FMO DATABASE

FMODB ID: 19Z8Z

Calculation Name: 5NMS-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5NMS

Chain ID: A

ChEMBL ID:

UniProt ID: P31170

Base Structure: ElectronMicroscopy

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1192322.767353
FMO2-HF: Nuclear repulsion	1133488.01943
FMO2-HF: Total energy	-58834.747922
FMO2-MP2: Total energy	-59000.993068

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:42:LEU)

Summations of interaction energy for fragment #1(A:42:LEU)

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.
-37.562	-29.311	6.734	-5.222	-9.765	-0.041

Interaction energy analysis for fragmet #1(A:42:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.919

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	44	ASP	-1	-0.722	-0.866	3.232	-40.861	-38.639	0.066	-0.895	-1.394	-0.002
4	A	45	PRO	0	-0.041	-0.017	5.270	0.925	0.945	-0.001	-0.003	-0.015	0.000
74	A	115	ASP	-1	-0.862	-0.937	4.555	-35.017	-34.908	-0.001	-0.004	-0.104	0.000
76	A	117	VAL	0	-0.030	-0.008	2.321	-1.842	-2.466	3.669	-0.624	-2.422	-0.006
77	A	118	LEU	0	0.028	0.017	5.018	2.803	2.847	-0.001	-0.004	-0.039	0.000
103	A	144	ARG	1	0.888	0.929	2.516	41.745	43.155	1.357	-0.692	-2.076	-0.003
104	A	145	LEU	0	-0.039	-0.008	2.563	-19.314	-16.333	1.206	-2.236	-1.951	-0.025
105	A	146	GLN	0	-0.024	-0.032	2.574	-2.110	-0.163	0.433	-0.700	-1.680	-0.005
106	A	147	LEU	0	-0.001	0.003	3.962	3.123	3.265	0.006	-0.064	-0.084	0.000
5	A	46	LEU	0	0.026	0.004	8.752	2.925	2.925	0.000	0.000	0.000	0.000
6	A	47	SER	0	-0.039	-0.046	6.717	2.310	2.310	0.000	0.000	0.000	0.000
7	A	48	PRO	0	0.036	0.008	8.823	0.738	0.738	0.000	0.000	0.000	0.000
8	A	49	MET	0	-0.020	0.025	4.957	0.543	0.543	0.000	0.000	0.000	0.000
9	A	50	ARG	1	0.926	0.960	7.706	34.012	34.012	0.000	0.000	0.000	0.000
10	A	51	THR	0	0.001	0.021	11.650	1.083	1.083	0.000	0.000	0.000	0.000
11	A	52	MET	0	-0.001	-0.002	12.814	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	53	ARG	1	0.956	0.981	17.323	13.662	13.662	0.000	0.000	0.000	0.000
13	A	54	GLN	0	-0.003	-0.020	12.632	-0.176	-0.176	0.000	0.000	0.000	0.000
14	A	55	MET	0	-0.001	-0.012	17.367	0.531	0.531	0.000	0.000	0.000	0.000
15	A	56	LEU	0	-0.044	0.001	13.987	0.370	0.370	0.000	0.000	0.000	0.000
16	A	57	ASP	-1	-0.845	-0.926	17.025	-14.649	-14.649	0.000	0.000	0.000	0.000
17	A	58	THR	0	0.033	-0.005	13.954	0.163	0.163	0.000	0.000	0.000	0.000
18	A	59	MET	0	-0.112	-0.041	16.680	0.038	0.038	0.000	0.000	0.000	0.000
19	A	60	ASP	-1	-0.789	-0.907	17.795	-16.536	-16.536	0.000	0.000	0.000	0.000
20	A	61	ARG	1	0.963	0.976	18.868	13.913	13.913	0.000	0.000	0.000	0.000
21	A	62	MET	0	-0.037	-0.003	12.121	-0.818	-0.818	0.000	0.000	0.000	0.000
22	A	63	PHE	0	-0.023	-0.008	16.457	-0.364	-0.364	0.000	0.000	0.000	0.000
23	A	64	GLU	-1	-0.945	-0.979	18.007	-12.935	-12.935	0.000	0.000	0.000	0.000
24	A	65	ASP	-1	-0.980	-0.976	18.669	-15.210	-15.210	0.000	0.000	0.000	0.000
25	A	66	THR	0	-0.098	-0.056	15.799	-0.343	-0.343	0.000	0.000	0.000	0.000
