FMO DATABASE

FMODB ID: 17NKZ

Calculation Name: 2CE3-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CE3

Chain ID: F

ChEMBL ID:

UniProt ID: P9WPC5

Base Structure: X-ray

Registration Date: 2023-06-22

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1660877.778027
FMO2-HF: Nuclear repulsion	1595298.981194
FMO2-HF: Total energy	-65578.796834
FMO2-MP2: Total energy	-65766.500272

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(F:15:SER)

Summations of interaction energy for fragment #1(F:15: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.
-45.098	-45.226	25.098	-14.604	-10.365	-0.055

Interaction energy analysis for fragmet #1(F:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.031

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	F	17	THR	0	0.015	-0.007	2.773	-4.841	-0.713	0.786	-2.223	-2.690	0.015
4	F	18	ASP	-1	-0.819	-0.879	1.609	-40.015	-44.890	24.300	-12.166	-7.259	-0.070
5	F	19	SER	0	-0.024	0.001	3.686	0.285	0.904	0.012	-0.215	-0.416	0.000
6	F	20	VAL	0	-0.018	-0.016	5.630	0.393	0.393	0.000	0.000	0.000	0.000
7	F	21	TYR	0	0.007	0.000	6.173	0.112	0.112	0.000	0.000	0.000	0.000
8	F	22	GLU	-1	-0.911	-0.940	7.832	-1.480	-1.480	0.000	0.000	0.000	0.000
9	F	23	ARG	1	0.952	0.964	9.504	0.863	0.863	0.000	0.000	0.000	0.000
10	F	24	LEU	0	-0.032	-0.018	11.091	0.121	0.121	0.000	0.000	0.000	0.000
11	F	25	LEU	0	0.020	0.015	12.257	0.073	0.073	0.000	0.000	0.000	0.000
12	F	26	SER	0	-0.036	-0.020	13.515	0.049	0.049	0.000	0.000	0.000	0.000
13	F	27	GLU	-1	-1.006	-0.988	15.805	-0.255	-0.255	0.000	0.000	0.000	0.000
14	F	28	ARG	1	0.754	0.851	17.576	0.339	0.339	0.000	0.000	0.000	0.000
15	F	29	ILE	0	-0.030	-0.005	15.716	0.052	0.052	0.000	0.000	0.000	0.000
16	F	30	ILE	0	0.019	0.010	14.123	-0.080	-0.080	0.000	0.000	0.000	0.000
17	F	31	PHE	0	0.012	-0.011	12.248	0.090	0.090	0.000	0.000	0.000	0.000
18	F	32	LEU	0	0.007	0.012	13.920	-0.071	-0.071	0.000	0.000	0.000	0.000
19	F	33	GLY	0	0.001	-0.007	13.313	0.056	0.056	0.000	0.000	0.000	0.000
20	F	34	SER	0	-0.013	-0.014	13.294	0.026	0.026	0.000	0.000	0.000	0.000
21	F	35	GLU	-1	-0.911	-0.912	15.344	-0.171	-0.171	0.000	0.000	0.000	0.000
22	F	36	VAL	0	0.006	-0.005	16.865	-0.048	-0.048	0.000	0.000	0.000	0.000
23	F	37	ASN	0	-0.006	-0.022	15.825	-0.015	-0.015	0.000	0.000	0.000	0.000
24	F	38	ASP	-1	-0.836	-0.950	18.834	-0.245	-0.245	0.000	0.000	0.000	0.000
25	F	39	GLU	-1	-0.908	-0.943	14.592	-0.507	-0.507	0.000	0.000	0.000	0.000
26	F	40	ILE	0	-0.057	-0.020	12.266	-0.093	-0.093	0.000	0.000	0.000	0.000
27	F	41	ALA	0	0.046	0.026	15.040	-0.033	-0.033	0.000	0.000	0.000	0.000
