FMO DATABASE

FMODB ID: QV4RY

Calculation Name: 2EDM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EDM

Chain ID: A

ChEMBL ID:

UniProt ID: Q0PW17

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	OptAll
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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1474473.47979
FMO2-HF: Nuclear repulsion	1411916.595795
FMO2-HF: Total energy	-62556.883995
FMO2-MP2: Total energy	-62734.363524

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:41:SER)

Summations of interaction energy for fragment #1(A:41: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.
-35.308	-34.846	23.51	-12.933	-11.041	-0.071

Interaction energy analysis for fragmet #1(A:41:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.042

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	43	VAL	0	0.010	0.003	3.798	-0.166	1.507	-0.014	-0.784	-0.875	0.004
4	A	44	ALA	0	-0.014	-0.002	5.899	0.640	0.640	0.000	0.000	0.000	0.000
5	A	45	ASN	0	-0.024	-0.021	9.446	0.000	0.000	0.000	0.000	0.000	0.000
6	A	46	TYR	0	0.014	0.002	12.333	0.019	0.019	0.000	0.000	0.000	0.000
7	A	47	ASP	-1	-0.745	-0.849	16.104	-0.686	-0.686	0.000	0.000	0.000	0.000
8	A	48	GLN	0	0.032	0.044	18.922	0.008	0.008	0.000	0.000	0.000	0.000
9	A	49	MET	0	0.001	0.038	22.699	0.032	0.032	0.000	0.000	0.000	0.000
10	A	50	MET	0	-0.023	-0.008	25.996	0.009	0.009	0.000	0.000	0.000	0.000
11	A	51	ARG	1	0.974	0.982	29.266	0.238	0.238	0.000	0.000	0.000	0.000
12	A	52	VAL	0	0.056	0.023	32.542	0.008	0.008	0.000	0.000	0.000	0.000
13	A	53	PRO	0	-0.013	-0.002	35.073	0.000	0.000	0.000	0.000	0.000	0.000
14	A	54	ILE	0	0.028	0.011	37.603	0.007	0.007	0.000	0.000	0.000	0.000
15	A	55	GLN	0	-0.021	-0.021	40.417	0.005	0.005	0.000	0.000	0.000	0.000
16	A	56	ARG	1	0.795	0.909	43.266	0.105	0.105	0.000	0.000	0.000	0.000
17	A	57	ARG	1	0.896	0.910	44.686	0.089	0.089	0.000	0.000	0.000	0.000
18	A	58	ALA	0	0.090	0.047	47.572	0.003	0.003	0.000	0.000	0.000	0.000
19	A	59	LYS	1	0.849	0.937	44.849	0.072	0.072	0.000	0.000	0.000	0.000
20	A	60	VAL	0	-0.012	0.009	43.567	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	61	MET	0	-0.015	0.003	37.569	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	62	SER	0	-0.021	-0.009	41.257	0.004	0.004	0.000	0.000	0.000	0.000
23	A	63	ILE	0	0.031	0.002	36.470	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	64	ARG	1	0.746	0.859	40.354	0.142	0.142	0.000	0.000	0.000	0.000
25	A	65	GLY	0	0.004	0.000	41.837	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	66	GLU	-1	-0.836	-0.916	39.681	-0.099	-0.099	0.000	0.000	0.000	0.000
27	A	67	ARG	1	0.860	0.937	32.990	0.188	0.188	0.000	0.000	0.000	0.000
28	A	68	SER	0	-0.027	-0.033	35.124	0.003	0.003	0.000	0.000	0.000	0.000
29	A	69	TYR	0	-0.013	-0.006	29.917	0.008	0.008	0.000	0.000	0.000	0.000
30	A	70	ASN	0	0.038	0.016	30.111	0.008	0.008	0.000	0.000	0.000	0.000
31	A	71	THR	0	-0.029	-0.025	25.209	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	72	PRO	0	-0.002	-0.012	21.972	0.021	0.021	0.000	0.000	0.000	0.000
33	A	73	LEU	0	-0.007	0.021	21.375	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	74	GLY	0	0.067	0.032	23.387	0.024	0.024	0.000	0.000	0.000	0.000
35	A	75	LYS	1	0.844	0.914	27.141	0.107	0.107	0.000	0.000	0.000	0.000
