FMO DATABASE

FMODB ID: QVR4Y

Calculation Name: 2V9U-A-Xray372

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: 2023-09-24

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1014321.253624
FMO2-HF: Nuclear repulsion	965819.660794
FMO2-HF: Total energy	-48501.59283
FMO2-MP2: Total energy	-48645.679985

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.
-12.604	-12.049	10.72	-5.843	-5.433	-0.046

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 : 0.022 / 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	3	ASP	-1	-0.793	-0.884	3.801	-5.466	-4.258	-0.008	-0.612	-0.589	0.002
4	A	4	ASN	0	-0.044	-0.009	5.741	1.224	1.224	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.875	-0.934	9.211	-0.986	-0.986	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.027	0.003	11.628	0.114	0.114	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.014	-0.010	15.361	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.041	-0.021	17.768	0.013	0.013	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.021	0.003	21.472	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.778	-0.884	24.328	-0.216	-0.216	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.005	0.002	26.133	0.017	0.017	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.099	-0.061	28.369	0.015	0.015	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.927	-0.958	28.029	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.819	0.901	23.884	0.213	0.213	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.056	-0.017	19.563	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.011	-0.005	19.528	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.034	0.009	13.278	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.030	-0.003	13.353	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	19	GLN	0	0.012	-0.021	8.430	-0.193	-0.193	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.042	-0.039	8.282	0.261	0.261	0.000	0.000	0.000	0.000
21	A	21	TRP	0	0.003	-0.025	2.320	-0.825	-0.581	1.672	-0.885	-1.031	-0.002
22	A	22	ASP	-1	-0.850	-0.943	1.893	-10.585	-11.691	9.053	-4.301	-3.646	-0.046
23	A	23	THR	0	-0.049	-0.041	3.870	1.906	2.115	0.003	-0.045	-0.167	0.000
24	A	24	PHE	0	-0.070	-0.033	7.219	0.252	0.252	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.001	0.000	9.493	0.085	0.085	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.023	-0.007	13.157	0.117	0.117	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.050	0.023	15.144	0.020	0.020	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.021	-0.011	18.743	0.033	0.033	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.050	-0.034	21.396	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.014	0.033	25.164	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.033	0.027	26.753	0.023	0.023	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.793	-0.902	28.499	-0.138	-0.138	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.847	0.908	27.563	0.117	0.117	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.025	0.036	31.163	0.014	0.014	0.000	0.000	0.000	0.000
35	A	35	ARG	1	1.005	0.992	30.184	0.092	0.092	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.034	-0.014	30.382	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.043	-0.033	27.204	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.755	0.876	22.990	0.195	0.195	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.745	-0.874	22.588	-0.205	-0.205	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.017	-0.005	16.982	0.039	0.039	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.023	-0.015	15.906	0.027	0.027	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.001	0.006	11.704	0.097	0.097	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.017	-0.013	9.860	0.167	0.167	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.077	0.055	7.517	-0.222	-0.222	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.879	0.936	5.540	1.933	1.933	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.036	0.047	8.207	-0.431	-0.431	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.848	0.925	5.419	1.234	1.234	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.019	-0.010	10.846	-0.111	-0.111	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.011	0.011	12.035	0.038	0.038	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.014	0.022	15.754	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.003	0.012	19.480	0.031	0.031	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.034	0.006	21.754	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.054	-0.041	25.531	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.065	0.033	28.158	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.044	-0.013	22.509	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.937	-0.973	23.369	-0.127	-0.127	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.982	-0.995	25.010	-0.114	-0.114	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.047	-0.008	20.677	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.874	-0.940	23.882	-0.194	-0.194	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.010	-0.002	22.551	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.028	-0.005	21.115	0.010	0.010	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.018	0.002	13.592	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.806	-0.874	17.102	-0.434	-0.434	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.034	-0.008	10.992	-0.106	-0.106	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.014	0.008	14.730	0.106	0.106	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.026	0.004	14.785	-0.084	-0.084	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.033	-0.014	17.076	0.060	0.060	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.004	-0.008	19.555	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.018	0.004	22.094	0.023	0.023	0.000	0.000	0.000	0.000
