FMO DATABASE

FMODB ID: R8KZ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1475282.239691
FMO2-HF: Nuclear repulsion	1412725.869431
FMO2-HF: Total energy	-62556.37026
FMO2-MP2: Total energy	-62733.857364

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.
-18.969	-12.933	8.856	-7.278	-7.614	-0.04

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 : 0.002 / q_NPA : 0.002

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	0.023	0.008	3.789	-1.311	1.145	-0.028	-1.306	-1.122	0.006
4	A	44	ALA	0	-0.012	0.003	5.799	0.570	0.570	0.000	0.000	0.000	0.000
5	A	45	ASN	0	-0.034	-0.014	9.413	0.010	0.010	0.000	0.000	0.000	0.000
6	A	46	TYR	0	0.007	-0.008	12.349	0.046	0.046	0.000	0.000	0.000	0.000
7	A	47	ASP	-1	-0.777	-0.873	16.056	-0.748	-0.748	0.000	0.000	0.000	0.000
8	A	48	GLN	0	0.047	0.032	19.006	0.024	0.024	0.000	0.000	0.000	0.000
9	A	49	MET	0	-0.019	0.040	22.710	0.032	0.032	0.000	0.000	0.000	0.000
10	A	50	MET	0	-0.013	0.003	25.930	0.017	0.017	0.000	0.000	0.000	0.000
11	A	51	ARG	1	0.960	0.973	29.144	0.240	0.240	0.000	0.000	0.000	0.000
12	A	52	VAL	0	0.033	0.007	32.311	0.012	0.012	0.000	0.000	0.000	0.000
13	A	53	PRO	0	-0.016	0.010	34.862	0.000	0.000	0.000	0.000	0.000	0.000
14	A	54	ILE	0	0.030	0.009	37.403	0.006	0.006	0.000	0.000	0.000	0.000
15	A	55	GLN	0	-0.031	-0.023	40.239	0.007	0.007	0.000	0.000	0.000	0.000
16	A	56	ARG	1	0.792	0.905	43.152	0.119	0.119	0.000	0.000	0.000	0.000
17	A	57	ARG	1	0.924	0.939	44.565	0.100	0.100	0.000	0.000	0.000	0.000
18	A	58	ALA	0	0.072	0.038	47.518	0.002	0.002	0.000	0.000	0.000	0.000
19	A	59	LYS	1	0.901	0.953	44.760	0.098	0.098	0.000	0.000	0.000	0.000
20	A	60	VAL	0	-0.001	0.015	43.487	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	61	MET	0	0.004	0.016	37.901	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	62	SER	0	-0.024	-0.015	40.875	0.002	0.002	0.000	0.000	0.000	0.000
23	A	63	ILE	0	0.026	0.002	36.191	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	64	ARG	1	0.755	0.868	40.117	0.149	0.149	0.000	0.000	0.000	0.000
25	A	65	GLY	0	0.002	-0.002	41.642	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	66	GLU	-1	-0.833	-0.911	39.740	-0.106	-0.106	0.000	0.000	0.000	0.000
27	A	67	ARG	1	0.860	0.939	33.092	0.190	0.190	0.000	0.000	0.000	0.000
28	A	68	SER	0	0.013	-0.009	35.470	0.002	0.002	0.000	0.000	0.000	0.000
29	A	69	TYR	0	-0.032	-0.008	29.713	0.008	0.008	0.000	0.000	0.000	0.000
30	A	70	ASN	0	0.037	0.020	30.253	0.003	0.003	0.000	0.000	0.000	0.000
31	A	71	THR	0	-0.025	-0.021	25.079	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	72	PRO	0	0.016	0.016	21.861	0.021	0.021	0.000	0.000	0.000	0.000
33	A	73	LEU	0	-0.018	0.005	21.638	0.005	0.005	0.000	0.000	0.000	0.000
34	A	74	GLY	0	0.053	0.024	23.540	0.019	0.019	0.000	0.000	0.000	0.000
35	A	75	LYS	1	0.838	0.906	27.202	0.105	0.105	0.000	0.000	0.000	0.000
36	A	76	VAL	0	-0.015	-0.013	28.509	0.000	0.000	0.000	0.000	0.000	0.000
37	A	77	ALA	0	0.008	-0.005	31.240	0.008	0.008	0.000	0.000	0.000	0.000
38	A	78	MET	0	-0.012	0.009	32.851	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	79	LYS	1	0.914	0.930	36.027	0.101	0.101	0.000	0.000	0.000	0.000