28	F	42	ASN	0	-0.004	0.002	16.850	0.018	0.018	0.000	0.000	0.000	0.000
29	F	43	ARG	1	0.952	0.967	10.085	1.010	1.010	0.000	0.000	0.000	0.000
30	F	44	LEU	0	-0.032	-0.010	14.374	-0.035	-0.035	0.000	0.000	0.000	0.000
31	F	45	CYS	0	-0.031	-0.011	16.115	0.020	0.020	0.000	0.000	0.000	0.000
32	F	46	ALA	0	0.011	0.000	15.728	0.022	0.022	0.000	0.000	0.000	0.000
33	F	47	GLN	0	-0.051	-0.034	12.611	-0.037	-0.037	0.000	0.000	0.000	0.000
34	F	48	ILE	0	0.016	0.011	16.230	0.025	0.025	0.000	0.000	0.000	0.000
35	F	49	LEU	0	-0.007	-0.009	19.756	0.025	0.025	0.000	0.000	0.000	0.000
36	F	50	LEU	0	-0.021	0.002	15.488	0.021	0.021	0.000	0.000	0.000	0.000
37	F	51	LEU	0	0.027	0.016	17.287	0.036	0.036	0.000	0.000	0.000	0.000
38	F	52	ALA	0	0.010	0.006	20.394	0.034	0.034	0.000	0.000	0.000	0.000
39	F	53	ALA	0	-0.077	-0.028	22.481	0.028	0.028	0.000	0.000	0.000	0.000
40	F	54	GLU	-1	-0.958	-0.983	17.952	-0.471	-0.471	0.000	0.000	0.000	0.000
41	F	55	ASP	-1	-0.824	-0.901	22.784	-0.191	-0.191	0.000	0.000	0.000	0.000
42	F	56	ALA	0	0.027	0.025	25.187	-0.009	-0.009	0.000	0.000	0.000	0.000
43	F	57	SER	0	-0.109	-0.056	27.791	0.016	0.016	0.000	0.000	0.000	0.000
44	F	58	LYS	1	0.863	0.915	24.402	0.240	0.240	0.000	0.000	0.000	0.000
45	F	59	ASP	-1	-0.803	-0.875	25.088	-0.173	-0.173	0.000	0.000	0.000	0.000
46	F	60	ILE	0	0.009	0.020	19.628	-0.023	-0.023	0.000	0.000	0.000	0.000
47	F	61	SER	0	-0.040	-0.019	19.899	0.037	0.037	0.000	0.000	0.000	0.000
48	F	62	LEU	0	0.037	0.017	17.746	-0.032	-0.032	0.000	0.000	0.000	0.000
49	F	63	TYR	0	-0.013	-0.013	16.752	0.055	0.055	0.000	0.000	0.000	0.000
50	F	64	ILE	0	-0.010	0.003	17.182	-0.028	-0.028	0.000	0.000	0.000	0.000
51	F	65	ASN	0	-0.021	-0.022	16.387	0.032	0.032	0.000	0.000	0.000	0.000
52	F	66	SER	0	-0.006	-0.014	17.096	0.002	0.002	0.000	0.000	0.000	0.000
53	F	67	PRO	0	0.011	-0.023	18.942	0.006	0.006	0.000	0.000	0.000	0.000
54	F	68	GLY	0	0.012	0.024	20.935	0.006	0.006	0.000	0.000	0.000	0.000
55	F	69	GLY	0	0.011	0.005	21.201	-0.009	-0.009	0.000	0.000	0.000	0.000
56	F	70	SER	0	-0.009	0.001	22.754	0.014	0.014	0.000	0.000	0.000	0.000
57	F	71	ILE	0	0.061	0.017	24.497	-0.012	-0.012	0.000	0.000	0.000	0.000
58	F	72	SER	0	0.046	0.018	26.456	-0.002	-0.002	0.000	0.000	0.000	0.000
59	F	73	ALA	0	-0.020	0.002	21.421	-0.009	-0.009	0.000	0.000	0.000	0.000
60	F	74	GLY	0	0.030	-0.007	22.776	-0.020	-0.020	0.000	0.000	0.000	0.000
61	F	75	MET	0	-0.015	-0.008	24.084	-0.002	-0.002	0.000	0.000	0.000	0.000
62	F	76	ALA	0	0.058	0.050	23.344	0.000	0.000	0.000	0.000	0.000	0.000
63	F	77	ILE	0	-0.016	-0.006	19.377	-0.011	-0.011	0.000	0.000	0.000	0.000
