FMO DATABASE

FMODB ID: YZ5M2

Calculation Name: 3E29-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E29

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1136519.864409
FMO2-HF: Nuclear repulsion	1084779.934989
FMO2-HF: Total energy	-51739.92942
FMO2-MP2: Total energy	-51889.366744

3D Structure Molmil

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-3.708	-2.13	8.064	-3.177	-6.464	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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	3	SER	0	0.066	0.033	3.908	-0.479	1.562	-0.020	-1.151	-0.869	0.000
4	A	4	THR	0	0.017	-0.003	6.683	0.352	0.352	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.039	0.026	4.795	0.109	0.188	-0.001	-0.008	-0.070	0.000
6	A	6	LEU	0	0.035	0.010	5.446	0.155	0.155	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.807	-0.864	7.033	0.010	0.010	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.012	0.006	10.159	0.076	0.076	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.043	0.022	8.890	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.003	0.004	10.716	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.787	0.857	12.532	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.072	-0.039	13.174	-0.046	-0.046	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.042	0.025	13.220	-0.029	-0.029	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.007	-0.016	15.718	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.931	0.983	18.424	-0.162	-0.162	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.020	0.022	20.458	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.017	-0.013	22.318	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.032	0.026	24.170	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.024	0.002	18.068	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.890	0.934	20.631	-0.111	-0.111	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.025	-0.003	22.087	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.014	0.014	21.237	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.018	0.015	20.602	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.058	-0.021	15.634	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.046	-0.017	13.657	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.014	-0.017	7.653	0.058	0.058	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.030	-0.010	8.897	-0.111	-0.111	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.828	-0.906	4.369	0.480	0.615	-0.001	-0.010	-0.124	0.000
29	A	29	ALA	0	0.015	-0.004	3.113	-0.312	0.025	0.012	-0.128	-0.221	0.000
30	A	30	GLY	0	0.025	0.003	2.470	1.130	0.367	7.209	-3.450	-2.996	-0.002
31	A	31	GLU	-1	-0.858	-0.911	2.222	-1.491	-2.718	0.806	1.871	-1.449	0.000
32	A	32	GLN	0	-0.002	-0.005	3.268	-2.418	-1.442	0.059	-0.301	-0.735	-0.001
33	A	33	GLY	0	0.005	0.019	5.719	-0.871	-0.871	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.041	-0.020	5.857	1.262	1.262	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.001	0.001	7.271	-0.245	-0.245	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.001	0.001	9.181	-0.079	-0.079	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.047	0.016	12.040	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.055	-0.018	14.896	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.837	0.912	18.322	-0.156	-0.156	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.006	0.003	21.450	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.815	0.876	24.568	-0.120	-0.120	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.780	-0.907	28.050	0.098	0.098	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.855	-0.905	30.381	0.099	0.099	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.033	-0.015	24.422	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.057	-0.003	28.990	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.055	-0.031	31.920	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.056	-0.048	33.622	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.019	0.002	35.275	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.875	-0.921	37.256	0.087	0.087	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.035	-0.021	33.659	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.864	0.932	32.575	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.030	0.027	30.431	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.017	0.003	24.867	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.056	0.024	28.185	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.067	0.027	27.024	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.028	0.011	26.282	0.016	0.016	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.002	0.012	22.901	0.012	0.012	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.031	0.006	21.980	0.023	0.023	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.019	0.015	21.445	0.029	0.029	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.010	-0.021	20.893	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.035	-0.016	17.265	0.028	0.028	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.010	-0.004	17.115	0.058	0.058	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.783	-0.853	17.608	0.361	0.361	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.019	-0.003	16.655	0.027	0.027	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.002	-0.006	13.360	0.062	0.062	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.028	0.006	13.222	0.132	0.132	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.803	-0.910	15.136	0.439	0.439	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.010	-0.020	11.973	0.011	0.011	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.000	0.014	10.360	0.169	0.169	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.013	-0.013	11.125	0.071	0.071	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.009	0.004	13.260	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.058	-0.027	6.647	-0.083	-0.083	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.812	0.898	7.208	-1.300	-1.300	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.037	-0.013	11.604	-0.094	-0.094	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.000	0.014	13.751	-0.077	-0.077	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.117	-0.078	14.829	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.010	-0.001	16.663	0.032	0.032	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.056	-0.010	17.545	-0.050	-0.050	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.036	-0.008	20.243	0.007	0.007	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.032	-0.029	22.558	0.002	0.002	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.131	-0.051	23.679	-0.031	-0.031	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.803	-0.881	25.314	0.211	0.211	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.019	-0.004	22.655	0.024	0.024	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.073	-0.041	23.982	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.009	-0.010	23.178	0.030	0.030	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.879	-0.910	23.888	0.218	0.218	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.021	-0.028	24.277	0.015	0.015	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.034	-0.001	22.908	0.009	0.009	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.892	0.951	24.234	-0.229	-0.229	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.010	0.009	27.143	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.041	0.028	24.635	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.034	0.015	26.095	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.038	-0.022	26.413	0.009	0.009	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.031	0.025	24.535	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.819	-0.906	19.298	0.167	0.167	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.019	-0.005	19.075	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.772	0.871	9.039	-0.632	-0.632	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.007	-0.011	13.838	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.781	-0.863	10.753	0.747	0.747	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.034	0.016	10.374	-0.135	-0.135	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.055	-0.039	8.913	0.135	0.135	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.005	0.003	11.511	-0.174	-0.174	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.020	-0.004	13.126	0.018	0.018	0.000	0.000	0.000	0.000
104	A	104	HIS	0	0.024	0.013	15.940	-0.075	-0.075	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.056	0.019	14.795	0.026	0.026	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.038	0.016	17.228	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.941	0.952	20.134	-0.113	-0.113	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.816	0.907	21.850	-0.207	-0.207	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.019	0.017	21.931	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.022	0.030	16.942	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.016	-0.005	18.226	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.001	0.016	15.075	0.042	0.042	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.053	0.018	15.538	-0.058	-0.058	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.015	0.007	14.678	0.098	0.098	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.867	0.922	14.134	-0.586	-0.586	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.002	0.001	15.339	0.041	0.041	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.023	-0.017	14.603	-0.024	-0.024	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.765	-0.879	18.349	0.226	0.226	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.013	-0.020	18.180	0.027	0.027	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.948	-0.956	19.110	0.181	0.181	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.016	0.001	17.624	0.006	0.006	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.101	-0.066	18.500	0.018	0.018	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.018	-0.016	18.161	0.012	0.012	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.013	-0.003	20.576	-0.026	-0.026	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.012	-0.003	21.244	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.012	-0.020	19.497	0.036	0.036	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.068	0.038	19.583	-0.034	-0.034	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.750	0.853	19.269	-0.222	-0.222	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.044	0.026	19.999	-0.036	-0.036	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.030	-0.008	20.753	0.028	0.028	0.000	0.000	0.000	0.000
131	A	131	TYR	0	0.037	-0.009	18.422	0.006	0.006	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.024	-0.021	21.713	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.020	-0.005	18.067	0.008	0.008	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.965	0.983	21.828	-0.163	-0.163	0.000	0.000	0.000	0.000

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