FMO DATABASE

FMODB ID: K96Q3

Calculation Name: 3DO8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DO8

Chain ID: A

ChEMBL ID:

UniProt ID: O28077

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:

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1263342.895491
FMO2-HF: Nuclear repulsion	1208808.272688
FMO2-HF: Total energy	-54534.622804
FMO2-MP2: Total energy	-54693.01471

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: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.
-12.222	-28.258	46.453	-3.017	-27.402	-0.099

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 : -0.031 / q_NPA : 0.031

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	VAL	0	-0.015	-0.020	3.297	-2.539	-0.211	0.452	-0.957	-1.822	0.007
4	A	4	ALA	0	-0.003	0.005	3.901	0.883	1.962	0.180	-0.463	-0.796	-0.004
5	A	5	LEU	0	0.033	0.019	6.031	-0.833	-0.819	-0.001	-0.003	-0.010	0.000
6	A	6	GLY	0	-0.004	-0.003	8.847	0.085	0.085	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.002	-0.002	11.567	-0.081	-0.081	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.004	0.014	14.849	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.012	-0.007	12.064	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.757	-0.819	17.785	0.051	0.051	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.040	0.001	21.480	0.005	0.005	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.010	-0.007	15.880	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.050	0.020	19.747	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.812	-0.937	19.613	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.075	0.029	19.782	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.052	0.013	15.863	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.893	0.959	15.042	0.021	0.021	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.871	0.940	15.680	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.009	0.008	13.156	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.015	0.003	10.806	0.032	0.032	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.758	-0.840	11.000	-0.123	-0.123	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.003	0.002	12.445	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.014	0.000	7.616	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.003	0.000	7.971	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.807	0.901	9.086	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.056	-0.016	9.326	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.003	-0.025	5.926	-0.086	-0.086	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.054	0.046	6.132	-0.381	-0.381	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.928	0.940	6.059	1.022	1.022	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.859	-0.919	2.329	-12.788	-8.816	4.520	-3.246	-5.246	-0.046
31	A	31	ILE	0	-0.013	-0.046	2.141	9.729	-3.450	15.200	3.160	-5.181	-0.014
32	A	32	THR	0	-0.027	-0.018	2.140	9.457	-3.298	14.582	3.541	-5.369	-0.024
33	A	33	ILE	0	-0.020	-0.009	3.830	0.309	0.505	0.010	0.052	-0.258	0.001
34	A	34	GLY	0	-0.006	-0.020	7.388	-0.167	-0.167	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.026	-0.007	10.031	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.019	-0.020	13.367	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.043	0.011	16.384	-0.049	-0.049	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.776	-0.901	18.372	0.094	0.094	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.912	0.951	21.781	-0.129	-0.129	0.000	0.000	0.000	0.000
40	A	40	MET	0	-0.009	0.009	17.681	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.008	-0.003	20.563	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.981	0.977	21.913	-0.101	-0.101	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.011	0.019	23.941	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.904	0.968	19.614	-0.194	-0.194	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.040	0.027	23.311	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.999	0.993	26.369	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.130	-0.082	23.714	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.004	-0.030	25.946	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.038	-0.005	22.346	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.060	0.026	22.672	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.009	-0.017	13.619	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.009	0.005	17.758	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.024	0.020	18.467	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.798	0.901	17.805	-0.136	-0.136	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.019	0.008	13.899	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.833	-0.920	14.630	-0.139	-0.139	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.065	-0.031	16.994	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.024	-0.007	11.614	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.933	0.967	11.775	0.140	0.140	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.988	0.989	13.627	0.038	0.038	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.066	-0.038	14.500	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.036	0.005	9.955	0.011	0.011	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.029	0.041	13.365	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.886	0.944	15.040	0.087	0.087	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.857	0.924	16.023	0.095	0.095	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.042	-0.056	12.388	0.038	0.038	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.047	0.054	13.813	-0.036	-0.036	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.018	-0.023	6.963	-0.066	-0.066	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.906	-0.962	11.068	-0.279	-0.279	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.063	-0.023	7.271	-0.144	-0.144	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.789	-0.886	3.018	-4.032	-2.843	0.112	-0.479	-0.822	-0.005