64	F	78	TYR	0	0.023	-0.001	22.663	0.000	0.000	0.000	0.000	0.000	0.000
65	F	79	ASP	-1	-0.892	-0.951	25.895	-0.164	-0.164	0.000	0.000	0.000	0.000
66	F	80	THR	0	-0.059	-0.035	21.896	-0.005	-0.005	0.000	0.000	0.000	0.000
67	F	81	MET	0	-0.073	-0.039	23.370	-0.008	-0.008	0.000	0.000	0.000	0.000
68	F	82	VAL	0	0.000	0.012	25.421	0.007	0.007	0.000	0.000	0.000	0.000
69	F	83	LEU	0	-0.082	-0.032	26.263	0.006	0.006	0.000	0.000	0.000	0.000
70	F	84	ALA	0	-0.040	-0.026	24.808	0.002	0.002	0.000	0.000	0.000	0.000
71	F	85	PRO	0	-0.011	-0.005	26.881	0.009	0.009	0.000	0.000	0.000	0.000
72	F	86	CYS	0	-0.062	-0.009	25.462	0.003	0.003	0.000	0.000	0.000	0.000
73	F	87	ASP	-1	-0.733	-0.840	27.457	-0.143	-0.143	0.000	0.000	0.000	0.000
74	F	88	ILE	0	-0.018	-0.005	22.609	-0.020	-0.020	0.000	0.000	0.000	0.000
75	F	89	ALA	0	0.017	0.018	24.429	0.018	0.018	0.000	0.000	0.000	0.000
76	F	90	THR	0	-0.031	-0.018	22.850	-0.018	-0.018	0.000	0.000	0.000	0.000
77	F	91	TYR	0	0.001	-0.002	21.272	0.027	0.027	0.000	0.000	0.000	0.000
78	F	92	ALA	0	-0.002	0.002	21.612	-0.006	-0.006	0.000	0.000	0.000	0.000
79	F	93	MET	0	-0.006	-0.012	15.599	0.030	0.030	0.000	0.000	0.000	0.000
80	F	94	GLY	0	0.026	0.008	20.875	0.024	0.024	0.000	0.000	0.000	0.000
81	F	95	MET	0	-0.102	-0.038	21.122	0.001	0.001	0.000	0.000	0.000	0.000
82	F	96	ALA	0	0.059	0.035	21.666	-0.015	-0.015	0.000	0.000	0.000	0.000
83	F	97	ALA	0	0.007	0.002	23.541	0.008	0.008	0.000	0.000	0.000	0.000
84	F	98	SER	0	0.035	0.011	24.594	-0.018	-0.018	0.000	0.000	0.000	0.000
85	F	99	MET	0	0.016	0.035	23.887	-0.003	-0.003	0.000	0.000	0.000	0.000
86	F	100	GLY	0	0.045	0.030	22.420	-0.012	-0.012	0.000	0.000	0.000	0.000
87	F	101	GLU	-1	-0.895	-0.952	23.145	-0.088	-0.088	0.000	0.000	0.000	0.000
88	F	102	PHE	0	0.026	0.005	26.594	-0.002	-0.002	0.000	0.000	0.000	0.000
89	F	103	LEU	0	0.001	-0.016	21.480	-0.003	-0.003	0.000	0.000	0.000	0.000
90	F	104	LEU	0	-0.049	-0.024	24.598	-0.005	-0.005	0.000	0.000	0.000	0.000
91	F	105	ALA	0	-0.009	0.001	25.697	0.000	0.000	0.000	0.000	0.000	0.000
92	F	106	ALA	0	0.006	-0.001	26.923	0.004	0.004	0.000	0.000	0.000	0.000
93	F	107	GLY	0	-0.031	0.001	27.042	-0.007	-0.007	0.000	0.000	0.000	0.000
94	F	108	THR	0	0.005	-0.014	27.638	0.008	0.008	0.000	0.000	0.000	0.000
95	F	109	LYS	1	0.844	0.918	30.096	0.091	0.091	0.000	0.000	0.000	0.000
96	F	110	GLY	0	-0.036	-0.009	33.103	0.000	0.000	0.000	0.000	0.000	0.000
97	F	111	LYS	1	0.707	0.808	28.231	0.144	0.144	0.000	0.000	0.000	0.000
98	F	112	ARG	1	0.830	0.928	27.658	0.082	0.082	0.000	0.000	0.000	0.000
