FMO DATABASE

FMODB ID: 8QLRY

Calculation Name: 5DQ0-A-Xray547

Preferred Name: Neuropilin-2

Target Type: SINGLE PROTEIN

Ligand Name: 2-(n-morpholino)-ethanesulfonic acid | 1,2-ethanediol | zinc ion | chloride ion

Ligand 3-letter code: MES | EDO | ZN | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DQ0

Chain ID: A

ChEMBL ID: CHEMBL4295667

UniProt ID: O60462

Base Structure: X-ray

Registration Date: 2025-10-05

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1593224.781988
FMO2-HF: Nuclear repulsion	1530779.525965
FMO2-HF: Total energy	-62445.256023
FMO2-MP2: Total energy	-62627.38788

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:277:CYS)

Summations of interaction energy for fragment #1(A:277: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.
-1.814	11.179	13.006	-7.396	-18.601	-0.02

Interaction energy analysis for fragmet #1(A:277:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.757 / q_NPA : 0.873

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	279	VAL	0	0.046	0.044	2.041	-5.812	-1.281	4.848	-4.483	-4.896	0.031
4	A	280	PRO	0	0.027	0.020	3.648	-3.341	-2.916	0.035	-0.150	-0.310	0.000
5	A	281	LEU	0	-0.030	-0.039	3.174	0.573	1.168	0.271	0.103	-0.968	0.002
61	A	337	THR	0	-0.031	-0.029	3.311	-2.947	-2.338	0.029	-0.162	-0.476	-0.001
62	A	338	MET	0	-0.008	-0.001	2.928	3.353	4.911	4.080	-1.448	-4.190	-0.006
63	A	339	LEU	0	0.004	0.005	2.127	-20.795	-23.308	3.250	2.160	-2.897	-0.033
64	A	340	THR	0	-0.045	-0.061	3.019	5.705	6.996	0.151	-0.227	-1.216	-0.001
65	A	341	ALA	0	-0.015	-0.008	4.731	5.339	5.494	-0.002	-0.015	-0.138	0.000
149	A	425	PHE	0	0.026	0.008	3.820	-2.916	0.429	-0.030	-1.827	-1.487	-0.008
152	A	429	VAL	0	-0.020	-0.010	3.361	-4.011	-1.045	0.376	-1.341	-2.000	-0.004
153	A	430	THR	0	-0.022	-0.007	5.827	2.144	2.175	-0.002	-0.006	-0.023	0.000
6	A	282	GLY	0	-0.006	-0.003	6.622	1.451	1.451	0.000	0.000	0.000	0.000
7	A	283	MET	0	-0.027	-0.005	10.259	1.370	1.370	0.000	0.000	0.000	0.000
8	A	284	GLU	-1	-0.863	-0.928	12.210	-17.011	-17.011	0.000	0.000	0.000	0.000
9	A	285	SER	0	-0.049	-0.035	10.725	0.962	0.962	0.000	0.000	0.000	0.000
10	A	286	GLY	0	0.045	0.026	13.704	0.564	0.564	0.000	0.000	0.000	0.000
11	A	287	ARG	1	0.901	0.950	9.957	20.093	20.093	0.000	0.000	0.000	0.000
12	A	288	ILE	0	-0.048	-0.003	8.932	-0.284	-0.284	0.000	0.000	0.000	0.000
13	A	289	ALA	0	0.088	0.045	12.629	0.734	0.734	0.000	0.000	0.000	0.000
14	A	290	ASN	0	0.066	0.025	16.185	-0.788	-0.788	0.000	0.000	0.000	0.000
