FMO DATABASE

FMODB ID: 76VMK

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	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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1164821.755663
FMO2-HF: Nuclear repulsion	1112447.532904
FMO2-HF: Total energy	-52374.222759
FMO2-MP2: Total energy	-52524.270456

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.
-4.906	-2.392	3.664	-2.891	-3.287	0.007

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 : 0.036 / q_NPA : 0.027

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	-0.065	-0.006	3.474	-2.612	0.253	0.005	-1.634	-1.236	0.003
4	A	120	LEU	0	0.031	0.024	6.294	0.263	0.263	0.000	0.000	0.000	0.000
5	A	121	PRO	0	0.045	0.005	9.584	-0.207	-0.207	0.000	0.000	0.000	0.000
6	A	122	ASN	0	-0.027	-0.020	12.796	0.078	0.078	0.000	0.000	0.000	0.000
7	A	123	TRP	0	-0.040	-0.005	9.811	0.080	0.080	0.000	0.000	0.000	0.000
8	A	124	ILE	0	-0.020	-0.011	9.870	-0.146	-0.146	0.000	0.000	0.000	0.000
9	A	125	MET	0	0.013	-0.001	2.448	-2.235	-2.586	3.659	-1.257	-2.051	0.004
10	A	126	HIS	0	-0.012	-0.006	6.835	0.298	0.298	0.000	0.000	0.000	0.000
11	A	127	GLY	0	0.029	0.012	8.159	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	128	LYS	1	0.877	0.931	6.969	0.857	0.857	0.000	0.000	0.000	0.000
13	A	129	SER	0	0.043	0.021	7.111	-0.084	-0.084	0.000	0.000	0.000	0.000
14	A	131	TYR	0	0.013	-0.027	7.747	0.294	0.294	0.000	0.000	0.000	0.000
15	A	132	LEU	0	-0.013	-0.007	11.449	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	133	PHE	0	0.038	0.011	13.980	0.070	0.070	0.000	0.000	0.000	0.000
17	A	134	SER	0	0.017	0.016	17.494	0.014	0.014	0.000	0.000	0.000	0.000
18	A	135	PHE	0	0.000	-0.011	19.081	0.023	0.023	0.000	0.000	0.000	0.000
19	A	136	SER	0	0.001	-0.012	23.015	0.016	0.016	0.000	0.000	0.000	0.000
20	A	137	GLY	0	-0.032	-0.002	25.414	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	138	ASN	0	0.004	-0.007	25.961	0.020	0.020	0.000	0.000	0.000	0.000
22	A	139	SER	0	0.038	0.037	28.219	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	140	TRP	0	0.035	0.021	24.661	0.010	0.010	0.000	0.000	0.000	0.000
24	A	141	TYR	0	0.046	0.001	25.762	0.004	0.004	0.000	0.000	0.000	0.000
25	A	142	GLY	0	-0.056	-0.023	26.394	0.014	0.014	0.000	0.000	0.000	0.000
26	A	143	SER	0	-0.004	-0.018	22.841	0.003	0.003	0.000	0.000	0.000	0.000
27	A	144	LYS	1	0.936	0.955	21.690	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	145	ARG	1	0.893	0.959	21.418	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	146	HIS	0	0.030	0.017	19.837	0.054	0.054	0.000	0.000	0.000	0.000
30	A	147	CYS	0	-0.028	0.005	15.679	0.051	0.051	0.000	0.000	0.000	0.000
31	A	148	SER	0	0.003	0.013	16.842	0.043	0.043	0.000	0.000	0.000	0.000
32	A	149	GLN	0	-0.023	-0.029	18.040	0.046	0.046	0.000	0.000	0.000	0.000
33	A	150	LEU	0	-0.035	0.006	14.596	0.042	0.042	0.000	0.000	0.000	0.000
34	A	151	GLY	0	-0.012	0.001	13.604	0.075	0.075	0.000	0.000	0.000	0.000
35	A	152	ALA	0	-0.074	-0.035	12.971	0.088	0.088	0.000	0.000	0.000	0.000
36	A	153	HIS	1	0.816	0.880	13.200	0.147	0.147	0.000	0.000	0.000	0.000
37	A	154	LEU	0	-0.007	-0.021	16.235	-0.046	-0.046	0.000	0.000	0.000	0.000
38	A	155	LEU	0	-0.047	-0.012	15.222	0.004	0.004	0.000	0.000	0.000	0.000
39	A	156	LYS	1	0.800	0.894	16.006	0.218	0.218	0.000	0.000	0.000	0.000