36	A	76	VAL	0	0.001	-0.001	28.565	0.002	0.002	0.000	0.000	0.000	0.000
37	A	77	ALA	0	0.015	0.008	31.216	0.009	0.009	0.000	0.000	0.000	0.000
38	A	78	MET	0	-0.034	-0.001	32.410	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	79	LYS	1	0.929	0.948	36.034	0.095	0.095	0.000	0.000	0.000	0.000
40	A	80	ASN	0	0.016	0.041	39.059	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	81	GLY	0	0.010	-0.005	40.880	0.004	0.004	0.000	0.000	0.000	0.000
42	A	82	LEU	0	0.022	0.031	38.216	0.006	0.006	0.000	0.000	0.000	0.000
43	A	83	SER	0	0.001	-0.041	40.373	0.001	0.001	0.000	0.000	0.000	0.000
44	A	84	ASP	-1	-0.818	-0.915	37.812	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	85	LYS	1	0.856	0.927	38.120	0.043	0.043	0.000	0.000	0.000	0.000
46	A	86	ASP	-1	-0.708	-0.808	40.120	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	87	MET	0	-0.087	-0.056	33.978	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	88	LYS	1	0.796	0.903	34.233	0.050	0.050	0.000	0.000	0.000	0.000
49	A	89	ASP	-1	-0.857	-0.915	36.967	-0.050	-0.050	0.000	0.000	0.000	0.000
50	A	90	VAL	0	-0.086	-0.041	35.718	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	91	SER	0	0.044	0.029	35.827	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	92	ALA	0	-0.059	-0.039	32.480	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	93	ASP	-1	-0.774	-0.868	27.479	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	94	LEU	0	-0.011	-0.002	25.841	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	95	VAL	0	-0.028	-0.009	29.123	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	96	ILE	0	0.006	-0.001	29.847	0.002	0.002	0.000	0.000	0.000	0.000
57	A	97	SER	0	-0.013	-0.037	33.280	0.009	0.009	0.000	0.000	0.000	0.000
58	A	98	THR	0	0.008	-0.016	35.733	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	99	VAL	0	-0.005	0.001	38.006	0.006	0.006	0.000	0.000	0.000	0.000
60	A	100	THR	0	-0.003	-0.010	40.390	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	101	ALA	0	0.006	0.013	43.796	0.000	0.000	0.000	0.000	0.000	0.000
62	A	102	PRO	0	0.000	0.007	40.633	0.004	0.004	0.000	0.000	0.000	0.000
63	A	103	ARG	1	0.942	0.950	42.143	0.046	0.046	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.018	0.008	37.757	0.006	0.006	0.000	0.000	0.000	0.000
65	A	105	ASP	-1	-0.733	-0.821	40.774	-0.085	-0.085	0.000	0.000	0.000	0.000
66	A	106	PRO	0	-0.011	-0.008	38.416	0.005	0.005	0.000	0.000	0.000	0.000
67	A	107	ALA	0	0.022	0.009	41.014	0.000	0.000	0.000	0.000	0.000	0.000
68	A	108	GLY	0	0.017	0.008	42.794	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	109	THR	0	-0.105	-0.066	41.597	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	110	GLY	0	0.061	0.040	44.078	0.005	0.005	0.000	0.000	0.000	0.000
71	A	111	ALA	0	-0.016	-0.020	46.576	0.000	0.000	0.000	0.000	0.000	0.000
72	A	112	GLU	-1	-0.777	-0.891	44.975	-0.093	-0.093	0.000	0.000	0.000	0.000
73	A	113	ASN	0	-0.035	-0.021	40.428	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	114	SER	0	-0.028	-0.034	41.503	0.004	0.004	0.000	0.000	0.000	0.000
75	A	115	ASN	0	0.012	0.003	39.388	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	116	MET	0	-0.007	-0.009	35.702	0.004	0.004	0.000	0.000	0.000	0.000
77	A	117	THR	0	-0.022	-0.006	35.439	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	118	LEU	0	0.007	0.001	31.475	0.005	0.005	0.000	0.000	0.000	0.000
