FMO DATABASE

FMODB ID: 2NN5R

Calculation Name: 5EXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EXV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KL40

Base Structure: X-ray

Registration Date: 2023-09-21

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1600184.755825
FMO2-HF: Nuclear repulsion	1536114.540277
FMO2-HF: Total energy	-64070.215548
FMO2-MP2: Total energy	-64257.048435

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-8.521	-6.24	14.487	-7.273	-9.496	-0.04

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.016

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	5	GLN	0	0.146	0.073	2.391	-10.706	-7.727	4.805	-3.397	-4.388	-0.023
4	A	6	GLN	0	-0.058	-0.041	2.250	0.310	-1.046	9.684	-3.679	-4.649	-0.017
5	A	7	GLN	0	-0.118	-0.037	4.095	0.570	1.127	-0.001	-0.191	-0.365	0.000
6	A	8	VAL	0	-0.022	-0.032	5.357	0.750	0.851	-0.001	-0.006	-0.094	0.000
7	A	9	ALA	0	0.077	0.037	8.693	0.208	0.208	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.061	-0.021	10.000	0.149	0.149	0.000	0.000	0.000	0.000
9	A	11	LEU	0	0.051	-0.007	12.206	0.069	0.069	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.053	0.052	11.067	0.081	0.081	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.857	-0.970	13.682	-0.330	-0.330	0.000	0.000	0.000	0.000
12	A	14	GLN	0	-0.018	-0.024	16.257	0.044	0.044	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.086	-0.019	17.216	0.044	0.044	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.051	0.032	18.683	0.006	0.006	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.026	-0.043	20.494	0.021	0.021	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.005	0.007	17.375	0.023	0.023	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.020	-0.020	17.533	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.048	-0.002	14.355	0.003	0.003	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.026	0.017	15.245	0.032	0.032	0.000	0.000	0.000	0.000
20	A	22	ALA	0	0.027	0.014	17.430	0.020	0.020	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.043	-0.004	12.613	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.007	0.013	13.112	0.013	0.013	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.899	-0.946	14.197	0.159	0.159	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.074	-0.035	14.882	0.022	0.022	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.062	-0.030	10.007	-0.039	-0.039	0.000	0.000	0.000	0.000
26	A	28	ASN	0	-0.059	-0.015	11.435	0.103	0.103	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.063	-0.026	8.361	0.132	0.132	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.047	-0.079	11.496	-0.140	-0.140	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.855	-0.952	11.957	0.095	0.095	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.016	0.001	11.458	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.766	-0.819	7.996	0.802	0.802	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.035	-0.015	7.798	0.146	0.146	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.025	-0.018	9.908	-0.135	-0.135	0.000	0.000	0.000	0.000
34	A	36	HIS	0	0.022	0.000	5.759	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	37	ALA	0	-0.083	-0.028	5.665	-0.174	-0.174	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.014	-0.005	6.615	-0.466	-0.466	0.000	0.000	0.000	0.000
37	A	39	PRO	0	-0.012	-0.016	8.859	-0.089	-0.089	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.890	-0.959	10.249	-0.265	-0.265	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.977	-0.979	11.739	-0.350	-0.350	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.077	-0.023	13.148	0.061	0.061	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.038	-0.018	11.344	0.068	0.068	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.064	0.028	14.334	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.043	-0.020	11.282	0.038	0.038	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.037	-0.016	14.564	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.868	-0.938	16.622	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.008	-0.016	18.095	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.073	-0.035	19.699	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	HIS	0	0.001	-0.003	22.600	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.094	0.047	23.216	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.067	-0.072	25.149	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.035	0.026	27.239	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.023	0.026	23.840	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.017	-0.005	26.783	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.868	-0.907	28.869	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.083	-0.057	29.046	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.006	-0.008	27.319	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.062	-0.029	31.325	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.984	-0.974	34.229	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	61	TRP	0	0.003	0.004	27.924	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.061	0.060	33.426	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	63	PRO	0	-0.034	-0.035	34.735	0.002	0.002	0.000	0.000	0.000	0.000
62	A	64	VAL	0	0.006	0.010	29.490	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.031	-0.021	30.048	0.003	0.003	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.035	-0.007	28.669	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.006	-0.001	26.454	0.001	0.001	0.000	0.000	0.000	0.000
66	A	68	MET	0	0.022	0.009	26.393	0.003	0.003	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.028	-0.009	24.036	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	70	ILE	0	0.084	0.032	26.278	0.009	0.009	0.000	0.000	0.000	0.000
69	A	71	ALA	0	-0.016	-0.013	28.050	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	72	GLY	0	0.046	0.034	27.286	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.059	-0.020	28.295	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.009	-0.017	26.882	0.004	0.004	0.000	0.000	0.000	0.000
73	A	75	PHE	0	-0.032	-0.006	30.040	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.895	-0.960	30.595	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.029	-0.012	32.177	0.000	0.000	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.919	0.949	33.320	0.029	0.029	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.032	0.016	34.970	0.001	0.001	0.000	0.000	0.000	0.000
