	40.378	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	THR	0	0.015	0.000	45.318	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	93	LYS	1	0.909	0.963	39.969	-0.089	-0.089	0.000	0.000	0.000	0.000
88	A	94	PRO	0	0.052	0.021	44.030	0.003	0.003	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.040	0.020	42.423	0.000	0.000	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.023	-0.001	38.537	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	ARG	1	0.830	0.915	40.909	-0.062	-0.062	0.000	0.000	0.000	0.000
92	A	98	GLU	-1	-0.830	-0.907	43.156	0.067	0.067	0.000	0.000	0.000	0.000
93	A	99	LEU	0	-0.022	-0.015	38.924	0.000	0.000	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.017	-0.004	36.276	0.003	0.003	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.007	-0.011	39.798	0.001	0.001	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.919	0.976	41.618	-0.073	-0.073	0.000	0.000	0.000	0.000
97	A	103	GLU	-1	-0.891	-0.940	35.251	0.114	0.114	0.000	0.000	0.000	0.000
98	A	104	GLY	0	-0.018	-0.012	39.204	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	ILE	0	-0.047	-0.036	35.949	0.000	0.000	0.000	0.000	0.000	0.000
100	A	106	LYS	1	0.832	0.921	39.787	-0.086	-0.086	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.002	-0.011	39.434	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	108	PHE	0	-0.047	-0.038	35.122	0.004	0.004	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.024	0.017	34.235	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	110	HIS	0	0.023	0.026	31.107	0.016	0.016	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.039	0.015	29.638	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	112	PRO	0	0.014	0.016	28.120	0.016	0.016	0.000	0.000	0.000	0.000
107	A	113	ILE	0	-0.021	0.009	21.775	0.001	0.001	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.025	0.011	24.096	0.012	0.012	0.000	0.000	0.000	0.000
109	A	115	ARG	1	0.900	0.957	23.237	-0.197	-0.197	0.000	0.000	0.000	0.000
110	A	116	LYS	1	0.967	0.960	25.340	-0.127	-0.127	0.000	0.000	0.000	0.000
111	A	117	GLY	0	-0.009	-0.004	28.709	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.844	-0.893	22.993	0.209	0.209	0.000	0.000	0.000	0.000
113	A	119	PRO	0	0.030	0.002	25.313	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	120	PRO	0	-0.027	0.004	24.935	0.016	0.016	0.000	0.000	0.000	0.000
115	A	121	PHE	0	0.005	-0.003	20.014	0.000	0.000	0.000	0.000	0.000	0.000
116	A	122	GLY	0	0.040	0.004	20.997	0.037	0.037	0.000	0.000	0.000	0.000
117	A	123	ILE	0	-0.059	-0.013	23.236	-0.023	-0.023	0.000	0.000	0.000	0.000
118	A	124	LEU	0	0.032	0.037	25.013	0.017	0.017	0.000	0.000	0.000	0.000
119	A	125	SER	0	-0.023	-0.031	26.682	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	126	VAL	0	-0.004	-0.005	28.718	0.009	0.009	0.000	0.000	0.000	0.000
121	A	127	PHE	0	0.041	0.004	30.057	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	128	SER	0	0.038	-0.001	34.315	0.001	0.001	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.752	0.861	33.787	-0.120	-0.120	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.037	-0.008	38.601	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	131	ILE	0	-0.078	-0.040	40.582	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	132	VAL	0	0.039	0.020	41.900	0.003	0.003	0.000	0.000	0.000	0.000
127	A	133	GLY	0	-0.014	-0.018	43.870	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	134	LEU	0	-0.015	-0.007	37.316	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	135	PHE	0	0.011	0.011	34.644	0.003	0.003	0.000	0.000	0.000	0.000
130	A	136	ASN	0	0.023	0.024	39.583	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.813	-0.928	40.014	0.090	0.090	0.000	0.000	0.000	0.000
132	A	138	PRO	0	-0.027	-0.002	39.241	0.005	0.005	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.018	0.017	33.957	0.006	0.006	0.000	0.000	0.000	0.000
134	A	140	LEU	0	0.005	0.004	35.304	0.009	0.009	0.000	0.000	0.000	0.000
135	A	141	ASN	0	0.009	-0.013	34.577	0.007	0.007	0.000	0.000	0.000	0.000
136	A	142	LEU	0	-0.023	0.019	31.635	0.007	0.007	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.008	-0.006	30.873	0.012	0.012	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.897	-0.956	29.720	0.140	0.140	0.000	0.000	0.000	0.000
139	A	145	SER	0	-0.070	-0.041	29.395	0.009	0.009	0.000	0.000	0.000	0.000
140	A	146	LEU	0	-0.031	-0.011	25.123	0.012	0.012	0.000	0.000	0.000	0.000
141	A	147	ALA	0	0.035	0.012	25.347	0.021	0.021	0.000	0.000	0.000	0.000
142	A	148	GLY	0	0.037	0.019	24.766	0.018	0.018	0.000	0.000	0.000	0.000
143	A	149	GLN	0	-0.057	-0.034	23.846	0.020	0.020	0.000	0.000	0.000	0.000
144	A	150	LEU	0	0.015	0.013	20.732	0.027	0.027	0.000	0.000	0.000	0.000
145	A	151	ALA	0	0.012	0.009	19.968	0.039	0.039	0.000	0.000	0.000	0.000
146	A	152	GLN	0	-0.025	-0.014	19.266	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	153	ALA	0	0.027	0.012	17.425	0.018	0.018	0.000	0.000	0.000	0.000
148	A	154	VAL	0	0.039	0.011	15.656	0.061	0.061	0.000	0.000	0.000	0.000
149	A	155	LYS	1	0.782	0.871	14.928	-0.186	-0.186	0.000	0.000	0.000	0.000
150	A	156	ILE	0	-0.046	0.006	13.597	-0.012	-0.012	0.000	0.000	0.000	0.000
151	A	157	VAL	0	-0.065	-0.022	9.523	0.089	0.089	0.000	0.000	0.000	0.000

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