FMO DATABASE

FMODB ID: ZVGJN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1475181.953317
FMO2-HF: Nuclear repulsion	1412626.780885
FMO2-HF: Total energy	-62555.172432
FMO2-MP2: Total energy	-62732.800486

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.
-8.043	-2.182	6.201	-5.616	-6.447	-0.029

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 : -0.021

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	0.025	0.012	3.434	-0.225	1.517	-0.023	-0.781	-0.938	0.001
4	A	44	ALA	0	-0.020	-0.006	5.415	0.584	0.584	0.000	0.000	0.000	0.000
5	A	45	ASN	0	-0.023	-0.012	9.116	0.058	0.058	0.000	0.000	0.000	0.000
6	A	46	TYR	0	-0.019	-0.042	12.114	0.049	0.049	0.000	0.000	0.000	0.000
7	A	47	ASP	-1	-0.813	-0.912	15.842	-0.494	-0.494	0.000	0.000	0.000	0.000
8	A	48	GLN	0	0.060	0.069	18.702	0.032	0.032	0.000	0.000	0.000	0.000
9	A	49	MET	0	-0.040	0.006	22.431	0.011	0.011	0.000	0.000	0.000	0.000
10	A	50	MET	0	-0.024	0.002	25.598	0.016	0.016	0.000	0.000	0.000	0.000
11	A	51	ARG	1	0.947	0.964	28.856	0.122	0.122	0.000	0.000	0.000	0.000
12	A	52	VAL	0	0.040	0.009	32.053	0.010	0.010	0.000	0.000	0.000	0.000
13	A	53	PRO	0	-0.020	0.007	34.570	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	54	ILE	0	0.053	0.021	37.074	0.003	0.003	0.000	0.000	0.000	0.000
15	A	55	GLN	0	-0.014	-0.011	39.919	0.003	0.003	0.000	0.000	0.000	0.000
16	A	56	ARG	1	0.799	0.921	42.830	0.074	0.074	0.000	0.000	0.000	0.000
17	A	57	ARG	1	0.957	0.956	44.204	0.057	0.057	0.000	0.000	0.000	0.000
18	A	58	ALA	0	0.047	0.030	47.181	0.001	0.001	0.000	0.000	0.000	0.000
19	A	59	LYS	1	1.037	1.007	45.208	0.061	0.061	0.000	0.000	0.000	0.000
20	A	60	VAL	0	-0.031	0.014	43.080	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	61	MET	0	0.004	0.016	37.263	0.001	0.001	0.000	0.000	0.000	0.000
22	A	62	SER	0	-0.040	-0.020	40.597	0.001	0.001	0.000	0.000	0.000	0.000
23	A	63	ILE	0	0.034	0.008	36.064	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	64	ARG	1	0.836	0.917	39.867	0.079	0.079	0.000	0.000	0.000	0.000
25	A	65	GLY	0	-0.009	-0.009	41.398	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	66	GLU	-1	-0.903	-0.970	39.530	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	67	ARG	1	0.843	0.928	33.501	0.091	0.091	0.000	0.000	0.000	0.000
28	A	68	SER	0	0.023	0.001	35.401	0.001	0.001	0.000	0.000	0.000	0.000
29	A	69	TYR	0	-0.028	-0.009	29.656	0.004	0.004	0.000	0.000	0.000	0.000
30	A	70	ASN	0	0.035	0.017	30.162	0.000	0.000	0.000	0.000	0.000	0.000
31	A	71	THR	0	-0.062	-0.031	25.104	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	72	PRO	0	0.018	0.018	21.746	0.013	0.013	0.000	0.000	0.000	0.000
33	A	73	LEU	0	0.018	0.015	21.738	0.008	0.008	0.000	0.000	0.000	0.000
34	A	74	GLY	0	0.067	0.031	23.544	0.008	0.008	0.000	0.000	0.000	0.000
35	A	75	LYS	1	0.820	0.904	27.230	0.030	0.030	0.000	0.000	0.000	0.000
36	A	76	VAL	0	-0.014	-0.009	28.436	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	77	ALA	0	0.004	-0.006	31.166	0.005	0.005	0.000	0.000	0.000	0.000
38	A	78	MET	0	-0.009	0.013	32.768	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	79	LYS	1	1.001	0.992	35.886	0.047	0.047	0.000	0.000	0.000	0.000
