FMO DATABASE

FMODB ID: KR163

Calculation Name: 2V9U-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V9U

Chain ID: A

ChEMBL ID:

UniProt ID: A0QR29

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	132
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1013973.896534
FMO2-HF: Nuclear repulsion	965473.536693
FMO2-HF: Total energy	-48500.359841
FMO2-MP2: Total energy	-48644.450302

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:GLY )

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

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.
-13.568	-10.531	5.84	-4.281	-4.596	-0.035

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.004

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	ASP	-1	-0.793	-0.899	3.801	-6.093	-4.927	-0.005	-0.590	-0.570	0.002
4	A	4	ASN	0	-0.045	0.009	5.732	1.184	1.184	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.882	-0.942	9.211	-0.889	-0.889	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.016	0.000	11.628	0.118	0.118	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.021	-0.007	15.361	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.050	-0.029	17.768	0.013	0.013	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.020	0.007	21.472	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.777	-0.867	24.362	-0.197	-0.197	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.019	-0.004	26.130	0.017	0.017	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.109	-0.071	28.351	0.015	0.015	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.916	-0.957	28.014	-0.109	-0.109	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.809	0.907	23.865	0.200	0.200	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.056	-0.021	19.849	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.013	-0.005	19.507	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.017	0.010	13.384	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.023	-0.001	13.248	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	19	GLN	0	0.009	-0.024	8.593	-0.133	-0.133	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.044	-0.043	8.157	0.218	0.218	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.014	-0.030	2.308	-0.880	-0.760	1.607	-0.750	-0.978	-0.001
22	A	22	ASP	-1	-0.853	-0.939	2.061	-10.960	-9.394	4.235	-2.902	-2.899	-0.036
23	A	23	THR	0	-0.068	-0.046	3.957	2.026	2.211	0.003	-0.039	-0.149	0.000
24	A	24	PHE	0	-0.058	-0.026	7.142	0.242	0.242	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.001	-0.005	9.516	0.100	0.100	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.032	-0.009	13.077	0.126	0.126	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.068	0.031	15.180	0.024	0.024	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.014	0.000	18.684	0.032	0.032	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.057	-0.045	21.422	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.021	0.026	25.188	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.021	0.018	26.790	0.023	0.023	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.821	-0.923	28.532	-0.147	-0.147	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.887	0.942	27.875	0.129	0.129	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.034	0.048	31.212	0.013	0.013	0.000	0.000	0.000	0.000
35	A	35	ARG	1	1.006	0.990	30.116	0.100	0.100	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.055	-0.040	30.323	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.044	-0.010	27.191	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.804	0.925	22.930	0.213	0.213	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.783	-0.906	22.387	-0.223	-0.223	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.012	0.000	17.253	0.035	0.035	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.019	-0.017	15.973	0.026	0.026	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.005	0.011	11.626	0.087	0.087	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.042	-0.032	9.697	0.166	0.166	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.086	0.058	7.598	-0.248	-0.248	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.867	0.935	5.250	2.015	2.015	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.046	0.046	8.191	-0.411	-0.411	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.875	0.935	5.327	1.146	1.146	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.004	0.013	10.839	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.021	0.011	12.211	0.046	0.046	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.012	0.029	15.755	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.004	0.010	19.481	0.032	0.032	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.030	0.001	21.758	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.052	-0.040	25.535	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.068	0.036	28.159	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.042	-0.019	22.497	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.941	-0.971	23.370	-0.109	-0.109	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.980	-0.993	25.012	-0.101	-0.101	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.065	-0.017	20.522	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.854	-0.939	23.879	-0.185	-0.185	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.022	-0.027	22.543	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.026	-0.001	20.978	0.010	0.010	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.019	0.001	13.704	-0.038	-0.038	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.875	-0.942	17.084	-0.430	-0.430	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.023	-0.009	11.072	-0.105	-0.105	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.011	0.008	14.647	0.101	0.101	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.009	0.001	14.691	-0.084	-0.084	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.016	-0.002	16.989	0.050	0.050	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.011	-0.008	19.481	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.003	0.002	22.018	0.026	0.026	0.000	0.000	0.000	0.000
