FMO DATABASE

FMODB ID: 98VM2

Calculation Name: 2BPD-A-Xray372

Preferred Name: C-type lectin domain family 7 member A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2BPD

Chain ID: A

ChEMBL ID: CHEMBL2034809

UniProt ID: Q6QLQ4

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1164508.259095
FMO2-HF: Nuclear repulsion	1112134.914386
FMO2-HF: Total energy	-52373.344708
FMO2-MP2: Total energy	-52523.449054

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:117:GLN)

Summations of interaction energy for fragment #1(A:117:GLN)

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	0.666	1.729	-1.801	-2.594	-0.006

Interaction energy analysis for fragmet #1(A:117:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.007

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	119	CYS	0	-0.050	-0.009	3.660	0.110	2.062	-0.015	-0.869	-1.068	-0.001
4	A	120	LEU	0	0.002	0.001	6.281	-0.111	-0.111	0.000	0.000	0.000	0.000
5	A	121	PRO	0	0.043	0.009	9.619	-0.229	-0.229	0.000	0.000	0.000	0.000
6	A	122	ASN	0	-0.010	-0.010	12.910	0.087	0.087	0.000	0.000	0.000	0.000
7	A	123	TRP	0	-0.042	-0.006	10.006	0.170	0.170	0.000	0.000	0.000	0.000
8	A	124	ILE	0	-0.017	-0.010	9.765	-0.266	-0.266	0.000	0.000	0.000	0.000
9	A	125	MET	0	0.021	0.000	2.763	-2.824	-2.110	1.744	-0.932	-1.526	-0.005
10	A	126	HIS	0	-0.013	-0.004	6.857	-0.055	-0.055	0.000	0.000	0.000	0.000
11	A	127	GLY	0	0.024	0.017	8.353	0.319	0.319	0.000	0.000	0.000	0.000
12	A	128	LYS	1	0.892	0.936	6.573	-0.295	-0.295	0.000	0.000	0.000	0.000
13	A	129	SER	0	0.040	0.024	7.046	0.847	0.847	0.000	0.000	0.000	0.000
14	A	131	TYR	0	-0.006	-0.022	8.198	0.244	0.244	0.000	0.000	0.000	0.000
15	A	132	LEU	0	-0.019	-0.013	12.057	-0.153	-0.153	0.000	0.000	0.000	0.000
16	A	133	PHE	0	0.005	0.002	14.287	0.051	0.051	0.000	0.000	0.000	0.000
17	A	134	SER	0	-0.015	-0.003	17.733	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	135	PHE	0	0.009	-0.016	19.533	0.004	0.004	0.000	0.000	0.000	0.000
19	A	136	SER	0	0.008	0.005	23.450	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	137	GLY	0	-0.010	0.005	25.482	0.010	0.010	0.000	0.000	0.000	0.000
21	A	138	ASN	0	0.006	-0.003	25.418	0.007	0.007	0.000	0.000	0.000	0.000
22	A	139	SER	0	0.029	0.033	28.065	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	140	TRP	0	0.064	0.019	24.659	0.018	0.018	0.000	0.000	0.000	0.000
24	A	141	TYR	0	0.022	-0.007	25.685	0.027	0.027	0.000	0.000	0.000	0.000
25	A	142	GLY	0	-0.060	-0.037	26.043	0.031	0.031	0.000	0.000	0.000	0.000
26	A	143	SER	0	0.005	0.000	22.810	0.018	0.018	0.000	0.000	0.000	0.000
27	A	144	LYS	1	1.009	1.012	21.524	-0.401	-0.401	0.000	0.000	0.000	0.000
28	A	145	ARG	1	0.899	0.953	21.161	-0.227	-0.227	0.000	0.000	0.000	0.000
29	A	146	HIS	0	0.006	0.006	19.194	0.067	0.067	0.000	0.000	0.000	0.000
30	A	147	CYS	0	-0.032	-0.001	15.083	0.049	0.049	0.000	0.000	0.000	0.000
31	A	148	SER	0	0.014	0.019	16.551	0.140	0.140	0.000	0.000	0.000	0.000
32	A	149	GLN	0	-0.031	-0.031	17.554	0.077	0.077	0.000	0.000	0.000	0.000
33	A	150	LEU	0	-0.055	0.001	14.343	0.020	0.020	0.000	0.000	0.000	0.000
34	A	151	GLY	0	-0.057	-0.038	13.272	0.194	0.194	0.000	0.000	0.000	0.000
35	A	152	ALA	0	-0.079	-0.028	12.688	0.281	0.281	0.000	0.000	0.000	0.000
36	A	153	HIS	1	0.795	0.866	13.006	-1.048	-1.048	0.000	0.000	0.000	0.000
37	A	154	LEU	0	-0.026	-0.023	15.978	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	155	LEU	0	-0.044	-0.009	15.732	0.047	0.047	0.000	0.000	0.000	0.000
