FMO DATABASE

FMODB ID: 5JYLZ

Calculation Name: 2DUM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DUM

Chain ID: A

ChEMBL ID:

UniProt ID: O58553

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1426465.678205
FMO2-HF: Nuclear repulsion	1367845.639856
FMO2-HF: Total energy	-58620.038349
FMO2-MP2: Total energy	-58792.875207

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:4:MET)

Summations of interaction energy for fragment #1(A:4:MET)

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.
-19.237	-18.461	17.109	-6.581	-11.305	0.022

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.006

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	6	ARG	1	0.966	0.985	2.052	-16.913	-17.864	9.444	-3.891	-4.602	0.033
4	A	7	LYS	1	0.863	0.928	4.924	-0.995	-0.808	-0.001	-0.020	-0.166	0.000
5	A	8	VAL	0	-0.018	0.029	5.109	-0.478	-0.478	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.041	0.031	7.256	0.427	0.427	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.017	-0.014	9.399	-0.236	-0.236	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.000	0.000	11.961	0.105	0.105	0.000	0.000	0.000	0.000
9	A	12	THR	0	0.025	0.033	15.177	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.853	-0.897	18.177	-0.240	-0.240	0.000	0.000	0.000	0.000
11	A	14	PHE	0	-0.047	-0.028	20.925	0.020	0.020	0.000	0.000	0.000	0.000
12	A	15	SER	0	-0.043	-0.061	21.860	0.005	0.005	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.820	-0.927	23.001	-0.210	-0.210	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.033	0.004	20.970	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	18	ALA	0	-0.015	-0.014	18.238	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	19	TYR	0	0.056	0.007	18.264	-0.048	-0.048	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.869	0.916	19.951	0.271	0.271	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.071	-0.026	14.909	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	22	VAL	0	0.028	0.013	15.360	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.800	-0.897	16.371	-0.309	-0.309	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.033	0.008	15.232	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.034	-0.020	7.886	-0.062	-0.062	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.765	-0.860	13.449	-0.410	-0.410	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.871	0.944	15.722	0.327	0.327	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.736	0.843	13.317	0.418	0.418	0.000	0.000	0.000	0.000
26	A	29	ASN	0	-0.007	-0.008	9.462	-0.084	-0.084	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.825	0.891	11.390	0.595	0.595	0.000	0.000	0.000	0.000
28	A	31	MET	0	-0.024	0.016	5.093	0.104	0.104	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.791	-0.876	8.286	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.011	-0.008	6.717	-0.152	-0.152	0.000	0.000	0.000	0.000
31	A	34	GLY	0	-0.065	-0.030	6.766	0.320	0.320	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.834	-0.931	8.240	0.124	0.124	0.000	0.000	0.000	0.000
33	A	36	VAL	0	0.019	-0.006	9.362	-0.165	-0.165	0.000	0.000	0.000	0.000
34	A	37	ILE	0	-0.031	-0.010	11.108	0.118	0.118	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.001	-0.002	13.377	-0.114	-0.114	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.028	-0.011	15.188	0.053	0.053	0.000	0.000	0.000	0.000
37	A	40	HIS	0	0.002	-0.028	17.038	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.045	-0.010	19.158	0.023	0.023	0.000	0.000	0.000	0.000
39	A	42	ILE	0	0.024	0.014	21.808	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	43	ASP	-1	-0.830	-0.930	24.870	-0.135	-0.135	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.845	-0.931	26.099	-0.085	-0.085	0.000	0.000	0.000	0.000
42	A	45	GLY	0	-0.003	0.009	27.954	0.008	0.008	0.000	0.000	0.000	0.000
