FMO DATABASE

FMODB ID: G7L11

Calculation Name: 3FF7-C-Xray547

Preferred Name: Cadherin-1

Target Type: SINGLE PROTEIN

Ligand Name: acetic acid

Ligand 3-letter code: ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FF7

Chain ID: C

ChEMBL ID: CHEMBL2321609

UniProt ID: P12830

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-962453.546609
FMO2-HF: Nuclear repulsion	915688.383198
FMO2-HF: Total energy	-46765.163411
FMO2-MP2: Total energy	-46897.326692

3D Structure Molmil

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(C:75:CYS)

Summations of interaction energy for fragment #1(C:75:CYS)

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.
-126.384	-114.591	28.084	-15.833	-24.042	-0.052

Interaction energy analysis for fragmet #1(C:75:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.703 / q_NPA : 0.846

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	C	77	ASP	-1	-0.848	-0.931	3.466	-44.481	-42.873	0.051	-0.746	-0.914	-0.001
5	C	79	TRP	0	-0.038	0.004	2.130	-0.177	1.654	2.648	-1.364	-3.114	-0.012
6	C	80	MET	0	-0.030	0.011	2.964	-8.322	-6.351	0.211	-0.929	-1.252	-0.008
7	C	81	LYS	1	0.927	0.944	2.408	18.366	24.061	7.358	-5.619	-7.433	-0.001
8	C	82	TYR	0	0.037	0.015	2.078	-8.511	-8.868	3.749	-0.777	-2.615	0.034
9	C	83	GLY	0	0.042	0.029	3.169	-1.989	-1.457	0.405	-0.040	-0.897	0.000
10	C	84	ASN	0	-0.077	-0.052	3.883	2.719	4.568	-0.022	-0.944	-0.883	-0.002
13	C	88	TYR	0	-0.007	0.016	3.849	-1.920	0.361	-0.023	-1.150	-1.107	0.003
108	C	185	LYS	1	0.854	0.903	4.400	26.197	26.376	-0.002	-0.035	-0.142	0.000
109	C	186	LYS	0	0.019	0.023	1.765	-30.779	-34.575	13.709	-4.229	-5.685	-0.065
4	C	78	ARG	1	0.909	0.938	5.996	27.647	27.647	0.000	0.000	0.000	0.000
14	C	89	PHE	0	0.040	0.007	6.511	1.793	1.793	0.000	0.000	0.000	0.000
15	C	90	SER	0	-0.036	-0.011	10.092	-0.438	-0.438	0.000	0.000	0.000	0.000
16	C	91	VAL	0	-0.008	-0.011	12.919	0.410	0.410	0.000	0.000	0.000	0.000
17	C	92	GLU	-1	-0.887	-0.946	15.621	-16.566	-16.566	0.000	0.000	0.000	0.000
18	C	93	GLU	-1	-0.900	-0.944	17.152	-13.857	-13.857	0.000	0.000	0.000	0.000
19	C	94	LYS	1	0.826	0.915	16.297	16.538	16.538	0.000	0.000	0.000	0.000
20	C	95	ASP	-1	-0.780	-0.845	19.877	-13.007	-13.007	0.000	0.000	0.000	0.000
21	C	96	TRP	0	0.016	0.000	17.506	-0.680	-0.680	0.000	0.000	0.000	0.000
22	C	97	ASN	0	-0.004	-0.010	18.384	-0.879	-0.879	0.000	0.000	0.000	0.000
23	C	98	SER	0	0.029	-0.011	18.563	-0.585	-0.585	0.000	0.000	0.000	0.000
24	C	99	SER	0	-0.073	-0.052	15.282	-1.032	-1.032	0.000	0.000	0.000	0.000
25	C	100	LEU	0	-0.008	-0.005	14.067	-1.573	-1.573	0.000	0.000	0.000	0.000
26	C	101	GLU	-1	-0.925	-0.965	14.081	-15.501	-15.501	0.000	0.000	0.000	0.000
27	C	102	PHE	0	-0.028	-0.017	10.051	-0.722	-0.722	0.000	0.000	0.000	0.000
28	C	103	CYS	0	-0.089	-0.007	7.139	0.211	0.211	0.000	0.000	0.000	0.000
29	C	104	LEU	0	0.065	0.051	10.025	-1.687	-1.687	0.000	0.000	0.000	0.000