40	A	80	ASN	0	0.013	0.034	39.148	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	81	GLY	0	-0.019	-0.011	41.123	0.004	0.004	0.000	0.000	0.000	0.000
42	A	82	LEU	0	0.050	0.057	38.471	0.006	0.006	0.000	0.000	0.000	0.000
43	A	83	SER	0	0.013	-0.035	40.705	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	84	ASP	-1	-0.838	-0.917	38.191	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	85	LYS	1	0.842	0.898	38.914	0.064	0.064	0.000	0.000	0.000	0.000
46	A	86	ASP	-1	-0.716	-0.812	40.659	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	87	MET	0	-0.080	-0.043	34.379	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	88	LYS	1	0.861	0.921	34.930	0.070	0.070	0.000	0.000	0.000	0.000
49	A	89	ASP	-1	-0.863	-0.909	37.224	-0.060	-0.060	0.000	0.000	0.000	0.000
50	A	90	VAL	0	-0.098	-0.040	36.183	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	91	SER	0	0.034	0.023	36.284	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	92	ALA	0	-0.069	-0.049	32.671	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	93	ASP	-1	-0.776	-0.862	27.746	-0.137	-0.137	0.000	0.000	0.000	0.000
54	A	94	LEU	0	-0.012	0.000	26.026	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	95	VAL	0	-0.012	-0.002	29.503	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	96	ILE	0	-0.009	-0.009	29.667	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	97	SER	0	0.003	-0.029	33.217	0.009	0.009	0.000	0.000	0.000	0.000
58	A	98	THR	0	0.003	-0.023	35.793	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	99	VAL	0	0.001	0.003	38.085	0.007	0.007	0.000	0.000	0.000	0.000
60	A	100	THR	0	0.006	-0.007	40.553	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	101	ALA	0	0.005	0.018	43.937	0.000	0.000	0.000	0.000	0.000	0.000
62	A	102	PRO	0	-0.002	0.014	40.863	0.003	0.003	0.000	0.000	0.000	0.000
63	A	103	ARG	1	0.927	0.926	42.160	0.068	0.068	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.022	0.007	38.429	0.004	0.004	0.000	0.000	0.000	0.000
65	A	105	ASP	-1	-0.791	-0.894	41.328	-0.111	-0.111	0.000	0.000	0.000	0.000
66	A	106	PRO	0	-0.014	-0.003	38.663	0.005	0.005	0.000	0.000	0.000	0.000
67	A	107	ALA	0	0.029	0.020	41.323	0.002	0.002	0.000	0.000	0.000	0.000
68	A	108	GLY	0	0.005	-0.004	42.793	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	109	THR	0	-0.048	-0.012	41.811	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	110	GLY	0	0.058	0.030	44.500	0.006	0.006	0.000	0.000	0.000	0.000
71	A	111	ALA	0	-0.036	-0.021	46.659	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	112	GLU	-1	-0.805	-0.904	45.073	-0.115	-0.115	0.000	0.000	0.000	0.000
73	A	113	ASN	0	-0.034	-0.015	40.891	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	114	SER	0	-0.044	-0.043	41.565	0.006	0.006	0.000	0.000	0.000	0.000
75	A	115	ASN	0	-0.001	-0.001	39.460	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	116	MET	0	0.014	0.006	35.369	0.005	0.005	0.000	0.000	0.000	0.000
77	A	117	THR	0	0.010	0.016	36.021	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	118	LEU	0	0.006	0.000	31.146	0.007	0.007	0.000	0.000	0.000	0.000
79	A	119	LYS	1	0.802	0.886	33.780	0.101	0.101	0.000	0.000	0.000	0.000
80	A	120	ILE	0	0.010	-0.011	28.051	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	121	LEU	0	-0.005	0.014	30.705	0.007	0.007	0.000	0.000	0.000	0.000
