FMO DATABASE

FMODB ID: 2NG3R

Calculation Name: 5EPW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EPW

Chain ID: A

ChEMBL ID:

UniProt ID: Q6Q1R8

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-735306.031483
FMO2-HF: Nuclear repulsion	693874.43345
FMO2-HF: Total energy	-41431.598033
FMO2-MP2: Total energy	-41552.676541

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:228:PRO)

Summations of interaction energy for fragment #1(A:228:PRO)

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.
-1.747	1.323	0.286	-1.381	-1.973	0.003

Interaction energy analysis for fragmet #1(A:228:PRO)

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 : -0.009

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	230	GLN	0	0.129	0.039	3.450	-1.726	0.464	0.011	-1.150	-1.050	0.002
4	A	231	LEU	0	-0.057	-0.029	6.182	0.392	0.392	0.000	0.000	0.000	0.000
5	A	232	LYS	1	0.849	0.925	2.712	-0.455	0.316	0.276	-0.227	-0.820	0.001
6	A	233	LYS	1	0.866	0.959	5.153	1.811	1.920	-0.001	-0.004	-0.103	0.000
7	A	234	PRO	0	0.050	0.014	7.166	0.091	0.091	0.000	0.000	0.000	0.000
8	A	235	ARG	1	0.928	0.949	10.910	0.205	0.205	0.000	0.000	0.000	0.000
9	A	236	TRP	0	0.092	0.041	12.817	-0.059	-0.059	0.000	0.000	0.000	0.000
10	A	237	LYS	1	0.936	0.972	10.454	0.582	0.582	0.000	0.000	0.000	0.000
11	A	238	ARG	1	0.816	0.927	9.039	0.505	0.505	0.000	0.000	0.000	0.000
12	A	239	VAL	0	-0.010	-0.016	10.012	0.159	0.159	0.000	0.000	0.000	0.000
13	A	240	PRO	0	-0.018	0.005	10.710	-0.146	-0.146	0.000	0.000	0.000	0.000
14	A	241	THR	0	0.006	-0.011	10.088	0.010	0.010	0.000	0.000	0.000	0.000
15	A	242	ARG	1	0.855	0.905	12.753	0.188	0.188	0.000	0.000	0.000	0.000
16	A	243	GLU	-1	-0.888	-0.935	9.188	-0.550	-0.550	0.000	0.000	0.000	0.000
17	A	244	GLU	-1	-0.745	-0.842	6.775	-1.865	-1.865	0.000	0.000	0.000	0.000
18	A	245	ASN	0	0.045	0.028	10.573	-0.094	-0.094	0.000	0.000	0.000	0.000
19	A	246	VAL	0	0.036	0.008	14.015	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	247	ILE	0	-0.013	-0.009	16.385	0.001	0.001	0.000	0.000	0.000	0.000
21	A	248	GLN	0	-0.003	0.011	11.366	0.002	0.002	0.000	0.000	0.000	0.000
22	A	249	CYS	0	-0.083	-0.020	11.238	-0.099	-0.099	0.000	0.000	0.000	0.000
23	A	250	PHE	0	-0.039	-0.014	12.532	0.009	0.009	0.000	0.000	0.000	0.000
24	A	251	GLY	0	0.087	0.049	15.873	0.034	0.034	0.000	0.000	0.000	0.000
25	A	252	PRO	0	0.019	0.005	18.730	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	253	ARG	1	0.824	0.918	20.105	0.223	0.223	0.000	0.000	0.000	0.000
27	A	254	ASP	-1	-0.710	-0.837	24.317	-0.130	-0.130	0.000	0.000	0.000	0.000
28	A	255	PHE	0	0.024	-0.003	26.834	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	256	ASN	0	-0.038	-0.009	26.025	0.002	0.002	0.000	0.000	0.000	0.000
30	A	257	HIS	1	0.755	0.844	22.088	0.164	0.164	0.000	0.000	0.000	0.000
31	A	258	ASN	0	0.039	0.009	24.203	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	259	MET	0	-0.030	0.014	23.916	0.014	0.014	0.000	0.000	0.000	0.000
33	A	260	GLY	0	0.023	0.021	23.734	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	261	ASP	-1	-0.768	-0.872	24.805	-0.152	-0.152	0.000	0.000	0.000	0.000
35	A	262	SER	0	-0.004	-0.025	23.985	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	263	ASP	-1	-0.876	-0.923	22.639	-0.190	-0.190	0.000	0.000	0.000	0.000
37	A	264	LEU	0	0.025	-0.009	21.040	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	265	VAL	0	-0.068	-0.027	19.419	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	266	GLN	0	-0.004	0.010	18.140	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	267	ASN	0	0.008	-0.011	16.810	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	268	GLY	0	0.005	0.008	15.691	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	269	VAL	0	-0.035	-0.026	14.022	0.048	0.048	0.000	0.000	0.000	0.000
43	A	270	ASP	-1	-0.821	-0.893	14.187	-0.466	-0.466	0.000	0.000	0.000	0.000
44	A	271	ALA	0	-0.013	-0.002	17.149	0.054	0.054	0.000	0.000	0.000	0.000
45	A	272	LYS	1	0.893	0.917	19.564	0.222	0.222	0.000	0.000	0.000	0.000
46	A	273	GLY	0	-0.027	-0.022	23.385	0.006	0.006	0.000	0.000	0.000	0.000
47	A	274	PHE	0	0.042	0.028	18.760	0.004	0.004	0.000	0.000	0.000	0.000
48	A	275	PRO	0	0.040	0.015	21.722	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	276	GLN	0	-0.006	-0.014	23.546	0.004	0.004	0.000	0.000	0.000	0.000
