FMO DATABASE

FMODB ID: 2J41R

Calculation Name: 1O6D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O6D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZU8

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptAll
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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1472787.298684
FMO2-HF: Nuclear repulsion	1413372.43949
FMO2-HF: Total energy	-59414.859195
FMO2-MP2: Total energy	-59588.217189

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:LEU)

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

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.
-13.299	-1.599	7.644	-5.504	-13.838	-0.035

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.026

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	0.030	0.013	2.356	-3.059	-0.654	1.673	-1.530	-2.548	-0.004
4	A	4	ARG	1	0.816	0.896	4.813	-0.326	-0.255	-0.001	-0.010	-0.060	0.000
5	A	5	ILE	0	0.019	0.005	8.347	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.003	0.016	11.381	0.047	0.047	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.001	-0.009	14.401	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.033	0.004	17.591	0.022	0.022	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.024	0.003	21.226	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.754	0.854	22.231	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.021	0.020	17.910	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.861	-0.930	22.453	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.056	-0.033	23.223	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.149	0.054	23.233	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.002	0.026	19.091	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.951	0.971	18.956	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.955	-0.973	18.952	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.042	0.018	18.861	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.015	-0.001	13.773	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.916	0.962	14.630	-0.083	-0.083	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.038	-0.017	16.258	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.007	-0.036	12.637	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.868	-0.931	10.962	0.091	0.091	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.831	0.927	11.497	0.042	0.042	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.039	0.012	12.736	0.023	0.023	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.019	0.014	7.089	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.866	0.916	7.240	-0.267	-0.267	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.784	0.885	8.004	0.375	0.375	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.013	-0.004	5.587	0.085	0.085	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.034	0.006	2.798	-2.472	-0.555	0.342	-0.704	-1.555	-0.003
31	A	31	LYS	1	0.827	0.895	3.663	-0.460	0.171	0.004	-0.184	-0.450	0.000
32	A	32	PRO	0	0.035	0.025	5.912	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.764	-0.862	7.487	0.959	0.959	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.046	0.035	10.055	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.044	-0.023	12.817	0.043	0.043	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.770	-0.860	15.447	0.018	0.018	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.027	-0.005	17.629	0.022	0.022	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.971	0.978	21.148	-0.082	-0.082	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.851	0.910	24.940	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.037	-0.020	26.876	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.021	-0.003	25.299	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.932	0.952	30.392	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.026	0.015	33.971	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.002	-0.014	35.763	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.031	0.005	32.036	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.801	-0.886	31.303	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.778	-0.859	30.488	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.047	-0.014	29.054	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.040	0.021	26.209	0.002	0.002	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.767	0.857	25.723	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.835	0.905	25.639	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.787	-0.904	23.700	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.003	-0.007	21.329	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.791	-0.859	20.920	0.024	0.024	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.815	-0.883	20.942	0.070	0.070	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.035	-0.011	16.490	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.004	-0.013	16.230	0.009	0.009	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.054	-0.032	16.668	0.018	0.018	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.791	0.872	14.458	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.005	0.016	11.470	0.025	0.025	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.027	-0.002	6.443	0.085	0.085	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.023	0.009	10.104	-0.115	-0.115	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.031	0.027	9.992	0.096	0.096	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.046	-0.017	6.721	-0.136	-0.136	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.004	-0.015	6.688	0.051	0.051	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.013	0.004	8.119	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.010	0.009	7.096	0.021	0.021	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.013	0.005	11.658	0.040	0.040	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.029	-0.005	13.994	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.763	-0.886	16.639	-0.080	-0.080	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.814	0.903	20.283	0.087	