40	A	80	ASN	0	0.019	0.038	39.007	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	81	GLY	0	-0.011	-0.007	40.950	0.003	0.003	0.000	0.000	0.000	0.000
42	A	82	LEU	0	0.051	0.056	38.390	0.004	0.004	0.000	0.000	0.000	0.000
43	A	83	SER	0	0.004	-0.015	40.629	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	84	ASP	-1	-0.917	-0.988	37.564	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	85	LYS	1	0.903	0.936	38.964	0.035	0.035	0.000	0.000	0.000	0.000
46	A	86	ASP	-1	-0.735	-0.837	40.723	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	87	MET	0	-0.078	-0.036	34.269	0.000	0.000	0.000	0.000	0.000	0.000
48	A	88	LYS	1	0.884	0.931	34.940	0.031	0.031	0.000	0.000	0.000	0.000
49	A	89	ASP	-1	-0.878	-0.912	37.302	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	90	VAL	0	-0.089	-0.034	36.375	0.001	0.001	0.000	0.000	0.000	0.000
51	A	91	SER	0	0.037	0.024	36.353	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	92	ALA	0	-0.059	-0.050	32.629	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	93	ASP	-1	-0.789	-0.876	27.741	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	94	LEU	0	-0.013	-0.001	26.222	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	95	VAL	0	-0.024	-0.003	29.482	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	96	ILE	0	0.018	-0.005	29.588	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	97	SER	0	-0.003	-0.037	33.090	0.006	0.006	0.000	0.000	0.000	0.000
58	A	98	THR	0	-0.005	-0.026	35.623	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	99	VAL	0	0.015	0.013	37.988	0.005	0.005	0.000	0.000	0.000	0.000
60	A	100	THR	0	-0.004	-0.012	40.391	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	101	ALA	0	0.000	0.013	43.760	0.000	0.000	0.000	0.000	0.000	0.000
62	A	102	PRO	0	0.000	0.014	40.778	0.001	0.001	0.000	0.000	0.000	0.000
63	A	103	ARG	1	0.923	0.923	41.911	0.046	0.046	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.021	0.009	38.181	0.003	0.003	0.000	0.000	0.000	0.000
65	A	105	ASP	-1	-0.851	-0.918	41.049	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	106	PRO	0	-0.010	-0.006	38.454	0.002	0.002	0.000	0.000	0.000	0.000
67	A	107	ALA	0	0.036	0.023	40.980	0.002	0.002	0.000	0.000	0.000	0.000
68	A	108	GLY	0	-0.009	-0.014	42.402	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	109	THR	0	-0.090	-0.041	41.487	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	110	GLY	0	0.070	0.030	44.086	0.004	0.004	0.000	0.000	0.000	0.000
71	A	111	ALA	0	-0.110	-0.062	46.240	0.000	0.000	0.000	0.000	0.000	0.000
72	A	112	GLU	-1	-0.838	-0.933	44.541	-0.079	-0.079	0.000	0.000	0.000	0.000
73	A	113	ASN	0	-0.007	0.008	40.549	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	114	SER	0	-0.048	-0.030	41.165	0.005	0.005	0.000	0.000	0.000	0.000
75	A	115	ASN	0	0.048	0.025	39.118	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	116	MET	0	0.012	0.003	34.520	0.005	0.005	0.000	0.000	0.000	0.000
77	A	117	THR	0	0.017	0.026	35.834	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	118	LEU	0	-0.015	-0.017	30.910	0.006	0.006	0.000	0.000	0.000	0.000
79	A	119	LYS	1	0.832	0.909	33.612	0.056	0.056	0.000	0.000	0.000	0.000
80	A	120	ILE	0	0.012	-0.008	27.896	0.000	0.000	0.000	0.000	0.000	0.000