39	A	156	LYS	1	0.836	0.924	16.295	-0.530	-0.530	0.000	0.000	0.000	0.000
40	A	157	ILE	0	0.021	0.026	16.508	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	158	ASP	-1	-0.903	-0.948	16.184	0.408	0.408	0.000	0.000	0.000	0.000
42	A	159	ASN	0	-0.035	-0.035	15.556	-0.093	-0.093	0.000	0.000	0.000	0.000
43	A	160	SER	0	0.065	0.011	19.237	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	161	LYS	1	0.927	0.970	15.873	0.259	0.259	0.000	0.000	0.000	0.000
45	A	162	GLU	-1	-0.784	-0.877	13.995	0.165	0.165	0.000	0.000	0.000	0.000
46	A	163	PHE	0	-0.009	-0.017	16.145	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	164	GLU	-1	-0.938	-0.957	18.672	-0.307	-0.307	0.000	0.000	0.000	0.000
48	A	165	PHE	0	0.002	0.008	12.557	-0.041	-0.041	0.000	0.000	0.000	0.000
49	A	166	ILE	0	-0.005	-0.005	15.321	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	167	GLU	-1	-0.833	-0.874	17.773	-0.167	-0.167	0.000	0.000	0.000	0.000
51	A	168	SER	0	0.046	0.023	18.285	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	169	GLN	0	-0.041	-0.008	16.287	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	170	THR	0	-0.008	-0.018	19.616	0.013	0.013	0.000	0.000	0.000	0.000
54	A	171	SER	0	-0.033	-0.023	22.477	0.013	0.013	0.000	0.000	0.000	0.000
55	A	172	SER	0	-0.073	-0.036	21.807	0.002	0.002	0.000	0.000	0.000	0.000
56	A	173	HIS	1	0.834	0.902	20.516	0.181	0.181	0.000	0.000	0.000	0.000
57	A	174	ARG	1	1.036	1.018	25.256	0.105	0.105	0.000	0.000	0.000	0.000
58	A	175	ILE	0	-0.017	-0.004	28.024	0.011	0.011	0.000	0.000	0.000	0.000
59	A	176	ASN	0	-0.035	-0.014	25.992	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	177	ALA	0	0.029	0.028	26.951	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	178	PHE	0	-0.021	-0.017	21.908	0.003	0.003	0.000	0.000	0.000	0.000
62	A	179	TRP	0	-0.037	-0.030	23.937	0.005	0.005	0.000	0.000	0.000	0.000
63	A	180	ILE	0	0.037	0.013	21.030	0.012	0.012	0.000	0.000	0.000	0.000
64	A	181	GLY	0	-0.012	-0.013	20.787	0.001	0.001	0.000	0.000	0.000	0.000
65	A	182	LEU	0	-0.040	-0.003	21.851	0.020	0.020	0.000	0.000	0.000	0.000
66	A	183	SER	0	-0.053	-0.034	24.938	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	184	ARG	1	0.975	0.986	28.197	-0.119	-0.119	0.000	0.000	0.000	0.000
68	A	185	ASN	0	0.011	-0.006	30.829	0.004	0.004	0.000	0.000	0.000	0.000
69	A	186	GLN	0	0.002	-0.011	33.536	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	187	SER	0	-0.010	-0.011	36.068	0.002	0.002	0.000	0.000	0.000	0.000
71	A	188	GLU	-1	-0.893	-0.941	37.959	0.093	0.093	0.000	0.000	0.000	0.000
72	A	189	GLY	0	-0.052	0.001	35.351	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	190	PRO	0	-0.022	-0.023	31.531	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	191	TRP	0	-0.034	-0.025	28.303	0.014	0.014	0.000	0.000	0.000	0.000
75	A	192	PHE	0	-0.041	-0.012	25.505	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	193	TRP	0	0.038	0.015	20.939	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	194	GLU	-1	-0.831	-0.934	19.846	0.531	0.531	0.000	0.000	0.000	0.000
78	A	195	ASP	-1	-0.837	-0.908	17.992	0.593	0.593	0.000	0.000	0.000	0.000
79	A	196	GLY	0	-0.021	-0.010	20.120	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	197	SER	0	-0.088	-0.032	21.282	-0.055	-0.055	0.000	0.000	0.000	0.000
81	A	198	ALA	0	0.055	0.012	23.339	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	199	PHE	0	-0.007	-0.002	24.986	0.005	0.005	0.000	0.000	0.000	0.000
