FMO DATABASE

FMODB ID: MN19Z

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1164436.789533
FMO2-HF: Nuclear repulsion	1112062.752063
FMO2-HF: Total energy	-52374.03747
FMO2-MP2: Total energy	-52524.105238

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.
-3.946	-0.616	1.902	-2.281	-2.952	0.005

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 : 0.027 / q_NPA : 0.011

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	-0.056	-0.011	3.465	-1.879	0.904	-0.003	-1.435	-1.346	0.002
4	A	120	LEU	0	0.009	0.006	6.136	0.187	0.187	0.000	0.000	0.000	0.000
5	A	121	PRO	0	0.049	0.010	9.404	-0.234	-0.234	0.000	0.000	0.000	0.000
6	A	122	ASN	0	-0.024	-0.017	12.704	0.091	0.091	0.000	0.000	0.000	0.000
7	A	123	TRP	0	-0.041	-0.007	9.931	0.136	0.136	0.000	0.000	0.000	0.000
8	A	124	ILE	0	-0.027	-0.016	10.132	-0.204	-0.204	0.000	0.000	0.000	0.000
9	A	125	MET	0	0.025	0.005	2.406	-2.134	-1.587	1.905	-0.846	-1.606	0.003
10	A	126	HIS	0	-0.024	-0.011	7.108	0.290	0.290	0.000	0.000	0.000	0.000
11	A	127	GLY	0	0.030	0.020	8.301	0.106	0.106	0.000	0.000	0.000	0.000
12	A	128	LYS	1	0.895	0.936	6.394	0.285	0.285	0.000	0.000	0.000	0.000
13	A	129	SER	0	0.042	0.017	7.011	0.279	0.279	0.000	0.000	0.000	0.000
14	A	131	TYR	0	-0.012	-0.049	8.166	0.331	0.331	0.000	0.000	0.000	0.000
15	A	132	LEU	0	-0.011	-0.003	11.892	-0.095	-0.095	0.000	0.000	0.000	0.000
16	A	133	PHE	0	0.013	0.002	14.392	0.067	0.067	0.000	0.000	0.000	0.000
17	A	134	SER	0	-0.011	0.001	17.753	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	135	PHE	0	0.010	-0.015	19.520	0.015	0.015	0.000	0.000	0.000	0.000
19	A	136	SER	0	0.032	0.013	23.514	0.009	0.009	0.000	0.000	0.000	0.000
20	A	137	GLY	0	-0.041	-0.006	25.504	0.000	0.000	0.000	0.000	0.000	0.000
21	A	138	ASN	0	0.000	-0.010	25.567	0.018	0.018	0.000	0.000	0.000	0.000
22	A	139	SER	0	0.043	0.042	28.095	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	140	TRP	0	0.057	0.028	24.832	0.014	0.014	0.000	0.000	0.000	0.000
24	A	141	TYR	0	0.029	-0.005	25.772	0.011	0.011	0.000	0.000	0.000	0.000
25	A	142	GLY	0	-0.051	-0.026	26.086	0.020	0.020	0.000	0.000	0.000	0.000
26	A	143	SER	0	-0.008	-0.017	22.862	0.008	0.008	0.000	0.000	0.000	0.000
27	A	144	LYS	1	0.952	0.967	21.567	-0.160	-0.160	0.000	0.000	0.000	0.000
28	A	145	ARG	1	0.910	0.958	21.199	-0.079	-0.079	0.000	0.000	0.000	0.000
29	A	146	HIS	0	0.011	0.010	19.165	0.063	0.063	0.000	0.000	0.000	0.000
30	A	147	CYS	0	-0.042	-0.006	15.187	0.058	0.058	0.000	0.000	0.000	0.000
31	A	148	SER	0	-0.003	0.017	16.540	0.068	0.068	0.000	0.000	0.000	0.000
32	A	149	GLN	0	-0.016	-0.031	17.504	0.068	0.068	0.000	0.000	0.000	0.000
33	A	150	LEU	0	-0.035	0.013	14.333	0.039	0.039	0.000	0.000	0.000	0.000
34	A	151	GLY	0	-0.018	-0.011	13.183	0.128	0.128	0.000	0.000	0.000	0.000
35	A	152	ALA	0	-0.065	-0.026	12.728	0.156	0.156	0.000	0.000	0.000	0.000
36	A	153	HIS	1	0.808	0.873	13.509	-0.212	-0.212	0.000	0.000	0.000	0.000
37	A	154	LEU	0	-0.016	-0.020	16.109	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	155	LEU	0	-0.040	-0.007	15.592	0.021	0.021	0.000	0.000	0.000	0.000
39	A	156	LYS	1	0.817	0.923	16.275	0.004	0.004	0.000	0.000	0.000	0.000