81	A	121	LEU	0	0.006	0.013	30.665	0.002	0.002	0.000	0.000	0.000	0.000
82	A	122	ASN	0	-0.031	0.001	23.031	0.003	0.003	0.000	0.000	0.000	0.000
83	A	123	ASN	0	0.021	0.010	27.221	0.009	0.009	0.000	0.000	0.000	0.000
84	A	124	THR	0	0.015	-0.027	23.308	0.003	0.003	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.016	0.009	22.830	0.007	0.007	0.000	0.000	0.000	0.000
86	A	126	VAL	0	0.017	0.003	18.507	0.001	0.001	0.000	0.000	0.000	0.000
87	A	127	ASP	-1	-0.935	-0.948	17.845	-0.111	-0.111	0.000	0.000	0.000	0.000
88	A	128	LEU	0	-0.009	-0.004	18.684	-0.039	-0.039	0.000	0.000	0.000	0.000
89	A	129	LEU	0	-0.015	-0.008	18.484	0.020	0.020	0.000	0.000	0.000	0.000
90	A	130	ILE	0	-0.027	-0.004	21.270	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	131	ASN	0	0.013	-0.006	19.988	0.030	0.030	0.000	0.000	0.000	0.000
92	A	132	ASP	-1	-0.904	-0.956	22.210	-0.235	-0.235	0.000	0.000	0.000	0.000
93	A	133	ILE	0	0.027	0.021	25.456	0.016	0.016	0.000	0.000	0.000	0.000
94	A	134	THR	0	-0.033	-0.007	29.123	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	135	VAL	0	-0.023	0.000	31.730	0.005	0.005	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.941	0.972	29.874	0.161	0.161	0.000	0.000	0.000	0.000
97	A	137	PRO	0	0.085	0.039	36.583	0.004	0.004	0.000	0.000	0.000	0.000
98	A	138	THR	0	-0.081	-0.049	38.591	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	139	VAL	0	0.027	0.013	40.658	0.003	0.003	0.000	0.000	0.000	0.000
100	A	140	ILE	0	-0.033	-0.021	42.724	0.000	0.000	0.000	0.000	0.000	0.000
101	A	141	ALA	0	0.020	0.006	45.241	0.002	0.002	0.000	0.000	0.000	0.000
102	A	142	GLY	0	0.032	0.021	46.516	0.002	0.002	0.000	0.000	0.000	0.000
103	A	143	ASN	0	-0.035	-0.016	47.242	0.001	0.001	0.000	0.000	0.000	0.000
104	A	144	ILE	0	0.008	0.018	42.156	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	145	LYS	1	0.915	0.958	43.866	0.064	0.064	0.000	0.000	0.000	0.000
106	A	146	GLY	0	0.085	0.045	42.390	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	147	ASN	0	-0.077	-0.036	41.953	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	148	THR	0	0.037	0.002	41.588	0.004	0.004	0.000	0.000	0.000	0.000
109	A	149	MET	0	-0.058	-0.018	39.881	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.015	-0.027	37.195	0.002	0.002	0.000	0.000	0.000	0.000
111	A	151	ASN	0	0.020	0.013	33.500	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	152	THR	0	-0.039	-0.011	32.360	0.013	0.013	0.000	0.000	0.000	0.000
113	A	153	TYR	0	0.057	0.051	30.875	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	154	PHE	0	0.009	-0.020	25.355	0.011	0.011	0.000	0.000	0.000	0.000
115	A	155	SER	0	-0.036	0.011	28.932	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	156	SER	0	0.031	0.002	23.753	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	157	LYS	1	0.913	0.958	25.358	0.115	0.115	0.000	0.000	0.000	0.000
118	A	158	ASP	-1	-0.821	-0.917	20.683	-0.209	-0.209	0.000	0.000	0.000	0.000
119	A	159	ILE	0	-0.080	-0.058	22.750	0.024	0.024	0.000	0.000	0.000	0.000
120	A	160	LYS	1	0.944	0.962	23.146	0.097	0.097	0.000	0.000	0.000	0.000
121	A	161	SER	0	-0.011	0.017	22.554	0.001	0.001	0.000	0.000	0.000	0.000
