FMO DATABASE

FMODB ID: 8938Y

Calculation Name: 3MC9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MC9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YUR6

Base Structure: X-ray

Registration Date: 2023-09-24

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	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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1439653.703094
FMO2-HF: Nuclear repulsion	1377748.932427
FMO2-HF: Total energy	-61904.770667
FMO2-MP2: Total energy	-62090.090106

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:217:THR)

Summations of interaction energy for fragment #1(A:217: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.
-6.185	-2.373	0.091	-1.905	-1.998	0.002

Interaction energy analysis for fragmet #1(A:217:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.013

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	219	PRO	0	-0.012	-0.006	3.266	-2.341	0.822	0.041	-1.695	-1.509	0.001
4	A	220	ARG	1	0.927	0.968	3.178	-3.173	-2.524	0.050	-0.210	-0.489	0.001
5	A	221	VAL	0	0.055	0.031	7.319	-0.187	-0.187	0.000	0.000	0.000	0.000
6	A	222	LEU	0	-0.019	0.000	11.044	0.122	0.122	0.000	0.000	0.000	0.000
7	A	223	VAL	0	0.014	0.020	13.651	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	224	SER	0	-0.013	-0.008	16.134	0.020	0.020	0.000	0.000	0.000	0.000
9	A	225	GLU	-1	-0.825	-0.893	19.747	0.007	0.007	0.000	0.000	0.000	0.000
10	A	226	VAL	0	0.004	0.013	19.224	0.000	0.000	0.000	0.000	0.000	0.000
11	A	227	LEU	0	-0.038	-0.002	21.865	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	228	VAL	0	0.034	0.028	24.182	0.003	0.003	0.000	0.000	0.000	0.000
13	A	229	ARG	1	0.888	0.930	26.371	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	230	PRO	0	0.013	0.030	28.856	0.004	0.004	0.000	0.000	0.000	0.000
15	A	231	GLN	0	0.017	0.006	29.941	0.000	0.000	0.000	0.000	0.000	0.000
16	A	232	SER	0	-0.054	-0.028	31.460	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	233	GLY	0	0.028	0.020	35.263	0.004	0.004	0.000	0.000	0.000	0.000
18	A	234	GLN	0	-0.019	-0.022	36.557	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	235	LEU	0	0.009	0.006	29.922	0.001	0.001	0.000	0.000	0.000	0.000
20	A	236	THR	0	-0.032	-0.041	34.384	0.000	0.000	0.000	0.000	0.000	0.000
21	A	237	PRO	0	0.099	0.042	33.725	0.003	0.003	0.000	0.000	0.000	0.000
22	A	238	GLU	-1	-0.841	-0.892	33.002	0.049	0.049	0.000	0.000	0.000	0.000
23	A	239	LEU	0	-0.006	-0.013	31.526	0.007	0.007	0.000	0.000	0.000	0.000
24	A	240	GLU	-1	-0.885	-0.955	28.968	0.053	0.053	0.000	0.000	0.000	0.000
25	A	241	THR	0	-0.029	-0.032	27.992	0.009	0.009	0.000	0.000	0.000	0.000
26	A	242	GLN	0	-0.055	-0.018	27.782	0.016	0.016	0.000	0.000	0.000	0.000
27	A	243	VAL	0	0.009	0.009	23.599	0.012	0.012	0.000	0.000	0.000	0.000
28	A	244	TYR	0	-0.044	-0.043	23.503	0.015	0.015	0.000	0.000	0.000	0.000
29	A	245	ASN	0	-0.056	-0.026	23.314	0.015	0.015	0.000	0.000	0.000	0.000
30	A	246	VAL	0	-0.050	-0.015	21.871	0.012	0.012	0.000	0.000	0.000	0.000
31	A	247	ILE	0	-0.070	0.000	18.732	0.026	0.026	0.000	0.000	0.000	0.000
32	A	248	ARG	1	0.848	0.911	11.397	-0.638	-0.638	0.000	0.000	0.000	0.000
33	A	249	THR	0	-0.049	-0.047	14.945	0.013	0.013	0.000	0.000	0.000	0.000
34	A	250	GLN	0	-0.030	-0.018	16.096	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	251	PRO	0	0.030	0.019	17.077	0.004	0.004	0.000	0.000	0.000	0.000