79	A	119	LYS	1	0.800	0.881	33.705	0.082	0.082	0.000	0.000	0.000	0.000
80	A	120	ILE	0	0.016	-0.003	27.976	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	121	LEU	0	-0.021	0.007	30.301	0.011	0.011	0.000	0.000	0.000	0.000
82	A	122	ASN	0	-0.011	-0.014	22.800	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	123	ASN	0	0.036	0.025	26.437	0.021	0.021	0.000	0.000	0.000	0.000
84	A	124	THR	0	-0.023	-0.025	23.244	0.000	0.000	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.026	0.033	22.221	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	126	VAL	0	-0.023	-0.008	17.614	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	127	ASP	-1	-0.845	-0.907	17.974	-0.116	-0.116	0.000	0.000	0.000	0.000
88	A	128	LEU	0	-0.010	-0.005	18.557	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	129	LEU	0	-0.026	-0.018	19.158	0.048	0.048	0.000	0.000	0.000	0.000
90	A	130	ILE	0	-0.037	-0.007	21.451	-0.034	-0.034	0.000	0.000	0.000	0.000
91	A	131	ASN	0	-0.018	-0.016	19.707	0.053	0.053	0.000	0.000	0.000	0.000
92	A	132	ASP	-1	-0.818	-0.894	22.805	-0.298	-0.298	0.000	0.000	0.000	0.000
93	A	133	ILE	0	-0.015	-0.011	26.137	0.011	0.011	0.000	0.000	0.000	0.000
94	A	134	THR	0	0.009	-0.001	29.802	0.009	0.009	0.000	0.000	0.000	0.000
95	A	135	VAL	0	-0.023	-0.007	32.219	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.870	0.929	29.415	0.266	0.266	0.000	0.000	0.000	0.000
97	A	137	PRO	0	0.082	0.040	37.079	0.006	0.006	0.000	0.000	0.000	0.000
98	A	138	THR	0	-0.095	-0.041	38.978	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	139	VAL	0	0.040	0.029	41.203	0.007	0.007	0.000	0.000	0.000	0.000
100	A	140	ILE	0	-0.018	-0.019	43.236	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	141	ALA	0	0.030	0.013	45.854	0.004	0.004	0.000	0.000	0.000	0.000
102	A	142	GLY	0	0.027	0.019	47.461	0.004	0.004	0.000	0.000	0.000	0.000
103	A	143	ASN	0	-0.043	-0.015	48.607	0.002	0.002	0.000	0.000	0.000	0.000
104	A	144	ILE	0	0.009	0.006	42.915	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	145	LYS	1	0.878	0.932	44.731	0.121	0.121	0.000	0.000	0.000	0.000
106	A	146	GLY	0	0.063	0.024	42.670	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	147	ASN	0	-0.074	-0.040	42.303	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	148	THR	0	0.012	0.007	41.964	0.009	0.009	0.000	0.000	0.000	0.000
109	A	149	MET	0	-0.019	-0.009	40.115	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.022	-0.027	37.368	0.005	0.005	0.000	0.000	0.000	0.000
111	A	151	ASN	0	0.010	0.009	33.967	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	152	THR	0	-0.027	-0.014	32.696	0.013	0.013	0.000	0.000	0.000	0.000
113	A	153	TYR	0	0.052	0.050	31.642	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	154	PHE	0	0.013	-0.016	25.616	0.008	0.008	0.000	0.000	0.000	0.000
115	A	155	SER	0	-0.025	0.000	29.454	0.001	0.001	0.000	0.000	0.000	0.000
116	A	156	SER	0	0.044	0.020	24.108	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	157	LYS	1	0.808	0.882	25.360	0.120	0.120	0.000	0.000	0.000	0.000
118	A	158	ASP	-1	-0.760	-0.864	20.403	-0.179	-0.179	0.000	0.000	0.000	0.000
119	A	159	ILE	0	-0.083	-0.045	22.947	0.030	0.030	0.000	0.000	0.000	0.000
120	A	160	LYS	1	0.933	0.937	22.335	0.071	0.071	0.000	0.000	0.000	0.000