0.087	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.790	0.869	22.843	0.093	0.093	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.004	0.005	19.488	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.863	-0.916	17.354	-0.293	-0.293	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.823	-0.895	18.486	-0.166	-0.166	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.033	-0.007	14.764	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.016	-0.030	17.873	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.020	-0.062	15.078	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.897	-0.950	14.264	-0.345	-0.345	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.797	-0.868	14.841	-0.325	-0.325	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.039	-0.018	9.396	-0.084	-0.084	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.014	0.006	10.235	-0.127	-0.127	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.812	-0.900	10.291	-0.623	-0.623	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.041	-0.032	9.708	-0.072	-0.072	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.019	-0.008	3.994	-0.368	-0.196	0.000	-0.020	-0.153	0.000
86	A	86	LYS	1	0.876	0.928	5.720	0.050	0.050	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.831	-0.895	7.386	-0.849	-0.849	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.017	-0.017	3.852	-0.114	0.075	0.000	-0.024	-0.166	0.000
89	A	89	GLU	-1	-0.855	-0.920	2.915	-3.373	-2.061	0.322	-0.533	-1.101	-0.003
90	A	90	MET	0	-0.039	-0.015	3.840	0.174	0.342	0.001	0.039	-0.208	0.000
91	A	91	LYS	1	0.746	0.859	5.381	1.006	1.006	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.007	0.007	2.387	0.020	0.067	1.008	-0.419	-0.636	-0.001
93	A	93	LYS	1	0.805	0.908	3.010	0.522	1.068	1.179	-0.028	-1.697	-0.006
94	A	94	ASP	-1	-0.788	-0.898	2.395	-2.986	0.053	2.775	-2.203	-3.610	-0.019
95	A	95	ILE	0	0.006	-0.003	2.658	-0.339	0.282	0.292	0.199	-1.112	0.001
96	A	96	THR	0	-0.028	-0.019	5.115	0.358	0.346	-0.001	-0.001	0.015	0.000
97	A	97	ILE	0	0.015	0.012	7.210	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.029	-0.015	10.685	0.075	0.075	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.006	0.004	14.433	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.076	0.022	17.283	0.023	0.023	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.048	0.022	20.925	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.051	-0.039	24.187	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.006	-0.004	27.098	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.024	0.032	24.980	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.017	-0.010	19.574	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.020	0.000	23.905	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.880	-0.950	23.494	-0.072	-0.072	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.828	-0.905	22.963	-0.039	-0.039	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.024	-0.021	17.645	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.006	-0.008	18.575	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.024	0.002	19.353	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.774	0.882	17.031	0.046	0.046	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.013	0.001	14.613	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.006	0.012	11.566	-0.045	-0.045	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.850	0.911	12.364	0.327	0.327	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.023	0.014	14.245	0.016	0.016	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.016	0.011	11.153	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.006	-0.002	16.513	0.025	0.025	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.030	-0.003	15.439	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	120	SER	0	0.003	0.000	19.269	0.006	0.006	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.900	0.930	23.077	0.140	0.140	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.018	0.002	25.858	0.009	0.009	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.001	-0.003	25.179	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	124	PHE	0	0.030	0.019	20.998	0.006	0.006	0.000	0.000	0.000	0.000
125	A	125	THR	0	0.047	0.020	23.714	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	HIS	0	0.068	0.033	20.549	-0.023	-0.023	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.041	0.003	19.042	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.006	-0.011	18.882	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	THR	0	0.008	-0.008	16.379	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.008	0.004	13.808	-0.026	-0.026	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.048	-0.013	14.049	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.016	0.018	15.212	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.023	0.013	10.456	-0.033	-0.033	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.017	-0.010	9.666	-0.054	-0.054	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.821	-0.875	10.976	-0.239	-0.239	0.000	0.000	0.000	0.000
136	A	136	GLN	0	0.045	0.043	12.562	-0.055	-0.055	0.000	0.000	0.000	0.000
137	A	137	ILE	0	0.029	0.014	5.973	-0.045	-0.045	0.000	0.000	0.000	0.000
138	A	138	PHE	0	-0.017	-0.015	8.661	-0.070	-0.070	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.869	0.921	10.379	0.232	0.232	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.050	0.036	9.340	0.011	0.011	0.000	0.000	0.000	0.000
141	A	141	PHE	0	0.032	0.000	3.152	-0.578	0.016	0.050	-0.086	-0.557	0.000
142	A	142	LYS	1	0.791	0.901	8.893	0.330	0.330	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.013	0.016	12.564	0.032	0.032	0.000	0.000	0.000	0.000
144	A	144	ILE	0	-0.032	-0.009	7.813	0.045	0.045	0.000	0.000	0.000	0.000
145	A	145	HIS	0	-0.096	-0.062	6.990	0.191	0.191	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.018	0.032	12.079	0.064	0.064	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.890	-0.929	15.004	-0.226	-0.226	0.000	0.000	0.000	0.000

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