FMO DATABASE

FMODB ID: KGMM3

Calculation Name: 3KYE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KYE

Chain ID: A

ChEMBL ID:

UniProt ID: Q82MM8

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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-878351.38782
FMO2-HF: Nuclear repulsion	833538.433224
FMO2-HF: Total energy	-44812.954596
FMO2-MP2: Total energy	-44939.933244

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:10:VAL)

Summations of interaction energy for fragment #1(A:10:VAL)

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.
-20.442	-15.955	10.827	-6.936	-8.376	-0.036

Interaction energy analysis for fragmet #1(A:10:VAL)

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 : -0.024

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

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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	12	ASP	-1	-0.886	-0.941	1.913	-10.142	-9.618	9.546	-5.204	-4.866	-0.047
4	A	13	LEU	0	0.001	-0.010	2.689	-5.509	-2.751	1.277	-1.359	-2.676	0.011
5	A	14	ASP	-1	-0.790	-0.900	4.130	-3.417	-2.742	0.003	-0.275	-0.403	0.000
6	A	15	TRP	0	-0.025	-0.003	6.169	0.045	0.045	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.025	-0.014	6.917	-0.141	-0.141	0.000	0.000	0.000	0.000
8	A	17	MET	0	-0.073	-0.008	7.458	-0.202	-0.202	0.000	0.000	0.000	0.000
9	A	18	SER	0	-0.009	-0.029	10.189	-0.104	-0.104	0.000	0.000	0.000	0.000
10	A	19	GLY	0	0.002	-0.003	11.810	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.043	-0.022	13.180	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	21	VAL	0	0.035	0.017	14.787	-0.040	-0.040	0.000	0.000	0.000	0.000
13	A	22	GLN	0	-0.079	-0.044	14.693	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	23	ARG	1	0.780	0.866	14.456	-0.336	-0.336	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.021	0.008	19.230	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	25	PRO	0	0.018	0.013	21.291	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	26	HIS	0	0.017	0.005	23.862	0.002	0.002	0.000	0.000	0.000	0.000
18	A	27	THR	0	-0.007	-0.012	18.770	0.001	0.001	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.055	-0.037	19.488	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	29	SER	0	-0.011	-0.001	14.927	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	30	ALA	0	-0.008	0.003	12.521	0.025	0.025	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.029	0.010	10.263	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.005	0.009	6.511	0.032	0.032	0.000	0.000	0.000	0.000
24	A	33	LEU	0	-0.004	0.001	8.933	-0.100	-0.100	0.000	0.000	0.000	0.000
25	A	34	SER	0	-0.008	-0.042	10.936	0.085	0.085	0.000	0.000	0.000	0.000
26	A	35	CYS	0	-0.072	-0.045	12.506	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.888	-0.925	13.870	0.099	0.099	0.000	0.000	0.000	0.000
28	A	37	GLY	0	0.011	0.007	15.173	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.012	0.007	10.560	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	39	VAL	0	0.040	0.014	7.035	0.087	0.087	0.000	0.000	0.000	0.000
31	A	40	LYS	1	0.793	0.893	6.013	-0.622	-0.622	0.000	0.000	0.000	0.000
32	A	41	SER	0	0.039	0.011	3.911	-0.127	0.206	0.001	-0.074	-0.259	0.000
33	A	42	VAL	0	-0.056	-0.035	5.555	0.172	0.172	0.000	0.000	0.000	0.000
