FMO DATABASE

FMODB ID: R8ZK8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1014181.097884
FMO2-HF: Nuclear repulsion	965680.00153
FMO2-HF: Total energy	-48501.096354
FMO2-MP2: Total energy	-48645.192788

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.
-13.317	-10.295	5.872	-4.289	-4.604	-0.034

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 : 0.028 / q_NPA : -0.003

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

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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	-0.796	-0.901	3.801	-6.109	-4.929	-0.008	-0.591	-0.581	0.002
4	A	4	ASN	0	-0.046	0.007	5.733	1.149	1.149	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.884	-0.943	9.211	-0.927	-0.927	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.013	0.001	11.628	0.112	0.112	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.021	-0.007	15.361	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.050	-0.028	17.768	0.012	0.012	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.017	0.007	21.472	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.779	-0.868	24.362	-0.201	-0.201	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.021	-0.003	26.130	0.017	0.017	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.109	-0.070	28.351	0.015	0.015	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.913	-0.956	28.014	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.811	0.908	23.865	0.203	0.203	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.058	-0.022	19.849	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.014	-0.005	19.507	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.019	0.010	13.385	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.029	-0.002	13.248	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	19	GLN	0	0.013	-0.022	8.593	-0.131	-0.131	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.045	-0.044	8.165	0.241	0.241	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.015	-0.030	2.308	-0.892	-0.763	1.634	-0.780	-0.983	-0.001
22	A	22	ASP	-1	-0.847	-0.936	2.060	-10.752	-9.227	4.244	-2.879	-2.890	-0.035
23	A	23	THR	0	-0.070	-0.047	3.950	1.958	2.146	0.002	-0.039	-0.150	0.000
24	A	24	PHE	0	-0.057	-0.026	7.150	0.235	0.235	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.001	-0.006	9.524	0.094	0.094	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.031	-0.009	13.085	0.122	0.122	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.054	0.024	15.175	0.022	0.022	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.010	0.003	18.691	0.030	0.030	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.063	-0.048	21.417	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.016	0.022	25.184	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.027	0.021	26.785	0.022	0.022	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.815	-0.920	28.527	-0.145	-0.145	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.892	0.944	27.870	0.125	0.125	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.041	0.052	31.209	0.013	0.013	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.999	0.988	30.122	0.098	0.098	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.053	-0.041	30.329	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.042	-0.009	27.200	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.799	0.920	22.937	0.212	0.212	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.777	-0.903	22.382	-0.220	-0.220	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.017	-0.003	17.246	0.038	0.038	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.017	-0.014	15.969	0.028	0.028	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.003	0.011	11.637	0.092	0.092	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.042	-0.031	9.693	0.171	0.171	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.083	0.056	7.592	-0.232	-0.232	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.872	0.938	5.250	2.000	2.000	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.043	0.045	8.191	-0.419	-0.419	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.878	0.936	5.327	1.164	1.164	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.002	0.013	10.839	-0.106	-0.106	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.021	0.011	12.211	0.041	0.041	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.017	0.028	15.755	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.005	0.011	19.481	0.030	0.030	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.031	0.002	21.758	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.050	-0.039	25.535	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.071	0.038	28.159	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.043	-0.021	22.497	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.942	-0.971	23.370	-0.112	-0.112	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.980	-0.992	25.012	-0.103	-0.103	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.065	-0.017	20.522	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.859	-0.940	23.879	-0.186	-0.186	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.018	-0.025	22.543	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.025	-0.001	20.977	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	-0.872	-0.941	17.084	-0.431	-0.431	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.029	-0.012	11.082	-0.103	-0.103	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.014	0.009	14.658	0.100	0.100	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.006	0.000	14.701	-0.082	-0.082	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.009	0.001	16.998	0.047	0.047	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.007	-0.011	19.489	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.002	0.002	22.026	0.024	0.024	0.000	0.000	0.000	0.000