50	A	277	LEU	0	-0.050	-0.013	24.312	0.008	0.008	0.000	0.000	0.000	0.000
51	A	278	ALA	0	0.006	0.000	21.868	0.003	0.003	0.000	0.000	0.000	0.000
52	A	279	GLU	-1	-0.884	-0.938	23.750	-0.169	-0.169	0.000	0.000	0.000	0.000
53	A	280	LEU	0	-0.097	-0.047	26.795	0.014	0.014	0.000	0.000	0.000	0.000
54	A	281	ILE	0	-0.036	-0.006	21.542	0.001	0.001	0.000	0.000	0.000	0.000
55	A	282	PRO	0	0.013	0.031	24.478	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	283	ASN	0	0.026	0.007	22.244	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	284	GLN	0	0.041	-0.010	16.128	0.019	0.019	0.000	0.000	0.000	0.000
58	A	285	ALA	0	0.013	0.011	21.820	0.012	0.012	0.000	0.000	0.000	0.000
59	A	286	ALA	0	0.025	0.016	25.065	0.013	0.013	0.000	0.000	0.000	0.000
60	A	287	LEU	0	0.001	0.011	21.930	0.008	0.008	0.000	0.000	0.000	0.000
61	A	288	PHE	0	-0.032	-0.013	24.244	0.012	0.012	0.000	0.000	0.000	0.000
62	A	289	PHE	0	-0.038	-0.020	26.044	0.010	0.010	0.000	0.000	0.000	0.000
63	A	290	ASP	-1	-0.882	-0.937	29.102	-0.130	-0.130	0.000	0.000	0.000	0.000
64	A	291	SER	0	-0.101	-0.066	27.449	0.001	0.001	0.000	0.000	0.000	0.000
65	A	292	GLU	-1	-0.871	-0.905	30.119	-0.116	-0.116	0.000	0.000	0.000	0.000
66	A	293	VAL	0	-0.031	-0.027	26.708	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	294	SER	0	0.009	0.002	28.829	0.008	0.008	0.000	0.000	0.000	0.000
68	A	295	THR	0	-0.069	-0.052	26.691	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	296	ASP	-1	-0.903	-0.945	27.552	-0.081	-0.081	0.000	0.000	0.000	0.000
70	A	297	GLU	-1	-0.943	-0.957	27.135	-0.082	-0.082	0.000	0.000	0.000	0.000
71	A	298	VAL	0	0.000	-0.009	24.911	0.004	0.004	0.000	0.000	0.000	0.000
72	A	299	GLY	0	-0.064	-0.042	24.721	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	300	ASP	-1	-0.953	-0.968	21.798	-0.061	-0.061	0.000	0.000	0.000	0.000
74	A	301	ASN	0	-0.075	-0.032	19.614	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	302	VAL	0	0.044	0.025	22.402	0.008	0.008	0.000	0.000	0.000	0.000
76	A	303	GLN	0	-0.065	-0.032	22.393	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	304	ILE	0	0.007	-0.002	21.618	0.007	0.007	0.000	0.000	0.000	0.000
78	A	305	THR	0	-0.009	0.004	23.638	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	306	TYR	0	0.008	0.003	22.145	0.003	0.003	0.000	0.000	0.000	0.000
80	A	307	THR	0	-0.053	-0.038	26.513	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	308	TYR	0	-0.061	-0.048	27.790	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	309	LYS	1	0.908	0.951	29.781	0.112	0.112	0.000	0.000	0.000	0.000
83	A	310	MET	0	0.066	0.052	29.454	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	311	LEU	0	-0.008	-0.012	33.122	0.004	0.004	0.000	0.000	0.000	0.000
85	A	312	VAL	0	0.002	0.005	32.979	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	313	ALA	0	0.014	0.019	36.206	0.005	0.005	0.000	0.000	0.000	0.000
87	A	314	LYS	1	0.996	0.972	38.365	0.075	0.075	0.000	0.000	0.000	0.000
88	A	315	ASP	-1	-0.845	-0.926	40.025	-0.091	-0.091	0.000	0.000	0.000	0.000
89	A	316	ASN	0	0.003	0.014	33.713	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	317	LYS	1	0.891	0.920	35.230	0.095	0.095	0.000	0.000	0.000	0.000
91	A	318	ASN	0	0.060	0.044	30.593	0.006	0.006	0.000	0.000	0.000	0.000
92	A	319	LEU	0	-0.045	-0.018	31.920	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	320	PRO	0	0.015	0.004	33.664	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	321	LYS	1	0.985	1.007	27.604	0.150	0.150	0.000	0.000	0.000	0.000
95	A	322	PHE	0	0.045	0.015	26.327	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	323	ILE	0	0.020	-0.011	30.326	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	324	GLU	-1	-0.939	-0.974	31.853	-0.108	-0.108	0.000	0.000	0.000	0.000
98	A	325	GLN	0	-0.005	-0.021	26.423	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	326	ILE	0	0.016	0.020	28.353	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	327	SER	0	0.025	0.010	29.150	0.008	0.008	0.000	0.000	0.000	0.000
101	A	328	ALA	0	0.028	0.038	28.161	0.011	0.011	0.000	0.000	0.000	0.000
102	A	329	PHE	0	-0.039	-0.029	27.356	0.007	0.007	0.000	0.000	0.000	0.000
103	A	330	THR	0	-0.079	-0.045	29.353	0.008	0.008	0.000	0.000	0.000	0.000
104	A	331	LYS	1	0.836	0.945	32.664	0.121	0.121	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:228:PRO)