15	A	291	GLU	-1	-0.877	-0.942	19.260	-13.107	-13.107	0.000	0.000	0.000	0.000
16	A	292	GLN	0	-0.090	-0.045	11.900	0.717	0.717	0.000	0.000	0.000	0.000
17	A	293	ILE	0	-0.011	0.008	15.135	-0.690	-0.690	0.000	0.000	0.000	0.000
18	A	294	SER	0	-0.005	-0.006	17.331	0.844	0.844	0.000	0.000	0.000	0.000
19	A	295	ALA	0	0.021	-0.004	19.128	-0.594	-0.594	0.000	0.000	0.000	0.000
20	A	296	SER	0	-0.058	-0.035	21.516	0.084	0.084	0.000	0.000	0.000	0.000
21	A	297	SER	0	-0.007	-0.026	24.266	0.532	0.532	0.000	0.000	0.000	0.000
22	A	298	THR	0	-0.042	-0.029	24.880	-0.446	-0.446	0.000	0.000	0.000	0.000
23	A	299	TYR	0	0.022	0.019	26.889	0.352	0.352	0.000	0.000	0.000	0.000
24	A	300	SER	0	0.007	0.002	29.810	-0.052	-0.052	0.000	0.000	0.000	0.000
25	A	301	ASP	-1	-0.815	-0.907	31.555	-9.069	-9.069	0.000	0.000	0.000	0.000
26	A	302	GLY	0	-0.019	-0.004	29.920	0.077	0.077	0.000	0.000	0.000	0.000
27	A	303	ARG	1	0.688	0.792	28.855	9.507	9.507	0.000	0.000	0.000	0.000
28	A	304	TRP	0	0.013	0.013	25.641	-0.351	-0.351	0.000	0.000	0.000	0.000
29	A	305	THR	0	0.032	0.001	24.296	-0.421	-0.421	0.000	0.000	0.000	0.000
30	A	306	PRO	0	0.015	-0.013	20.082	-0.382	-0.382	0.000	0.000	0.000	0.000
31	A	307	GLN	0	-0.019	-0.005	19.235	-0.454	-0.454	0.000	0.000	0.000	0.000
32	A	308	GLN	0	0.036	0.029	19.980	-0.193	-0.193	0.000	0.000	0.000	0.000
33	A	309	SER	0	-0.065	-0.042	17.227	-0.442	-0.442	0.000	0.000	0.000	0.000
34	A	310	ARG	1	0.806	0.875	15.076	15.009	15.009	0.000	0.000	0.000	0.000
35	A	311	LEU	0	-0.031	-0.017	12.558	0.526	0.526	0.000	0.000	0.000	0.000
36	A	312	HIS	0	-0.004	-0.011	15.613	0.757	0.757	0.000	0.000	0.000	0.000
37	A	313	GLY	0	-0.018	0.014	18.676	0.594	0.594	0.000	0.000	0.000	0.000
38	A	314	ASP	-1	-0.862	-0.938	20.554	-11.373	-11.373	0.000	0.000	0.000	0.000
39	A	315	ASP	-1	-0.822	-0.876	24.097	-9.758	-9.758	0.000	0.000	0.000	0.000
40	A	316	ASN	0	-0.003	0.015	24.792	-0.203	-0.203	0.000	0.000	0.000	0.000
41	A	317	GLY	0	0.028	0.007	21.858	-0.459	-0.459	0.000	0.000	0.000	0.000
42	A	318	TRP	0	-0.079	-0.038	20.309	0.036	0.036	0.000	0.000	0.000	0.000
43	A	319	THR	0	0.015	-0.024	22.246	-0.228	-0.228	0.000	0.000	0.000	0.000
44	A	320	PRO	0	-0.049	-0.007	24.299	0.134	0.134	0.000	0.000	0.000	0.000
45	A	321	ASN	0	0.015	-0.009	26.461	0.331	0.331	0.000	0.000	0.000	0.000
46	A	322	LEU	0	-0.013	-0.011	29.263	0.365	0.365	0.000	0.000	0.000	0.000
47	A	323	ASP	-1	-0.801	-0.887	28.162	-10.628	-10.628	0.000	0.000	0.000	0.000