82	A	122	ASN	0	-0.019	-0.014	23.001	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	123	ASN	0	0.044	0.034	27.138	0.019	0.019	0.000	0.000	0.000	0.000
84	A	124	THR	0	0.009	-0.020	23.403	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.010	0.017	22.660	0.000	0.000	0.000	0.000	0.000	0.000
86	A	126	VAL	0	0.003	-0.006	18.355	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	127	ASP	-1	-0.902	-0.943	17.937	-0.189	-0.189	0.000	0.000	0.000	0.000
88	A	128	LEU	0	-0.023	-0.008	18.736	-0.061	-0.061	0.000	0.000	0.000	0.000
89	A	129	LEU	0	-0.007	-0.008	18.910	0.041	0.041	0.000	0.000	0.000	0.000
90	A	130	ILE	0	-0.038	-0.006	21.501	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	131	ASN	0	0.004	-0.005	19.646	0.054	0.054	0.000	0.000	0.000	0.000
92	A	132	ASP	-1	-0.869	-0.943	22.602	-0.345	-0.345	0.000	0.000	0.000	0.000
93	A	133	ILE	0	-0.003	0.000	25.884	0.015	0.015	0.000	0.000	0.000	0.000
94	A	134	THR	0	0.035	0.029	29.537	0.005	0.005	0.000	0.000	0.000	0.000
95	A	135	VAL	0	-0.038	-0.006	32.184	0.004	0.004	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.906	0.953	29.911	0.284	0.284	0.000	0.000	0.000	0.000
97	A	137	PRO	0	0.091	0.042	37.046	0.006	0.006	0.000	0.000	0.000	0.000
98	A	138	THR	0	-0.105	-0.057	39.034	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	139	VAL	0	0.048	0.023	41.077	0.006	0.006	0.000	0.000	0.000	0.000
100	A	140	ILE	0	-0.035	-0.026	43.108	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	141	ALA	0	0.025	0.012	45.615	0.004	0.004	0.000	0.000	0.000	0.000
102	A	142	GLY	0	0.033	0.022	46.906	0.004	0.004	0.000	0.000	0.000	0.000
103	A	143	ASN	0	-0.036	-0.019	47.646	0.004	0.004	0.000	0.000	0.000	0.000
104	A	144	ILE	0	0.008	0.020	42.622	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	145	LYS	1	0.872	0.927	44.309	0.124	0.124	0.000	0.000	0.000	0.000
106	A	146	GLY	0	0.084	0.047	42.833	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	147	ASN	0	-0.069	-0.035	42.428	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	148	THR	0	0.006	-0.008	42.203	0.008	0.008	0.000	0.000	0.000	0.000
109	A	149	MET	0	-0.030	-0.007	40.423	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.019	-0.028	37.427	0.004	0.004	0.000	0.000	0.000	0.000
111	A	151	ASN	0	-0.003	0.003	34.185	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	152	THR	0	-0.028	-0.026	32.680	0.013	0.013	0.000	0.000	0.000	0.000
113	A	153	TYR	0	0.047	0.038	31.559	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	154	PHE	0	0.010	-0.021	25.701	0.012	0.012	0.000	0.000	0.000	0.000
115	A	155	SER	0	-0.042	0.011	29.294	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	156	SER	0	0.045	0.011	24.081	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	157	LYS	1	0.812	0.886	25.490	0.171	0.171	0.000	0.000	0.000	0.000
118	A	158	ASP	-1	-0.772	-0.876	20.477	-0.296	-0.296	0.000	0.000	0.000	0.000
119	A	159	ILE	0	-0.069	-0.055	22.856	0.036	0.036	0.000	0.000	0.000	0.000
120	A	160	LYS	1	0.915	0.925	23.100	0.136	0.136	0.000	0.000	0.000	0.000
121	A	161	SER	0	-0.008	0.020	22.459	0.000	0.000	0.000	0.000	0.000	0.000