34	A	43	HIS	0	0.039	0.045	8.703	-0.143	-0.143	0.000	0.000	0.000	0.000
35	A	44	GLY	0	0.020	-0.003	11.391	0.046	0.046	0.000	0.000	0.000	0.000
36	A	45	LEU	0	-0.039	-0.019	13.302	0.015	0.015	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.829	-0.876	12.715	-0.131	-0.131	0.000	0.000	0.000	0.000
38	A	47	PRO	0	0.036	-0.010	10.757	0.014	0.014	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.867	-0.919	12.250	-0.106	-0.106	0.000	0.000	0.000	0.000
40	A	49	SER	0	-0.053	-0.064	15.492	0.027	0.027	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.033	-0.008	11.159	0.032	0.032	0.000	0.000	0.000	0.000
42	A	51	ASP	-1	-0.853	-0.936	11.681	-0.083	-0.083	0.000	0.000	0.000	0.000
43	A	52	HIS	0	-0.051	-0.025	13.789	0.034	0.034	0.000	0.000	0.000	0.000
44	A	53	MET	0	-0.012	0.000	14.974	0.024	0.024	0.000	0.000	0.000	0.000
45	A	54	ALA	0	0.010	0.008	12.604	0.030	0.030	0.000	0.000	0.000	0.000
46	A	55	ALA	0	0.056	0.039	14.717	0.020	0.020	0.000	0.000	0.000	0.000
47	A	56	LEU	0	-0.031	-0.015	17.821	0.009	0.009	0.000	0.000	0.000	0.000
48	A	57	ALA	0	0.004	-0.003	16.368	0.007	0.007	0.000	0.000	0.000	0.000
49	A	58	SER	0	-0.007	-0.012	16.761	0.009	0.009	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.006	0.010	18.442	0.000	0.000	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.004	-0.012	21.262	0.000	0.000	0.000	0.000	0.000	0.000
52	A	61	TYR	0	-0.022	-0.035	19.294	0.001	0.001	0.000	0.000	0.000	0.000
53	A	62	SER	0	0.037	0.013	21.329	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.043	-0.005	23.335	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	64	GLY	0	0.038	0.016	25.048	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.891	0.927	22.984	-0.125	-0.125	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.052	-0.036	25.679	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	67	ALA	0	-0.023	-0.010	28.689	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.012	0.000	28.572	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.035	-0.027	27.125	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	70	ARG	1	0.888	0.949	30.881	-0.054	-0.054	0.000	0.000	0.000	0.000
62	A	71	PHE	0	-0.055	-0.031	33.191	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	72	GLY	0	0.006	0.024	31.824	0.000	0.000	0.000	0.000	0.000	0.000
64	A	73	ASP	-1	-0.928	-0.971	32.613	0.084	0.084	0.000	0.000	0.000	0.000
65	A	74	GLY	0	0.007	0.001	31.192	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	75	GLY	0	-0.083	-0.027	27.438	0.007	0.007	0.000	0.000	0.000	0.000
67	A	76	ASP	-1	-0.790	-0.866	22.042	0.149	0.149	0.000	0.000	0.000	0.000
68	A	77	VAL	0	-0.006	0.004	22.347	0.000	0.000	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.936	0.975	22.477	-0.139	-0.139	0.000	0.000	0.000	0.000
70	A	79	GLN	0	-0.011	-0.027	20.460	0.008	0.008	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.019	0.007	21.999	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.000	-0.005	22.539	0.012	0.012	0.000	0.000	0.000	0.000
73	A	82	VAL	0	-0.010	-0.003	24.674	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	83	GLU	-1	-0.835	-0.893	25.915	0.063	0.063	0.000	0.000	0.000	0.000
75	A	84	LEU	0	-0.025	-0.009	26.190	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.899	-0.954	29.922	0.031	0.031	0.000	0.000	0.000	0.000
77	A	86	SER	0	-0.022	-0.018	30.025	0.001	0.001	0.000	0.000	0.000	0.000
