FMO DATABASE

FMODB ID: RY568

Calculation Name: 3KML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KML

Chain ID: A

ChEMBL ID:

UniProt ID: P69687

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1190705.965414
FMO2-HF: Nuclear repulsion	1136600.68332
FMO2-HF: Total energy	-54105.282095
FMO2-MP2: Total energy	-54265.498394

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:13:THR)

Summations of interaction energy for fragment #1(A:13: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.
2.525	4.458	-0.028	-0.782	-1.123	0.003

Interaction energy analysis for fragmet #1(A:13:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.017

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	15	ARG	1	1.040	1.020	3.793	0.789	2.635	-0.027	-0.779	-1.040	0.003
4	A	16	VAL	0	-0.069	-0.036	5.429	0.693	0.693	0.000	0.000	0.000	0.000
5	A	17	ASP	-1	-0.798	-0.883	7.594	0.143	0.143	0.000	0.000	0.000	0.000
6	A	18	ASP	-1	-0.930	-0.948	7.333	-0.548	-0.548	0.000	0.000	0.000	0.000
7	A	19	ALA	0	-0.016	-0.018	9.844	0.117	0.117	0.000	0.000	0.000	0.000
8	A	20	THR	0	-0.009	-0.003	11.752	0.088	0.088	0.000	0.000	0.000	0.000
9	A	21	VAL	0	0.030	0.010	12.971	0.068	0.068	0.000	0.000	0.000	0.000
10	A	22	ALA	0	-0.010	-0.005	14.007	0.043	0.043	0.000	0.000	0.000	0.000
11	A	23	ILE	0	0.014	0.001	15.042	0.039	0.039	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.845	0.931	17.518	0.184	0.184	0.000	0.000	0.000	0.000
13	A	25	CYS	0	-0.022	-0.014	18.267	0.030	0.030	0.000	0.000	0.000	0.000
14	A	26	ALA	0	-0.014	0.013	19.959	0.017	0.017	0.000	0.000	0.000	0.000
15	A	27	ILE	0	0.017	0.000	21.697	0.015	0.015	0.000	0.000	0.000	0.000
16	A	28	ASN	0	0.006	-0.005	22.687	0.017	0.017	0.000	0.000	0.000	0.000
17	A	29	ASN	0	0.002	-0.007	22.861	0.019	0.019	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.004	0.021	26.122	0.007	0.007	0.000	0.000	0.000	0.000
19	A	31	ILE	0	0.023	0.004	27.323	0.009	0.009	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.029	-0.012	28.891	0.008	0.008	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.873	-0.942	31.161	-0.066	-0.066	0.000	0.000	0.000	0.000
22	A	34	LEU	0	-0.004	-0.009	31.140	0.005	0.005	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.034	-0.006	32.957	0.005	0.005	0.000	0.000	0.000	0.000
24	A	36	ARG	1	0.886	0.947	35.622	0.056	0.056	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.012	0.024	37.255	0.003	0.003	0.000	0.000	0.000	0.000
26	A	38	THR	0	-0.064	-0.045	35.537	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	39	GLY	0	0.047	0.019	36.326	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	40	SER	0	-0.029	-0.015	37.690	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	41	TYR	0	-0.015	-0.009	39.360	0.001	0.001	0.000	0.000	0.000	0.000
30	A	42	ASN	0	0.087	0.043	43.397	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	43	ARG	1	0.982	0.990	46.732	0.036	0.036	0.000	0.000	0.000	0.000
32	A	44	SER	0	-0.033	-0.011	49.424	0.000	0.000	0.000	0.000	0.000	0.000
33	A	45	SER	0	0.055	0.011	46.040	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.010	0.019	43.965	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	47	GLU	-1	-0.778	-0.873	46.326	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	48	SER	0	-0.060	-0.010	49.194	0.000	0.000	0.000	0.000	0.000	0.000
37	A	49	SER	0	-0.044	-0.041	44.807	0.000	0.000	0.000	0.000	0.000	0.000
38	A	50	SER	0	-0.012	0.001	45.338	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	51	GLY	0	0.019	0.011	46.295	0.000	0.000	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.075	-0.021	46.479	0.002	0.002	0.000	0.000	0.000	0.000
41	A	53	VAL	0	0.043	0.010	50.567	0.001	0.001	0.000	0.000	0.000	0.000
42	A	54	TRP	0	-0.022	0.004	52.518	0.000	0.000	0.000	0.000	0.000	0.000
