FMO DATABASE

FMODB ID: 2JV5R

Calculation Name: 3DKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DKZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W9W5

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	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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-976563.399211
FMO2-HF: Nuclear repulsion	929417.670176
FMO2-HF: Total energy	-47145.729035
FMO2-MP2: Total energy	-47280.838746

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:39:THR)

Summations of interaction energy for fragment #1(A:39:THR)

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.
-15.425	-13.642	10.808	-5.178	-7.413	0.01

Interaction energy analysis for fragmet #1(A:39:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.013

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	41	PHE	0	-0.050	-0.035	2.679	-4.132	-1.224	0.881	-1.718	-2.071	-0.009
4	A	42	PHE	0	0.033	0.013	5.675	0.835	0.835	0.000	0.000	0.000	0.000
5	A	43	GLY	0	0.041	0.019	7.981	0.413	0.413	0.000	0.000	0.000	0.000
6	A	44	LEU	0	-0.035	-0.015	6.947	0.471	0.471	0.000	0.000	0.000	0.000
7	A	45	THR	0	0.020	0.011	2.804	-2.766	-1.812	0.699	-0.583	-1.070	-0.004
8	A	46	ILE	0	0.047	0.019	4.145	0.941	1.121	-0.001	-0.024	-0.155	0.000
9	A	47	PRO	0	0.022	0.003	4.835	0.060	0.060	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.029	0.019	5.747	0.326	0.326	0.000	0.000	0.000	0.000
11	A	49	MET	0	0.040	0.023	5.830	0.221	0.221	0.000	0.000	0.000	0.000
12	A	50	GLN	0	-0.026	-0.028	1.889	-11.111	-13.466	9.231	-2.843	-4.033	0.023
13	A	51	LEU	0	-0.021	0.007	4.694	0.048	0.093	-0.001	-0.008	-0.037	0.000
14	A	52	LEU	0	0.026	0.004	8.451	-0.056	-0.056	0.000	0.000	0.000	0.000
15	A	53	GLY	0	-0.034	-0.001	6.636	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	54	VAL	0	-0.043	-0.017	6.697	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	55	VAL	0	0.014	-0.005	5.347	-0.859	-0.859	0.000	0.000	0.000	0.000
18	A	56	PRO	0	-0.013	0.005	4.726	0.445	0.496	-0.001	-0.002	-0.047	0.000
19	A	57	GLU	-1	-0.875	-0.947	7.492	-0.417	-0.417	0.000	0.000	0.000	0.000
20	A	58	HIS	0	-0.054	-0.033	10.637	0.110	0.110	0.000	0.000	0.000	0.000
21	A	59	SER	0	-0.015	-0.005	12.075	-0.110	-0.110	0.000	0.000	0.000	0.000
22	A	60	GLY	0	0.045	0.025	13.790	0.012	0.012	0.000	0.000	0.000	0.000
23	A	61	ASN	0	-0.071	-0.039	17.273	0.045	0.045	0.000	0.000	0.000	0.000
24	A	62	GLY	0	0.022	0.011	20.679	0.022	0.022	0.000	0.000	0.000	0.000
25	A	63	THR	0	-0.031	-0.014	18.810	0.014	0.014	0.000	0.000	0.000	0.000
26	A	64	ALA	0	-0.011	-0.003	13.399	-0.051	-0.051	0.000	0.000	0.000	0.000
27	A	65	ARG	1	0.814	0.896	13.366	0.611	0.611	0.000	0.000	0.000	0.000
28	A	66	THR	0	0.001	-0.012	8.857	-0.237	-0.237	0.000	0.000	0.000	0.000
29	A	67	ARG	1	0.832	0.907	9.969	0.619	0.619	0.000	0.000	0.000	0.000
30	A	68	LEU	0	0.002	-0.006	9.944	-0.181	-0.181	0.000	0.000	0.000	0.000
31	A	69	PRO	0	0.007	0.016	9.972	0.089	0.089	0.000	0.000	0.000	0.000
32	A	70	ALA	0	-0.006	-0.006	13.070	0.032	0.032	0.000	0.000	0.000	0.000
33	A	71	ARG	1	0.777	0.858	10.528	-0.196	-0.196	0.000	0.000	0.000	0.000
34	A	72	ALA	0	0.023	0.007	15.899	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	73	ASP	-1	-0.849	-0.922	14.685	0.264	0.264	0.000	0.000	0.000	0.000
