FMO DATABASE

FMODB ID: YVRK2

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	OptHSide
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	-1129554.228081
FMO2-HF: Nuclear repulsion	1077383.862537
FMO2-HF: Total energy	-52170.365544
FMO2-MP2: Total energy	-52323.255898

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.
-3.996	3.294	5.441	-3.862	-8.867	-0.018

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 : -0.002 / q_NPA : 0.009

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	0.013	0.004	3.458	-3.022	-0.133	0.002	-1.575	-1.316	0.004
4	A	4	THR	0	0.063	0.009	5.747	0.240	0.240	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.029	-0.048	2.850	-2.095	0.642	1.306	-1.586	-2.456	-0.013
6	A	6	LYS	1	0.891	0.952	2.338	0.418	2.824	3.947	-2.092	-4.260	-0.008
7	A	7	VAL	0	0.055	0.029	2.917	2.196	0.908	0.102	1.503	-0.318	-0.001
8	A	8	ASN	0	0.077	0.041	5.676	0.398	0.398	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.822	0.909	2.980	0.170	0.673	0.085	-0.109	-0.479	0.000
10	A	10	LEU	0	-0.039	-0.025	4.945	0.395	0.438	-0.001	-0.003	-0.038	0.000
11	A	11	LEU	0	0.040	0.004	7.928	0.219	0.219	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.008	0.015	7.950	0.148	0.148	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.891	-0.941	9.402	-0.187	-0.187	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.007	-0.002	11.112	0.064	0.064	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.024	0.016	13.026	0.048	0.048	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.002	0.003	13.767	0.042	0.042	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.724	0.824	14.578	0.251	0.251	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.022	-0.001	17.385	0.015	0.015	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.028	0.006	18.705	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.023	-0.012	17.333	0.014	0.014	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.042	-0.026	16.998	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.036	-0.027	13.153	0.017	0.017	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.037	0.017	12.362	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.105	-0.054	10.425	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.053	-0.014	9.301	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.876	-0.928	12.447	-0.210	-0.210	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.973	-0.990	13.717	-0.230	-0.230	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.936	-0.974	15.528	-0.336	-0.336	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.066	-0.038	12.898	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.057	-0.033	13.816	-0.047	-0.047	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.098	0.050	14.815	0.017	0.017	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.006	-0.002	16.809	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.052	-0.023	17.439	0.017	0.017	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.010	-0.012	21.389	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.022	0.002	20.690	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.877	-0.944	26.390	-0.109	-0.109	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-1.007	-0.996	28.817	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.093	-0.049	30.052	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.002	0.008	26.536	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.036	0.028	25.552	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.020	-0.025	20.307	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.035	0.020	19.762	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.053	-0.022	14.279	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.054	0.026	16.317	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.010	0.004	9.028	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.007	-0.005	13.450	0.035	0.035	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.027	-0.004	10.655	-0.050	-0.050	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.820	-0.886	12.074	-0.678	-0.678	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.762	0.852	14.317	0.552	0.552	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.937	-0.960	10.866	-1.392	-1.392	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.864	0.925	13.152	0.611	0.611	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.008	0.013	11.825	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.033	-0.032	14.508	0.058	0.058	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.003	-0.003	16.325	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.891	-0.947	19.745	-0.284	-0.284	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.024	0.013	23.001	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.833	-0.917	25.423	-0.167	-0.167	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.069	-0.036	28.793	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.005	-0.015	31.609	0.009	0.009	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.030	0.040	34.997	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.017	-0.018	36.965	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.928	-0.961	39.491	-0.091	-0.091	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.015	-0.005	40.003	0.005	0.005	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.037	0.001	37.966	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.025	0.007	42.423	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.936	-0.971	44.696	-0.089	-0.089	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.025	-0.016	44.785	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.036	0.020	39.411	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.088	0.032	36.188	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.923	0.964	39.411	0.096	0.096	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.023	-0.021	41.029	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.075	0.040	35.186	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.003	0.017	36.020	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.074	-0.041	37.569	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.017	-0.002	31.580	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.079	0.037	32.504	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.888	0.961	33.252	0.134	0.134	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.122	-0.080	35.102	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	TRP	0	0.078	0.045	27.097	0.012	0.012	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.017	-0.002	29.373	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.881	0.944	30.000	0.149	0.149	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.014	-0.017	29.680	0.009	0.009	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.937	-0.950	24.639	-0.309	-0.309	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.012	0.003	25.028	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	85	HIS	0	-0.072	-0.035	25.284	0.018	0.018	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.030	-0.006	28.507	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.001	-0.004	29.867	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.062	-0.046	30.845	0.010	0.010	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.751	-0.842	29.864	-0.168	-0.168	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.920	-0.977	31.978	-0.116	-0.116	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.092	-0.035	30.793	0.011	0.011	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.046	-0.049	30.498	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.005	0.004	33.700	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.932	0.985	31.295	0.136	0.136	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.009	-0.008	32.336	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	96	GLN	0	-0.010	0.001	26.873	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.011	-0.007	27.236	0.004	0.004	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.026	-0.013	24.213	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.062	0.022	21.374	0.011	0.011	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.015	-0.001	18.728	-0.050	-0.050	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.009	0.009	14.758	0.022	0.022	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.004	-0.001	14.913	-0.072	-0.072	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.043	0.014	10.159	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.061	-0.023	11.036	-0.088	-0.088	0.000	0.000	0.000	0.000
105	A	105	GLN	0	0.014	-0.010	13.444	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.009	0.026	9.499	0.059	0.059	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.044	0.016	10.642	-0.095	-0.095	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.044	0.016	11.084	0.018	0.018	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.943	-0.968	12.606	-0.259	-0.259	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.056	-0.026	14.911	0.042	0.042	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.001	0.002	13.308	0.007	0.007	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.756	-0.848	15.429	-0.243	-0.243	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.001	0.014	18.005	0.031	0.031	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.016	-0.029	18.390	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.018	0.001	18.128	0.020	0.020	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.026	0.007	20.557	0.023	0.023	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.044	0.024	23.324	0.034	0.034	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.027	-0.013	22.073	0.015	0.015	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.000	-0.003	23.267	0.014	0.014	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.878	-0.926	26.443	-0.157	-0.157	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.105	-0.065	28.258	0.020	0.020	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.028	-0.014	27.961	0.011	0.011	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.820	-0.917	29.928	-0.119	-0.119	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.063	-0.025	32.190	0.013	0.013	0.000	0.000	0.000	0.000
125	A	125	TRP	0	0.002	-0.015	32.001	0.014	0.014	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.050	-0.014	32.349	0.011	0.011	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.848	0.925	34.445	0.118	0.118	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.079	-0.034	37.978	0.006	0.006	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.043	-0.027	36.214	0.003	0.003	0.000	0.000	0.000	0.000
130	A	130	PRO	0	-0.033	0.000	39.023	0.003	0.003	0.000	0.000	0.000	0.000
131	A	131	CYS	0	-0.061	-0.016	42.000	0.003	0.003	0.000	0.000	0.000	0.000
132	A	132	ALA	0	-0.019	-0.013	45.679	0.003	0.003	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.008	0.007	45.862	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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