122	A	162	SER	0	-0.055	-0.014	24.402	0.015	0.015	0.000	0.000	0.000	0.000
123	A	163	SER	0	0.096	0.043	27.526	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	164	SER	0	-0.065	-0.044	30.868	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	165	LYN	0	0.004	0.007	29.779	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	166	ILE	0	0.002	0.016	30.959	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	167	THR	0	-0.029	-0.023	27.528	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	168	LEU	0	0.005	0.001	30.617	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	169	ILE	0	-0.024	-0.014	27.757	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	170	ASP	-1	-0.903	-0.947	31.445	-0.091	-0.091	0.000	0.000	0.000	0.000
131	A	171	VAL	0	-0.009	-0.016	32.151	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	172	CYS	0	-0.032	-0.008	34.436	0.009	0.009	0.000	0.000	0.000	0.000
133	A	173	SER	0	0.029	-0.003	35.677	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	174	LYS	1	0.925	0.962	37.677	0.104	0.104	0.000	0.000	0.000	0.000
135	A	175	PHE	0	-0.039	-0.034	39.044	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	176	GLU	-1	-0.788	-0.885	42.401	-0.087	-0.087	0.000	0.000	0.000	0.000
137	A	177	ASP	-1	-0.814	-0.891	45.324	-0.067	-0.067	0.000	0.000	0.000	0.000
138	A	178	GLY	0	0.008	0.003	46.807	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	179	ALA	0	-0.051	-0.016	49.026	0.003	0.003	0.000	0.000	0.000	0.000
140	A	180	ALA	0	-0.051	-0.032	47.592	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	181	PHE	0	-0.011	-0.012	41.341	0.001	0.001	0.000	0.000	0.000	0.000
142	A	182	GLU	-1	-0.945	-0.972	43.644	-0.064	-0.064	0.000	0.000	0.000	0.000
143	A	183	ALA	0	0.000	-0.009	39.238	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	184	THR	0	-0.038	-0.017	34.386	0.005	0.005	0.000	0.000	0.000	0.000
145	A	185	MET	0	0.025	0.026	31.841	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	186	ASN	0	-0.027	-0.040	29.527	0.011	0.011	0.000	0.000	0.000	0.000
147	A	187	ILE	0	0.048	0.022	26.592	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	188	GLY	0	-0.003	0.005	24.070	0.005	0.005	0.000	0.000	0.000	0.000
149	A	189	PHE	0	-0.002	-0.021	22.264	0.004	0.004	0.000	0.000	0.000	0.000
150	A	190	THR	0	0.045	0.029	16.048	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	191	SER	0	-0.022	-0.012	14.844	0.042	0.042	0.000	0.000	0.000	0.000
152	A	192	LYS	1	0.867	0.925	14.599	0.196	0.196	0.000	0.000	0.000	0.000
153	A	193	ASN	0	0.002	0.006	13.243	-0.014	-0.014	0.000	0.000	0.000	0.000
154	A	194	VAL	0	-0.020	-0.011	7.596	0.008	0.008	0.000	0.000	0.000	0.000
155	A	195	ILE	0	-0.008	0.004	7.930	0.208	0.208	0.000	0.000	0.000	0.000
156	A	196	ASP	-1	-0.874	-0.962	2.512	-3.100	-1.383	0.916	-1.214	-1.419	-0.014
157	A	197	ILE	0	-0.015	0.000	4.219	0.968	1.228	-0.001	-0.078	-0.181	0.000
158	A	198	LYS	1	0.936	0.961	2.294	-8.978	-6.682	5.292	-3.758	-3.830	-0.016
159	A	199	ASP	-1	-0.963	-0.971	3.303	1.328	1.174	0.017	0.215	-0.079	0.000
160	A	200	GLU	-1	-0.965	-0.983	5.816	1.283	1.283	0.000	0.000	0.000	0.000
161	A	201	ILE	0	-0.021	-0.004	8.215	-0.147	-0.147	0.000	0.000	0.000	0.000

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