48	A	324	SER	0	-0.003	-0.019	27.508	0.200	0.200	0.000	0.000	0.000	0.000
49	A	325	ASN	0	0.005	-0.002	24.974	-0.219	-0.219	0.000	0.000	0.000	0.000
50	A	326	LYS	1	0.932	0.962	24.518	9.315	9.315	0.000	0.000	0.000	0.000
51	A	327	GLU	-1	-0.802	-0.831	24.014	-11.105	-11.105	0.000	0.000	0.000	0.000
52	A	328	TYR	0	-0.036	-0.050	18.796	-0.400	-0.400	0.000	0.000	0.000	0.000
53	A	329	LEU	0	0.026	0.046	16.036	0.441	0.441	0.000	0.000	0.000	0.000
54	A	330	GLN	0	0.007	-0.009	15.829	-0.657	-0.657	0.000	0.000	0.000	0.000
55	A	331	VAL	0	0.020	0.008	10.983	0.360	0.360	0.000	0.000	0.000	0.000
56	A	332	ASP	-1	-0.753	-0.838	13.060	-18.719	-18.719	0.000	0.000	0.000	0.000
57	A	333	LEU	0	0.017	0.004	6.340	-0.245	-0.245	0.000	0.000	0.000	0.000
58	A	334	ARG	1	0.879	0.949	9.709	15.442	15.442	0.000	0.000	0.000	0.000
59	A	335	PHE	0	-0.029	-0.031	8.463	1.045	1.045	0.000	0.000	0.000	0.000
60	A	336	LEU	0	0.025	0.017	8.584	-1.501	-1.501	0.000	0.000	0.000	0.000
66	A	342	ILE	0	-0.004	0.004	6.236	-1.728	-1.728	0.000	0.000	0.000	0.000
67	A	343	ALA	0	-0.017	0.001	9.090	0.711	0.711	0.000	0.000	0.000	0.000
68	A	344	THR	0	-0.014	-0.024	11.690	0.023	0.023	0.000	0.000	0.000	0.000
69	A	345	GLN	0	0.021	0.022	15.198	-0.181	-0.181	0.000	0.000	0.000	0.000
70	A	346	GLY	0	0.030	0.013	18.570	0.007	0.007	0.000	0.000	0.000	0.000
71	A	347	ALA	0	0.001	0.009	21.473	-0.390	-0.390	0.000	0.000	0.000	0.000
72	A	348	ILE	0	0.023	0.003	24.099	0.267	0.267	0.000	0.000	0.000	0.000
73	A	349	SER	0	-0.023	0.006	27.681	0.001	0.001	0.000	0.000	0.000	0.000
74	A	350	ARG	1	0.886	0.933	27.608	10.562	10.562	0.000	0.000	0.000	0.000
75	A	351	GLU	-1	-0.788	-0.875	31.653	-9.131	-9.131	0.000	0.000	0.000	0.000
76	A	352	THR	0	-0.024	-0.028	33.687	0.227	0.227	0.000	0.000	0.000	0.000
77	A	353	GLN	0	-0.037	-0.012	32.478	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	354	ASN	0	-0.010	0.013	32.520	-0.094	-0.094	0.000	0.000	0.000	0.000
79	A	355	GLY	0	0.015	0.006	28.509	-0.259	-0.259	0.000	0.000	0.000	0.000
80	A	356	TYR	0	-0.022	-0.012	26.819	0.251	0.251	0.000	0.000	0.000	0.000
81	A	357	TYR	0	0.042	0.019	23.033	-0.402	-0.402	0.000	0.000	0.000	0.000
82	A	358	VAL	0	0.004	0.008	19.580	0.355	0.355	0.000	0.000	0.000	0.000
83	A	359	LYS	1	0.946	0.982	21.586	10.617	10.617	0.000	0.000	0.000	0.000
84	A	360	SER	0	-0.039	-0.028	20.218	-0.365	-0.365	0.000	0.000	0.000	0.000
85	A	361	TYR	0	0.061	0.022	12.651	0.654	0.654	0.000	0.000	0.000	0.000