36	A	74	LEU	0	-0.016	0.010	12.560	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	75	VAL	0	-0.005	0.014	16.832	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	76	ASN	0	0.019	0.000	20.601	0.018	0.018	0.000	0.000	0.000	0.000
39	A	77	SER	0	-0.008	-0.015	23.769	0.007	0.007	0.000	0.000	0.000	0.000
40	A	78	ARG	1	0.894	0.943	26.795	0.039	0.039	0.000	0.000	0.000	0.000
41	A	79	GLY	0	0.014	0.019	24.617	0.000	0.000	0.000	0.000	0.000	0.000
42	A	80	ASP	-1	-0.825	-0.899	23.266	-0.075	-0.075	0.000	0.000	0.000	0.000
43	A	81	ILE	0	0.019	0.003	17.153	0.015	0.015	0.000	0.000	0.000	0.000
44	A	82	HIS	0	-0.009	0.000	19.260	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	83	GLY	0	0.066	0.027	19.381	-0.032	-0.032	0.000	0.000	0.000	0.000
46	A	84	GLY	0	0.024	0.007	19.102	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	85	THR	0	-0.006	0.005	14.358	-0.032	-0.032	0.000	0.000	0.000	0.000
48	A	86	LEU	0	-0.008	-0.007	15.173	-0.081	-0.081	0.000	0.000	0.000	0.000
49	A	87	MET	0	-0.001	-0.008	16.980	-0.044	-0.044	0.000	0.000	0.000	0.000
50	A	88	SER	0	-0.028	-0.018	12.917	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	89	VAL	0	0.029	0.013	11.284	-0.114	-0.114	0.000	0.000	0.000	0.000
52	A	90	LEU	0	-0.003	0.017	13.078	-0.093	-0.093	0.000	0.000	0.000	0.000
53	A	91	ASP	-1	-0.854	-0.910	14.684	-0.594	-0.594	0.000	0.000	0.000	0.000
54	A	92	PHE	0	0.013	0.008	7.479	-0.083	-0.083	0.000	0.000	0.000	0.000
55	A	93	THR	0	0.006	-0.009	12.348	-0.104	-0.104	0.000	0.000	0.000	0.000
56	A	94	LEU	0	-0.017	0.007	13.467	0.053	0.053	0.000	0.000	0.000	0.000
57	A	95	GLY	0	0.045	0.027	15.440	0.050	0.050	0.000	0.000	0.000	0.000
58	A	96	ALA	0	0.001	-0.003	11.926	0.022	0.022	0.000	0.000	0.000	0.000
59	A	97	ALA	0	-0.022	0.011	13.883	0.028	0.028	0.000	0.000	0.000	0.000
60	A	98	ILE	0	-0.019	-0.013	17.085	0.079	0.079	0.000	0.000	0.000	0.000
61	A	99	ARG	1	0.746	0.867	11.172	1.170	1.170	0.000	0.000	0.000	0.000
62	A	100	GLY	0	0.107	0.063	14.859	-0.090	-0.090	0.000	0.000	0.000	0.000
63	A	101	ASP	-1	-0.883	-0.943	15.722	-0.403	-0.403	0.000	0.000	0.000	0.000
64	A	102	THR	0	-0.063	-0.037	17.998	0.069	0.069	0.000	0.000	0.000	0.000
65	A	103	PRO	0	0.039	0.046	14.106	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	104	GLU	-1	-0.859	-0.941	14.796	-0.534	-0.534	0.000	0.000	0.000	0.000
67	A	105	VAL	0	-0.067	-0.021	17.421	0.052	0.052	0.000	0.000	0.000	0.000
68	A	106	GLY	0	0.036	0.017	16.039	-0.087	-0.087	0.000	0.000	0.000	0.000
69	A	107	VAL	0	-0.030	-0.033	15.932	0.055	0.055	0.000	0.000	0.000	0.000
70	A	108	ALA	0	0.004	0.004	16.874	-0.044	-0.044	0.000	0.000	0.000	0.000
71	A	109	THR	0	-0.015	-0.028	17.657	0.025	0.025	0.000	0.000	0.000	0.000
72	A	110	ILE	0	-0.079	-0.029	20.196	0.025	0.025	0.000	0.000	0.000	0.000
73	A	111	ASP	-1	-0.862	-0.914	23.876	-0.209	-0.209	0.000	0.000	0.000	0.000
74	A	112	MET	0	0.008	-0.005	18.293	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	113	ASN	0	-0.046	-0.011	23.771	0.023	0.023	0.000	0.000	0.000	0.000
76	A	114	THR	0	0.004	-0.017	21.695	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	115	SER	0	-0.017	0.013	24.402	0.025	0.025	0.000	0.000	0.000	0.000
78	A	116	PHE	0	0.007	-0.017	21.912	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	117	MET	0	-0.066	-0.022	26.281	0.008	0.008	0.000	0.000	0.000	0.000
80	A	118	SER	0	0.022	0.000	26.124	0.019	0.019	0.000	0.000	0.000	0.000