40	A	157	ILE	0	-0.018	-0.022	16.474	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	158	ASP	-1	-0.774	-0.869	16.598	-0.201	-0.201	0.000	0.000	0.000	0.000
42	A	159	ASN	0	-0.065	-0.028	14.944	0.013	0.013	0.000	0.000	0.000	0.000
43	A	160	SER	0	0.079	0.023	18.691	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	161	LYS	1	0.813	0.891	15.862	0.353	0.353	0.000	0.000	0.000	0.000
45	A	162	GLU	-1	-0.812	-0.882	13.621	-0.527	-0.527	0.000	0.000	0.000	0.000
46	A	163	PHE	0	0.010	-0.006	15.785	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	164	GLU	-1	-0.800	-0.871	18.604	-0.345	-0.345	0.000	0.000	0.000	0.000
48	A	165	PHE	0	-0.009	-0.003	12.323	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	166	ILE	0	-0.004	-0.009	14.893	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	167	GLU	-1	-0.796	-0.861	17.751	-0.239	-0.239	0.000	0.000	0.000	0.000
51	A	168	SER	0	0.025	0.011	18.092	0.017	0.017	0.000	0.000	0.000	0.000
52	A	169	GLN	0	-0.045	0.009	15.894	0.020	0.020	0.000	0.000	0.000	0.000
53	A	170	THR	0	-0.029	-0.022	19.331	0.020	0.020	0.000	0.000	0.000	0.000
54	A	171	SER	0	-0.043	-0.030	22.415	0.025	0.025	0.000	0.000	0.000	0.000
55	A	172	SER	0	-0.046	-0.044	21.228	0.022	0.022	0.000	0.000	0.000	0.000
56	A	173	HIS	1	0.845	0.905	20.798	0.309	0.309	0.000	0.000	0.000	0.000
57	A	174	ARG	1	0.970	0.993	25.165	0.175	0.175	0.000	0.000	0.000	0.000
58	A	175	ILE	0	-0.029	-0.006	27.916	0.013	0.013	0.000	0.000	0.000	0.000
59	A	176	ASN	0	-0.038	-0.018	26.054	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	177	ALA	0	0.024	0.024	26.726	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	178	PHE	0	-0.013	-0.001	21.720	0.004	0.004	0.000	0.000	0.000	0.000
62	A	179	TRP	0	-0.032	-0.027	23.904	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	180	ILE	0	0.031	0.011	20.779	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	181	GLY	0	0.009	0.001	20.559	0.028	0.028	0.000	0.000	0.000	0.000
65	A	182	LEU	0	-0.044	-0.018	21.531	0.011	0.011	0.000	0.000	0.000	0.000
66	A	183	SER	0	-0.054	-0.028	24.648	0.006	0.006	0.000	0.000	0.000	0.000
67	A	184	ARG	1	0.932	0.975	28.061	0.050	0.050	0.000	0.000	0.000	0.000
68	A	185	ASN	0	0.012	-0.003	31.193	0.003	0.003	0.000	0.000	0.000	0.000
69	A	186	GLN	0	0.000	-0.005	33.724	0.002	0.002	0.000	0.000	0.000	0.000
70	A	187	SER	0	0.028	0.005	36.087	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	188	GLU	-1	-0.909	-0.944	38.098	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	189	GLY	0	-0.044	-0.005	35.039	0.000	0.000	0.000	0.000	0.000	0.000
73	A	190	PRO	0	-0.026	-0.019	31.604	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	191	TRP	0	-0.009	-0.021	28.237	0.004	0.004	0.000	0.000	0.000	0.000
75	A	192	PHE	0	-0.032	-0.008	25.622	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	193	TRP	0	0.047	0.013	20.777	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	194	GLU	-1	-0.816	-0.894	19.364	0.008	0.008	0.000	0.000	0.000	0.000
78	A	195	ASP	-1	-0.806	-0.862	18.041	-0.066	-0.066	0.000	0.000	0.000	0.000
79	A	196	GLY	0	-0.017	-0.002	20.028	0.015	0.015	0.000	0.000	0.000	0.000
80	A	197	SER	0	-0.090	-0.065	20.829	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	198	ALA	0	0.026	-0.002	23.142	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	199	PHE	0	-0.021	-0.010	24.450	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	200	PHE	0	0.030	0.005	24.466	0.011	0.011	0.000	0.000	0.000	0.000
