FMO DATABASE

FMODB ID: 2JM1R

Calculation Name: 1C3K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1C3K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZQY5

Base Structure: X-ray

Registration Date: 2023-06-26

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

DOI:

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1230800.492323
FMO2-HF: Nuclear repulsion	1178457.743992
FMO2-HF: Total energy	-52342.748331
FMO2-MP2: Total energy	-52498.243082

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
-106.164	-100.547	11.083	-8.685	-8.013	0.081

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.869 / q_NPA : -0.938

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	7	ALA	0	-0.015	0.000	3.426	-11.468	-9.010	-0.006	-1.180	-1.272	0.003
4	A	8	VAL	0	-0.008	0.002	5.250	-5.499	-5.499	0.000	0.000	0.000	0.000
5	A	9	GLN	0	-0.037	-0.024	7.374	-0.343	-0.343	0.000	0.000	0.000	0.000
6	A	10	ALA	0	0.003	0.006	9.585	-2.298	-2.298	0.000	0.000	0.000	0.000
7	A	11	GLY	0	0.050	0.039	12.620	0.322	0.322	0.000	0.000	0.000	0.000
8	A	12	PRO	0	-0.075	-0.055	15.394	0.488	0.488	0.000	0.000	0.000	0.000
9	A	13	TRP	0	0.018	0.001	15.472	-0.600	-0.600	0.000	0.000	0.000	0.000
10	A	14	GLY	0	0.037	-0.001	19.964	0.355	0.355	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.003	-0.002	22.510	-0.381	-0.381	0.000	0.000	0.000	0.000
12	A	16	ASN	0	-0.060	-0.043	22.042	1.136	1.136	0.000	0.000	0.000	0.000
13	A	17	GLY	0	0.029	0.036	23.172	0.012	0.012	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.049	0.029	21.817	0.668	0.668	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.913	0.942	18.671	-14.584	-14.584	0.000	0.000	0.000	0.000
16	A	20	ARG	1	0.886	0.940	12.748	-21.501	-21.501	0.000	0.000	0.000	0.000
17	A	21	TRP	0	-0.046	0.002	10.989	0.700	0.700	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.021	-0.020	5.473	0.294	0.294	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.048	-0.020	7.561	-2.794	-2.794	0.000	0.000	0.000	0.000
20	A	24	THR	0	0.010	-0.012	1.794	-26.485	-26.866	10.328	-5.723	-4.223	0.069
21	A	25	ALA	0	0.014	0.014	4.554	-5.934	-5.918	-0.001	-0.015	0.000	0.000
22	A	26	HIS	0	-0.028	-0.005	3.490	-3.296	-2.370	0.026	-0.376	-0.576	0.002
23	A	27	GLY	0	-0.006	-0.003	3.634	-9.591	-9.166	0.003	-0.227	-0.201	0.001
24	A	28	GLY	0	-0.033	-0.016	5.479	-5.532	-5.497	-0.001	-0.001	-0.033	0.000
25	A	29	LYS	1	0.755	0.853	7.626	-18.615	-18.615	0.000	0.000	0.000	0.000
26	A	30	ILE	0	0.006	0.001	7.663	-0.694	-0.694	0.000	0.000	0.000	0.000
27	A	31	THR	0	0.002	-0.017	10.556	-1.023	-1.023	0.000	0.000	0.000	0.000
28	A	32	SER	0	0.033	0.019	14.160	-2.026	-2.026	0.000	0.000	0.000	0.000
29	A	33	ILE	0	-0.043	0.001	14.216	1.453	1.453	0.000	0.000	0.000	0.000
30	A	34	ILE	0	-0.021	-0.004	16.500	-1.183	-1.183	0.000	0.000	0.000	0.000
31	A	35	ILE	0	0.032	0.005	18.937	0.562	0.562	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.827	0.946	21.073	-13.152	-13.152	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.014	0.002	24.197	0.197	0.197	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.001	-0.012	25.908	-0.388	-0.388	0.000	0.000	0.000	0.000
35	A	39	THR	0	0.000	0.014	29.472	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	40	CYS	0	-0.055	-0.012	26.408	0.016	0.016	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.011	0.005	20.532	-0.157	-0.157	0.000	0.000	0.000	0.000
38	A	42	PHE	0	0.030	-0.004	23.320	0.204	0.204	0.000	0.000	0.000	0.000
39	A	43	SER	0	-0.042	-0.036	20.758	0.333	0.333	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.000	0.012	15.571	-0.328	-0.328	0.000	0.000	0.000	0.000
41	A	45	GLN	0	0.000	0.012	15.475	-0.705	-0.705	0.000	0.000	0.000	0.000
42	A	46	PHE	0	0.010	-0.008	11.539	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.019	0.033	13.508	0.156	0.156	0.000	0.000	0.000	0.000
44	A	48	TYR	0	-0.002	-0.005	8.517	1.341	1.341	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.913	0.972	10.759	-20.150	-20.150	0.000	0.000	0.000	0.000