36	A	252	GLY	0	0.006	-0.003	18.067	0.011	0.011	0.000	0.000	0.000	0.000
37	A	253	ARG	1	0.876	0.941	13.955	-0.167	-0.167	0.000	0.000	0.000	0.000
38	A	254	THR	0	0.014	-0.001	9.511	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	255	THR	0	-0.008	-0.006	10.560	0.117	0.117	0.000	0.000	0.000	0.000
40	A	256	THR	0	-0.011	-0.032	5.903	-0.118	-0.118	0.000	0.000	0.000	0.000
41	A	257	ARG	1	0.940	0.960	8.865	-0.139	-0.139	0.000	0.000	0.000	0.000
42	A	258	SER	0	-0.008	-0.037	7.869	-0.141	-0.141	0.000	0.000	0.000	0.000
43	A	259	GLN	0	-0.082	-0.023	9.573	0.040	0.040	0.000	0.000	0.000	0.000
44	A	260	LEU	0	0.040	0.020	11.213	-0.092	-0.092	0.000	0.000	0.000	0.000
45	A	261	GLN	0	-0.043	-0.025	13.209	-0.059	-0.059	0.000	0.000	0.000	0.000
46	A	262	GLU	-1	-0.850	-0.921	11.882	0.566	0.566	0.000	0.000	0.000	0.000
47	A	263	ASP	-1	-0.705	-0.840	14.745	0.285	0.285	0.000	0.000	0.000	0.000
48	A	264	ILE	0	-0.001	-0.004	17.156	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	265	ASN	0	-0.016	-0.015	16.192	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	266	ALA	0	0.026	0.026	18.823	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	267	ILE	0	0.037	0.020	20.570	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	268	PHE	0	-0.024	-0.003	22.134	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	269	GLY	0	-0.019	0.007	23.127	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	270	THR	0	-0.045	-0.042	24.448	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	271	GLY	0	-0.004	0.001	27.088	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	272	PHE	0	0.026	0.010	29.373	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	273	PHE	0	-0.017	-0.004	27.464	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	274	SER	0	0.033	0.029	29.153	0.002	0.002	0.000	0.000	0.000	0.000
59	A	275	ASN	0	-0.052	-0.045	26.678	0.001	0.001	0.000	0.000	0.000	0.000
60	A	276	VAL	0	0.009	0.010	22.270	0.003	0.003	0.000	0.000	0.000	0.000
61	A	277	GLN	0	-0.021	0.004	21.713	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	278	ALA	0	0.036	0.015	18.179	0.008	0.008	0.000	0.000	0.000	0.000
63	A	279	SER	0	-0.022	-0.017	20.062	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	280	PRO	0	-0.060	-0.020	16.775	0.013	0.013	0.000	0.000	0.000	0.000
65	A	281	GLU	-1	-0.845	-0.909	19.002	-0.082	-0.082	0.000	0.000	0.000	0.000
66	A	282	ASP	-1	-0.907	-0.959	17.314	-0.201	-0.201	0.000	0.000	0.000	0.000
67	A	283	THR	0	-0.035	-0.033	19.267	0.015	0.015	0.000	0.000	0.000	0.000
68	A	284	PRO	0	0.022	-0.007	19.634	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	285	LEU	0	-0.023	-0.003	20.297	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	286	GLY	0	-0.003	0.005	16.937	0.019	0.019	0.000	0.000	0.000	0.000
71	A	287	VAL	0	-0.024	-0.009	14.744	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	288	ARG	1	0.772	0.855	17.675	0.060	0.060	0.000	0.000	0.000	0.000
73	A	289	VAL	0	0.002	-0.011	16.364	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	290	SER	0	0.007	0.006	19.652	0.013	0.013	0.000	0.000	0.000	0.000
75	A	291	PHE	0	0.007	0.000	17.662	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	292	ILE	0	-0.028	-0.009	23.149	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	293	VAL	0	0.026	0.008	25.466	0.003	0.003	0.000	0.000	0.000	0.000
78	A	294	GLN	0	0.048	0.033	27.814	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	295	PRO	0	-0.021	-0.019	31.048	0.004	0.004	0.000	0.000	0.000	0.000