84	A	201	PRO	0	-0.014	0.012	25.633	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	202	ASN	0	-0.054	-0.030	21.439	0.000	0.000	0.000	0.000	0.000	0.000
86	A	203	SER	0	-0.013	-0.025	21.786	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	204	PHE	0	0.002	0.004	22.019	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	205	GLN	0	0.009	-0.005	26.283	0.012	0.012	0.000	0.000	0.000	0.000
89	A	206	VAL	0	-0.004	0.004	28.015	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	207	ARG	1	0.873	0.922	30.184	0.122	0.122	0.000	0.000	0.000	0.000
91	A	208	ASN	0	0.038	0.008	32.970	0.000	0.000	0.000	0.000	0.000	0.000
92	A	209	ALA	0	0.001	-0.007	35.605	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	210	VAL	0	-0.026	-0.001	37.310	0.001	0.001	0.000	0.000	0.000	0.000
94	A	211	PRO	0	-0.024	-0.007	39.408	0.002	0.002	0.000	0.000	0.000	0.000
95	A	212	GLN	0	-0.047	-0.026	42.801	0.002	0.002	0.000	0.000	0.000	0.000
96	A	213	GLU	-1	-0.866	-0.935	43.126	-0.040	-0.040	0.000	0.000	0.000	0.000
97	A	214	SER	0	-0.035	-0.052	39.226	0.002	0.002	0.000	0.000	0.000	0.000
98	A	215	LEU	0	0.020	0.011	40.630	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	216	LEU	0	0.018	0.006	37.538	0.002	0.002	0.000	0.000	0.000	0.000
100	A	217	HIS	0	0.019	0.050	35.035	0.003	0.003	0.000	0.000	0.000	0.000
101	A	218	ASN	0	0.020	0.001	33.077	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	219	CYS	0	0.017	0.027	28.351	0.002	0.002	0.000	0.000	0.000	0.000
103	A	220	VAL	0	0.042	0.017	26.296	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	221	TRP	0	0.008	0.012	25.364	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	222	ILE	0	0.033	0.018	21.841	0.004	0.004	0.000	0.000	0.000	0.000
106	A	223	HIS	0	0.009	-0.010	25.319	0.003	0.003	0.000	0.000	0.000	0.000
107	A	224	GLY	0	0.000	-0.012	26.297	0.008	0.008	0.000	0.000	0.000	0.000
108	A	225	SER	0	-0.021	-0.028	24.952	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	226	GLU	-1	-0.847	-0.866	26.752	-0.129	-0.129	0.000	0.000	0.000	0.000
110	A	227	VAL	0	-0.011	-0.002	24.628	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	228	TYR	0	-0.038	-0.038	27.543	0.009	0.009	0.000	0.000	0.000	0.000
112	A	229	ASN	0	-0.006	-0.011	29.543	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	230	GLN	0	-0.023	-0.007	30.944	0.008	0.008	0.000	0.000	0.000	0.000
114	A	231	ILE	0	0.021	0.011	32.631	0.004	0.004	0.000	0.000	0.000	0.000
115	A	233	ASN	0	0.018	-0.010	30.877	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	234	THR	0	-0.025	-0.014	31.967	0.002	0.002	0.000	0.000	0.000	0.000
117	A	235	SER	0	-0.022	-0.015	30.599	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	236	SER	0	-0.010	-0.022	27.407	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	237	TYR	0	-0.006	0.023	23.506	0.004	0.004	0.000	0.000	0.000	0.000
120	A	238	SER	0	0.007	0.002	21.797	0.005	0.005	0.000	0.000	0.000	0.000
121	A	239	ILE	0	0.009	0.009	15.959	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	241	GLU	-1	-0.776	-0.895	11.634	-0.537	-0.537	0.000	0.000	0.000	0.000
123	A	242	LYS	1	0.852	0.928	8.121	-0.385	-0.385	0.000	0.000	0.000	0.000
124	A	243	GLU	-1	-0.811	-0.864	5.654	-0.767	-0.767	0.000	0.000	0.000	0.000

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