46	A	50	ASP	-1	-0.724	-0.834	8.938	27.698	27.698	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.966	0.953	8.674	-29.503	-29.503	0.000	0.000	0.000	0.000
48	A	52	ASP	-1	-0.951	-0.951	11.425	20.226	20.226	0.000	0.000	0.000	0.000
49	A	53	ASN	0	-0.094	-0.055	13.399	-1.619	-1.619	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.023	0.019	13.949	-1.593	-1.593	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.928	-0.977	13.225	19.070	19.070	0.000	0.000	0.000	0.000
52	A	56	TYR	0	-0.063	-0.041	11.474	-0.925	-0.925	0.000	0.000	0.000	0.000
53	A	57	HIS	0	-0.028	-0.026	13.558	0.129	0.129	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.007	0.010	11.605	0.415	0.415	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.024	0.009	13.233	-1.738	-1.738	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.864	0.918	15.551	-14.281	-14.281	0.000	0.000	0.000	0.000
57	A	61	PHE	0	0.019	0.018	12.069	0.291	0.291	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.072	0.045	17.421	-0.267	-0.267	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.050	-0.027	21.028	0.233	0.233	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.021	0.032	23.553	-0.485	-0.485	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.028	0.000	25.232	0.445	0.445	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.892	-0.946	27.549	10.401	10.401	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.849	0.906	27.609	-11.074	-11.074	0.000	0.000	0.000	0.000
64	A	68	ALA	0	-0.048	-0.048	23.885	0.382	0.382	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.860	-0.905	24.130	11.364	11.364	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.010	-0.009	19.990	0.663	0.663	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.063	-0.010	18.130	-0.683	-0.683	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.032	-0.013	18.530	0.640	0.640	0.000	0.000	0.000	0.000
69	A	73	PHE	0	-0.084	-0.035	14.448	-0.525	-0.525	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.063	0.028	18.619	0.024	0.024	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.853	-0.941	18.136	15.041	15.041	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.877	-0.906	17.372	15.077	15.077	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.760	-0.825	17.966	14.778	14.778	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.863	-0.938	12.301	23.559	23.559	0.000	0.000	0.000	0.000
75	A	79	ILE	0	0.002	-0.001	11.985	-1.143	-1.143	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.032	-0.031	13.405	0.928	0.928	0.000	0.000	0.000	0.000
77	A	81	ALA	0	0.013	0.001	15.673	-0.192	-0.192	0.000	0.000	0.000	0.000
78	A	82	ILE	0	-0.023	0.027	14.272	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.027	-0.013	16.985	-0.400	-0.400	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.062	0.015	20.257	0.245	0.245	0.000	0.000	0.000	0.000
81	A	85	THR	0	-0.031	-0.009	22.708	-0.488	-0.488	0.000	0.000	0.000	0.000
82	A	86	PHE	0	0.018	0.017	23.709	0.427	0.427	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.015	0.000	25.693	-0.436	-0.436	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.026	-0.012	28.556	0.270	0.270	0.000	0.000	0.000	0.000
85	A	89	TYR	0	0.044	0.004	28.674	-0.075	-0.075	0.000	0.000	0.000	0.000
86	A	90	TYR	0	-0.005	-0.004	30.968	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	91	HIS	0	-0.006	-0.007	33.191	0.202	0.202	0.000	0.000	0.000	0.000
88	A	92	MET	0	0.018	0.026	28.465	0.260	0.260	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.009	0.000	25.878	-0.240	-0.240	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.002	0.006	24.110	0.426	0.426	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.025	0.011	19.636	-0.338	-0.338	0.000	0.000	0.000	0.000
92	A	96	THR	0	-0.005	-0.011	23.116	-0.114	-0.114	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.011	0.015	24.521	-0.209	-0.209	0.000	0.000	0.000	0.000