78	A	80	PRO	0	0.008	0.010	34.873	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.023	0.023	30.032	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	PRO	0	0.027	0.031	33.546	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.967	0.969	34.788	0.010	0.010	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.066	-0.012	35.529	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.950	0.983	36.446	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.055	0.035	33.499	0.001	0.001	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.021	-0.016	36.260	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.921	0.948	37.681	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.046	0.034	35.160	0.002	0.002	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.065	-0.021	32.698	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	TYR	0	0.084	0.078	30.050	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.041	-0.031	33.177	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.047	0.035	35.923	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.088	-0.031	37.802	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.037	0.045	39.653	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.861	0.925	40.373	0.011	0.011	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.950	-1.012	43.003	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.023	0.036	41.963	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.830	-0.901	38.410	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.020	-0.008	31.900	0.002	0.002	0.000	0.000	0.000	0.000
99	A	101	HIS	0	-0.040	-0.016	36.406	0.000	0.000	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.036	-0.012	35.477	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.067	-0.065	34.722	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.045	0.030	29.090	0.003	0.003	0.000	0.000	0.000	0.000
103	A	105	LYS	1	0.857	0.933	28.243	-0.043	-0.043	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.065	0.006	26.041	0.005	0.005	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.860	-0.918	24.764	0.038	0.038	0.000	0.000	0.000	0.000
106	A	108	ASN	0	-0.076	-0.045	24.024	0.000	0.000	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.055	-0.022	20.624	0.011	0.011	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.033	-0.024	16.388	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	111	HIS	0	-0.011	-0.001	12.661	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	112	VAL	0	0.012	0.006	17.179	0.007	0.007	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.005	0.008	14.966	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.017	-0.004	16.722	0.009	0.009	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.019	0.013	15.893	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.054	-0.089	17.550	0.015	0.015	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.971	1.034	16.378	0.172	0.172	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.007	0.066	18.812	0.030	0.030	0.000	0.000	0.000	0.000
117	A	119	PHE	0	0.010	0.013	20.970	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.029	-0.009	23.400	0.011	0.011	0.000	0.000	0.000	0.000
119	A	121	GLY	0	-0.010	-0.002	25.060	0.008	0.008	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.784	0.857	25.907	0.104	0.104	0.000	0.000	0.000	0.000
121	A	123	GLU	-1	-0.846	-0.912	23.518	-0.124	-0.124	0.000	0.000	0.000	0.000
122	A	124	SER	0	-0.108	-0.117	21.757	0.017	0.017	0.000	0.000	0.000	0.000
123	A	125	HIS	0	0.059	0.028	21.788	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	126	TYR	0	-0.005	-0.011	17.869	0.008	0.008	0.000	0.000	0.000	0.000
125	A	127	PHE	0	0.056	0.039	21.225	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.011	-0.001	18.771	0.008	0.008	0.000	0.000	0.000	0.000
127	A	129	PHE	0	-0.018	-0.002	18.866	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	130	PHE	0	0.030	0.009	15.593	0.008	0.008	0.000	0.000	0.000	0.000
129	A	131	THR	0	0.027	0.006	17.488	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	132	ALA	0	-0.025	0.009	16.525	0.016	0.016	0.000	0.000	0.000	0.000
131	A	133	GLN	0	0.016	0.000	15.655	0.034	0.034	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.036	0.012	14.350	0.037	0.037	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.944	-0.977	15.222	0.112	0.112	0.000	0.000	0.000	0.000
134	A	136	ASN	0	-0.015	-0.009	18.156	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	137	ALA	0	-0.009	0.014	19.627	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	138	PHE	0	-0.033	-0.033	22.554	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	139	LYS	1	0.949	0.969	21.212	0.007	0.007	0.000	0.000	0.000	0.000
138	A	140	ILE	0	-0.018	-0.001	23.836	0.000	0.000	0.000	0.000	0.000	0.000
139	A	141	TYR	0	0.018	0.006	22.676	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	142	LEU	0	0.038	0.009	25.866	0.005	0.005	0.000	0.000	0.000	0.000
141	A	143	GLY	0	-0.023	0.001	28.474	0.000	0.000	0.000	0.000	0.000	0.000
142	A	144	ARG	1	0.844	0.916	28.869	0.049	0.049	0.000	0.000	0.000	0.000
143	A	145	ASP	-1	-0.847	-0.909	34.045	-0.043	-0.043	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.949	-0.970	37.519	-0.037	-0.037	0.000	0.000	0.000	0.000
145	A	147	LYS	1	0.898	0.966	35.399	0.064	0.064	0.000	0.000	0.000	0.000
146	A	148	ARG	1	0.921	0.918	31.329	0.068	0.068	0.000	0.000	0.000	0.000
147	A	149	GLU	-1	-0.875	-0.943	29.896	-0.092	-0.092	0.000	0.000	0.000	0.000
148	A	150	LEU	0	0.051	0.038	27.736	0.006	0.006	0.000	0.000	0.000	0.000
149	A	151	ILE	0	0.033	0.035	31.760	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	152	PRO	0	0.002	-0.008	31.859	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	153	GLU	-1	-0.914	-0.956	32.038	-0.054	-0.054	0.000	0.000	0.000	0.000
152	A	154	GLN	0	-0.044	-0.057	29.817	-0.005	-0.005	0.000	0.000	0.000	0.000
153	A	155	VAL	0	-0.014	0.003	25.919	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	156	ALA	0	0.020	0.008	26.480	-0.009	-0.009	0.000	0.000	0.000	0.000
155	A	157	ARG	1	0.988	0.994	27.323	0.049	0.049	0.000	0.000	0.000	0.000
156	A	158	PHE	0	-0.056	-0.025	20.616	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	159	LYS	1	0.919	0.945	20.228	0.174	0.174	0.000	0.000	0.000	0.000
158	A	160	ALA	0	-0.017	0.005	22.846	-0.007	-0.007	0.000	0.000	0.000	0.000
159	A	161	MET	0	-0.085	-0.023	22.212	0.006	0.006	0.000	0.000	0.000	0.000
160	A	162	GLN	0	0.049	0.076	16.514	0.006	0.006	0.000	0.000	0.000	0.000
161	A	163	GLN	0	-0.033	-0.036	19.200	0.013	0.013	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.047	-0.003	20.221	0.003	0.003	0.000	0.000	0.000	0.000
163	A	165	HIS	0	-0.065	-0.015	23.106	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)