FMO DATABASE

FMODB ID: NN5VQ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1440620.315212
FMO2-HF: Nuclear repulsion	1378715.179854
FMO2-HF: Total energy	-61905.135359
FMO2-MP2: Total energy	-62090.465962

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.
-16.405	-11.973	4.344	-3.959	-4.817	0.014

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 : 0.032 / q_NPA : 0.019

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	0.006	-0.009	2.795	-1.636	1.947	0.379	-2.058	-1.905	-0.006
4	A	220	ARG	1	0.905	0.956	2.111	-14.745	-13.896	3.965	-1.901	-2.912	0.020
5	A	221	VAL	0	0.036	0.024	6.871	-0.231	-0.231	0.000	0.000	0.000	0.000
6	A	222	LEU	0	-0.019	-0.003	10.646	0.138	0.138	0.000	0.000	0.000	0.000
7	A	223	VAL	0	-0.001	0.014	13.448	-0.066	-0.066	0.000	0.000	0.000	0.000
8	A	224	SER	0	-0.035	-0.029	16.050	0.025	0.025	0.000	0.000	0.000	0.000
9	A	225	GLU	-1	-0.809	-0.887	19.602	0.056	0.056	0.000	0.000	0.000	0.000
10	A	226	VAL	0	-0.006	-0.001	18.975	0.006	0.006	0.000	0.000	0.000	0.000
11	A	227	LEU	0	-0.036	0.014	21.661	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	228	VAL	0	0.047	0.027	23.765	0.002	0.002	0.000	0.000	0.000	0.000
13	A	229	ARG	1	0.834	0.897	26.042	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	230	PRO	0	0.000	0.017	28.552	0.000	0.000	0.000	0.000	0.000	0.000
15	A	231	GLN	0	0.024	0.017	29.689	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	232	SER	0	-0.053	-0.039	31.257	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	233	GLY	0	0.024	0.020	35.068	0.005	0.005	0.000	0.000	0.000	0.000
18	A	234	GLN	0	-0.020	-0.026	36.022	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	235	LEU	0	0.003	0.012	29.290	0.000	0.000	0.000	0.000	0.000	0.000
20	A	236	THR	0	-0.017	-0.026	33.740	0.000	0.000	0.000	0.000	0.000	0.000
21	A	237	PRO	0	0.072	0.032	33.125	0.005	0.005	0.000	0.000	0.000	0.000
22	A	238	GLU	-1	-0.826	-0.891	32.317	0.070	0.070	0.000	0.000	0.000	0.000
23	A	239	LEU	0	-0.002	-0.005	30.834	0.009	0.009	0.000	0.000	0.000	0.000
24	A	240	GLU	-1	-0.840	-0.918	28.268	0.082	0.082	0.000	0.000	0.000	0.000
25	A	241	THR	0	-0.036	-0.038	27.422	0.014	0.014	0.000	0.000	0.000	0.000
26	A	242	GLN	0	-0.056	-0.032	27.201	0.020	0.020	0.000	0.000	0.000	0.000
27	A	243	VAL	0	0.000	0.014	22.872	0.010	0.010	0.000	0.000	0.000	0.000
28	A	244	TYR	0	-0.040	-0.052	22.925	0.019	0.019	0.000	0.000	0.000	0.000
29	A	245	ASN	0	-0.060	-0.021	23.122	0.023	0.023	0.000	0.000	0.000	0.000
30	A	246	VAL	0	-0.060	-0.023	21.251	0.012	0.012	0.000	0.000	0.000	0.000
31	A	247	ILE	0	-0.061	-0.002	18.151	0.025	0.025	0.000	0.000	0.000	0.000
32	A	248	ARG	1	0.834	0.891	10.281	-0.774	-0.774	0.000	0.000	0.000	0.000
33	A	249	THR	0	-0.067	-0.049	14.635	0.057	0.057	0.000	0.000	0.000	0.000
34	A	250	GLN	0	-0.003	-0.006	15.811	-0.065	-0.065	0.000	0.000	0.000	0.000
35	A	251	PRO	0	0.035	0.017	17.068	0.030	0.030	0.000	0.000	0.000	0.000
36	A	252	GLY	0	0.009	0.008	18.092	0.015	0.015	0.000	0.000	0.000	0.000
37	A	253	ARG	1	0.869	0.933	13.773	-0.342	-0.342	0.000	0.000	0.000	0.000
38	A	254	THR	0	0.006	0.002	9.186	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	255	THR	0	0.008	-0.001	10.605	0.152	0.152	0.000	0.000	0.000	0.000
40	A	256	THR	0	-0.020	-0.043	5.860	0.060	0.060	0.000	0.000	0.000	0.000