43	A	55	THR	0	-0.009	-0.011	55.345	0.001	0.001	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.027	-0.013	58.759	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	57	GLY	0	-0.011	-0.001	60.206	0.001	0.001	0.000	0.000	0.000	0.000
46	A	58	PRO	0	-0.017	0.024	61.577	0.000	0.000	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.009	-0.015	63.022	0.000	0.000	0.000	0.000	0.000	0.000
48	A	60	GLY	0	0.025	-0.012	60.887	0.000	0.000	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.935	-0.961	57.733	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	62	GLY	0	0.004	-0.014	56.792	0.001	0.001	0.000	0.000	0.000	0.000
51	A	63	SER	0	0.001	-0.023	53.931	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	64	TYR	0	-0.085	-0.036	49.647	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	SER	0	-0.035	-0.006	52.864	0.000	0.000	0.000	0.000	0.000	0.000
54	A	66	ILE	0	-0.012	-0.007	48.450	0.000	0.000	0.000	0.000	0.000	0.000
55	A	67	THR	0	-0.016	-0.001	50.793	0.000	0.000	0.000	0.000	0.000	0.000
56	A	68	THR	0	0.000	-0.008	47.525	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	69	PRO	0	0.044	0.009	44.844	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	70	SER	0	-0.005	-0.001	42.475	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	71	GLN	0	0.081	0.021	42.278	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	72	PHE	0	0.010	-0.002	42.803	0.000	0.000	0.000	0.000	0.000	0.000
61	A	73	VAL	0	0.031	0.029	37.265	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	74	PHE	0	-0.015	0.021	39.661	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	75	LEU	0	-0.029	0.002	41.738	0.001	0.001	0.000	0.000	0.000	0.000
64	A	76	SER	0	-0.035	-0.033	38.040	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.023	-0.032	35.686	0.003	0.003	0.000	0.000	0.000	0.000
66	A	78	ALA	0	-0.007	-0.004	35.393	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	79	TRP	0	0.000	-0.007	36.409	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	80	ALA	0	0.020	0.024	34.667	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.827	-0.932	36.717	-0.054	-0.054	0.000	0.000	0.000	0.000
70	A	82	PRO	0	0.033	0.006	36.905	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	83	ILE	0	0.014	0.009	36.550	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	84	GLU	-1	-0.941	-0.966	34.429	-0.077	-0.077	0.000	0.000	0.000	0.000
73	A	85	LEU	0	-0.002	-0.007	30.679	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.009	0.004	31.590	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	87	ASN	0	0.021	-0.001	32.156	0.000	0.000	0.000	0.000	0.000	0.000
76	A	88	LEU	0	-0.025	0.004	28.495	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	89	CYS	0	-0.045	-0.014	27.393	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	90	THR	0	-0.025	-0.002	27.373	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	91	ASN	0	-0.003	-0.015	28.243	0.005	0.005	0.000	0.000	0.000	0.000
80	A	92	ALA	0	-0.029	0.009	23.902	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	93	LEU	0	0.003	-0.009	22.530	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	94	GLY	0	0.007	0.017	23.107	0.005	0.005	0.000	0.000	0.000	0.000
83	A	95	ASN	0	0.004	0.006	20.595	0.004	0.004	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.017	0.001	17.197	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.010	-0.003	15.833	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	98	GLN	0	0.040	-0.001	10.043	0.004	0.004	0.000	0.000	0.000	0.000
87	A	99	THR	0	-0.066	-0.041	11.812	-0.108	-0.108	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.085	0.030	13.336	-0.084	-0.084	0.000	0.000	0.000	0.000
89	A	101	GLN	0	0.027	0.000	14.686	0.017	0.017	0.000	0.000	0.000	0.000
90	A	102	ALA	0	0.022	0.027	17.370	0.020	0.020	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.899	0.951	11.105	0.673	0.673	0.000	0.000	0.000	0.000
92	A	104	THR	0	-0.018	-0.006	17.542	0.002	0.002	0.000	0.000	0.000	0.000
