FMO DATABASE

FMODB ID: 3JQ1L

Calculation Name: 2A4C-A-Xray372

Preferred Name: Cadherin-11

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A4C

Chain ID: A

ChEMBL ID: CHEMBL2163173

UniProt ID: P55288

Base Structure: X-ray

Registration Date: 2023-09-21

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-690249.438272
FMO2-HF: Nuclear repulsion	651880.421338
FMO2-HF: Total energy	-38369.016934
FMO2-MP2: Total energy	-38482.773769

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-8.687	-3.44	1.258	-3.023	-3.481	0.016

Interaction energy analysis for fragmet #1(A:0:SER)

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 : 0.013

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	2	TRP	0	-0.016	-0.002	2.438	-6.830	-1.628	1.259	-3.013	-3.447	0.016
4	A	3	VAL	0	0.023	0.019	5.098	-0.799	-0.754	-0.001	-0.010	-0.034	0.000
5	A	4	TRP	0	0.033	-0.002	5.498	0.139	0.139	0.000	0.000	0.000	0.000
6	A	5	ASN	0	-0.044	-0.011	9.628	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.023	-0.032	11.548	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	7	PHE	0	0.009	0.014	14.708	0.063	0.063	0.000	0.000	0.000	0.000
9	A	8	PHE	0	-0.028	-0.018	18.033	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.021	0.014	21.145	0.011	0.011	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.009	0.009	24.067	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.734	-0.833	26.999	-0.063	-0.063	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.883	-0.923	30.145	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.098	-0.062	28.167	0.006	0.006	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.063	-0.016	29.298	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.056	0.022	32.057	0.002	0.002	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.056	-0.022	34.707	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.922	-0.963	35.618	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	18	PRO	0	-0.040	-0.028	31.647	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.001	0.014	27.534	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.031	-0.012	24.031	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.027	-0.016	21.235	0.005	0.005	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.031	0.008	19.698	0.001	0.001	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.831	0.935	18.912	0.036	0.036	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.027	0.002	17.216	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	25	HIS	0	-0.045	-0.054	16.357	0.049	0.049	0.000	0.000	0.000	0.000
27	A	26	SER	0	0.013	-0.022	15.218	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.932	-0.964	13.969	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.014	-0.004	16.601	0.037	0.037	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.847	-0.892	19.314	-0.062	-0.062	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.013	-0.007	21.435	0.022	0.022	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.005	-0.002	24.289	0.014	0.014	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.850	-0.919	25.909	-0.052	-0.052	0.000	0.000	0.000	0.000
34	A	33	GLY	0	-0.023	-0.012	26.977	0.002	0.002	0.000	0.000	0.000	0.000
35	A	34	ASN	0	-0.042	-0.038	27.679	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.021	0.030	20.029	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.774	0.877	24.347	0.133	0.133	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.042	-0.038	18.944	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.008	-0.020	22.100	0.017	0.017	0.000	0.000	0.000	0.000
40	A	39	LEU	0	-0.012	0.009	21.324	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.043	-0.039	22.243	0.015	0.015	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.053	0.025	22.450	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.780	-0.868	23.518	-0.227	-0.227	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.061	0.025	25.102	0.002	0.002	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.000	0.009	24.851	0.013	0.013	0.000	0.000	0.000	0.000
46	A	45	GLY	0	-0.035	-0.012	26.717	0.006	0.006	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.046	-0.025	29.625	0.010	0.010	0.000	0.000	0.000	0.000
48	A	47	ILE	0	0.002	0.034	28.233	0.010	0.010	0.000	0.000	0.000	0.000
49	A	48	PHE	0	0.016	0.009	25.094	0.006	0.006	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.012	-0.007	27.222	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.004	-0.008	22.377	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.800	-0.849	26.577	-0.066	-0.066	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.810	-0.892	25.920	-0.104	-0.104	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.881	0.936	25.863	0.039	0.039	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.065	-0.062	24.964	0.005	0.005	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.049	0.023	21.922	0.003	0.003	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.068	-0.046	22.099	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.005	-0.004	19.749	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	58	HIS	0	0.023	0.000	24.177	0.015	0.015	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.022	0.009	27.030	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	60	THR	0	-0.066	-0.062	28.410	0.011	0.011	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.792	0.895	31.610	0.096	0.096	0.000	0.000	0.000	0.000
63	A	62	THR	0	0.020	0.003	31.947	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.092	-0.055	27.528	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.822	-0.905	31.229	-0.067	-0.067	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.782	0.855	24.160	0.078	0.078	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.944	-0.961	29.234	-0.091	-0.091	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.900	-0.938	31.646	-0.099	-0.099	0.000	0.000	0.000	0.000
69	A	68	ARG	1	0.724	0.804	24.958	0.192	0.192	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.061	0.046	25.036	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.020	-0.003	18.746	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	71	TYR	0	0.040	0.032	22.191	0.008	0.008	0.000	0.000	0.000	0.000
73	A	72	THR	0	-0.002	-0.008	18.037	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.040	-0.014	18.982	0.032	0.032	0.000	0.000	0.000	0.000
75	A	74	MET	0	-0.008	0.013	16.323	-0.068	-0.068	0.000	0.000	0.000	0.000
76	A	75	ALA	0	0.030	0.011	15.909	0.064	0.064	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.010	-0.016	17.660	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	77	ALA	0	0.053	0.031	19.289	0.028	0.028	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.036	-0.012	20.831	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.741	-0.861	23.935	-0.092	-0.092	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.755	0.859	26.544	0.088	0.088	0.000	0.000	0.000	0.000
82	A	81	ASP	-1	-0.914	-0.952	29.420	-0.076	-0.076	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.014	-0.030	29.446	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.067	-0.024	28.384	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.905	0.957	26.133	0.111	0.111	0.000	0.000	0.000	0.000
86	A	85	PRO	0	0.012	-0.009	21.390	0.006	0.006	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.030	-0.012	20.838	0.013	0.013	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.807	-0.860	14.936	-0.393	-0.393	0.000	0.000	0.000	0.000
89	A	88	PRO	0	-0.085	-0.029	13.470	0.030	0.030	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.020	-0.024	15.607	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	90	SER	0	0.009	0.007	12.151	-0.145	-0.145	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.931	-0.972	13.889	-0.578	-0.578	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.039	-0.018	13.160	-0.108	-0.108	0.000	0.000	0.000	0.000
94	A	93	ILE	0	-0.017	0.000	14.377	0.051	0.051	0.000	0.000	0.000	0.000
95	A	94	VAL	0	0.005	0.003	17.406	0.024	0.024	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.873	0.934	16.230	0.307	0.307	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.021	0.017	21.793	0.019	0.019	0.000	0.000	0.000	0.000
98	A	97	GLN	0	-0.067	-0.023	22.541	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.870	-0.966	25.231	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)