99	F	113	TYR	0	0.014	0.004	25.861	0.018	0.018	0.000	0.000	0.000	0.000
100	F	114	ALA	0	0.026	0.007	26.334	-0.004	-0.004	0.000	0.000	0.000	0.000
101	F	115	LEU	0	-0.004	0.004	21.601	0.006	0.006	0.000	0.000	0.000	0.000
102	F	116	PRO	0	0.011	-0.004	26.108	0.003	0.003	0.000	0.000	0.000	0.000
103	F	117	HIS	0	-0.035	-0.019	26.105	-0.001	-0.001	0.000	0.000	0.000	0.000
104	F	118	ALA	0	-0.049	-0.006	25.137	0.006	0.006	0.000	0.000	0.000	0.000
105	F	119	ARG	1	0.903	0.953	23.300	-0.009	-0.009	0.000	0.000	0.000	0.000
106	F	120	ILE	0	0.035	0.027	26.196	-0.006	-0.006	0.000	0.000	0.000	0.000
107	F	121	LEU	0	-0.023	-0.028	26.963	0.008	0.008	0.000	0.000	0.000	0.000
108	F	122	MET	0	0.029	0.034	28.877	-0.007	-0.007	0.000	0.000	0.000	0.000
109	F	123	HIS	1	0.797	0.869	27.716	0.048	0.048	0.000	0.000	0.000	0.000
110	F	124	GLN	0	0.045	0.012	31.398	-0.013	-0.013	0.000	0.000	0.000	0.000
111	F	125	PRO	0	-0.027	0.008	29.879	0.002	0.002	0.000	0.000	0.000	0.000
112	F	136	ILE	0	0.009	-0.004	36.663	-0.001	-0.001	0.000	0.000	0.000	0.000
113	F	137	ALA	0	0.029	0.000	38.155	-0.002	-0.002	0.000	0.000	0.000	0.000
114	F	138	ILE	0	0.073	0.034	37.043	0.000	0.000	0.000	0.000	0.000	0.000
115	F	139	GLN	0	0.016	0.011	32.799	-0.006	-0.006	0.000	0.000	0.000	0.000
116	F	140	ALA	0	-0.018	-0.001	35.473	-0.004	-0.004	0.000	0.000	0.000	0.000
117	F	141	GLU	-1	-0.910	-0.950	37.858	-0.066	-0.066	0.000	0.000	0.000	0.000
118	F	142	GLN	0	-0.011	-0.013	33.271	0.002	0.002	0.000	0.000	0.000	0.000
119	F	143	PHE	0	0.002	0.000	31.185	-0.002	-0.002	0.000	0.000	0.000	0.000
120	F	144	ALA	0	-0.010	-0.007	34.601	-0.001	-0.001	0.000	0.000	0.000	0.000
121	F	145	VAL	0	-0.018	-0.004	36.699	0.001	0.001	0.000	0.000	0.000	0.000
122	F	146	ILE	0	0.035	0.001	30.726	0.000	0.000	0.000	0.000	0.000	0.000
123	F	147	LYS	1	0.877	0.944	33.682	0.059	0.059	0.000	0.000	0.000	0.000
124	F	148	LYS	1	0.907	0.959	34.714	0.061	0.061	0.000	0.000	0.000	0.000
125	F	149	GLU	-1	-0.774	-0.863	34.368	-0.093	-0.093	0.000	0.000	0.000	0.000
126	F	150	MET	0	-0.028	-0.003	30.904	-0.003	-0.003	0.000	0.000	0.000	0.000
127	F	151	PHE	0	0.015	-0.003	33.354	0.001	0.001	0.000	0.000	0.000	0.000
128	F	152	ARG	1	0.764	0.850	36.012	0.094	0.094	0.000	0.000	0.000	0.000
129	F	153	LEU	0	0.008	0.014	32.588	0.002	0.002	0.000	0.000	0.000	0.000
130	F	154	ASN	0	-0.019	-0.031	31.348	-0.002	-0.002	0.000	0.000	0.000	0.000
131	F	155	ALA	0	-0.027	0.007	34.041	0.003	0.003	0.000	0.000	0.000	0.000
132	F	156	GLU	-1	-0.870	-0.913	36.352	-0.090	-0.090	0.000	0.000	0.000	0.000
133	F	157	PHE	0	-0.014	-0.017	30.173	0.002	0.002	0.000	0.000	0.000	0.000
