FMO DATABASE

FMODB ID: YQK22

Calculation Name: 3DA5-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA5

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWU1

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1148122.872592
FMO2-HF: Nuclear repulsion	1098409.247652
FMO2-HF: Total energy	-49713.62494
FMO2-MP2: Total energy	-49864.146189

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:7:ACE )

Summations of interaction energy for fragment #1(A:7:ACE )

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.
1.317	2.202	-0.004	-0.431	-0.451	-0.001

Interaction energy analysis for fragmet #1(A:7:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.016

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	9	LYS	1	0.952	0.996	3.897	1.024	1.909	-0.004	-0.431	-0.451	-0.001
4	A	10	THR	0	0.027	0.022	6.830	-0.044	-0.044	0.000	0.000	0.000	0.000
5	A	11	LEU	0	0.037	0.000	9.875	0.033	0.033	0.000	0.000	0.000	0.000
6	A	12	TRP	0	-0.008	-0.007	13.380	0.019	0.019	0.000	0.000	0.000	0.000
7	A	13	GLU	-1	-0.911	-0.966	10.123	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	14	LEU	0	-0.098	-0.051	9.700	0.013	0.013	0.000	0.000	0.000	0.000
9	A	15	VAL	0	-0.007	0.007	13.041	0.025	0.025	0.000	0.000	0.000	0.000
10	A	16	GLY	0	0.006	0.012	15.627	0.026	0.026	0.000	0.000	0.000	0.000
11	A	17	ARG	1	0.872	0.934	13.735	0.065	0.065	0.000	0.000	0.000	0.000
12	A	18	ASN	0	0.072	0.059	18.174	0.013	0.013	0.000	0.000	0.000	0.000
13	A	19	LYS	1	0.937	0.946	21.233	0.044	0.044	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.828	-0.902	23.277	-0.074	-0.074	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.025	0.003	20.811	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.036	-0.016	18.267	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.873	0.933	20.911	0.068	0.068	0.000	0.000	0.000	0.000
18	A	24	ASP	-1	-0.907	-0.950	23.829	-0.102	-0.102	0.000	0.000	0.000	0.000
19	A	25	PHE	0	0.033	0.019	15.781	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	26	LEU	0	-0.014	-0.019	19.110	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	27	LYS	1	0.932	0.960	21.948	0.091	0.091	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.938	-0.967	22.666	-0.140	-0.140	0.000	0.000	0.000	0.000
23	A	29	HIS	1	0.860	0.926	18.896	0.226	0.226	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.882	0.959	22.099	0.098	0.098	0.000	0.000	0.000	0.000
25	A	31	GLY	0	-0.099	-0.055	23.950	0.009	0.009	0.000	0.000	0.000	0.000
26	A	32	THR	0	0.050	0.032	21.243	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	33	ILE	0	-0.051	0.003	16.677	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.060	-0.036	17.441	0.036	0.036	0.000	0.000	0.000	0.000
29	A	35	LEU	0	0.028	0.008	15.200	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	36	ARG	1	0.908	0.958	10.572	0.522	0.522	0.000	0.000	0.000	0.000
31	A	37	ASP	-1	-0.768	-0.880	12.579	-0.241	-0.241	0.000	0.000	0.000	0.000
32	A	38	ILE	0	-0.112	-0.083	7.342	-0.046	-0.046	0.000	0.000	0.000	0.000
33	A	39	ALA	0	0.069	0.033	10.491	0.043	0.043	0.000	0.000	0.000	0.000
34	A	40	SER	0	0.005	0.009	12.971	0.033	0.033	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.933	-0.955	13.967	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	42	HIS	0	-0.019	-0.011	14.769	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.962	1.002	8.599	0.214	0.214	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.000	-0.008	14.106	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	45	VAL	0	-0.025	-0.014	15.236	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	46	TYR	0	0.029	0.019	17.512	0.040	0.040	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.947	0.968	19.589	0.123	0.123	0.000	0.000	0.000	0.000
42	A	48	PRO	0	0.026	0.008	20.332	0.016	0.016	0.000	0.000	0.000	0.000
43	A	49	ILE	0	-0.021	0.010	22.980	0.005	0.005	0.000	0.000	0.000	0.000
44	A	50	PHE	0	-0.010	-0.018	24.707	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	51	LYS	1	1.000	0.999	28.886	0.074	0.074	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.942	0.955	31.996	0.051	0.051	0.000	0.000	0.000	0.000
47	A	53	TYR	0	0.019	0.001	34.932	0.001	0.001	0.000	0.000	0.000	0.000
48	A	54	ASN	0	-0.031	0.042	31.502	0.000	0.000	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.069	0.010	32.113	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	56	ASP	-1	-0.891	-0.949	29.263	-0.088	-0.088	0.000	0.000	0.000	0.000
51	A	57	PRO	0	-0.038	-0.029	24.867	0.002	0.002	0.000	0.000	0.000	0.000
52	A	58	ASP	-1	-0.929	-0.967	27.040	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	59	LEU	0	-0.049	-0.023	23.482	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	60	ILE	0	0.041	0.025	25.922	0.006	0.006	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.953	-1.006	26.129	-0.075	-0.075	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.931	-0.959	27.870	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	63	ASN	0	-0.017	-0.008	28.539	0.009	0.009	0.000	0.000	0.000	0.000