80	A	296	ASN	0	-0.024	-0.020	31.968	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	297	PRO	0	0.034	0.026	34.537	0.000	0.000	0.000	0.000	0.000	0.000
82	A	298	VAL	0	-0.027	-0.025	38.263	0.003	0.003	0.000	0.000	0.000	0.000
83	A	299	LEU	0	-0.021	-0.002	39.827	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	300	SER	0	-0.055	-0.040	41.434	0.000	0.000	0.000	0.000	0.000	0.000
85	A	301	LYS	1	0.860	0.905	43.882	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	302	VAL	0	0.012	0.016	41.051	0.000	0.000	0.000	0.000	0.000	0.000
87	A	303	GLU	-1	-0.897	-0.927	43.321	0.015	0.015	0.000	0.000	0.000	0.000
88	A	304	ILE	0	0.025	0.013	43.158	0.001	0.001	0.000	0.000	0.000	0.000
89	A	305	GLN	0	-0.025	-0.008	42.787	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	306	ALA	0	0.012	0.011	43.636	0.001	0.001	0.000	0.000	0.000	0.000
91	A	307	ASN	0	-0.064	-0.028	45.461	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	308	PRO	0	0.050	0.030	45.274	0.000	0.000	0.000	0.000	0.000	0.000
93	A	309	GLY	0	-0.021	-0.018	46.355	0.000	0.000	0.000	0.000	0.000	0.000
94	A	310	THR	0	-0.013	-0.012	47.733	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	311	ASN	0	0.035	0.021	47.783	0.000	0.000	0.000	0.000	0.000	0.000
96	A	312	VAL	0	-0.007	0.005	48.751	0.001	0.001	0.000	0.000	0.000	0.000
97	A	313	PRO	0	0.027	0.000	51.258	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	314	SER	0	-0.084	-0.069	47.810	0.000	0.000	0.000	0.000	0.000	0.000
99	A	315	VAL	0	-0.012	-0.011	48.806	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	316	LEU	0	-0.053	-0.013	46.610	0.000	0.000	0.000	0.000	0.000	0.000
101	A	317	PRO	0	0.002	-0.007	50.756	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	318	GLN	0	0.020	-0.003	51.231	0.000	0.000	0.000	0.000	0.000	0.000
103	A	319	ALA	0	-0.013	0.000	51.145	0.000	0.000	0.000	0.000	0.000	0.000
104	A	320	THR	0	0.019	0.016	47.615	0.001	0.001	0.000	0.000	0.000	0.000
105	A	321	ALA	0	0.034	0.017	45.305	0.002	0.002	0.000	0.000	0.000	0.000
106	A	322	ASP	-1	-0.838	-0.911	45.849	0.024	0.024	0.000	0.000	0.000	0.000
107	A	323	GLU	-1	-1.018	-1.029	47.896	0.026	0.026	0.000	0.000	0.000	0.000
108	A	324	ILE	0	-0.028	0.009	42.613	0.001	0.001	0.000	0.000	0.000	0.000
109	A	325	PHE	0	0.022	0.005	38.989	0.002	0.002	0.000	0.000	0.000	0.000
110	A	326	ARG	1	0.961	0.998	43.752	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	327	ALA	0	-0.017	0.002	44.265	0.000	0.000	0.000	0.000	0.000	0.000
112	A	328	GLN	0	-0.053	-0.048	38.674	0.000	0.000	0.000	0.000	0.000	0.000
113	A	329	TYR	0	-0.023	-0.031	42.160	0.000	0.000	0.000	0.000	0.000	0.000
114	A	330	GLY	0	-0.026	-0.009	44.536	0.000	0.000	0.000	0.000	0.000	0.000
115	A	331	LYS	1	0.865	0.926	40.603	-0.039	-0.039	0.000	0.000	0.000	0.000
116	A	332	ILE	0	-0.027	0.001	34.613	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	333	LEU	0	0.027	0.018	35.171	0.003	0.003	0.000	0.000	0.000	0.000
118	A	334	ASN	0	0.006	-0.006	31.292	0.004	0.004	0.000	0.000	0.000	0.000
119	A	335	LEU	0	0.034	0.002	29.490	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	336	ARG	1	0.935	0.974	28.496	-0.089	-0.089	0.000	0.000	0.000	0.000
121	A	337	ASP	-1	-0.878	-0.941	31.773	0.061	0.061	0.000	0.000	0.000	0.000