134	F	158	THR	0	-0.034	-0.040	34.017	0.003	0.003	0.000	0.000	0.000	0.000
135	F	159	GLY	0	-0.022	0.005	36.099	0.004	0.004	0.000	0.000	0.000	0.000
136	F	160	GLN	0	-0.059	-0.038	38.378	0.007	0.007	0.000	0.000	0.000	0.000
137	F	161	PRO	0	-0.006	-0.002	40.537	-0.003	-0.003	0.000	0.000	0.000	0.000
138	F	162	ILE	0	0.089	0.026	40.253	0.000	0.000	0.000	0.000	0.000	0.000
139	F	163	GLU	-1	-0.880	-0.951	40.697	-0.048	-0.048	0.000	0.000	0.000	0.000
140	F	164	ARG	1	0.789	0.878	40.341	0.039	0.039	0.000	0.000	0.000	0.000
141	F	165	ILE	0	0.010	0.010	35.645	0.002	0.002	0.000	0.000	0.000	0.000
142	F	166	GLU	-1	-0.898	-0.956	37.387	-0.055	-0.055	0.000	0.000	0.000	0.000
143	F	167	ALA	0	0.014	0.005	39.030	0.002	0.002	0.000	0.000	0.000	0.000
144	F	168	ASP	-1	-0.732	-0.826	37.052	-0.033	-0.033	0.000	0.000	0.000	0.000
145	F	169	SER	0	0.007	-0.002	34.395	0.001	0.001	0.000	0.000	0.000	0.000
146	F	170	ASP	-1	-0.906	-0.931	35.356	-0.036	-0.036	0.000	0.000	0.000	0.000
147	F	171	ARG	1	0.802	0.910	37.986	0.031	0.031	0.000	0.000	0.000	0.000
148	F	172	ASP	-1	-0.834	-0.904	33.208	-0.031	-0.031	0.000	0.000	0.000	0.000
149	F	173	ARG	1	0.827	0.928	34.063	0.038	0.038	0.000	0.000	0.000	0.000
150	F	174	TRP	0	-0.041	-0.033	31.112	-0.004	-0.004	0.000	0.000	0.000	0.000
151	F	175	PHE	0	-0.042	-0.019	31.574	0.002	0.002	0.000	0.000	0.000	0.000
152	F	176	THR	0	0.000	-0.039	30.999	0.000	0.000	0.000	0.000	0.000	0.000
153	F	177	ALA	0	0.049	0.018	29.824	-0.005	-0.005	0.000	0.000	0.000	0.000
154	F	178	ALA	0	0.009	-0.003	31.424	-0.005	-0.005	0.000	0.000	0.000	0.000
155	F	179	GLU	-1	-0.820	-0.884	35.196	-0.021	-0.021	0.000	0.000	0.000	0.000
156	F	180	ALA	0	-0.015	-0.016	31.473	-0.003	-0.003	0.000	0.000	0.000	0.000
157	F	181	LEU	0	-0.020	-0.015	33.506	-0.005	-0.005	0.000	0.000	0.000	0.000
158	F	182	GLU	-1	-0.973	-0.974	34.819	-0.037	-0.037	0.000	0.000	0.000	0.000
159	F	183	TYR	0	-0.084	-0.063	35.321	-0.001	-0.001	0.000	0.000	0.000	0.000
160	F	184	GLY	0	0.080	0.048	35.744	-0.002	-0.002	0.000	0.000	0.000	0.000
161	F	185	PHE	0	-0.038	-0.025	30.204	-0.004	-0.004	0.000	0.000	0.000	0.000
162	F	186	VAL	0	-0.046	-0.034	28.547	-0.008	-0.008	0.000	0.000	0.000	0.000
163	F	187	ASP	-1	-0.777	-0.868	31.352	-0.083	-0.083	0.000	0.000	0.000	0.000
164	F	188	HIS	0	-0.022	-0.009	31.090	0.010	0.010	0.000	0.000	0.000	0.000
165	F	189	ILE	0	-0.009	0.008	30.319	-0.003	-0.003	0.000	0.000	0.000	0.000
166	F	190	ILE	0	-0.009	0.005	25.094	0.003	0.003	0.000	0.000	0.000	0.000
167	F	191	THR	0	-0.013	-0.014	27.723	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:15:SER)