FMO DATABASE

FMODB ID: YVMQ2

Calculation Name: 1K8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K8F

Chain ID: A

ChEMBL ID:

UniProt ID: Q01518

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1457016.209881
FMO2-HF: Nuclear repulsion	1395884.879828
FMO2-HF: Total energy	-61131.330053
FMO2-MP2: Total energy	-61308.691488

3D Structure Molmil

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:319:PRO)

Summations of interaction energy for fragment #1(A:319:PRO)

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.
-2.908	-0.13	0.006	-1.106	-1.678	0.003

Interaction energy analysis for fragmet #1(A:319:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.002

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	321	VAL	0	-0.027	-0.002	3.760	-1.741	0.305	-0.004	-0.883	-1.159	0.004
4	A	322	LEU	0	0.015	-0.020	5.985	0.560	0.560	0.000	0.000	0.000	0.000
5	A	323	GLU	-1	-0.953	-0.959	7.965	-1.406	-1.406	0.000	0.000	0.000	0.000
6	A	324	LEU	0	-0.014	0.003	11.413	-0.022	-0.022	0.000	0.000	0.000	0.000
7	A	325	GLU	-1	-0.917	-0.967	11.594	-0.797	-0.797	0.000	0.000	0.000	0.000
8	A	326	GLY	0	0.010	0.006	14.242	0.041	0.041	0.000	0.000	0.000	0.000
9	A	327	LYS	1	0.864	0.915	17.962	0.312	0.312	0.000	0.000	0.000	0.000
10	A	328	LYS	1	0.939	0.970	13.050	0.653	0.653	0.000	0.000	0.000	0.000
11	A	329	TRP	0	0.039	0.016	14.188	-0.103	-0.103	0.000	0.000	0.000	0.000
12	A	330	ARG	1	0.808	0.919	6.557	1.727	1.727	0.000	0.000	0.000	0.000
13	A	331	VAL	0	0.032	0.029	9.984	-0.132	-0.132	0.000	0.000	0.000	0.000
14	A	332	GLU	-1	-0.858	-0.967	6.502	-1.630	-1.630	0.000	0.000	0.000	0.000
15	A	333	ASN	0	-0.057	-0.021	3.672	-0.619	0.113	0.010	-0.223	-0.519	-0.001
16	A	334	GLN	0	-0.003	-0.008	5.588	0.540	0.540	0.000	0.000	0.000	0.000
17	A	335	GLU	-1	-0.878	-0.967	7.468	0.649	0.649	0.000	0.000	0.000	0.000
18	A	336	ASN	0	-0.075	-0.011	9.285	0.032	0.032	0.000	0.000	0.000	0.000
19	A	337	VAL	0	0.036	0.045	9.720	0.031	0.031	0.000	0.000	0.000	0.000
20	A	338	SER	0	-0.027	-0.041	12.697	0.004	0.004	0.000	0.000	0.000	0.000
21	A	339	ASN	0	0.024	0.004	15.206	0.002	0.002	0.000	0.000	0.000	0.000
22	A	340	LEU	0	-0.002	0.009	11.066	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	341	VAL	0	0.006	-0.012	15.296	0.043	0.043	0.000	0.000	0.000	0.000
24	A	342	ILE	0	-0.047	-0.012	15.164	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	343	GLU	-1	-0.880	-0.959	18.084	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	344	ASP	-1	-0.862	-0.920	18.972	-0.385	-0.385	0.000	0.000	0.000	0.000
27	A	345	THR	0	0.035	0.015	21.251	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	346	GLU	-1	-0.952	-0.973	22.855	-0.245	-0.245	0.000	0.000	0.000	0.000
29	A	347	LEU	0	0.029	0.012	24.453	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	348	LYS	1	0.871	0.933	23.399	0.281	0.281	0.000	0.000	0.000	0.000
31	A	349	GLN	0	0.010	0.012	20.373	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	350	VAL	0	0.027	0.016	17.890	0.031	0.031	0.000	0.000	0.000	0.000
33	A	351	ALA	0	0.031	0.025	16.499	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	352	TYR	0	-0.080	-0.069	12.634	0.074	0.074	0.000	0.000	0.000	0.000