94	A	98	LEU	0	0.003	0.004	18.205	0.556	0.556	0.000	0.000	0.000	0.000
95	A	99	THR	0	-0.022	-0.015	20.942	-0.855	-0.855	0.000	0.000	0.000	0.000
96	A	100	PHE	0	0.028	0.015	14.421	0.610	0.610	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.007	0.007	18.313	-0.952	-0.952	0.000	0.000	0.000	0.000
98	A	102	THR	0	0.018	-0.010	17.053	0.894	0.894	0.000	0.000	0.000	0.000
99	A	103	ASN	0	-0.044	-0.022	18.341	-0.287	-0.287	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.812	0.897	20.030	-14.331	-14.331	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.887	0.938	21.855	-13.037	-13.037	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.050	0.032	21.855	0.730	0.730	0.000	0.000	0.000	0.000
103	A	107	TYR	0	-0.064	-0.061	20.523	-0.852	-0.852	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.050	0.044	22.807	0.497	0.497	0.000	0.000	0.000	0.000
105	A	109	PRO	0	-0.052	-0.044	25.005	-0.311	-0.311	0.000	0.000	0.000	0.000
106	A	110	PHE	0	0.014	0.012	21.648	-0.189	-0.189	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.025	0.006	25.143	0.327	0.327	0.000	0.000	0.000	0.000
108	A	112	THR	0	-0.019	-0.026	27.054	-0.502	-0.502	0.000	0.000	0.000	0.000
109	A	113	VAL	0	-0.050	-0.028	28.227	0.299	0.299	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.006	0.005	28.744	-0.453	-0.453	0.000	0.000	0.000	0.000
111	A	115	SER	0	0.013	-0.006	30.461	-0.093	-0.093	0.000	0.000	0.000	0.000
112	A	116	SER	0	-0.042	-0.008	27.696	-0.186	-0.186	0.000	0.000	0.000	0.000
113	A	117	SER	0	0.028	0.013	25.716	0.378	0.378	0.000	0.000	0.000	0.000
114	A	118	PHE	0	-0.012	0.001	18.046	-0.029	-0.029	0.000	0.000	0.000	0.000
115	A	119	SER	0	0.014	-0.022	20.198	0.159	0.159	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.016	0.007	12.726	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	121	PRO	0	0.044	0.018	15.919	0.897	0.897	0.000	0.000	0.000	0.000
118	A	122	LEU	0	-0.013	-0.002	10.772	0.327	0.327	0.000	0.000	0.000	0.000
119	A	123	THR	0	-0.015	-0.005	15.132	-0.419	-0.419	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.932	0.940	13.715	-17.117	-17.117	0.000	0.000	0.000	0.000
121	A	125	GLY	0	0.010	0.028	10.643	0.462	0.462	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.925	0.956	8.470	-24.329	-24.329	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.017	0.008	7.683	2.027	2.027	0.000	0.000	0.000	0.000
124	A	128	ALA	0	0.001	0.014	3.143	-2.575	-1.256	0.167	-0.747	-0.739	0.006
125	A	129	GLY	0	0.043	-0.005	5.082	3.772	3.946	-0.001	-0.004	-0.168	0.000
126	A	130	PHE	0	-0.031	-0.006	6.983	-2.956	-2.956	0.000	0.000	0.000	0.000
127	A	131	PHE	0	-0.009	0.000	8.980	2.668	2.668	0.000	0.000	0.000	0.000
128	A	132	GLY	0	0.060	0.025	11.074	-1.703	-1.703	0.000	0.000	0.000	0.000
129	A	133	ASN	0	-0.022	0.011	14.740	1.822	1.822	0.000	0.000	0.000	0.000
130	A	134	SER	0	-0.018	-0.002	17.762	-0.136	-0.136	0.000	0.000	0.000	0.000
131	A	135	GLY	0	0.061	0.018	19.666	0.140	0.140	0.000	0.000	0.000	0.000
132	A	136	ASP	-1	-0.904	-0.939	22.744	11.962	11.962	0.000	0.000	0.000	0.000
133	A	137	VAL	0	-0.042	-0.026	23.622	-0.082	-0.082	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.032	0.011	17.001	0.633	0.633	0.000	0.000	0.000	0.000
135	A	139	ASP	-1	-0.850	-0.931	20.830	13.894	13.894	0.000	0.000	0.000	0.000
136	A	140	SER	0	-0.017	-0.023	18.894	-0.097	-0.097	0.000	0.000	0.000	0.000
137	A	141	ILE	0	-0.010	-0.005	14.157	0.765	0.765	0.000	0.000	0.000	0.000
138	A	142	GLY	0	0.057	0.022	13.709	-1.381	-1.381	0.000	0.000	0.000	0.000
139	A	143	GLY	0	-0.032	-0.004	10.766	0.776	0.776	0.000	0.000	0.000	0.000
140	A	144	VAL	0	-0.016	0.016	4.688	-1.217	-1.092	-0.001	-0.032	-0.092	0.000
141	A	145	VAL	0	-0.031	-0.017	6.637	1.331	1.331	0.000	0.000	0.000	0.000
142	A	146	VAL	0	0.049	0.023	2.536	1.017	1.537	0.569	-0.380	-0.709	0.000
143	A	147	PRO	0	-0.007	0.001	5.816	-5.277	-5.277	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)