30	C	105	ALA	0	-0.055	-0.022	12.365	-0.343	-0.343	0.000	0.000	0.000	0.000
31	C	106	ARG	1	0.817	0.903	8.452	23.356	23.356	0.000	0.000	0.000	0.000
32	C	107	ASP	-1	-0.882	-0.916	7.640	-33.328	-33.328	0.000	0.000	0.000	0.000
33	C	108	SER	0	-0.053	-0.037	6.106	-3.625	-3.625	0.000	0.000	0.000	0.000
34	C	109	HIS	0	0.069	0.025	7.607	3.552	3.552	0.000	0.000	0.000	0.000
35	C	110	LEU	0	0.008	-0.001	8.871	-2.076	-2.076	0.000	0.000	0.000	0.000
36	C	111	LEU	0	-0.037	-0.024	8.135	0.323	0.323	0.000	0.000	0.000	0.000
37	C	112	VAL	0	0.027	0.021	9.544	1.825	1.825	0.000	0.000	0.000	0.000
38	C	113	ILE	0	-0.055	-0.029	9.742	-1.690	-1.690	0.000	0.000	0.000	0.000
39	C	114	THR	0	-0.035	-0.042	9.499	0.978	0.978	0.000	0.000	0.000	0.000
40	C	115	ASP	-1	-0.799	-0.889	11.907	-16.309	-16.309	0.000	0.000	0.000	0.000
41	C	116	ASN	0	0.048	0.000	13.544	-0.183	-0.183	0.000	0.000	0.000	0.000
42	C	117	GLN	0	-0.022	0.003	12.904	0.162	0.162	0.000	0.000	0.000	0.000
43	C	118	GLU	-1	-0.729	-0.805	7.459	-25.799	-25.799	0.000	0.000	0.000	0.000
44	C	119	MET	0	-0.045	-0.005	10.605	-0.276	-0.276	0.000	0.000	0.000	0.000
45	C	120	SER	0	-0.026	-0.033	13.601	0.173	0.173	0.000	0.000	0.000	0.000
46	C	121	LEU	0	-0.051	-0.009	7.747	0.086	0.086	0.000	0.000	0.000	0.000
47	C	122	LEU	0	0.014	-0.014	7.069	-0.303	-0.303	0.000	0.000	0.000	0.000
48	C	123	GLN	0	-0.013	-0.017	10.883	-0.032	-0.032	0.000	0.000	0.000	0.000
49	C	124	VAL	0	-0.048	-0.016	12.529	0.562	0.562	0.000	0.000	0.000	0.000
50	C	125	PHE	0	-0.036	-0.018	9.356	-0.249	-0.249	0.000	0.000	0.000	0.000
51	C	126	LEU	0	-0.031	0.011	12.889	-0.230	-0.230	0.000	0.000	0.000	0.000
52	C	127	SER	0	0.029	0.007	15.632	0.741	0.741	0.000	0.000	0.000	0.000
53	C	128	GLU	-1	-0.871	-0.942	19.326	-11.098	-11.098	0.000	0.000	0.000	0.000
54	C	129	ALA	0	0.011	0.018	20.001	0.309	0.309	0.000	0.000	0.000	0.000
55	C	130	PHE	0	-0.025	-0.013	19.165	-0.502	-0.502	0.000	0.000	0.000	0.000
56	C	131	SER	0	0.011	0.003	14.601	-0.358	-0.358	0.000	0.000	0.000	0.000
57	C	132	TRP	0	-0.028	-0.026	16.448	0.021	0.021	0.000	0.000	0.000	0.000
58	C	133	ILE	0	-0.005	-0.010	13.384	-1.282	-1.282	0.000	0.000	0.000	0.000
59	C	134	GLY	0	0.023	0.031	13.278	0.927	0.927	0.000	0.000	0.000	0.000
60	C	135	LEU	0	-0.033	-0.021	14.579	0.350	0.350	0.000	0.000	0.000	0.000
61	C	136	ARG	1	0.862	0.886	17.801	13.546	13.546	0.000	0.000	0.000	0.000
62	C	137	ASN	0	-0.021	-0.007	21.458	0.075	0.075	0.000	0.000	0.000	0.000
63	C	138	ASN	0	0.001	0.013	23.913	0.507	0.507	0.000	0.000	0.000	0.000
64	C	139	SER	0	-0.016	-0.005	25.689	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	140	GLY	0	0.053	0.036	26.864	-0.077	-0.077	0.000	0.000	0.000	0.000
66	C	141	TRP	0	-0.010	-0.016	21.955	-0.284	-0.284	0.000	0.000	0.000	0.000
67	C	142	ARG	1	0.814	0.892	20.435	11.611	11.611	0.000	0.000	0.000	0.000
68	C	143	TRP	0	0.062	0.024	14.301	-0.375	-0.375	0.000	0.000	0.000	0.000