41	A	257	ARG	1	0.913	0.945	8.837	0.242	0.242	0.000	0.000	0.000	0.000
42	A	258	SER	0	-0.017	-0.054	7.545	-0.102	-0.102	0.000	0.000	0.000	0.000
43	A	259	GLN	0	-0.098	-0.038	9.253	0.116	0.116	0.000	0.000	0.000	0.000
44	A	260	LEU	0	0.039	0.015	10.918	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	261	GLN	0	-0.024	-0.011	13.059	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	262	GLU	-1	-0.833	-0.897	11.567	0.569	0.569	0.000	0.000	0.000	0.000
47	A	263	ASP	-1	-0.694	-0.829	14.276	0.374	0.374	0.000	0.000	0.000	0.000
48	A	264	ILE	0	-0.007	-0.008	16.709	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	265	ASN	0	0.001	-0.006	16.576	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	266	ALA	0	0.015	0.014	18.133	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	267	ILE	0	0.028	0.018	19.949	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	268	PHE	0	-0.008	0.008	21.784	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	269	GLY	0	-0.013	0.007	22.645	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	270	THR	0	-0.046	-0.043	23.961	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	271	GLY	0	0.003	0.008	26.653	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	272	PHE	0	0.015	0.002	28.955	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	273	PHE	0	-0.020	-0.013	27.145	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	274	SER	0	0.019	0.017	28.742	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	275	ASN	0	-0.050	-0.050	26.253	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	276	VAL	0	-0.002	0.006	21.944	0.010	0.010	0.000	0.000	0.000	0.000
61	A	277	GLN	0	-0.005	0.012	21.409	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	278	ALA	0	0.016	0.012	17.915	0.012	0.012	0.000	0.000	0.000	0.000
63	A	279	SER	0	-0.017	-0.009	19.944	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	280	PRO	0	-0.059	-0.024	16.508	0.021	0.021	0.000	0.000	0.000	0.000
65	A	281	GLU	-1	-0.829	-0.897	18.777	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	282	ASP	-1	-0.901	-0.961	16.766	-0.103	-0.103	0.000	0.000	0.000	0.000
67	A	283	THR	0	-0.005	-0.015	18.737	0.001	0.001	0.000	0.000	0.000	0.000
68	A	284	PRO	0	-0.002	-0.014	19.109	0.002	0.002	0.000	0.000	0.000	0.000
69	A	285	LEU	0	-0.022	0.000	20.357	0.007	0.007	0.000	0.000	0.000	0.000
70	A	286	GLY	0	0.003	0.009	16.397	0.036	0.036	0.000	0.000	0.000	0.000
71	A	287	VAL	0	-0.022	-0.002	14.341	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	288	ARG	1	0.772	0.855	17.274	0.028	0.028	0.000	0.000	0.000	0.000
73	A	289	VAL	0	-0.005	-0.018	16.406	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	290	SER	0	0.014	0.011	19.632	0.017	0.017	0.000	0.000	0.000	0.000
75	A	291	PHE	0	0.012	-0.011	17.155	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	292	ILE	0	-0.003	0.008	22.745	0.001	0.001	0.000	0.000	0.000	0.000
77	A	293	VAL	0	0.008	-0.001	25.025	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	294	GLN	0	0.045	0.037	27.409	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	295	PRO	0	-0.011	-0.009	30.686	0.002	0.002	0.000	0.000	0.000	0.000
80	A	296	ASN	0	-0.007	-0.014	31.762	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	297	PRO	0	0.033	0.026	34.215	0.002	0.002	0.000	0.000	0.000	0.000
82	A	298	VAL	0	-0.027	-0.024	37.989	0.004	0.004	0.000	0.000	0.000	0.000
