FMO DATABASE

FMODB ID: 5J5LZ

Calculation Name: 3KXY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KXY

Chain ID: A

ChEMBL ID:

UniProt ID: P26995

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129259.955336
FMO2-HF: Nuclear repulsion	1077090.136917
FMO2-HF: Total energy	-52169.81842
FMO2-MP2: Total energy	-52322.6758

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.
-2.162	2.553	6.736	-3.6	-7.85	-0.016

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 : -0.052 / q_NPA : -0.030

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	LEU	0	0.003	-0.005	3.513	-2.818	-0.910	-0.002	-0.963	-0.943	0.001
4	A	4	THR	0	0.088	0.031	5.966	-0.152	-0.152	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.006	-0.003	2.838	-0.210	0.639	3.759	-1.807	-2.802	-0.017
6	A	6	LYS	1	0.915	0.959	2.291	0.159	2.162	2.862	-1.577	-3.288	0.001
7	A	7	VAL	0	0.057	0.031	3.053	1.163	0.560	0.048	0.850	-0.294	-0.001
8	A	8	ASN	0	0.084	0.040	6.079	0.076	0.076	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.908	0.958	3.006	0.406	0.929	0.070	-0.102	-0.491	0.000
10	A	10	LEU	0	-0.031	-0.002	5.104	0.225	0.260	-0.001	-0.001	-0.032	0.000
11	A	11	LEU	0	0.034	0.000	7.869	0.149	0.149	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.009	0.013	8.104	0.106	0.106	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.968	-0.987	9.453	-0.413	-0.413	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.005	-0.006	11.087	0.057	0.057	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.024	0.014	13.161	0.041	0.041	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.001	0.002	13.836	0.033	0.033	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.767	0.869	14.678	0.278	0.278	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.022	0.004	17.354	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.032	0.002	18.773	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.022	-0.013	17.624	0.020	0.020	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.048	-0.027	17.160	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.045	-0.030	13.485	0.015	0.015	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.040	0.021	12.673	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.105	-0.056	10.905	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.050	-0.009	9.600	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.881	-0.930	12.948	0.107	0.107	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.975	-0.990	14.302	0.213	0.213	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.936	-0.974	15.543	0.115	0.115	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.069	-0.039	13.463	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.032	-0.026	14.380	-0.071	-0.071	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.097	0.053	15.226	0.021	0.021	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.003	0.004	17.200	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.042	-0.017	17.694	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.011	-0.010	21.635	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.016	0.001	20.850	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.879	-0.939	26.570	-0.070	-0.070	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-1.027	-1.014	29.092	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.082	-0.044	30.265	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.019	0.022	26.691	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.032	0.023	25.766	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.011	-0.017	20.314	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.015	0.011	19.981	0.006	0.006	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.062	-0.036	14.444	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.053	0.022	16.699	0.021	0.021	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.004	0.010	9.640	-0.073	-0.073	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.019	-0.011	13.856	0.064	0.064	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.023	-0.007	10.687	-0.062	-0.062	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.933	-0.962	12.057	-0.177	-0.177	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.878	0.932	14.382	0.126	0.126	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.921	-0.953	11.223	-0.778	-0.778	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.864	0.926	13.094	0.240	0.240	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.007	0.012	12.131	0.015	0.015	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.033	-0.028	14.708	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.001	-0.005	16.672	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.905	-0.952	19.920	-0.100	-0.100	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.037	0.018	23.227	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.847	-0.915	25.603	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.050	-0.024	29.006	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.001	-0.024	31.767	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.001	0.024	35.185	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.034	-0.012	37.213	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.939	-0.965	39.757	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.014	-0.001	40.195	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.042	-0.003	38.215	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.023	0.009	42.626	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.940	-0.975	44.910	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.049	-0.026	45.000	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.061	0.029	39.595	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.082	0.029	36.350	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.921	0.965	39.613	0.042	0.042	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.008	-0.014	41.061	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.073	0.040	35.309	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.002	0.016	36.157	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.080	-0.044	37.705	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.014	-0.005	31.541	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.097	0.048	32.712	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.914	0.978	33.342	0.072	0.072	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.141	-0.087	35.115	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	TRP	0	0.072	0.037	27.196	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.020	-0.002	29.337	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.884	0.945	29.906	0.092	0.092	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.014	-0.014	29.572	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.946	-0.947	24.587	-0.207	-0.207	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.002	-0.002	24.864	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	85	HIS	0	-0.075	-0.032	25.587	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.039	-0.004	28.656	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.013	-0.013	30.141	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.067	-0.050	31.099	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.805	-0.887	30.108	-0.037	-0.037	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.909	-0.982	32.344	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.079	-0.025	31.475	0.004	0.004	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.016	-0.006	30.904	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.005	0.005	34.077	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.940	0.978	31.687	0.043	0.043	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.002	-0.001	32.627	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	GLN	0	-0.012	0.004	27.327	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.011	-0.005	27.282	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.019	-0.016	24.377	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.062	0.021	21.325	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.028	-0.013	18.835	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.007	0.010	14.223	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.014	-0.005	14.960	-0.027	-0.027	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.046	0.012	10.050	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.062	-0.024	10.895	-0.121	-0.121	0.000	0.000	0.000	0.000
105	A	105	GLN	0	0.014	-0.009	13.286	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.001	0.019	9.026	0.041	0.041	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.030	0.010	10.316	-0.108	-0.108	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.029	0.003	11.154	0.043	0.043	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.931	-0.967	12.476	-0.276	-0.276	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.055	-0.023	14.719	0.052	0.052	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.004	-0.013	13.165	0.022	0.022	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.790	-0.892	15.254	-0.234	-0.234	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.004	0.014	17.791	0.031	0.031	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.007	-0.009	18.260	0.029	0.029	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.024	-0.004	18.241	0.022	0.022	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.033	0.009	20.493	0.021	0.021	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.039	0.021	23.180	0.025	0.025	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.034	-0.016	22.237	0.013	0.013	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.006	-0.002	23.510	0.014	0.014	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.857	-0.915	26.425	-0.118	-0.118	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.121	-0.072	28.153	0.016	0.016	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.025	-0.012	28.029	0.010	0.010	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.876	-0.947	29.700	-0.084	-0.084	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.070	-0.026	32.205	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	TRP	0	-0.011	-0.020	32.171	0.010	0.010	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.031	0.000	32.984	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.903	0.959	35.374	0.073	0.073	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.075	-0.036	38.015	0.004	0.004	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.040	-0.032	36.364	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	PRO	0	-0.031	0.003	39.103	0.003	0.003	0.000	0.000	0.000	0.000
131	A	131	CYS	0	-0.040	-0.011	42.130	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	ALA	0	-0.029	-0.015	45.818	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.002	0.004	45.973	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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