70	A	122	GLY	0	0.011	-0.017	23.958	0.002	0.002	0.000	0.000	0.000	0.000
71	A	123	PRO	0	-0.047	-0.001	26.791	0.016	0.016	0.000	0.000	0.000	0.000
72	A	124	GLY	0	0.021	0.005	28.291	0.016	0.016	0.000	0.000	0.000	0.000
73	A	125	ILE	0	-0.019	-0.011	24.270	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	126	GLN	0	-0.023	-0.009	24.983	0.009	0.009	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.826	-0.910	20.977	-0.480	-0.480	0.000	0.000	0.000	0.000
76	A	128	VAL	0	-0.014	0.009	20.015	0.036	0.036	0.000	0.000	0.000	0.000
77	A	129	ALA	0	0.038	0.023	19.401	-0.064	-0.064	0.000	0.000	0.000	0.000
78	A	130	THR	0	-0.052	-0.053	15.958	0.054	0.054	0.000	0.000	0.000	0.000
79	A	131	PHE	0	-0.033	-0.018	13.165	0.042	0.042	0.000	0.000	0.000	0.000
80	A	132	SER	0	-0.035	-0.036	18.382	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	133	VAL	0	-0.039	-0.030	18.012	0.039	0.039	0.000	0.000	0.000	0.000
82	A	134	ASP	-1	-0.859	-0.915	20.324	-0.284	-0.284	0.000	0.000	0.000	0.000
83	A	135	VAL	0	-0.113	-0.054	17.698	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	136	SER	0	0.067	0.027	21.120	0.012	0.012	0.000	0.000	0.000	0.000
85	A	137	GLY	0	-0.001	0.011	21.082	0.000	0.000	0.000	0.000	0.000	0.000
86	A	138	ALA	0	0.033	-0.006	20.060	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.977	-0.998	14.990	-0.157	-0.157	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.038	0.017	14.515	0.038	0.038	0.000	0.000	0.000	0.000
89	A	141	GLY	0	-0.023	-0.026	11.549	-0.101	-0.101	0.000	0.000	0.000	0.000
90	A	142	VAL	0	-0.028	0.007	12.300	0.097	0.097	0.000	0.000	0.000	0.000
91	A	143	ALA	0	-0.036	-0.016	9.794	-0.200	-0.200	0.000	0.000	0.000	0.000
92	A	144	VAL	0	0.010	0.012	11.279	0.189	0.189	0.000	0.000	0.000	0.000
93	A	145	SER	0	-0.031	-0.031	11.574	-0.161	-0.161	0.000	0.000	0.000	0.000
94	A	146	ASN	0	0.013	-0.012	13.226	0.054	0.054	0.000	0.000	0.000	0.000
95	A	147	ALA	0	0.032	0.043	15.275	0.070	0.070	0.000	0.000	0.000	0.000
96	A	148	HIS	0	-0.040	-0.024	17.327	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	149	GLY	0	0.020	0.020	20.132	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	150	THR	0	-0.041	-0.029	21.228	0.025	0.025	0.000	0.000	0.000	0.000
99	A	151	VAL	0	0.008	0.007	24.140	0.000	0.000	0.000	0.000	0.000	0.000
100	A	152	THR	0	0.019	-0.015	26.340	0.013	0.013	0.000	0.000	0.000	0.000
101	A	153	GLY	0	-0.001	-0.002	29.595	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	154	ALA	0	-0.013	-0.001	27.093	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	155	ALA	0	-0.047	-0.004	29.053	0.011	0.011	0.000	0.000	0.000	0.000
104	A	156	GLY	0	-0.047	-0.041	29.130	0.004	0.004	0.000	0.000	0.000	0.000
105	A	157	GLY	0	-0.015	-0.006	24.777	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	158	VAL	0	0.021	0.005	21.320	0.005	0.005	0.000	0.000	0.000	0.000
107	A	159	LEU	0	-0.006	0.022	19.631	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	160	LEU	0	0.007	0.000	16.370	0.017	0.017	0.000	0.000	0.000	0.000
109	A	161	ARG	1	0.932	0.989	15.907	0.415	0.415	0.000	0.000	0.000	0.000
110	A	162	PRO	0	0.018	0.019	11.621	0.079	0.079	0.000	0.000	0.000	0.000
111	A	163	PHE	0	-0.003	0.010	13.387	-0.046	-0.046	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.035	0.013	11.856	-0.048	-0.048	0.000	0.000	0.000	0.000
113	A	165	ARG	1	0.814	0.900	13.972	0.562	0.562	0.000	0.000	0.000	0.000
114	A	166	LEU	0	0.023	0.016	16.814	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	167	ILE	0	-0.015	-0.016	18.433	0.029	0.029	0.000	0.000	0.000	0.000
116	A	168	ALA	0	0.035	0.023	22.147	0.006	0.006	0.000	0.000	0.000	0.000
117	A	169	SER	0	0.002	0.007	24.519	0.010	0.010	0.000	0.000	0.000	0.000
118	A	170	THR	0	-0.055	-0.043	27.525	0.011	0.011	0.000	0.000	0.000	0.000
119	A	171	GLY	0	-0.039	-0.015	28.026	0.012	0.012	0.000	0.000	0.000	0.000
120	A	172	ASP	-1	-0.842	-0.903	25.155	-0.223	-0.223	0.000	0.000	0.000	0.000
121	A	173	SER	0	-0.014	-0.006	22.335	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	174	VAL	0	0.014	0.017	17.794	0.013	0.013	0.000	0.000	0.000	0.000
123	A	175	THR	0	-0.052	-0.034	16.906	-0.027	-0.027	0.000	0.000	0.000	0.000
124	A	176	THR	0	-0.004	-0.001	11.738	0.107	0.107	0.000	0.000	0.000	0.000
125	A	177	TYR	0	-0.006	-0.027	14.024	-0.053	-0.053	0.000	0.000	0.000	0.000
126	A	178	GLY	0	0.025	0.022	11.202	-0.076	-0.076	0.000	0.000	0.000	0.000
127	A	179	GLU	-1	-0.979	-0.996	11.627	-0.350	-0.350	0.000	0.000	0.000	0.000
128	A	180	PRO	0	-0.060	-0.046	13.023	-0.074	-0.074	0.000	0.000	0.000	0.000
129	A	181	TRP	0	0.063	0.040	8.477	0.144	0.144	0.000	0.000	0.000	0.000
130	A	182	ASN	0	-0.010	-0.031	15.185	0.033	0.033	0.000	0.000	0.000	0.000
131	A	183	MET	0	-0.064	-0.041	16.045	0.020	0.020	0.000	0.000	0.000	0.000
132	A	184	ASN	-1	-0.922	-0.950	20.107	-0.171	-0.171	0.000	0.000	0.000	0.000

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