70	A	122	GLY	0	-0.003	-0.024	23.964	0.002	0.002	0.000	0.000	0.000	0.000
71	A	123	PRO	0	-0.040	0.001	26.798	0.015	0.015	0.000	0.000	0.000	0.000
72	A	124	GLY	0	0.025	0.007	28.298	0.016	0.016	0.000	0.000	0.000	0.000
73	A	125	ILE	0	-0.021	-0.013	24.277	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	126	GLN	0	-0.019	-0.007	24.991	0.009	0.009	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.823	-0.910	20.986	-0.481	-0.481	0.000	0.000	0.000	0.000
76	A	128	VAL	0	-0.015	0.008	20.026	0.037	0.037	0.000	0.000	0.000	0.000
77	A	129	ALA	0	0.038	0.023	19.411	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	130	THR	0	-0.050	-0.053	15.952	0.054	0.054	0.000	0.000	0.000	0.000
79	A	131	PHE	0	-0.031	-0.018	13.165	0.040	0.040	0.000	0.000	0.000	0.000
80	A	132	SER	0	-0.038	-0.037	18.382	-0.037	-0.037	0.000	0.000	0.000	0.000
81	A	133	VAL	0	-0.039	-0.029	18.012	0.038	0.038	0.000	0.000	0.000	0.000
82	A	134	ASP	-1	-0.856	-0.914	20.324	-0.287	-0.287	0.000	0.000	0.000	0.000
83	A	135	VAL	0	-0.110	-0.054	17.697	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	136	SER	0	0.067	0.028	21.120	0.011	0.011	0.000	0.000	0.000	0.000
85	A	137	GLY	0	0.000	0.012	21.082	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	138	ALA	0	0.032	-0.006	20.060	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.974	-0.997	14.990	-0.164	-0.164	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.039	0.017	14.515	0.040	0.040	0.000	0.000	0.000	0.000
89	A	141	GLY	0	-0.024	-0.026	11.549	-0.100	-0.100	0.000	0.000	0.000	0.000
90	A	142	VAL	0	-0.027	0.007	12.299	0.099	0.099	0.000	0.000	0.000	0.000
91	A	143	ALA	0	-0.036	-0.017	9.795	-0.197	-0.197	0.000	0.000	0.000	0.000
92	A	144	VAL	0	0.013	0.014	11.275	0.185	0.185	0.000	0.000	0.000	0.000
93	A	145	SER	0	-0.033	-0.032	11.571	-0.160	-0.160	0.000	0.000	0.000	0.000
94	A	146	ASN	0	0.014	-0.012	13.224	0.051	0.051	0.000	0.000	0.000	0.000
95	A	147	ALA	0	0.037	0.046	15.271	0.069	0.069	0.000	0.000	0.000	0.000
96	A	148	HIS	0	-0.044	-0.027	17.322	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	149	GLY	0	0.026	0.022	20.127	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	150	THR	0	-0.039	-0.030	21.222	0.024	0.024	0.000	0.000	0.000	0.000
99	A	151	VAL	0	0.010	0.008	24.150	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	152	THR	0	0.020	-0.015	26.349	0.012	0.012	0.000	0.000	0.000	0.000
101	A	153	GLY	0	0.005	0.003	29.603	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	154	ALA	0	-0.019	-0.004	27.099	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	155	ALA	0	-0.037	0.001	29.059	0.011	0.011	0.000	0.000	0.000	0.000
104	A	156	GLY	0	-0.045	-0.040	29.137	0.004	0.004	0.000	0.000	0.000	0.000
105	A	157	GLY	0	-0.039	-0.023	24.780	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	158	VAL	0	0.033	0.014	21.326	0.006	0.006	0.000	0.000	0.000	0.000
107	A	159	LEU	0	-0.007	0.020	19.635	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	160	LEU	0	0.014	0.004	16.378	0.020	0.020	0.000	0.000	0.000	0.000
109	A	161	ARG	1	0.931	0.989	15.912	0.420	0.420	0.000	0.000	0.000	0.000
110	A	162	PRO	0	0.019	0.019	11.627	0.085	0.085	0.000	0.000	0.000	0.000
111	A	163	PHE	0	0.001	0.011	13.393	-0.046	-0.046	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.026	0.010	11.856	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	165	ARG	1	0.823	0.903	13.972	0.558	0.558	0.000	0.000	0.000	0.000
114	A	166	LEU	0	0.020	0.016	16.814	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	167	ILE	0	-0.014	-0.016	18.433	0.026	0.026	0.000	0.000	0.000	0.000
116	A	168	ALA	0	0.033	0.023	22.147	0.005	0.005	0.000	0.000	0.000	0.000
117	A	169	SER	0	0.006	0.008	24.519	0.009	0.009	0.000	0.000	0.000	0.000
118	A	170	THR	0	-0.056	-0.044	27.525	0.011	0.011	0.000	0.000	0.000	0.000
119	A	171	GLY	0	-0.037	-0.014	28.026	0.013	0.013	0.000	0.000	0.000	0.000
120	A	172	ASP	-1	-0.840	-0.902	25.155	-0.225	-0.225	0.000	0.000	0.000	0.000
121	A	173	SER	0	-0.017	-0.008	22.335	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	174	VAL	0	0.016	0.018	17.794	0.014	0.014	0.000	0.000	0.000	0.000
123	A	175	THR	0	-0.051	-0.034	16.911	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	176	THR	0	-0.008	-0.001	11.741	0.109	0.109	0.000	0.000	0.000	0.000
125	A	177	TYR	0	-0.001	-0.025	14.030	-0.050	-0.050	0.000	0.000	0.000	0.000
126	A	178	GLY	0	0.025	0.023	11.207	-0.076	-0.076	0.000	0.000	0.000	0.000
127	A	179	GLU	-1	-0.978	-0.995	11.629	-0.358	-0.358	0.000	0.000	0.000	0.000
128	A	180	PRO	0	-0.054	-0.044	13.027	-0.072	-0.072	0.000	0.000	0.000	0.000
129	A	181	TRP	0	0.069	0.046	8.482	0.159	0.159	0.000	0.000	0.000	0.000
130	A	182	ASN	0	-0.004	-0.025	15.190	0.035	0.035	0.000	0.000	0.000	0.000
131	A	183	MET	0	-0.030	-0.021	16.052	0.026	0.026	0.000	0.000	0.000	0.000
132	A	184	ASN	0	-0.022	-0.001	20.113	0.036	0.036	0.000	0.000	0.000	0.000

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