35	A	353	ILE	0	0.015	0.007	12.471	-0.134	-0.134	0.000	0.000	0.000	0.000
36	A	354	TYR	0	0.040	0.001	8.430	0.199	0.199	0.000	0.000	0.000	0.000
37	A	355	LYS	1	0.978	0.993	7.766	0.065	0.065	0.000	0.000	0.000	0.000
38	A	356	CYS	0	-0.030	0.018	8.253	-0.170	-0.170	0.000	0.000	0.000	0.000
39	A	357	VAL	0	0.019	-0.014	10.397	0.117	0.117	0.000	0.000	0.000	0.000
40	A	358	ASN	0	-0.070	-0.066	12.307	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	359	THR	0	-0.006	0.011	11.728	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	360	THR	0	-0.035	-0.012	14.095	0.036	0.036	0.000	0.000	0.000	0.000
43	A	361	LEU	0	-0.042	-0.016	14.796	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	362	GLN	0	0.009	0.001	17.040	0.054	0.054	0.000	0.000	0.000	0.000
45	A	363	ILE	0	-0.033	-0.024	18.169	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	364	LYS	1	0.921	0.977	20.956	0.246	0.246	0.000	0.000	0.000	0.000
47	A	365	GLY	0	0.045	0.023	23.599	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	366	LYS	1	0.905	0.962	25.692	0.166	0.166	0.000	0.000	0.000	0.000
49	A	367	ILE	0	0.010	0.017	21.126	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	368	ASN	0	-0.035	-0.041	23.974	0.013	0.013	0.000	0.000	0.000	0.000
51	A	369	SER	0	0.006	-0.001	22.936	0.013	0.013	0.000	0.000	0.000	0.000
52	A	370	ILE	0	0.012	0.017	18.694	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	371	THR	0	0.036	0.020	17.044	0.037	0.037	0.000	0.000	0.000	0.000
54	A	372	VAL	0	-0.015	-0.008	15.972	-0.068	-0.068	0.000	0.000	0.000	0.000
55	A	373	ASP	-1	-0.794	-0.896	14.453	-0.312	-0.312	0.000	0.000	0.000	0.000
56	A	374	ASN	0	-0.070	-0.043	12.274	-0.045	-0.045	0.000	0.000	0.000	0.000
57	A	375	CYS	0	-0.031	0.032	12.542	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	376	LYS	1	0.954	0.966	14.073	0.063	0.063	0.000	0.000	0.000	0.000
59	A	377	LYS	1	0.926	0.979	15.360	0.016	0.016	0.000	0.000	0.000	0.000
60	A	378	LEU	0	0.032	0.027	14.052	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	379	GLY	0	0.006	0.002	17.061	0.030	0.030	0.000	0.000	0.000	0.000
62	A	380	LEU	0	-0.016	-0.013	18.584	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	381	VAL	0	-0.038	-0.021	20.281	0.034	0.034	0.000	0.000	0.000	0.000
64	A	382	PHE	0	0.023	-0.001	22.372	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	383	ASP	-1	-0.804	-0.899	24.229	-0.182	-0.182	0.000	0.000	0.000	0.000
66	A	384	ASP	-1	-0.892	-0.963	27.245	-0.150	-0.150	0.000	0.000	0.000	0.000
67	A	385	VAL	0	-0.019	-0.009	24.634	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	386	VAL	0	-0.113	-0.067	27.369	0.019	0.019	0.000	0.000	0.000	0.000
69	A	387	GLY	0	-0.015	-0.008	27.570	0.014	0.014	0.000	0.000	0.000	0.000
70	A	388	ILE	0	0.011	0.012	24.649	0.011	0.011	0.000	0.000	0.000	0.000
71	A	389	VAL	0	0.018	0.009	22.333	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	390	GLU	-1	-0.964	-0.979	21.294	-0.225	-0.225	0.000	0.000	0.000	0.000
73	A	391	ILE	0	0.018	0.022	20.038	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	392	ILE	0	0.001	-0.010	18.126	0.040	0.040	0.000	0.000	0.000	0.000
75	A	393	ASN	0	-0.070	-0.030	17.296	0.011	0.011	0.000	0.000	0.000	0.000