40	A	157	ILE	0	-0.006	0.003	16.433	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	158	ASP	-1	-0.816	-0.918	16.309	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	159	ASN	0	-0.034	-0.020	15.361	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	160	SER	0	0.090	0.020	18.976	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	161	LYS	1	0.827	0.903	15.817	0.368	0.368	0.000	0.000	0.000	0.000
45	A	162	GLU	-1	-0.797	-0.857	13.967	-0.400	-0.400	0.000	0.000	0.000	0.000
46	A	163	PHE	0	-0.002	-0.017	15.978	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	164	GLU	-1	-0.834	-0.886	18.628	-0.377	-0.377	0.000	0.000	0.000	0.000
48	A	165	PHE	0	0.003	0.005	12.644	-0.033	-0.033	0.000	0.000	0.000	0.000
49	A	166	ILE	0	0.000	-0.006	15.068	0.000	0.000	0.000	0.000	0.000	0.000
50	A	167	GLU	-1	-0.823	-0.882	17.803	-0.247	-0.247	0.000	0.000	0.000	0.000
51	A	168	SER	0	0.015	0.013	18.372	0.015	0.015	0.000	0.000	0.000	0.000
52	A	169	GLN	0	-0.043	-0.011	16.467	0.012	0.012	0.000	0.000	0.000	0.000
53	A	170	THR	0	-0.018	-0.026	19.875	0.024	0.024	0.000	0.000	0.000	0.000
54	A	171	SER	0	-0.032	-0.009	22.615	0.029	0.029	0.000	0.000	0.000	0.000
55	A	172	SER	0	-0.026	-0.011	21.803	0.018	0.018	0.000	0.000	0.000	0.000
56	A	173	HIS	1	0.801	0.882	21.259	0.309	0.309	0.000	0.000	0.000	0.000
57	A	174	ARG	1	1.038	1.018	25.513	0.172	0.172	0.000	0.000	0.000	0.000
58	A	175	ILE	0	-0.015	0.000	28.218	0.013	0.013	0.000	0.000	0.000	0.000
59	A	176	ASN	0	-0.040	-0.018	26.112	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	177	ALA	0	0.025	0.029	26.927	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	178	PHE	0	-0.018	-0.020	21.835	0.000	0.000	0.000	0.000	0.000	0.000
62	A	179	TRP	0	-0.037	-0.026	24.078	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	180	ILE	0	0.034	0.009	21.127	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	181	GLY	0	-0.014	-0.016	20.919	0.023	0.023	0.000	0.000	0.000	0.000
65	A	182	LEU	0	-0.045	-0.006	22.034	0.018	0.018	0.000	0.000	0.000	0.000
66	A	183	SER	0	-0.045	-0.029	24.990	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	184	ARG	1	0.950	0.981	28.332	0.004	0.004	0.000	0.000	0.000	0.000
68	A	185	ASN	0	0.005	-0.005	30.969	0.004	0.004	0.000	0.000	0.000	0.000
69	A	186	GLN	0	0.002	-0.008	33.778	0.000	0.000	0.000	0.000	0.000	0.000
70	A	187	SER	0	0.008	-0.009	36.151	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	188	GLU	-1	-0.897	-0.944	37.946	0.000	0.000	0.000	0.000	0.000	0.000
72	A	189	GLY	0	-0.054	-0.003	35.473	0.000	0.000	0.000	0.000	0.000	0.000
73	A	190	PRO	0	-0.014	-0.018	31.530	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	191	TRP	0	-0.029	-0.028	28.299	0.008	0.008	0.000	0.000	0.000	0.000
75	A	192	PHE	0	-0.037	-0.008	25.899	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	193	TRP	0	0.048	0.020	20.945	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	194	GLU	-1	-0.788	-0.891	19.956	0.179	0.179	0.000	0.000	0.000	0.000
78	A	195	ASP	-1	-0.828	-0.880	18.394	0.139	0.139	0.000	0.000	0.000	0.000
79	A	196	GLY	0	-0.023	-0.008	20.448	0.013	0.013	0.000	0.000	0.000	0.000
80	A	197	SER	0	-0.100	-0.068	21.227	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	198	ALA	0	0.025	-0.001	23.565	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	199	PHE	0	-0.015	-0.003	24.913	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	200	PHE	0	0.028	0.004	25.092	0.004	0.004	0.000	0.000	0.000	0.000