86	A	362	LYS	1	0.850	0.948	17.521	12.571	12.571	0.000	0.000	0.000	0.000
87	A	363	LEU	0	0.015	0.020	10.517	-0.119	-0.119	0.000	0.000	0.000	0.000
88	A	364	GLU	-1	-0.846	-0.901	14.781	-13.635	-13.635	0.000	0.000	0.000	0.000
89	A	365	VAL	0	-0.002	-0.007	11.005	-0.730	-0.730	0.000	0.000	0.000	0.000
90	A	366	SER	0	0.074	0.022	13.104	1.197	1.197	0.000	0.000	0.000	0.000
91	A	367	THR	0	0.014	-0.007	11.848	-1.155	-1.155	0.000	0.000	0.000	0.000
92	A	368	ASN	0	-0.005	-0.021	13.758	-0.494	-0.494	0.000	0.000	0.000	0.000
93	A	369	GLY	0	0.021	0.023	17.004	0.318	0.318	0.000	0.000	0.000	0.000
94	A	370	GLU	-1	-0.957	-0.960	18.289	-11.190	-11.190	0.000	0.000	0.000	0.000
95	A	371	ASP	-1	-0.848	-0.915	18.895	-13.061	-13.061	0.000	0.000	0.000	0.000
96	A	372	TRP	0	-0.076	-0.038	15.405	-1.505	-1.505	0.000	0.000	0.000	0.000
97	A	373	MET	0	-0.018	-0.010	15.129	0.939	0.939	0.000	0.000	0.000	0.000
98	A	374	VAL	0	-0.009	-0.005	16.639	-0.947	-0.947	0.000	0.000	0.000	0.000
99	A	375	TYR	0	0.010	0.005	12.705	0.202	0.202	0.000	0.000	0.000	0.000
100	A	376	ARG	1	0.967	0.975	16.120	15.690	15.690	0.000	0.000	0.000	0.000
101	A	377	HIS	0	-0.034	-0.010	15.153	-0.934	-0.934	0.000	0.000	0.000	0.000
102	A	378	GLY	0	0.047	0.021	19.674	0.820	0.820	0.000	0.000	0.000	0.000
103	A	379	LYS	1	0.958	0.964	22.205	10.836	10.836	0.000	0.000	0.000	0.000
104	A	380	ASN	0	0.026	0.026	23.098	0.434	0.434	0.000	0.000	0.000	0.000
105	A	381	HIS	0	0.059	0.019	20.326	-0.676	-0.676	0.000	0.000	0.000	0.000
106	A	382	LYS	1	0.879	0.952	15.287	18.496	18.496	0.000	0.000	0.000	0.000
107	A	383	VAL	0	-0.008	-0.002	17.452	-0.416	-0.416	0.000	0.000	0.000	0.000
108	A	384	PHE	0	-0.039	-0.027	12.324	-0.435	-0.435	0.000	0.000	0.000	0.000
109	A	385	GLN	0	0.034	0.007	17.194	0.968	0.968	0.000	0.000	0.000	0.000
110	A	386	ALA	0	-0.002	-0.005	17.644	-1.047	-1.047	0.000	0.000	0.000	0.000
111	A	387	ASN	0	-0.007	0.019	18.480	-0.208	-0.208	0.000	0.000	0.000	0.000
112	A	388	ASN	0	0.016	-0.017	21.314	0.036	0.036	0.000	0.000	0.000	0.000
113	A	389	ASP	-1	-0.811	-0.890	23.841	-12.147	-12.147	0.000	0.000	0.000	0.000
114	A	390	ALA	0	-0.015	-0.024	23.708	-0.388	-0.388	0.000	0.000	0.000	0.000
115	A	391	THR	0	-0.063	-0.041	22.850	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	392	GLU	-1	-0.863	-0.912	20.924	-14.061	-14.061	0.000	0.000	0.000	0.000
117	A	393	VAL	0	-0.030	-0.026	14.284	-0.396	-0.396	0.000	0.000	0.000	0.000
118	A	394	VAL	0	-0.021	0.000	16.032	-0.272	-0.272	0.000	0.000	0.000	0.000