83	A	200	PHE	0	0.001	-0.006	25.516	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	201	PRO	0	-0.003	0.021	25.863	0.000	0.000	0.000	0.000	0.000	0.000
85	A	202	ASN	0	-0.025	-0.022	22.787	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	203	SER	0	-0.021	-0.014	22.120	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	204	PHE	0	0.022	0.009	22.564	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	205	GLN	0	0.012	0.000	26.856	0.012	0.012	0.000	0.000	0.000	0.000
89	A	206	VAL	0	-0.008	0.003	28.561	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	207	ARG	1	0.957	0.979	30.768	0.003	0.003	0.000	0.000	0.000	0.000
91	A	208	ASN	0	0.031	0.014	33.607	0.006	0.006	0.000	0.000	0.000	0.000
92	A	209	ALA	0	-0.006	-0.009	36.413	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	210	VAL	0	-0.025	-0.018	37.578	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	211	PRO	0	-0.023	-0.002	39.872	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	212	GLN	0	-0.031	-0.017	43.224	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	213	GLU	-1	-0.897	-0.943	43.501	0.065	0.065	0.000	0.000	0.000	0.000
97	A	214	SER	0	-0.022	-0.048	39.511	0.004	0.004	0.000	0.000	0.000	0.000
98	A	215	LEU	0	0.014	0.011	40.814	0.001	0.001	0.000	0.000	0.000	0.000
99	A	216	LEU	0	0.020	-0.005	37.615	0.011	0.011	0.000	0.000	0.000	0.000
100	A	217	HIS	0	0.015	0.049	35.224	0.013	0.013	0.000	0.000	0.000	0.000
101	A	218	ASN	0	0.037	0.012	33.107	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	219	CYS	0	0.020	0.030	28.504	0.021	0.021	0.000	0.000	0.000	0.000
103	A	220	VAL	0	0.056	0.027	26.347	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	221	TRP	0	0.031	0.020	25.773	0.021	0.021	0.000	0.000	0.000	0.000
105	A	222	ILE	0	0.008	0.013	22.282	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	223	HIS	0	-0.063	-0.045	25.733	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	224	GLY	0	0.011	0.002	26.775	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	225	SER	0	-0.030	-0.059	25.335	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	226	GLU	-1	-0.957	-0.969	26.724	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	227	VAL	0	0.016	0.010	25.490	0.006	0.006	0.000	0.000	0.000	0.000
111	A	228	TYR	0	-0.010	0.002	28.188	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	229	ASN	0	-0.006	0.005	30.130	0.007	0.007	0.000	0.000	0.000	0.000
113	A	230	GLN	0	-0.013	-0.003	31.428	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	231	ILE	0	-0.013	-0.011	32.851	0.016	0.016	0.000	0.000	0.000	0.000
115	A	233	ASN	0	-0.017	-0.021	30.902	0.008	0.008	0.000	0.000	0.000	0.000
116	A	234	THR	0	-0.015	-0.001	32.271	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	235	SER	0	-0.029	-0.022	30.516	0.014	0.014	0.000	0.000	0.000	0.000
118	A	236	SER	0	0.001	-0.008	27.226	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	237	TYR	0	-0.007	0.020	23.738	0.007	0.007	0.000	0.000	0.000	0.000
120	A	238	SER	0	0.001	-0.002	21.497	0.025	0.025	0.000	0.000	0.000	0.000
121	A	239	ILE	0	0.029	0.022	16.367	-0.036	-0.036	0.000	0.000	0.000	0.000
122	A	241	GLU	-1	-0.718	-0.872	11.667	0.456	0.456	0.000	0.000	0.000	0.000
123	A	242	LYS	1	0.947	0.972	7.881	-2.142	-2.142	0.000	0.000	0.000	0.000
124	A	243	GLU	-1	-0.813	-0.862	5.554	1.598	1.598	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:117:GLN)