72	A	72	ILE	0	-0.055	-0.026	6.201	0.337	0.337	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.030	0.012	6.426	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.918	0.960	9.374	-0.087	-0.087	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.017	0.008	11.455	0.054	0.054	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.004	-0.031	13.337	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.034	0.017	13.654	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.041	-0.003	15.206	0.044	0.044	0.000	0.000	0.000	0.000
79	A	79	TYR	0	0.087	0.054	12.511	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.030	0.014	10.859	0.124	0.124	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.996	0.985	3.436	-1.936	-1.690	0.003	-0.046	-0.204	0.000
82	A	82	THR	0	-0.032	-0.029	7.339	0.060	0.060	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.012	0.001	8.393	-0.138	-0.138	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.913	-0.938	8.644	0.748	0.748	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.010	-0.016	2.499	-0.632	-0.088	1.094	-0.412	-1.226	0.002
86	A	86	ASP	-1	-0.883	-0.927	4.109	-0.415	-0.042	-0.001	-0.124	-0.249	0.000
87	A	87	PHE	0	-0.008	-0.017	1.980	-8.658	-9.003	10.302	-3.999	-5.958	-0.016
88	A	88	GLU	-1	-0.890	-0.939	4.035	-0.881	-0.579	0.000	-0.041	-0.261	0.000
89	A	89	TYR	0	-0.002	-0.015	6.403	0.366	0.366	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.017	-0.005	6.914	0.482	0.482	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.006	0.000	9.231	-0.188	-0.188	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.039	-0.017	11.570	0.074	0.074	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.039	0.026	14.614	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.014	-0.034	18.122	0.011	0.011	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.919	-0.951	20.482	0.124	0.124	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.044	-0.028	15.884	0.021	0.021	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.033	0.017	16.646	0.030	0.030	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.862	-0.931	17.950	0.123	0.123	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.047	-0.021	15.410	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.019	0.008	13.865	0.027	0.027	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.020	0.011	14.796	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.953	0.987	17.438	-0.180	-0.180	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.021	-0.019	10.834	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	104	ASN	0	0.053	0.016	12.574	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.040	-0.005	14.671	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.887	0.931	15.807	-0.196	-0.196	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.757	0.850	7.403	-0.226	-0.226	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.922	-0.962	13.961	0.065	0.065	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.892	-0.946	16.555	0.152	0.152	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.054	-0.024	14.641	0.002	0.002	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.017	0.031	15.817	0.011	0.011	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.845	0.938	8.188	-0.575	-0.575	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.984	0.994	5.898	0.407	0.407	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.914	0.954	10.187	-0.077	-0.077	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.030	0.001	7.486	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.041	0.026	9.873	0.116	0.116	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.034	-0.018	11.208	0.059	0.059	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.018	0.010	12.407	-0.048	-0.048	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.879	0.943	14.515	-0.023	-0.023	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.008	-0.005	15.193	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.776	-0.900	18.169	0.075	0.075	0.000	0.000	0.000	0.000
122	A	122	TRP	0	-0.065	-0.046	17.776	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.067	-0.033	21.309	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.040	0.046	22.486	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	132	SER	0	0.054	0.044	29.634	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	133	SER	0	-0.045	-0.044	25.327	0.007	0.007	0.000	0.000	0.000	0.000
127	A	134	THR	0	0.068	0.045	25.359	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.945	0.972	25.143	0.051	0.051	0.000	0.000	0.000	0.000
129	A	136	ILE	0	0.044	0.020	19.059	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	137	LYS	1	0.921	0.952	21.616	0.090	0.090	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.801	0.916	17.188	0.031	0.031	0.000	0.000	0.000	0.000
132	A	139	GLY	0	0.058	0.030	15.939	0.002	0.002	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.920	-0.968	11.140	-0.474	-0.474	0.000	0.000	0.000	0.000
134	A	141	ILE	0	-0.041	-0.041	14.790	0.024	0.024	0.000	0.000	0.000	0.000
135	A	142	ASP	-1	-0.929	-0.937	15.872	-0.266	-0.266	0.000	0.000	0.000	0.000

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