119	A	395	LEU	0	-0.026	-0.016	8.982	-1.141	-1.141	0.000	0.000	0.000	0.000
120	A	396	ASN	0	-0.029	-0.026	11.990	0.434	0.434	0.000	0.000	0.000	0.000
121	A	397	LYS	1	0.969	0.975	8.913	29.029	29.029	0.000	0.000	0.000	0.000
122	A	398	LEU	0	-0.030	-0.014	7.790	3.169	3.169	0.000	0.000	0.000	0.000
123	A	399	HIS	0	0.005	-0.005	9.755	-1.990	-1.990	0.000	0.000	0.000	0.000
124	A	400	ALA	0	0.003	0.002	8.814	0.129	0.129	0.000	0.000	0.000	0.000
125	A	401	PRO	0	-0.026	-0.018	4.816	-0.270	-0.270	0.000	0.000	0.000	0.000
126	A	402	LEU	0	-0.007	0.007	6.788	3.941	3.941	0.000	0.000	0.000	0.000
127	A	403	LEU	0	-0.015	0.000	6.684	-3.722	-3.722	0.000	0.000	0.000	0.000
128	A	404	THR	0	-0.015	-0.026	7.323	3.207	3.207	0.000	0.000	0.000	0.000
129	A	405	ARG	1	0.853	0.915	8.013	15.578	15.578	0.000	0.000	0.000	0.000
130	A	406	PHE	0	-0.007	0.005	10.208	-0.334	-0.334	0.000	0.000	0.000	0.000
131	A	407	VAL	0	0.004	-0.004	8.737	-0.892	-0.892	0.000	0.000	0.000	0.000
132	A	408	ARG	1	0.845	0.929	12.117	15.575	15.575	0.000	0.000	0.000	0.000
133	A	409	ILE	0	0.003	0.005	11.854	-0.609	-0.609	0.000	0.000	0.000	0.000
134	A	410	ARG	1	0.871	0.918	15.685	14.363	14.363	0.000	0.000	0.000	0.000
135	A	411	PRO	0	0.038	0.023	19.205	-0.165	-0.165	0.000	0.000	0.000	0.000
136	A	412	GLN	0	-0.106	-0.064	21.233	0.612	0.612	0.000	0.000	0.000	0.000
137	A	413	THR	0	0.024	0.025	23.481	0.378	0.378	0.000	0.000	0.000	0.000
138	A	414	TRP	0	0.012	0.013	23.815	-0.771	-0.771	0.000	0.000	0.000	0.000
139	A	415	HIS	0	0.004	0.002	25.889	0.279	0.279	0.000	0.000	0.000	0.000
140	A	416	SER	0	-0.014	0.005	28.224	-0.076	-0.076	0.000	0.000	0.000	0.000
141	A	417	GLY	0	0.050	0.017	28.656	0.304	0.304	0.000	0.000	0.000	0.000
142	A	418	ILE	0	-0.089	-0.044	22.829	-0.451	-0.451	0.000	0.000	0.000	0.000
143	A	419	ALA	0	0.043	0.036	23.567	0.180	0.180	0.000	0.000	0.000	0.000
144	A	420	LEU	0	-0.066	-0.035	16.493	-0.373	-0.373	0.000	0.000	0.000	0.000
145	A	421	ARG	1	0.844	0.929	17.531	13.810	13.810	0.000	0.000	0.000	0.000
146	A	422	LEU	0	-0.016	-0.009	11.525	-0.467	-0.467	0.000	0.000	0.000	0.000
147	A	423	GLU	-1	-0.739	-0.859	8.376	-24.153	-24.153	0.000	0.000	0.000	0.000
148	A	424	LEU	0	-0.024	-0.010	6.497	-0.730	-0.730	0.000	0.000	0.000	0.000
154	A	431	SER	0	-0.055	-0.054	9.471	-1.038	-1.038	0.000	0.000	0.000	0.000
155	A	432	GLY	0	0.010	0.003	12.106	0.174	0.174	0.000	0.000	0.000	0.000
156	A	433	SER	-1	-0.906	-0.913	14.437	-14.960	-14.960	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:277:CYS)