FMO DATABASE

FMODB ID: 8GZZY

Calculation Name: 2HAZ-A-Xray547

Preferred Name: Neural cell adhesion molecule 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HAZ

Chain ID: A

ChEMBL ID: CHEMBL3712938

UniProt ID: P13591

Base Structure: X-ray

Registration Date: 2025-10-04

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-735908.129775
FMO2-HF: Nuclear repulsion	696461.681782
FMO2-HF: Total energy	-39446.447993
FMO2-MP2: Total energy	-39562.444702

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(A:486:SER)

Summations of interaction energy for fragment #1(A:486: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.
-89.026	-86.58	-0.027	-1.32	-1.099	-0.004

Interaction energy analysis for fragmet #1(A:486:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.914

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	488	MET	0	0.049	0.047	3.853	-8.751	-6.305	-0.027	-1.320	-1.099	-0.004
4	A	489	ASP	-1	-0.872	-0.931	6.517	-33.890	-33.890	0.000	0.000	0.000	0.000
5	A	490	THR	0	-0.036	-0.012	9.530	0.517	0.517	0.000	0.000	0.000	0.000
6	A	491	PRO	0	-0.027	-0.008	13.156	-0.574	-0.574	0.000	0.000	0.000	0.000
7	A	492	SER	0	0.059	0.033	15.196	0.141	0.141	0.000	0.000	0.000	0.000
8	A	493	SER	0	-0.040	-0.022	16.936	0.431	0.431	0.000	0.000	0.000	0.000
9	A	494	PRO	0	-0.047	-0.014	20.741	-0.080	-0.080	0.000	0.000	0.000	0.000
10	A	495	SER	0	0.013	0.013	23.169	0.021	0.021	0.000	0.000	0.000	0.000
11	A	496	ILE	0	-0.085	-0.051	26.238	0.082	0.082	0.000	0.000	0.000	0.000
12	A	497	ASP	-1	-0.879	-0.918	29.792	-10.306	-10.306	0.000	0.000	0.000	0.000
13	A	498	GLN	0	-0.076	-0.053	32.311	0.527	0.527	0.000	0.000	0.000	0.000
14	A	499	VAL	0	-0.034	-0.018	34.747	-0.186	-0.186	0.000	0.000	0.000	0.000
15	A	500	GLU	-1	-0.873	-0.917	37.060	-8.134	-8.134	0.000	0.000	0.000	0.000
16	A	501	PRO	0	-0.034	-0.015	40.102	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	502	TYR	0	0.032	0.016	41.884	0.291	0.291	0.000	0.000	0.000	0.000
18	A	503	SER	0	-0.007	-0.007	45.041	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	504	SER	0	-0.002	-0.009	44.906	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	505	THR	0	-0.049	-0.025	40.950	-0.123	-0.123	0.000	0.000	0.000	0.000
21	A	506	ALA	0	0.034	0.011	38.285	0.159	0.159	0.000	0.000	0.000	0.000
22	A	507	GLN	0	0.062	0.069	36.557	-0.194	-0.194	0.000	0.000	0.000	0.000
23	A	508	VAL	0	-0.011	-0.009	31.380	0.117	0.117	0.000	0.000	0.000	0.000
24	A	509	GLN	0	0.007	-0.015	32.213	-0.365	-0.365	0.000	0.000	0.000	0.000
25	A	510	PHE	0	-0.097	-0.056	25.035	-0.044	-0.044	0.000	0.000	0.000	0.000
26	A	511	ASP	-1	-0.770	-0.856	24.670	-11.792	-11.792	0.000	0.000	0.000	0.000
27	A	512	GLU	-1	-0.938	-1.004	21.105	-13.160	-13.160	0.000	0.000	0.000	0.000
28	A	513	PRO	0	-0.088	-0.051	17.751	-0.097	-0.097	0.000	0.000	0.000	0.000