43	A	46	THR	0	-0.063	-0.068	28.059	0.006	0.006	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.044	-0.015	30.604	0.004	0.004	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.918	-0.960	32.984	-0.065	-0.065	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.927	-0.958	34.887	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.077	-0.025	36.331	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.110	-0.050	38.125	0.008	0.008	0.000	0.000	0.000	0.000
49	A	64	GLU	-1	-0.969	-0.993	41.457	-0.053	-0.053	0.000	0.000	0.000	0.000
50	A	65	LEU	0	0.016	-0.009	40.721	0.000	0.000	0.000	0.000	0.000	0.000
51	A	66	LYN	0	0.012	0.015	35.142	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	67	ASP	-1	-0.891	-0.954	36.272	-0.043	-0.043	0.000	0.000	0.000	0.000
53	A	68	ILE	0	0.015	0.014	36.058	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	69	LYS	1	0.878	0.935	30.162	0.071	0.071	0.000	0.000	0.000	0.000
55	A	70	GLU	-1	-0.877	-0.964	31.969	-0.070	-0.070	0.000	0.000	0.000	0.000
56	A	71	LYS	1	0.874	0.933	33.406	0.063	0.063	0.000	0.000	0.000	0.000
57	A	72	LEU	0	0.045	0.004	30.093	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	73	LYS	1	0.892	0.980	28.391	0.052	0.052	0.000	0.000	0.000	0.000
59	A	74	GLU	-1	-0.923	-0.958	28.463	-0.069	-0.069	0.000	0.000	0.000	0.000
60	A	75	GLU	-1	-0.772	-0.887	30.099	-0.119	-0.119	0.000	0.000	0.000	0.000
61	A	76	ALA	0	0.003	0.016	25.050	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	77	SER	0	-0.051	-0.053	25.695	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	78	ARG	1	0.896	0.962	26.731	0.106	0.106	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.877	0.920	25.670	0.134	0.134	0.000	0.000	0.000	0.000
65	A	80	LEU	0	-0.079	-0.011	20.166	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	81	GLN	0	-0.009	-0.033	22.592	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	82	GLU	-1	-0.894	-0.921	24.387	-0.127	-0.127	0.000	0.000	0.000	0.000
68	A	83	LYS	1	0.827	0.946	18.995	0.323	0.323	0.000	0.000	0.000	0.000
69	A	84	ALA	0	-0.013	-0.011	19.578	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	85	GLU	-1	-0.796	-0.906	19.058	-0.156	-0.156	0.000	0.000	0.000	0.000
71	A	86	GLU	-1	-0.838	-0.927	20.623	-0.298	-0.298	0.000	0.000	0.000	0.000
72	A	87	VAL	0	0.027	0.004	14.887	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	88	LYS	1	0.799	0.909	15.125	0.044	0.044	0.000	0.000	0.000	0.000
74	A	89	ARG	1	0.865	0.917	15.151	0.251	0.251	0.000	0.000	0.000	0.000
75	A	90	ALA	0	0.009	0.024	15.752	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	91	PHE	0	-0.086	-0.076	10.055	-0.093	-0.093	0.000	0.000	0.000	0.000
77	A	92	ARG	1	0.819	0.926	11.199	0.385	0.385	0.000	0.000	0.000	0.000
78	A	93	ALA	0	-0.003	0.002	11.013	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	94	LYS	1	0.827	0.903	8.611	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	95	ASN	0	-0.076	-0.034	12.461	0.003	0.003	0.000	0.000	0.000	0.000
81	A	96	VAL	0	0.033	0.019	13.412	-0.068	-0.068	0.000	0.000	0.000	0.000
82	A	97	ARG	1	0.762	0.873	14.637	0.043	0.043	0.000	0.000	0.000	0.000
83	A	98	THR	0	0.031	0.006	17.332	-0.050	-0.050	0.000	0.000	0.000	0.000
84	A	99	ILE	0	-0.008	0.001	16.550	0.028	0.028	0.000	0.000	0.000	0.000
85	A	100	ILE	0	0.041	0.020	19.914	-0.035	-0.035	0.000	0.000	0.000	0.000
86	A	101	ARG	1	0.761	0.880	19.316	0.129	0.129	0.000	0.000	0.000	0.000
87	A	102	PHE	0	0.046	0.020	23.110	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	103	GLY	0	0.110	0.051	24.357	0.002	0.002	0.000	0.000	0.000	0.000
89	A	104	ILE	0	0.007	0.026	22.446	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	105	PRO	0	0.092	0.044	20.266	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	106	TRP	0	-0.033	-0.043	17.221	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	107	ASP	-1	-0.841	-0.916	17.009	-0.164	-0.164	0.000	0.000	0.000	0.000
93	A	108	GLU	-1	-0.767	-0.867	18.537	-0.127	-0.127	0.000	0.000	0.000	0.000