76	A	394	SER	0	0.003	-0.002	17.290	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	395	LYS	1	0.891	0.936	18.161	0.109	0.109	0.000	0.000	0.000	0.000
78	A	396	ASP	-1	-0.878	-0.929	19.047	-0.072	-0.072	0.000	0.000	0.000	0.000
79	A	397	VAL	0	-0.020	-0.007	18.377	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	398	LYS	1	0.950	0.989	20.837	0.191	0.191	0.000	0.000	0.000	0.000
81	A	399	VAL	0	0.003	-0.002	21.918	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	400	GLN	0	-0.012	-0.004	23.893	0.021	0.021	0.000	0.000	0.000	0.000
83	A	401	VAL	0	0.012	0.028	25.821	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	402	MET	0	-0.030	-0.006	27.676	0.016	0.016	0.000	0.000	0.000	0.000
85	A	403	GLY	0	-0.009	-0.003	29.977	0.014	0.014	0.000	0.000	0.000	0.000
86	A	404	LYS	1	0.856	0.925	31.620	0.124	0.124	0.000	0.000	0.000	0.000
87	A	405	VAL	0	0.009	-0.018	27.523	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	406	PRO	0	-0.027	0.002	29.905	0.010	0.010	0.000	0.000	0.000	0.000
89	A	407	THR	0	0.034	0.022	29.617	0.005	0.005	0.000	0.000	0.000	0.000
90	A	408	ILE	0	0.051	0.016	25.804	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	409	SER	0	-0.028	-0.010	25.309	0.019	0.019	0.000	0.000	0.000	0.000
92	A	410	ILE	0	0.010	-0.003	24.538	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	411	ASN	0	0.038	-0.005	23.538	0.028	0.028	0.000	0.000	0.000	0.000
94	A	412	LYS	1	0.858	0.930	21.881	0.128	0.128	0.000	0.000	0.000	0.000
95	A	413	THR	0	0.015	0.006	21.496	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	414	ASP	-1	-0.890	-0.891	22.566	-0.052	-0.052	0.000	0.000	0.000	0.000
97	A	415	GLY	0	0.111	0.056	23.300	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	416	CYS	0	-0.108	-0.064	23.464	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	417	HIS	0	-0.003	0.011	25.178	0.011	0.011	0.000	0.000	0.000	0.000
100	A	418	ALA	0	0.018	0.003	26.281	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	419	TYR	0	-0.002	0.006	27.259	0.010	0.010	0.000	0.000	0.000	0.000
102	A	420	LEU	0	0.026	0.013	29.554	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	421	SER	0	0.032	-0.007	32.164	0.006	0.006	0.000	0.000	0.000	0.000
104	A	422	LYS	1	0.962	0.961	34.282	0.080	0.080	0.000	0.000	0.000	0.000
105	A	423	ASN	0	-0.054	-0.020	35.410	0.008	0.008	0.000	0.000	0.000	0.000
106	A	424	SER	0	0.042	0.020	32.891	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	425	LEU	0	-0.003	-0.003	34.669	0.000	0.000	0.000	0.000	0.000	0.000
108	A	426	ASP	-1	-0.942	-0.962	36.665	-0.104	-0.104	0.000	0.000	0.000	0.000
109	A	427	CYS	0	-0.042	0.008	30.822	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	428	GLU	-1	-0.963	-0.975	33.339	-0.099	-0.099	0.000	0.000	0.000	0.000
111	A	429	ILE	0	0.006	-0.014	29.877	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	430	VAL	0	0.003	0.019	29.698	0.009	0.009	0.000	0.000	0.000	0.000
113	A	431	SER	0	0.054	0.023	28.966	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	432	ALA	0	-0.013	-0.009	28.428	0.008	0.008	0.000	0.000	0.000	0.000
115	A	433	LYS	1	0.865	0.942	26.211	0.057	0.057	0.000	0.000	0.000	0.000
116	A	434	SER	0	0.002	-0.024	26.554	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	435	SER	0	-0.007	-0.025	27.103	0.006	0.006	0.000	0.000	0.000	0.000