29	A	514	GLU	-1	-0.892	-0.928	18.136	-15.671	-15.671	0.000	0.000	0.000	0.000
30	A	515	ALA	0	-0.019	-0.009	12.847	-1.090	-1.090	0.000	0.000	0.000	0.000
31	A	516	THR	0	0.023	-0.006	13.177	-0.377	-0.377	0.000	0.000	0.000	0.000
32	A	517	GLY	0	0.084	0.055	10.543	0.172	0.172	0.000	0.000	0.000	0.000
33	A	518	GLY	0	-0.036	-0.022	8.443	-4.678	-4.678	0.000	0.000	0.000	0.000
34	A	519	VAL	0	-0.094	-0.049	9.523	-0.250	-0.250	0.000	0.000	0.000	0.000
35	A	520	PRO	0	0.018	0.006	12.138	0.693	0.693	0.000	0.000	0.000	0.000
36	A	521	ILE	0	0.040	0.019	15.909	-0.374	-0.374	0.000	0.000	0.000	0.000
37	A	522	LEU	0	-0.061	-0.027	18.049	0.638	0.638	0.000	0.000	0.000	0.000
38	A	523	LYS	1	0.837	0.907	20.900	13.254	13.254	0.000	0.000	0.000	0.000
39	A	524	TYR	0	0.089	0.060	22.181	-0.890	-0.890	0.000	0.000	0.000	0.000
40	A	525	LYS	1	0.823	0.902	24.636	12.595	12.595	0.000	0.000	0.000	0.000
41	A	526	ALA	0	0.054	0.037	26.395	-0.144	-0.144	0.000	0.000	0.000	0.000
42	A	527	GLU	-1	-0.803	-0.894	27.523	-11.808	-11.808	0.000	0.000	0.000	0.000
43	A	528	TRP	0	0.021	0.004	30.861	-0.111	-0.111	0.000	0.000	0.000	0.000
44	A	529	ARG	1	0.913	0.961	34.366	9.130	9.130	0.000	0.000	0.000	0.000
45	A	530	ALA	0	0.044	0.035	37.300	0.001	0.001	0.000	0.000	0.000	0.000
46	A	531	VAL	0	-0.011	-0.021	39.098	-0.127	-0.127	0.000	0.000	0.000	0.000
47	A	532	GLY	0	-0.019	-0.009	40.511	0.215	0.215	0.000	0.000	0.000	0.000
48	A	533	GLU	-1	-0.920	-0.956	40.640	-7.603	-7.603	0.000	0.000	0.000	0.000
49	A	534	GLU	-1	-0.939	-0.972	37.645	-8.436	-8.436	0.000	0.000	0.000	0.000
50	A	535	VAL	0	-0.048	-0.026	36.078	-0.296	-0.296	0.000	0.000	0.000	0.000
51	A	536	TRP	0	-0.002	-0.001	32.122	0.045	0.045	0.000	0.000	0.000	0.000
52	A	537	HIS	0	0.010	0.016	34.279	-0.102	-0.102	0.000	0.000	0.000	0.000
53	A	538	SER	0	-0.045	-0.027	30.142	-0.398	-0.398	0.000	0.000	0.000	0.000
54	A	539	LYS	1	0.939	0.977	30.988	9.615	9.615	0.000	0.000	0.000	0.000
55	A	540	TRP	0	0.001	0.001	23.419	-0.393	-0.393	0.000	0.000	0.000	0.000
56	A	541	TYR	0	-0.035	-0.049	27.570	0.472	0.472	0.000	0.000	0.000	0.000
57	A	542	ASP	-1	-0.850	-0.927	26.583	-11.934	-11.934	0.000	0.000	0.000	0.000
58	A	543	ALA	0	0.016	0.004	22.743	0.195	0.195	0.000	0.000	0.000	0.000
59	A	544	LYS	1	0.938	0.994	24.741	10.964	10.964	0.000	0.000	0.000	0.000
60	A	545	GLU	-1	-0.870	-0.950	26.632	-10.720	-10.720	0.000	0.000	0.000	0.000
61	A	546	ALA	0	-0.014	0.002	27.068	0.218	0.218	0.000	0.000	0.000	0.000
62	A	547	SER	0	0.003	-0.015	25.039	0.152	0.152	0.000	0.000	0.000	0.000
63	A	548	MET	0	-0.124	-0.054	27.185	0.146	0.146	0.000	0.000	0.000	0.000
64	A	549	GLU	-1	-0.949	-0.978	30.129	-8.789	-8.789	0.000	0.000	0.000	0.000
65	A	550	GLY	0	0.042	0.038	29.899	0.246	0.246	0.000	0.000	0.000	0.000
66	A	551	ILE	0	-0.013	-0.015	30.960	0.080	0.080	0.000	0.000	0.000	0.000