93	A	105	VAL	0	-0.024	-0.010	19.402	0.022	0.022	0.000	0.000	0.000	0.000
94	A	106	VAL	0	0.029	0.009	20.742	0.014	0.014	0.000	0.000	0.000	0.000
95	A	107	GLN	0	-0.039	0.000	19.730	0.021	0.021	0.000	0.000	0.000	0.000
96	A	108	ARG	1	0.945	0.974	22.444	0.163	0.163	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.014	0.002	25.133	0.007	0.007	0.000	0.000	0.000	0.000
98	A	110	PHE	0	0.011	-0.002	24.689	0.011	0.011	0.000	0.000	0.000	0.000
99	A	111	SER	0	-0.062	-0.021	26.219	0.004	0.004	0.000	0.000	0.000	0.000
100	A	112	GLU	-1	-0.875	-0.954	28.016	-0.105	-0.105	0.000	0.000	0.000	0.000
101	A	113	VAL	0	-0.030	-0.010	30.577	0.009	0.009	0.000	0.000	0.000	0.000
102	A	114	TRP	0	-0.080	-0.035	29.211	0.010	0.010	0.000	0.000	0.000	0.000
103	A	115	LYS	1	0.959	0.982	34.167	0.080	0.080	0.000	0.000	0.000	0.000
104	A	116	PRO	0	-0.015	-0.003	37.372	0.001	0.001	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.032	-0.007	40.495	0.003	0.003	0.000	0.000	0.000	0.000
106	A	118	PRO	0	-0.032	-0.017	42.721	0.002	0.002	0.000	0.000	0.000	0.000
107	A	119	GLN	0	0.056	0.025	44.357	0.000	0.000	0.000	0.000	0.000	0.000
108	A	120	VAL	0	0.044	0.016	46.993	0.002	0.002	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.008	0.000	49.715	0.001	0.001	0.000	0.000	0.000	0.000
110	A	122	VAL	0	-0.002	0.005	48.553	0.001	0.001	0.000	0.000	0.000	0.000
111	A	123	ARG	1	0.843	0.920	49.133	0.033	0.033	0.000	0.000	0.000	0.000
112	A	124	PHE	0	-0.013	-0.002	43.863	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	125	PRO	0	0.004	-0.001	45.516	0.002	0.002	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.948	-0.988	48.832	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	127	SER	0	0.023	0.014	50.564	0.001	0.001	0.000	0.000	0.000	0.000
116	A	128	ASP	-1	-0.958	-0.961	45.294	-0.043	-0.043	0.000	0.000	0.000	0.000
117	A	129	PHE	0	-0.006	-0.019	42.693	0.000	0.000	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.900	0.949	40.463	0.054	0.054	0.000	0.000	0.000	0.000
119	A	131	VAL	0	0.013	0.019	34.832	0.001	0.001	0.000	0.000	0.000	0.000
120	A	132	TYR	0	0.006	-0.002	36.903	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.900	0.957	27.595	0.122	0.122	0.000	0.000	0.000	0.000
122	A	134	TYR	0	-0.004	-0.010	31.638	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	135	ASN	0	-0.003	-0.003	34.472	0.000	0.000	0.000	0.000	0.000	0.000
124	A	136	ALA	0	0.016	-0.005	34.015	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	137	VAL	0	0.007	0.012	32.737	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	138	LEU	0	0.024	0.012	31.135	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.875	-0.922	29.643	-0.119	-0.119	0.000	0.000	0.000	0.000
128	A	140	PRO	0	0.011	-0.010	27.288	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	141	LEU	0	-0.017	-0.009	25.523	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	142	VAL	0	0.007	-0.006	25.035	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	143	THR	0	-0.015	0.001	23.525	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	144	ALA	0	-0.005	-0.007	21.255	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	145	LEU	0	-0.012	0.002	20.062	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	146	LEU	0	-0.018	-0.016	20.238	-0.028	-0.028	0.000	0.000	0.000	0.000
135	A	147	GLY	0	0.005	0.004	19.140	-0.017	-0.017	0.000	0.000	0.000	0.000
136	A	148	ALA	0	-0.020	-0.006	16.006	-0.045	-0.045	0.000	0.000	0.000	0.000
137	A	149	PHE	0	-0.036	-0.027	15.181	-0.058	-0.058	0.000	0.000	0.000	0.000
138	A	150	ASP	-1	-0.937	-0.941	15.552	-0.393	-0.393	0.000	0.000	0.000	0.000
139	A	151	THR	0	-0.065	-0.042	9.272	-0.107	-0.107	0.000	0.000	0.000	0.000
140	A	152	ARG	1	0.943	0.972	8.163	0.453	0.453	0.000	0.000	0.000	0.000
141	A	153	ASN	0	0.048	0.022	4.469	0.585	0.672	-0.001	-0.003	-0.083	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:THR)