121	A	161	SER	0	0.003	0.021	22.015	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	162	SER	0	-0.058	-0.021	23.858	0.023	0.023	0.000	0.000	0.000	0.000
123	A	163	SER	0	0.047	0.006	27.145	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	164	SER	0	-0.031	-0.019	30.215	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	165	LYN	0	0.005	0.013	29.133	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	166	ILE	0	0.034	0.012	30.403	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	167	THR	0	0.001	0.008	27.186	0.010	0.010	0.000	0.000	0.000	0.000
128	A	168	LEU	0	0.009	0.007	30.231	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	169	ILE	0	-0.008	0.003	27.514	0.002	0.002	0.000	0.000	0.000	0.000
130	A	170	ASP	-1	-0.823	-0.895	31.446	-0.094	-0.094	0.000	0.000	0.000	0.000
131	A	171	VAL	0	-0.005	-0.005	32.450	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	172	CYS	0	-0.062	-0.022	34.731	0.011	0.011	0.000	0.000	0.000	0.000
133	A	173	SER	0	0.027	0.002	36.226	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	174	LYS	1	0.836	0.904	37.982	0.116	0.116	0.000	0.000	0.000	0.000
135	A	175	PHE	0	-0.027	-0.013	39.643	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	176	GLU	-1	-0.802	-0.896	42.712	-0.123	-0.123	0.000	0.000	0.000	0.000
137	A	177	ASP	-1	-0.831	-0.922	45.562	-0.091	-0.091	0.000	0.000	0.000	0.000
138	A	178	GLY	0	0.001	0.022	47.066	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	179	ALA	0	-0.002	0.006	49.385	0.002	0.002	0.000	0.000	0.000	0.000
140	A	180	ALA	0	-0.048	-0.027	48.090	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	181	PHE	0	0.029	0.012	42.183	0.000	0.000	0.000	0.000	0.000	0.000
142	A	182	GLU	-1	-0.848	-0.894	44.391	-0.115	-0.115	0.000	0.000	0.000	0.000
143	A	183	ALA	0	0.029	0.010	40.112	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	184	THR	0	-0.030	-0.019	34.940	0.003	0.003	0.000	0.000	0.000	0.000
145	A	185	MET	0	0.019	0.021	32.608	0.002	0.002	0.000	0.000	0.000	0.000
146	A	186	ASN	0	-0.055	-0.061	30.190	0.011	0.011	0.000	0.000	0.000	0.000
147	A	187	ILE	0	0.023	0.016	27.068	0.007	0.007	0.000	0.000	0.000	0.000
148	A	188	GLY	0	0.010	0.012	24.580	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	189	PHE	0	0.003	-0.026	22.507	0.033	0.033	0.000	0.000	0.000	0.000
150	A	190	THR	0	0.004	-0.019	16.041	-0.014	-0.014	0.000	0.000	0.000	0.000
151	A	191	SER	0	-0.064	-0.047	15.688	0.041	0.041	0.000	0.000	0.000	0.000
152	A	192	LYS	1	0.856	0.894	14.711	0.145	0.145	0.000	0.000	0.000	0.000
153	A	193	ASN	0	-0.042	-0.011	13.226	-0.014	-0.014	0.000	0.000	0.000	0.000
154	A	194	VAL	0	-0.017	-0.009	7.719	-0.029	-0.029	0.000	0.000	0.000	0.000
155	A	195	ILE	0	-0.006	0.006	7.862	0.262	0.262	0.000	0.000	0.000	0.000
156	A	196	ASP	-1	-0.797	-0.887	1.679	-20.619	-25.802	17.132	-7.765	-4.185	-0.078
157	A	197	ILE	0	-0.019	-0.003	3.734	1.760	2.172	0.001	-0.122	-0.291	0.000
158	A	198	LYS	1	0.872	0.935	2.318	-20.576	-16.788	6.322	-4.720	-5.391	0.003
159	A	199	ASP	-1	-0.936	-0.958	3.126	-1.938	-2.259	0.070	0.459	-0.208	0.000
160	A	200	GLU	-1	-0.952	-0.982	5.293	5.972	6.065	-0.001	-0.001	-0.091	0.000
161	A	201	ILE	0	-0.035	-0.013	8.189	-0.608	-0.608	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:41:SER)