81	A	119	PRO	0	-0.043	-0.023	25.268	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	120	GLY	0	0.061	0.041	21.501	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	121	ARG	1	0.812	0.875	21.618	0.094	0.094	0.000	0.000	0.000	0.000
84	A	122	GLY	0	0.046	0.026	19.964	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	123	ASP	-1	-0.806	-0.898	14.900	-0.255	-0.255	0.000	0.000	0.000	0.000
86	A	124	LEU	0	-0.049	-0.005	15.693	0.018	0.018	0.000	0.000	0.000	0.000
87	A	125	VAL	0	0.010	0.005	14.737	-0.079	-0.079	0.000	0.000	0.000	0.000
88	A	126	ILE	0	-0.006	-0.008	13.043	0.055	0.055	0.000	0.000	0.000	0.000
89	A	127	GLU	-1	-0.847	-0.913	14.984	-0.494	-0.494	0.000	0.000	0.000	0.000
90	A	128	THR	0	-0.045	-0.053	16.283	0.050	0.050	0.000	0.000	0.000	0.000
91	A	129	ARG	1	0.820	0.886	18.742	0.310	0.310	0.000	0.000	0.000	0.000
92	A	130	CYS	0	-0.022	-0.004	21.315	0.022	0.022	0.000	0.000	0.000	0.000
93	A	131	LEU	0	-0.017	0.000	22.910	0.022	0.022	0.000	0.000	0.000	0.000
94	A	132	ARG	1	0.937	0.960	26.126	0.221	0.221	0.000	0.000	0.000	0.000
95	A	133	ARG	1	0.932	0.961	20.597	0.383	0.383	0.000	0.000	0.000	0.000
96	A	134	GLY	0	0.006	-0.001	26.656	0.024	0.024	0.000	0.000	0.000	0.000
97	A	135	ALA	0	0.010	-0.001	27.183	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	136	SER	0	-0.027	-0.004	26.847	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	137	ILE	0	0.024	0.010	25.930	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	138	ALA	0	-0.012	0.000	23.012	0.008	0.008	0.000	0.000	0.000	0.000
101	A	139	PHE	0	0.013	0.010	24.695	0.003	0.003	0.000	0.000	0.000	0.000
102	A	140	CYS	0	-0.032	-0.006	19.604	0.006	0.006	0.000	0.000	0.000	0.000
103	A	141	GLU	-1	-0.775	-0.875	22.567	-0.250	-0.250	0.000	0.000	0.000	0.000
104	A	142	GLY	0	0.065	0.023	20.190	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	143	GLU	-1	-0.865	-0.912	20.050	-0.227	-0.227	0.000	0.000	0.000	0.000
106	A	144	ILE	0	0.010	0.010	17.488	-0.047	-0.047	0.000	0.000	0.000	0.000
107	A	145	ARG	1	0.826	0.891	19.278	0.256	0.256	0.000	0.000	0.000	0.000
108	A	146	ASP	-1	-0.757	-0.887	19.427	-0.191	-0.191	0.000	0.000	0.000	0.000
109	A	147	SER	0	-0.057	-0.017	21.167	0.000	0.000	0.000	0.000	0.000	0.000
110	A	148	ALA	0	-0.049	-0.028	21.972	0.005	0.005	0.000	0.000	0.000	0.000
111	A	149	GLY	0	0.013	0.021	23.483	0.006	0.006	0.000	0.000	0.000	0.000
112	A	150	GLU	-1	-0.868	-0.919	24.509	-0.156	-0.156	0.000	0.000	0.000	0.000
113	A	151	LEU	0	-0.053	-0.044	24.032	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	152	VAL	0	-0.009	0.016	21.019	0.017	0.017	0.000	0.000	0.000	0.000
115	A	153	ALA	0	0.005	-0.007	21.503	0.018	0.018	0.000	0.000	0.000	0.000
116	A	154	LYS	1	0.828	0.905	22.757	0.240	0.240	0.000	0.000	0.000	0.000
117	A	155	ALA	0	0.004	0.010	21.192	0.017	0.017	0.000	0.000	0.000	0.000
118	A	156	THR	0	-0.013	-0.013	23.346	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	157	ALA	0	0.030	0.017	21.187	0.004	0.004	0.000	0.000	0.000	0.000
120	A	158	THR	0	-0.043	-0.027	23.234	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	159	PHE	0	0.038	0.011	17.360	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	160	LYS	1	0.868	0.929	22.382	0.278	0.278	0.000	0.000	0.000	0.000
123	A	161	ILE	0	0.022	0.007	21.279	-0.036	-0.036	0.000	0.000	0.000	0.000
124	A	162	ILE	0	-0.081	-0.037	19.044	0.046	0.046	0.000	0.000	0.000	0.000
125	A	163	GLN	0	-0.002	0.008	21.202	0.027	0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:THR)