67	A	552	VAL	0	-0.029	-0.013	29.226	-0.198	-0.198	0.000	0.000	0.000	0.000
68	A	553	THR	0	-0.015	-0.018	32.311	0.147	0.147	0.000	0.000	0.000	0.000
69	A	554	ILE	0	-0.043	0.012	33.940	-0.118	-0.118	0.000	0.000	0.000	0.000
70	A	555	VAL	0	-0.007	-0.027	36.355	0.266	0.266	0.000	0.000	0.000	0.000
71	A	556	GLY	0	-0.003	0.000	39.353	-0.117	-0.117	0.000	0.000	0.000	0.000
72	A	557	LEU	0	-0.058	-0.012	38.735	0.009	0.009	0.000	0.000	0.000	0.000
73	A	558	LYS	1	0.915	0.949	42.683	7.514	7.514	0.000	0.000	0.000	0.000
74	A	559	PRO	0	0.094	0.056	45.638	-0.115	-0.115	0.000	0.000	0.000	0.000
75	A	560	GLU	-1	-0.971	-0.961	48.213	-6.205	-6.205	0.000	0.000	0.000	0.000
76	A	561	THR	0	-0.068	-0.039	43.581	0.042	0.042	0.000	0.000	0.000	0.000
77	A	562	THR	0	-0.024	-0.018	41.436	-0.045	-0.045	0.000	0.000	0.000	0.000
78	A	563	TYR	0	0.009	0.012	38.327	0.070	0.070	0.000	0.000	0.000	0.000
79	A	564	ALA	0	0.028	0.030	34.766	0.004	0.004	0.000	0.000	0.000	0.000
80	A	565	VAL	0	-0.042	-0.027	31.746	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	566	ARG	1	0.878	0.923	27.543	11.573	11.573	0.000	0.000	0.000	0.000
82	A	567	LEU	0	0.043	0.020	25.937	0.178	0.178	0.000	0.000	0.000	0.000
83	A	568	ALA	0	0.035	0.019	21.950	-0.343	-0.343	0.000	0.000	0.000	0.000
84	A	569	ALA	0	0.059	0.037	19.243	0.478	0.478	0.000	0.000	0.000	0.000
85	A	570	LEU	0	-0.035	-0.013	19.068	-0.685	-0.685	0.000	0.000	0.000	0.000
86	A	571	ASN	0	0.056	0.006	12.359	0.763	0.763	0.000	0.000	0.000	0.000
87	A	572	GLY	0	0.001	-0.009	14.718	0.423	0.423	0.000	0.000	0.000	0.000
88	A	573	LYS	1	0.787	0.908	8.976	32.264	32.264	0.000	0.000	0.000	0.000
89	A	574	GLY	0	0.008	0.014	13.490	0.196	0.196	0.000	0.000	0.000	0.000
90	A	575	LEU	0	-0.050	-0.036	16.967	0.124	0.124	0.000	0.000	0.000	0.000
91	A	576	GLY	0	0.029	0.006	16.651	-0.861	-0.861	0.000	0.000	0.000	0.000
92	A	577	GLU	-1	-0.922	-0.956	17.643	-15.922	-15.922	0.000	0.000	0.000	0.000
93	A	578	ILE	0	-0.071	-0.042	19.415	0.368	0.368	0.000	0.000	0.000	0.000
94	A	579	SER	0	0.044	0.012	23.204	-0.164	-0.164	0.000	0.000	0.000	0.000
95	A	580	ALA	0	-0.006	0.000	25.210	0.153	0.153	0.000	0.000	0.000	0.000
96	A	581	ALA	0	-0.038	-0.010	27.884	0.013	0.013	0.000	0.000	0.000	0.000
97	A	582	SER	0	0.036	0.028	31.058	0.131	0.131	0.000	0.000	0.000	0.000
98	A	583	GLU	-1	-0.914	-0.978	33.780	-9.177	-9.177	0.000	0.000	0.000	0.000
99	A	584	PHE	0	-0.001	0.004	36.662	0.122	0.122	0.000	0.000	0.000	0.000
100	A	585	LYS	1	0.904	0.947	39.996	6.824	6.824	0.000	0.000	0.000	0.000
101	A	586	THR	0	-0.016	-0.021	42.870	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	587	GLN	0	-0.057	-0.041	44.833	0.262	0.262	0.000	0.000	0.000	0.000
103	A	588	PRO	0	0.035	0.000	48.103	-0.044	-0.044	0.000	0.000	0.000	0.000
104	A	589	VAL	-1	-0.932	-0.953	51.159	-6.068	-6.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:486:SER)