69	C	144	GLU	-1	-0.801	-0.875	15.126	-13.658	-13.658	0.000	0.000	0.000	0.000
70	C	145	ASP	-1	-0.868	-0.925	14.162	-16.530	-16.530	0.000	0.000	0.000	0.000
71	C	146	GLY	0	-0.002	0.001	16.223	0.563	0.563	0.000	0.000	0.000	0.000
72	C	147	SER	0	-0.026	-0.002	17.212	0.939	0.939	0.000	0.000	0.000	0.000
73	C	148	PRO	0	-0.041	-0.025	19.250	-0.179	-0.179	0.000	0.000	0.000	0.000
74	C	149	LEU	0	-0.003	-0.008	18.592	-0.426	-0.426	0.000	0.000	0.000	0.000
75	C	150	ASN	0	-0.037	-0.022	17.986	0.348	0.348	0.000	0.000	0.000	0.000
76	C	151	PHE	0	0.005	0.003	14.757	0.459	0.459	0.000	0.000	0.000	0.000
77	C	152	SER	0	0.044	0.015	18.973	0.036	0.036	0.000	0.000	0.000	0.000
78	C	153	ARG	1	0.913	0.944	20.969	10.439	10.439	0.000	0.000	0.000	0.000
79	C	154	ILE	0	0.012	0.035	21.246	-0.218	-0.218	0.000	0.000	0.000	0.000
80	C	155	SER	0	-0.048	-0.020	23.932	0.373	0.373	0.000	0.000	0.000	0.000
81	C	156	SER	0	0.020	-0.014	26.240	-0.218	-0.218	0.000	0.000	0.000	0.000
82	C	157	ASN	0	0.006	0.006	28.865	0.024	0.024	0.000	0.000	0.000	0.000
83	C	158	SER	0	-0.025	-0.025	31.142	0.371	0.371	0.000	0.000	0.000	0.000
84	C	159	PHE	0	0.020	0.012	31.049	-0.270	-0.270	0.000	0.000	0.000	0.000
85	C	160	VAL	0	0.028	0.020	31.176	-0.114	-0.114	0.000	0.000	0.000	0.000
86	C	161	GLN	0	0.005	0.022	26.972	-0.195	-0.195	0.000	0.000	0.000	0.000
87	C	162	THR	0	0.020	0.001	25.992	-0.104	-0.104	0.000	0.000	0.000	0.000
88	C	163	CYS	0	-0.003	0.019	21.059	-0.458	-0.458	0.000	0.000	0.000	0.000
89	C	164	GLY	0	0.034	0.012	19.662	0.439	0.439	0.000	0.000	0.000	0.000
90	C	165	ALA	0	-0.006	-0.004	17.920	-0.692	-0.692	0.000	0.000	0.000	0.000
91	C	166	ILE	0	-0.014	-0.007	14.258	0.485	0.485	0.000	0.000	0.000	0.000
92	C	167	ASN	0	0.026	0.014	17.513	-0.323	-0.323	0.000	0.000	0.000	0.000
93	C	168	LYS	1	0.896	0.939	17.806	11.868	11.868	0.000	0.000	0.000	0.000
94	C	169	ASN	0	-0.037	-0.015	18.788	0.072	0.072	0.000	0.000	0.000	0.000
95	C	170	GLY	0	-0.003	-0.011	20.561	0.306	0.306	0.000	0.000	0.000	0.000
96	C	171	LEU	0	0.014	0.011	17.043	-0.430	-0.430	0.000	0.000	0.000	0.000
97	C	172	GLN	0	-0.031	-0.029	20.807	0.663	0.663	0.000	0.000	0.000	0.000
98	C	173	ALA	0	-0.002	0.010	22.154	-0.474	-0.474	0.000	0.000	0.000	0.000
99	C	174	SER	0	-0.015	-0.013	23.326	0.450	0.450	0.000	0.000	0.000	0.000
100	C	175	SER	0	0.005	-0.003	25.051	-0.087	-0.087	0.000	0.000	0.000	0.000
101	C	177	GLU	-1	-0.838	-0.931	23.720	-10.830	-10.830	0.000	0.000	0.000	0.000
102	C	178	VAL	0	-0.062	-0.022	24.628	0.080	0.080	0.000	0.000	0.000	0.000
103	C	179	PRO	0	-0.013	-0.009	22.477	-0.498	-0.498	0.000	0.000	0.000	0.000
104	C	180	LEU	0	0.018	0.003	19.720	0.383	0.383	0.000	0.000	0.000	0.000
105	C	181	HIS	0	-0.007	0.010	15.904	-0.709	-0.709	0.000	0.000	0.000	0.000
106	C	182	TRP	0	-0.005	-0.018	11.546	0.742	0.742	0.000	0.000	0.000	0.000
107	C	183	VAL	0	0.024	0.013	8.357	-0.870	-0.870	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:75:CYS)