70	A	122	GLY	0	0.004	-0.021	24.019	0.002	0.002	0.000	0.000	0.000	0.000
71	A	123	PRO	0	-0.044	0.002	26.854	0.015	0.015	0.000	0.000	0.000	0.000
72	A	124	GLY	0	0.027	0.006	28.365	0.015	0.015	0.000	0.000	0.000	0.000
73	A	125	ILE	0	-0.022	-0.013	24.358	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	126	GLN	0	-0.018	-0.004	25.068	0.009	0.009	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.791	-0.868	20.905	-0.496	-0.496	0.000	0.000	0.000	0.000
76	A	128	VAL	0	-0.018	0.003	20.205	0.038	0.038	0.000	0.000	0.000	0.000
77	A	129	ALA	0	0.028	0.016	19.477	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	130	THR	0	-0.055	-0.048	15.755	0.063	0.063	0.000	0.000	0.000	0.000
79	A	131	PHE	0	-0.026	-0.020	12.882	0.047	0.047	0.000	0.000	0.000	0.000
80	A	132	SER	0	-0.043	-0.061	18.399	-0.038	-0.038	0.000	0.000	0.000	0.000
81	A	133	VAL	0	-0.036	-0.026	17.968	0.040	0.040	0.000	0.000	0.000	0.000
82	A	134	ASP	-1	-0.850	-0.913	20.336	-0.300	-0.300	0.000	0.000	0.000	0.000
83	A	135	VAL	0	-0.107	-0.055	17.720	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	136	SER	0	0.062	0.027	21.128	0.010	0.010	0.000	0.000	0.000	0.000
85	A	137	GLY	0	0.017	0.021	21.080	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	138	ALA	0	0.039	0.011	20.059	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.971	-0.992	14.949	-0.201	-0.201	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.038	0.015	14.513	0.044	0.044	0.000	0.000	0.000	0.000
89	A	141	GLY	0	-0.015	-0.021	11.548	-0.106	-0.106	0.000	0.000	0.000	0.000
90	A	142	VAL	0	-0.027	0.013	12.319	0.104	0.104	0.000	0.000	0.000	0.000
91	A	143	ALA	0	-0.034	-0.022	9.870	-0.200	-0.200	0.000	0.000	0.000	0.000
92	A	144	VAL	0	0.009	0.009	11.214	0.185	0.185	0.000	0.000	0.000	0.000
93	A	145	SER	0	-0.038	-0.023	11.523	-0.102	-0.102	0.000	0.000	0.000	0.000
94	A	146	ASN	0	-0.015	-0.032	13.193	0.042	0.042	0.000	0.000	0.000	0.000
95	A	147	ALA	0	0.050	0.049	15.227	0.067	0.067	0.000	0.000	0.000	0.000
96	A	148	HIS	0	-0.050	-0.039	17.269	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	149	GLY	0	0.030	0.028	20.075	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	150	THR	0	-0.041	-0.032	21.159	0.024	0.024	0.000	0.000	0.000	0.000
99	A	151	VAL	0	0.013	0.012	24.103	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	152	THR	0	0.015	-0.013	26.427	0.012	0.012	0.000	0.000	0.000	0.000
101	A	153	GLY	0	0.006	0.009	29.676	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	154	ALA	0	-0.017	-0.005	27.136	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	155	ALA	0	-0.039	0.001	29.118	0.011	0.011	0.000	0.000	0.000	0.000
104	A	156	GLY	0	-0.040	-0.038	29.174	0.003	0.003	0.000	0.000	0.000	0.000
105	A	157	GLY	0	-0.022	-0.013	24.822	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	158	VAL	0	0.034	0.011	21.390	0.004	0.004	0.000	0.000	0.000	0.000
107	A	159	LEU	0	-0.017	0.017	19.679	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	160	LEU	0	0.016	0.004	16.288	0.018	0.018	0.000	0.000	0.000	0.000
109	A	161	ARG	1	0.896	0.962	15.963	0.441	0.441	0.000	0.000	0.000	0.000
110	A	162	PRO	0	0.013	0.017	11.665	0.085	0.085	0.000	0.000	0.000	0.000
111	A	163	PHE	0	-0.013	0.004	13.449	-0.047	-0.047	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.029	0.015	11.876	-0.047	-0.047	0.000	0.000	0.000	0.000
113	A	165	ARG	1	0.760	0.843	13.988	0.557	0.557	0.000	0.000	0.000	0.000
114	A	166	LEU	0	0.033	0.019	16.795	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	167	ILE	0	-0.030	-0.020	18.443	0.028	0.028	0.000	0.000	0.000	0.000
116	A	168	ALA	0	0.040	0.027	22.157	0.005	0.005	0.000	0.000	0.000	0.000
117	A	169	SER	0	-0.026	-0.024	24.528	0.014	0.014	0.000	0.000	0.000	0.000
118	A	170	THR	0	-0.068	-0.057	27.536	0.013	0.013	0.000	0.000	0.000	0.000
119	A	171	GLY	0	-0.033	-0.015	28.032	0.013	0.013	0.000	0.000	0.000	0.000
120	A	172	ASP	-1	-0.827	-0.884	24.994	-0.237	-0.237	0.000	0.000	0.000	0.000
121	A	173	SER	0	-0.014	-0.007	22.299	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	174	VAL	0	0.005	0.014	17.795	0.013	0.013	0.000	0.000	0.000	0.000
123	A	175	THR	0	0.005	-0.015	17.055	-0.043	-0.043	0.000	0.000	0.000	0.000
124	A	176	THR	0	-0.037	-0.009	11.734	0.111	0.111	0.000	0.000	0.000	0.000
125	A	177	TYR	0	-0.011	-0.019	14.079	-0.048	-0.048	0.000	0.000	0.000	0.000
126	A	178	GLY	0	0.031	0.022	11.239	-0.079	-0.079	0.000	0.000	0.000	0.000
127	A	179	GLU	-1	-0.970	-0.989	11.647	-0.405	-0.405	0.000	0.000	0.000	0.000
128	A	180	PRO	0	-0.056	-0.048	13.054	-0.067	-0.067	0.000	0.000	0.000	0.000
129	A	181	TRP	0	0.060	0.041	8.509	0.163	0.163	0.000	0.000	0.000	0.000
130	A	182	ASN	0	-0.009	-0.027	15.227	0.038	0.038	0.000	0.000	0.000	0.000
131	A	183	MET	0	-0.031	-0.021	15.980	0.025	0.025	0.000	0.000	0.000	0.000
132	A	184	ASN	0	0.008	0.024	20.161	0.039	0.039	0.000	0.000	0.000	0.000

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