94	A	109	ILE	0	-0.052	-0.026	12.989	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	110	VAL	0	-0.035	-0.022	13.468	-0.045	-0.045	0.000	0.000	0.000	0.000
96	A	111	LYS	1	0.762	0.873	14.433	0.133	0.133	0.000	0.000	0.000	0.000
97	A	112	VAL	0	0.044	0.005	14.359	0.023	0.023	0.000	0.000	0.000	0.000
98	A	113	ALA	0	-0.060	-0.032	10.162	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	114	GLU	-1	-0.881	-0.957	11.487	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.815	-0.898	12.733	0.016	0.016	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.840	-0.895	12.219	0.105	0.105	0.000	0.000	0.000	0.000
102	A	117	ASN	0	-0.021	-0.006	9.620	0.020	0.020	0.000	0.000	0.000	0.000
103	A	118	VAL	0	0.022	0.029	7.332	0.288	0.288	0.000	0.000	0.000	0.000
104	A	119	SER	0	-0.095	-0.051	2.300	0.822	1.556	1.217	-0.904	-1.047	0.002
105	A	120	LEU	0	-0.023	-0.022	2.273	-4.050	-2.402	2.713	-1.143	-3.219	-0.011
106	A	121	ILE	0	-0.012	0.013	4.214	0.734	0.873	0.003	-0.029	-0.113	0.000
107	A	122	ILE	0	-0.014	0.007	6.536	-0.219	-0.219	0.000	0.000	0.000	0.000
108	A	123	LEU	0	0.053	0.014	8.771	0.195	0.195	0.000	0.000	0.000	0.000
109	A	124	PRO	0	0.024	0.016	12.176	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	125	SER	0	-0.024	-0.010	15.213	0.028	0.028	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.875	0.958	16.396	0.268	0.268	0.000	0.000	0.000	0.000
112	A	127	GLY	0	0.030	0.009	19.888	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	128	LYS	1	0.965	0.972	21.519	0.231	0.231	0.000	0.000	0.000	0.000
114	A	129	LEU	0	0.020	0.014	23.138	0.006	0.006	0.000	0.000	0.000	0.000
115	A	130	SER	0	0.069	0.033	25.043	0.006	0.006	0.000	0.000	0.000	0.000
116	A	131	LEU	0	-0.011	-0.011	26.894	0.004	0.004	0.000	0.000	0.000	0.000
117	A	132	SER	0	0.030	0.002	25.549	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	133	HIS	0	0.012	0.017	21.010	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	134	GLU	-1	-0.880	-0.939	21.083	-0.164	-0.164	0.000	0.000	0.000	0.000
120	A	135	PHE	0	0.005	0.003	21.882	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	136	LEU	0	-0.025	-0.011	15.554	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	137	GLY	0	0.094	0.056	18.667	-0.026	-0.026	0.000	0.000	0.000	0.000
123	A	138	SER	0	-0.003	-0.030	19.195	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	139	THR	0	0.066	0.023	17.182	0.011	0.011	0.000	0.000	0.000	0.000
125	A	140	VAL	0	0.032	0.026	13.635	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	141	MET	0	0.011	0.008	14.847	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	142	ARG	1	0.865	0.943	16.172	0.196	0.196	0.000	0.000	0.000	0.000
128	A	143	VAL	0	0.042	0.023	11.490	0.021	0.021	0.000	0.000	0.000	0.000
129	A	144	LEU	0	-0.064	-0.039	11.073	0.008	0.008	0.000	0.000	0.000	0.000
130	A	145	ARG	1	0.937	0.969	12.214	0.192	0.192	0.000	0.000	0.000	0.000
131	A	146	LYS	1	0.945	0.994	14.684	0.196	0.196	0.000	0.000	0.000	0.000
132	A	147	THR	0	-0.022	-0.007	9.405	0.071	0.071	0.000	0.000	0.000	0.000
133	A	148	LYS	1	0.904	0.947	10.399	0.143	0.143	0.000	0.000	0.000	0.000
134	A	149	LYS	1	0.824	0.924	6.599	0.176	0.176	0.000	0.000	0.000	0.000
135	A	150	PRO	0	0.016	0.025	2.375	0.089	-0.971	3.734	-0.588	-2.086	-0.002
136	A	151	VAL	0	0.029	-0.014	4.301	-0.170	-0.091	-0.001	-0.006	-0.072	0.000
137	A	152	LEU	0	0.004	0.002	5.991	0.237	0.237	0.000	0.000	0.000	0.000
138	A	153	ILE	0	-0.039	-0.012	7.252	0.128	0.128	0.000	0.000	0.000	0.000
139	A	154	ILE	0	0.011	0.009	10.746	0.072	0.072	0.000	0.000	0.000	0.000
140	A	155	LYS	1	0.837	0.884	12.892	0.358	0.358	0.000	0.000	0.000	0.000
141	A	156	GLU	-1	-0.752	-0.847	16.563	-0.291	-0.291	0.000	0.000	0.000	0.000
142	A	157	VAL	0	-0.007	-0.016	18.371	-0.018	-0.018	0.000	0.000	0.000	0.000
143	A	158	ASP	-1	-0.828	-0.899	18.455	-0.327	-0.327	0.000	0.000	0.000	0.000
144	A	159	GLU	-1	-0.830	-0.895	21.097	-0.215	-0.215	0.000	0.000	0.000	0.000
145	A	160	ASN	0	-0.099	-0.056	24.095	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)