84	A	201	PRO	0	-0.008	0.016	25.865	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	202	ASN	0	-0.040	-0.028	21.865	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	203	SER	0	-0.031	-0.018	21.962	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	204	PHE	0	-0.001	-0.006	22.431	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	205	GLN	0	0.019	0.006	26.601	0.013	0.013	0.000	0.000	0.000	0.000
89	A	206	VAL	0	-0.009	-0.001	28.411	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	207	ARG	1	0.855	0.912	30.563	0.097	0.097	0.000	0.000	0.000	0.000
91	A	208	ASN	0	0.051	0.017	33.355	0.002	0.002	0.000	0.000	0.000	0.000
92	A	209	ALA	0	-0.007	-0.010	36.154	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	210	VAL	0	-0.016	-0.013	37.484	0.000	0.000	0.000	0.000	0.000	0.000
94	A	211	PRO	0	-0.029	-0.007	39.680	0.001	0.001	0.000	0.000	0.000	0.000
95	A	212	GLN	0	-0.039	-0.016	43.130	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	213	GLU	-1	-0.889	-0.942	43.534	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	214	SER	0	-0.015	-0.037	39.744	0.003	0.003	0.000	0.000	0.000	0.000
98	A	215	LEU	0	0.012	0.008	40.937	0.000	0.000	0.000	0.000	0.000	0.000
99	A	216	LEU	0	0.016	0.000	37.809	0.005	0.005	0.000	0.000	0.000	0.000
100	A	217	HIS	0	0.013	0.044	35.417	0.007	0.007	0.000	0.000	0.000	0.000
101	A	218	ASN	0	0.039	0.011	33.283	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	219	CYS	0	0.019	0.032	28.614	0.008	0.008	0.000	0.000	0.000	0.000
103	A	220	VAL	0	0.057	0.027	26.524	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	221	TRP	0	0.012	0.016	25.684	0.005	0.005	0.000	0.000	0.000	0.000
105	A	222	ILE	0	0.017	0.012	22.107	0.001	0.001	0.000	0.000	0.000	0.000
106	A	223	HIS	0	-0.039	-0.032	25.593	0.001	0.001	0.000	0.000	0.000	0.000
107	A	224	GLY	0	0.015	0.004	26.843	0.005	0.005	0.000	0.000	0.000	0.000
108	A	225	SER	0	-0.016	-0.038	25.411	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	226	GLU	-1	-0.843	-0.873	26.781	-0.108	-0.108	0.000	0.000	0.000	0.000
110	A	227	VAL	0	0.002	0.005	25.176	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	228	TYR	0	-0.046	-0.040	27.991	0.007	0.007	0.000	0.000	0.000	0.000
112	A	229	ASN	0	-0.016	-0.007	29.977	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	230	GLN	0	-0.005	-0.001	31.486	0.004	0.004	0.000	0.000	0.000	0.000
114	A	231	ILE	0	-0.001	-0.002	33.033	0.008	0.008	0.000	0.000	0.000	0.000
115	A	233	ASN	0	-0.002	-0.015	31.009	0.000	0.000	0.000	0.000	0.000	0.000
116	A	234	THR	0	-0.022	-0.007	32.384	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	235	SER	0	-0.021	-0.020	30.584	0.001	0.001	0.000	0.000	0.000	0.000
118	A	236	SER	0	-0.011	-0.014	27.296	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	237	TYR	0	-0.003	0.022	23.743	0.006	0.006	0.000	0.000	0.000	0.000
120	A	238	SER	0	0.014	0.002	21.539	0.015	0.015	0.000	0.000	0.000	0.000
121	A	239	ILE	0	0.012	0.014	16.285	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	241	GLU	-1	-0.743	-0.880	11.820	-0.290	-0.290	0.000	0.000	0.000	0.000
123	A	242	LYS	1	0.866	0.928	8.052	-0.980	-0.980	0.000	0.000	0.000	0.000
124	A	243	GLU	-1	-0.829	-0.871	5.966	-0.092	-0.092	0.000	0.000	0.000	0.000

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