83	A	299	LEU	0	-0.029	0.002	39.628	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	300	SER	0	-0.057	-0.046	41.233	0.001	0.001	0.000	0.000	0.000	0.000
85	A	301	LYS	1	0.799	0.884	44.029	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	302	VAL	0	-0.002	0.003	41.118	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	303	GLU	-1	-0.900	-0.932	43.192	0.006	0.006	0.000	0.000	0.000	0.000
88	A	304	ILE	0	0.016	-0.001	43.086	0.001	0.001	0.000	0.000	0.000	0.000
89	A	305	GLN	0	-0.024	-0.017	42.458	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	306	ALA	0	0.035	0.027	43.770	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	307	ASN	0	-0.053	-0.018	46.104	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	308	PRO	0	0.029	0.015	45.025	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	309	GLY	0	-0.028	-0.015	46.051	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	310	THR	0	-0.004	-0.017	48.087	0.000	0.000	0.000	0.000	0.000	0.000
95	A	311	ASN	0	0.023	0.018	47.624	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	312	VAL	0	-0.040	0.013	48.666	0.002	0.002	0.000	0.000	0.000	0.000
97	A	313	PRO	0	-0.003	-0.010	51.837	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	314	SER	0	0.003	-0.041	48.158	0.000	0.000	0.000	0.000	0.000	0.000
99	A	315	VAL	0	-0.035	-0.028	48.883	0.000	0.000	0.000	0.000	0.000	0.000
100	A	316	LEU	0	-0.036	-0.007	46.698	0.001	0.001	0.000	0.000	0.000	0.000
101	A	317	PRO	0	-0.005	-0.012	50.984	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	318	GLN	0	0.023	0.009	51.270	0.000	0.000	0.000	0.000	0.000	0.000
103	A	319	ALA	0	-0.012	0.001	50.938	0.000	0.000	0.000	0.000	0.000	0.000
104	A	320	THR	0	-0.020	-0.040	47.617	0.002	0.002	0.000	0.000	0.000	0.000
105	A	321	ALA	0	0.048	0.025	45.440	0.002	0.002	0.000	0.000	0.000	0.000
106	A	322	ASP	-1	-0.795	-0.886	45.772	0.018	0.018	0.000	0.000	0.000	0.000
107	A	323	GLU	-1	-0.990	-0.993	48.068	0.021	0.021	0.000	0.000	0.000	0.000
108	A	324	ILE	0	-0.010	0.028	42.454	0.002	0.002	0.000	0.000	0.000	0.000
109	A	325	PHE	0	0.009	-0.008	39.035	0.003	0.003	0.000	0.000	0.000	0.000
110	A	326	ARG	1	0.962	0.996	43.619	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	327	ALA	0	-0.006	0.011	43.825	0.000	0.000	0.000	0.000	0.000	0.000
112	A	328	GLN	0	-0.042	-0.037	38.394	0.001	0.001	0.000	0.000	0.000	0.000
113	A	329	TYR	0	-0.022	-0.033	41.682	0.000	0.000	0.000	0.000	0.000	0.000
114	A	330	GLY	0	-0.008	0.000	44.149	0.002	0.002	0.000	0.000	0.000	0.000
115	A	331	LYS	1	0.841	0.914	40.174	-0.040	-0.040	0.000	0.000	0.000	0.000
116	A	332	ILE	0	-0.023	0.003	34.039	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	333	LEU	0	0.032	0.022	35.016	0.003	0.003	0.000	0.000	0.000	0.000
118	A	334	ASN	0	-0.012	-0.013	30.817	0.002	0.002	0.000	0.000	0.000	0.000
119	A	335	LEU	0	0.032	0.001	29.052	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	336	ARG	1	0.869	0.938	28.241	-0.088	-0.088	0.000	0.000	0.000	0.000
121	A	337	ASP	-1	-0.817	-0.910	31.351	0.067	0.067	0.000	0.000	0.000	0.000
122	A	338	LEU	0	0.008	0.023	34.392	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	339	GLN	0	-0.006	-0.011	30.899	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	340	GLU	-1	-0.852	-0.907	33.114	0.064	0.064	0.000	0.000	0.000	0.000