118	A	436	GLU	-1	-0.896	-0.942	27.606	-0.052	-0.052	0.000	0.000	0.000	0.000
119	A	437	MET	0	-0.034	0.001	27.642	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	438	ASN	0	0.027	0.009	29.437	0.013	0.013	0.000	0.000	0.000	0.000
121	A	439	VAL	0	0.004	0.004	30.174	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	440	LEU	0	-0.026	-0.023	30.506	0.007	0.007	0.000	0.000	0.000	0.000
123	A	441	ILE	0	-0.006	-0.011	33.315	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	442	PRO	0	-0.026	0.011	35.065	0.004	0.004	0.000	0.000	0.000	0.000
125	A	443	THR	0	-0.038	-0.028	36.975	0.003	0.003	0.000	0.000	0.000	0.000
126	A	444	GLU	-1	-0.994	-1.026	39.724	-0.064	-0.064	0.000	0.000	0.000	0.000
127	A	445	GLY	0	-0.004	0.011	40.102	0.004	0.004	0.000	0.000	0.000	0.000
128	A	446	GLY	0	-0.047	-0.005	36.170	0.000	0.000	0.000	0.000	0.000	0.000
129	A	447	ASP	-1	-0.872	-0.926	35.404	-0.062	-0.062	0.000	0.000	0.000	0.000
130	A	448	PHE	0	-0.041	-0.045	32.460	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	449	ASN	0	-0.015	0.011	36.109	0.007	0.007	0.000	0.000	0.000	0.000
132	A	450	GLU	-1	-0.906	-0.970	32.284	-0.069	-0.069	0.000	0.000	0.000	0.000
133	A	451	PHE	0	-0.042	-0.018	35.158	0.006	0.006	0.000	0.000	0.000	0.000
134	A	452	PRO	0	0.040	0.044	34.097	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	453	VAL	0	-0.022	-0.018	31.755	0.002	0.002	0.000	0.000	0.000	0.000
136	A	454	PRO	0	-0.028	-0.046	34.021	0.002	0.002	0.000	0.000	0.000	0.000
137	A	455	GLU	-1	-0.844	-0.920	32.396	-0.056	-0.056	0.000	0.000	0.000	0.000
138	A	456	GLN	0	-0.038	-0.017	34.256	0.002	0.002	0.000	0.000	0.000	0.000
139	A	457	PHE	0	-0.001	-0.007	34.848	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	458	LYS	1	0.950	1.007	39.958	0.037	0.037	0.000	0.000	0.000	0.000
141	A	459	THR	0	-0.008	-0.026	42.416	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	460	LEU	0	0.015	0.003	44.619	0.003	0.003	0.000	0.000	0.000	0.000
143	A	461	TRP	0	0.013	0.032	48.261	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	462	ASN	0	-0.007	-0.020	50.374	0.001	0.001	0.000	0.000	0.000	0.000
145	A	463	GLY	0	0.027	0.029	52.933	0.001	0.001	0.000	0.000	0.000	0.000
146	A	464	GLN	0	-0.063	-0.037	53.520	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	465	LYS	1	0.973	0.964	48.153	0.040	0.040	0.000	0.000	0.000	0.000
148	A	466	LEU	0	0.048	0.031	44.075	0.002	0.002	0.000	0.000	0.000	0.000
149	A	467	VAL	0	-0.044	-0.020	46.721	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	468	THR	0	0.000	-0.024	40.914	0.003	0.003	0.000	0.000	0.000	0.000
151	A	469	THR	0	-0.032	-0.001	43.986	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	470	VAL	0	0.019	0.002	39.019	0.000	0.000	0.000	0.000	0.000	0.000
153	A	471	THR	0	-0.037	-0.015	39.720	0.002	0.002	0.000	0.000	0.000	0.000
154	A	472	GLU	-1	-0.915	-0.966	39.827	-0.038	-0.038	0.000	0.000	0.000	0.000
155	A	473	ILE	0	0.024	0.043	35.990	0.003	0.003	0.000	0.000	0.000	0.000
156	A	474	ALA	0	0.005	-0.003	39.159	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	475	GLY	0	-0.003	0.005	37.927	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:319:PRO)