58	A	64	SER	0	0.060	0.013	26.074	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	65	ASN	0	0.063	0.038	26.202	0.004	0.004	0.000	0.000	0.000	0.000
60	A	66	ASP	-1	-0.864	-0.930	26.530	-0.042	-0.042	0.000	0.000	0.000	0.000
61	A	67	VAL	0	-0.089	-0.044	21.082	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.922	-0.966	22.021	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	69	HIS	0	0.002	0.021	23.217	0.007	0.007	0.000	0.000	0.000	0.000
64	A	70	TRP	0	-0.016	-0.031	20.909	0.001	0.001	0.000	0.000	0.000	0.000
65	A	71	TYR	0	-0.040	-0.038	16.053	0.000	0.000	0.000	0.000	0.000	0.000
66	A	72	ASP	-1	-0.869	-0.941	19.118	0.012	0.012	0.000	0.000	0.000	0.000
67	A	73	TYR	0	-0.077	-0.027	21.096	0.009	0.009	0.000	0.000	0.000	0.000
68	A	74	HIS	0	-0.002	-0.018	16.415	0.015	0.015	0.000	0.000	0.000	0.000
69	A	75	LEU	0	-0.037	0.001	17.117	0.013	0.013	0.000	0.000	0.000	0.000
70	A	76	GLU	-1	-0.814	-0.905	18.455	0.012	0.012	0.000	0.000	0.000	0.000
71	A	77	ARG	1	0.745	0.868	21.031	0.014	0.014	0.000	0.000	0.000	0.000
72	A	78	TYR	0	-0.029	-0.029	16.545	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	79	TRP	0	-0.081	-0.046	10.090	0.019	0.019	0.000	0.000	0.000	0.000
74	A	80	ASN	0	0.008	0.011	17.130	0.018	0.018	0.000	0.000	0.000	0.000
75	A	81	THR	0	0.044	0.015	19.094	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	82	PRO	0	0.042	0.021	19.248	0.008	0.008	0.000	0.000	0.000	0.000
77	A	83	GLU	-1	-0.917	-0.966	16.824	0.136	0.136	0.000	0.000	0.000	0.000
78	A	84	LEU	0	0.025	0.017	14.419	0.036	0.036	0.000	0.000	0.000	0.000
79	A	85	LYS	1	1.027	1.024	14.624	-0.068	-0.068	0.000	0.000	0.000	0.000
80	A	86	LYS	1	0.904	0.955	13.773	-0.276	-0.276	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.989	-0.994	9.205	0.382	0.382	0.000	0.000	0.000	0.000
82	A	88	PHE	0	0.049	0.018	10.764	0.040	0.040	0.000	0.000	0.000	0.000
83	A	89	TYR	0	0.006	0.005	11.917	0.005	0.005	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.892	0.936	10.537	-0.337	-0.337	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.792	0.940	6.365	0.155	0.155	0.000	0.000	0.000	0.000
86	A	92	PHE	0	0.001	-0.020	8.654	-0.072	-0.072	0.000	0.000	0.000	0.000
87	A	93	GLY	0	0.007	0.021	11.198	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	94	PRO	0	-0.013	-0.013	14.123	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.051	0.041	17.139	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	96	ASP	-1	-0.837	-0.906	18.188	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.052	0.010	19.870	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	98	ASN	0	0.005	0.005	22.507	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	99	GLN	0	-0.062	-0.046	17.618	-0.031	-0.031	0.000	0.000	0.000	0.000
94	A	100	PRO	0	-0.017	0.010	20.877	0.007	0.007	0.000	0.000	0.000	0.000
95	A	101	ILE	0	0.020	-0.004	21.353	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	102	ILE	0	-0.037	-0.031	18.353	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	103	LEU	0	0.052	0.047	22.348	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	104	ALA	0	-0.020	-0.012	21.636	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.998	0.998	23.550	0.116	0.116	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.002	0.016	22.937	-0.019	-0.019	0.000	0.000	0.000	0.000
101	A	107	LEU	0	-0.004	-0.013	20.861	0.007	0.007	0.000	0.000	0.000	0.000
102	A	108	ARG	1	0.898	0.954	23.135	0.112	0.112	0.000	0.000	0.000	0.000
103	A	109	GLN	0	0.060	0.028	26.628	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	110	HIS	0	0.023	0.019	22.022	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	111	ASN	0	0.033	-0.002	26.504	0.005	0.005	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.903	0.962	24.639	0.055	0.055	0.000	0.000	0.000	0.000
107	A	113	GLY	0	0.024	0.034	27.420	0.001	0.001	0.000	0.000	0.000	0.000
108	A	114	ASP	-1	-0.877	-0.971	27.464	-0.088	-0.088	0.000	0.000	0.000	0.000
109	A	115	LEU	0	-0.042	-0.033	26.723	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	116	VAL	0	-0.050	-0.013	21.164	0.005	0.005	0.000	0.000	0.000	0.000
111	A	117	HIS	0	0.047	0.026	23.137	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	118	LEU	0	-0.034	-0.012	17.649	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	119	LEU	0	0.051	0.032	16.856	0.005	0.005	0.000	0.000	0.000	0.000
114	A	120	PRO	0	0.027	-0.001	15.873	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	121	GLN	0	-0.037	-0.021	13.500	-0.064	-0.064	0.000	0.000	0.000	0.000
116	A	122	PHE	0	0.007	0.011	12.028	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	123	VAL	0	-0.004	0.022	12.249	-0.046	-0.046	0.000	0.000	0.000	0.000
118	A	124	VAL	0	-0.032	-0.018	7.538	-0.093	-0.093	0.000	0.000	0.000	0.000
119	A	125	PRO	0	0.036	0.020	10.657	0.069	0.069	0.000	0.000	0.000	0.000
120	A	126	VAL	0	-0.109	-0.058	11.868	-0.127	-0.127	0.000	0.000	0.000	0.000
121	A	127	TYR	0	-0.006	-0.013	12.308	0.075	0.075	0.000	0.000	0.000	0.000
122	A	128	ASN	-1	-0.882	-0.936	16.517	-0.218	-0.218	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ACE )