122	A	338	LEU	0	-0.010	0.008	34.618	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	339	GLN	0	-0.023	-0.020	31.191	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	340	GLU	-1	-0.899	-0.959	33.968	0.067	0.067	0.000	0.000	0.000	0.000
125	A	341	GLY	0	0.060	0.033	36.369	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	342	ILE	0	0.003	-0.003	35.034	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	343	LYS	1	0.876	0.963	32.113	-0.071	-0.071	0.000	0.000	0.000	0.000
128	A	344	GLU	-1	-0.918	-0.954	37.989	0.039	0.039	0.000	0.000	0.000	0.000
129	A	345	LEU	0	0.008	-0.010	41.275	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	346	THR	0	-0.047	-0.033	38.487	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	347	LYS	1	0.824	0.902	41.219	-0.039	-0.039	0.000	0.000	0.000	0.000
132	A	348	ARG	1	0.913	0.949	43.219	-0.031	-0.031	0.000	0.000	0.000	0.000
133	A	349	TYR	0	-0.018	-0.045	43.074	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	350	GLN	0	-0.025	-0.009	42.050	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	351	ASP	-1	-0.850	-0.910	45.865	0.033	0.033	0.000	0.000	0.000	0.000
136	A	352	GLN	0	-0.040	-0.001	48.905	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	353	GLY	0	0.018	0.007	49.517	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	354	TYR	0	-0.025	-0.005	46.430	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	355	VAL	0	-0.012	-0.023	44.444	0.001	0.001	0.000	0.000	0.000	0.000
140	A	356	LEU	0	-0.047	-0.024	41.254	0.002	0.002	0.000	0.000	0.000	0.000
141	A	357	ALA	0	0.003	0.029	41.036	0.000	0.000	0.000	0.000	0.000	0.000
142	A	358	ASN	0	-0.051	-0.031	36.279	0.005	0.005	0.000	0.000	0.000	0.000
143	A	359	VAL	0	0.015	0.009	35.572	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	360	VAL	0	-0.040	-0.026	35.678	0.002	0.002	0.000	0.000	0.000	0.000
145	A	361	GLY	0	-0.012	-0.003	32.419	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	362	ALA	0	-0.010	-0.009	30.483	0.004	0.004	0.000	0.000	0.000	0.000
147	A	363	PRO	0	0.026	0.001	32.450	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	364	GLN	0	-0.020	0.007	34.245	0.001	0.001	0.000	0.000	0.000	0.000
149	A	365	VAL	0	-0.001	-0.003	34.883	0.000	0.000	0.000	0.000	0.000	0.000
150	A	366	SER	0	-0.018	0.007	37.321	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	367	GLU	-1	-0.877	-0.947	38.291	0.008	0.008	0.000	0.000	0.000	0.000
152	A	368	ASN	0	-0.061	-0.037	40.045	0.001	0.001	0.000	0.000	0.000	0.000
153	A	369	GLY	0	0.045	0.024	40.341	0.001	0.001	0.000	0.000	0.000	0.000
154	A	370	VAL	0	-0.014	0.004	41.422	0.002	0.002	0.000	0.000	0.000	0.000
155	A	371	VAL	0	0.019	-0.003	37.659	0.000	0.000	0.000	0.000	0.000	0.000
156	A	372	THR	0	-0.011	0.000	39.811	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	373	LEU	0	0.004	-0.008	37.511	0.001	0.001	0.000	0.000	0.000	0.000
158	A	374	GLN	0	0.024	0.013	38.736	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	375	VAL	0	-0.009	0.000	39.050	0.003	0.003	0.000	0.000	0.000	0.000
160	A	376	ALA	0	0.010	0.019	40.271	-0.002	-0.002	0.000	0.000	0.000	0.000
161	A	377	GLU	-1	-0.723	-0.830	42.047	0.024	0.024	0.000	0.000	0.000	0.000
162	A	378	GLY	0	0.014	0.010	44.759	0.001	0.001	0.000	0.000	0.000	0.000
163	A	379	VAL	0	-0.001	-0.012	46.150	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	380	VAL	0	-0.014	-0.008	49.530	0.001	0.001	0.000	0.000	0.000	0.000
165	A	381	GLU	-1	-0.987	-0.980	51.963	0.015	0.015	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:217:THR)