122	A	162	SER	0	-0.049	-0.016	24.302	0.022	0.022	0.000	0.000	0.000	0.000
123	A	163	SER	0	0.077	0.015	27.377	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	164	SER	0	-0.042	-0.025	30.710	0.000	0.000	0.000	0.000	0.000	0.000
125	A	165	LYN	0	-0.009	0.025	29.575	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	166	ILE	0	0.013	0.010	30.918	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	167	THR	0	-0.017	-0.007	27.570	0.005	0.005	0.000	0.000	0.000	0.000
128	A	168	LEU	0	0.022	0.011	30.685	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	169	ILE	0	-0.014	-0.004	27.733	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	170	ASP	-1	-0.876	-0.926	31.664	-0.136	-0.136	0.000	0.000	0.000	0.000
131	A	171	VAL	0	0.005	-0.006	32.401	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	172	CYS	0	-0.044	-0.013	34.768	0.013	0.013	0.000	0.000	0.000	0.000
133	A	173	SER	0	0.044	0.026	36.326	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	174	LYS	1	0.873	0.935	38.103	0.143	0.143	0.000	0.000	0.000	0.000
135	A	175	PHE	0	-0.036	-0.034	39.523	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	176	GLU	-1	-0.798	-0.894	42.883	-0.136	-0.136	0.000	0.000	0.000	0.000
137	A	177	ASP	-1	-0.820	-0.898	45.834	-0.105	-0.105	0.000	0.000	0.000	0.000
138	A	178	GLY	0	0.011	0.014	47.265	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	179	ALA	0	-0.040	-0.007	49.465	0.003	0.003	0.000	0.000	0.000	0.000
140	A	180	ALA	0	-0.046	-0.023	48.017	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	181	PHE	0	0.029	0.007	41.887	0.000	0.000	0.000	0.000	0.000	0.000
142	A	182	GLU	-1	-0.825	-0.891	44.003	-0.121	-0.121	0.000	0.000	0.000	0.000
143	A	183	ALA	0	0.008	0.004	39.728	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	184	THR	0	-0.038	-0.024	34.670	0.004	0.004	0.000	0.000	0.000	0.000
145	A	185	MET	0	0.013	0.018	32.267	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	186	ASN	0	-0.054	-0.067	29.951	0.013	0.013	0.000	0.000	0.000	0.000
147	A	187	ILE	0	0.041	0.020	26.895	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	188	GLY	0	0.013	0.010	24.460	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	189	PHE	0	-0.003	-0.028	22.518	0.016	0.016	0.000	0.000	0.000	0.000
150	A	190	THR	0	0.015	-0.010	16.287	-0.013	-0.013	0.000	0.000	0.000	0.000
151	A	191	SER	0	-0.033	-0.019	15.828	0.038	0.038	0.000	0.000	0.000	0.000
152	A	192	LYS	1	0.851	0.905	14.716	0.279	0.279	0.000	0.000	0.000	0.000
153	A	193	ASN	0	-0.010	0.005	13.261	-0.023	-0.023	0.000	0.000	0.000	0.000
154	A	194	VAL	0	-0.013	-0.008	7.632	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	195	ILE	0	-0.015	-0.002	7.986	0.228	0.228	0.000	0.000	0.000	0.000
156	A	196	ASP	-1	-0.826	-0.918	2.124	-11.475	-9.841	2.755	-2.230	-2.159	-0.032
157	A	197	ILE	0	-0.026	-0.003	4.087	1.502	1.764	-0.001	-0.075	-0.186	0.000
158	A	198	LYS	1	0.904	0.938	2.283	-11.416	-9.650	6.107	-3.848	-4.025	-0.014
159	A	199	ASP	-1	-0.955	-0.975	3.299	-0.388	-0.470	0.023	0.181	-0.122	0.000
160	A	200	GLU	-1	-0.967	-0.983	5.793	3.820	3.820	0.000	0.000	0.000	0.000
161	A	201	ILE	0	-0.018	-0.005	8.434	-0.509	-0.509	0.000	0.000	0.000	0.000

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