125	A	341	GLY	0	0.041	0.021	36.074	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	342	ILE	0	0.027	0.003	35.109	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	343	LYS	1	0.796	0.903	32.722	-0.062	-0.062	0.000	0.000	0.000	0.000
128	A	344	GLU	-1	-0.910	-0.949	38.050	0.035	0.035	0.000	0.000	0.000	0.000
129	A	345	LEU	0	0.021	-0.005	41.223	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	346	THR	0	-0.040	-0.028	38.671	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	347	LYS	1	0.803	0.888	41.281	-0.033	-0.033	0.000	0.000	0.000	0.000
132	A	348	ARG	1	0.908	0.946	43.360	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	349	TYR	0	-0.009	-0.043	43.003	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	350	GLN	0	-0.039	-0.017	42.078	0.000	0.000	0.000	0.000	0.000	0.000
135	A	351	ASP	-1	-0.818	-0.896	45.983	0.028	0.028	0.000	0.000	0.000	0.000
136	A	352	GLN	0	-0.043	-0.003	49.058	0.000	0.000	0.000	0.000	0.000	0.000
137	A	353	GLY	0	0.033	0.015	49.739	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	354	TYR	0	-0.005	0.008	46.757	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	355	VAL	0	-0.058	-0.048	44.778	0.001	0.001	0.000	0.000	0.000	0.000
140	A	356	LEU	0	-0.030	-0.015	41.524	0.002	0.002	0.000	0.000	0.000	0.000
141	A	357	ALA	0	-0.002	0.033	41.432	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	358	ASN	0	-0.064	-0.042	36.708	0.005	0.005	0.000	0.000	0.000	0.000
143	A	359	VAL	0	0.009	0.004	35.577	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	360	VAL	0	-0.019	-0.008	36.049	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	361	GLY	0	-0.023	-0.008	32.637	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	362	ALA	0	-0.004	-0.009	30.791	0.005	0.005	0.000	0.000	0.000	0.000
147	A	363	PRO	0	0.008	-0.002	32.647	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	364	GLN	0	-0.005	0.023	34.268	0.001	0.001	0.000	0.000	0.000	0.000
149	A	365	VAL	0	-0.007	-0.019	34.738	0.003	0.003	0.000	0.000	0.000	0.000
150	A	366	SER	0	-0.007	-0.001	37.173	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	367	GLU	-1	-0.899	-0.956	38.143	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	368	ASN	0	-0.058	-0.038	39.955	0.002	0.002	0.000	0.000	0.000	0.000
153	A	369	GLY	0	0.065	0.040	40.644	0.001	0.001	0.000	0.000	0.000	0.000
154	A	370	VAL	0	-0.022	-0.001	41.619	0.002	0.002	0.000	0.000	0.000	0.000
155	A	371	VAL	0	0.028	0.020	37.632	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	372	THR	0	-0.039	-0.026	39.470	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	373	LEU	0	0.015	0.007	37.741	0.000	0.000	0.000	0.000	0.000	0.000
158	A	374	GLN	0	0.016	0.006	38.805	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	375	VAL	0	-0.017	-0.016	39.275	0.002	0.002	0.000	0.000	0.000	0.000
160	A	376	ALA	0	0.030	0.029	40.576	-0.002	-0.002	0.000	0.000	0.000	0.000
161	A	377	GLU	-1	-0.719	-0.821	42.334	0.010	0.010	0.000	0.000	0.000	0.000
162	A	378	GLY	0	0.017	0.008	45.019	0.002	0.002	0.000	0.000	0.000	0.000
163	A	379	VAL	0	-0.016	-0.020	46.509	0.000	0.000	0.000	0.000	0.000	0.000
164	A	380	VAL	0	-0.009	-0.003	49.923	0.001	0.001	0.000	0.000	0.000	0.000
165	A	381	GLU	-1	-0.993	-0.981	52.374	0.001	0.001	0.000	0.000	0.000	0.000

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