78	A	87	THR	0	-0.003	-0.004	25.127	0.002	0.002	0.000	0.000	0.000	0.000
79	A	88	LEU	0	0.003	0.003	24.501	0.000	0.000	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.002	0.013	18.947	0.002	0.002	0.000	0.000	0.000	0.000
81	A	90	PHE	0	0.012	0.002	19.928	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	91	VAL	0	0.031	0.003	17.267	0.016	0.016	0.000	0.000	0.000	0.000
83	A	92	SER	0	-0.008	0.007	17.229	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	93	THR	0	-0.024	-0.040	16.520	0.032	0.032	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.003	-0.010	13.556	0.010	0.010	0.000	0.000	0.000	0.000
86	A	95	GLY	0	-0.017	0.003	15.278	0.020	0.020	0.000	0.000	0.000	0.000
87	A	96	SER	0	-0.022	-0.035	13.371	0.009	0.009	0.000	0.000	0.000	0.000
88	A	97	GLY	0	0.034	0.031	13.278	0.035	0.035	0.000	0.000	0.000	0.000
89	A	98	THR	0	0.003	0.010	10.271	0.027	0.027	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.029	-0.007	12.696	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	100	LEU	0	-0.001	0.011	11.807	0.072	0.072	0.000	0.000	0.000	0.000
92	A	101	ALA	0	0.001	0.012	13.519	-0.044	-0.044	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.010	-0.011	14.393	0.026	0.026	0.000	0.000	0.000	0.000
94	A	103	LEU	0	0.000	0.015	16.938	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	104	ALA	0	0.021	-0.003	19.680	0.008	0.008	0.000	0.000	0.000	0.000
96	A	105	GLY	0	0.052	0.040	22.529	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	106	ARG	1	0.754	0.851	26.106	-0.042	-0.042	0.000	0.000	0.000	0.000
98	A	107	GLU	-1	-0.911	-0.955	28.523	0.047	0.047	0.000	0.000	0.000	0.000
99	A	108	ALA	0	-0.046	-0.010	24.336	0.002	0.002	0.000	0.000	0.000	0.000
100	A	109	ASP	-1	-0.811	-0.908	26.385	0.103	0.103	0.000	0.000	0.000	0.000
101	A	110	ALA	0	0.032	0.007	25.562	0.013	0.013	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.054	-0.016	25.705	0.012	0.012	0.000	0.000	0.000	0.000
103	A	112	VAL	0	0.000	-0.013	22.905	0.016	0.016	0.000	0.000	0.000	0.000
104	A	113	LEU	0	0.020	0.020	20.739	0.024	0.024	0.000	0.000	0.000	0.000
105	A	114	GLY	0	0.022	0.006	20.720	0.026	0.026	0.000	0.000	0.000	0.000
106	A	115	TYR	0	-0.039	-0.025	21.425	0.021	0.021	0.000	0.000	0.000	0.000
107	A	116	GLU	-1	-0.766	-0.872	18.200	0.303	0.303	0.000	0.000	0.000	0.000
108	A	117	MET	0	-0.024	0.006	16.602	0.052	0.052	0.000	0.000	0.000	0.000
109	A	118	ALA	0	-0.029	-0.011	16.660	0.053	0.053	0.000	0.000	0.000	0.000
110	A	119	MET	0	-0.034	-0.009	17.327	0.018	0.018	0.000	0.000	0.000	0.000
111	A	120	LEU	0	0.031	0.020	10.498	0.062	0.062	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.010	0.008	12.329	0.151	0.151	0.000	0.000	0.000	0.000
113	A	122	LYS	1	0.847	0.914	13.223	-0.241	-0.241	0.000	0.000	0.000	0.000
114	A	123	SER	0	-0.012	-0.009	11.193	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	124	VAL	0	0.032	0.010	8.072	0.126	0.126	0.000	0.000	0.000	0.000
116	A	125	ARG	1	0.926	0.962	8.204	-0.224	-0.224	0.000	0.000	0.000	0.000
117	A	126	PRO	0	-0.004	-0.012	9.566	-0.060	-0.060	0.000	0.000	0.000	0.000
118	A	127	TYR	0	0.000	0.009	4.271	-0.242	-0.045	0.000	-0.024	-0.172	0.000
119	A	128	LEU	0	-0.037	-0.005	5.260	0.136	0.136	0.000	0.000	0.000	0.000
120	A	129	MET	0	-0.059	-0.008	8.047	-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:10:VAL)