26	A	67	MET	0	0.013	0.034	17.281	-0.532	-0.532	0.000	0.000	0.000	0.000
27	A	68	PRO	0	-0.044	-0.025	19.068	-0.186	-0.186	0.000	0.000	0.000	0.000
28	A	69	VAL	0	0.013	0.011	14.933	-0.545	-0.545	0.000	0.000	0.000	0.000
29	A	70	SER	0	-0.042	-0.030	16.859	0.225	0.225	0.000	0.000	0.000	0.000
30	A	71	GLY	0	0.055	0.015	16.058	0.014	0.014	0.000	0.000	0.000	0.000
31	A	72	ARG	1	0.904	0.970	7.363	32.314	32.314	0.000	0.000	0.000	0.000
32	A	73	ASN	0	0.071	0.035	12.897	-0.323	-0.323	0.000	0.000	0.000	0.000
33	A	74	ARG	1	0.959	0.960	7.004	31.585	31.585	0.000	0.000	0.000	0.000
34	A	75	GLY	0	0.020	0.011	8.986	-3.395	-3.395	0.000	0.000	0.000	0.000
35	A	76	GLY	0	-0.024	-0.018	10.422	-0.122	-0.122	0.000	0.000	0.000	0.000
36	A	77	SER	0	0.036	0.006	12.300	0.142	0.142	0.000	0.000	0.000	0.000
37	A	78	GLY	0	0.078	0.050	12.503	0.759	0.759	0.000	0.000	0.000	0.000
38	A	79	VAL	0	-0.026	-0.028	8.214	-0.241	-0.241	0.000	0.000	0.000	0.000
39	A	80	SER	0	-0.070	-0.029	11.591	0.735	0.735	0.000	0.000	0.000	0.000
40	A	81	GLU	-1	-0.851	-0.916	14.988	-15.397	-15.397	0.000	0.000	0.000	0.000
41	A	82	ILE	0	-0.015	0.000	12.862	0.544	0.544	0.000	0.000	0.000	0.000
42	A	83	ARG	1	0.888	0.940	12.499	17.019	17.019	0.000	0.000	0.000	0.000
43	A	84	ALA	0	0.051	0.006	11.058	1.014	1.014	0.000	0.000	0.000	0.000
44	A	85	PRO	0	-0.070	-0.025	11.917	-1.553	-1.553	0.000	0.000	0.000	0.000
45	A	86	TRP	0	0.012	-0.011	8.073	-2.284	-2.284	0.000	0.000	0.000	0.000
46	A	87	ASP	-1	-0.801	-0.873	13.057	-16.455	-16.455	0.000	0.000	0.000	0.000
47	A	88	ILE	0	-0.031	-0.015	13.481	-0.492	-0.492	0.000	0.000	0.000	0.000
48	A	89	LYS	1	0.927	0.964	15.951	13.516	13.516	0.000	0.000	0.000	0.000
49	A	90	GLU	-1	-0.851	-0.913	18.853	-14.116	-14.116	0.000	0.000	0.000	0.000
50	A	91	GLU	-1	-0.836	-0.923	21.285	-12.853	-12.853	0.000	0.000	0.000	0.000
51	A	92	GLU	-1	-0.862	-0.959	18.388	-13.416	-13.416	0.000	0.000	0.000	0.000
52	A	93	HIS	0	0.029	0.017	12.899	-0.068	-0.068	0.000	0.000	0.000	0.000
53	A	94	GLU	-1	-0.826	-0.921	14.904	-14.699	-14.699	0.000	0.000	0.000	0.000
54	A	95	ILE	0	-0.040	-0.006	10.986	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.858	0.933	14.733	16.209	16.209	0.000	0.000	0.000	0.000
56	A	97	MET	0	-0.063	-0.039	8.602	-0.754	-0.754	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.926	0.963	13.882	14.856	14.856	0.000	0.000	0.000	0.000
58	A	99	PHE	0	0.025	-0.004	13.439	-1.236	-1.236	0.000	0.000	0.000	0.000
59	A	100	ASP	-1	-0.901	-0.939	15.746	-14.259	-14.259	0.000	0.000	0.000	0.000
60	A	101	MET	0	-0.045	-0.008	17.102	-0.937	-0.937	0.000	0.000	0.000	0.000
61	A	102	PRO	0	0.023	0.006	19.398	0.558	0.558	0.000	0.000	0.000	0.000
62	A	103	GLY	0	0.025	0.001	23.205	-0.063	-0.063	0.000	0.000	0.000	0.000
63	A	104	LEU	0	-0.050	0.001	19.246	0.152	0.152	0.000	0.000	0.000	0.000
64	A	105	SER	0	0.011	-0.015	22.733	0.260	0.260	0.000	0.000	0.000	0.000
65	A	106	LYS	1	0.865	0.895	21.232	11.094	11.094	0.000	0.000	0.000	0.000
66	A	107	GLU	-1	-0.849	-0.896	21.033	-12.317	-12.317	0.000	0.000	0.000	0.000
67	A	108	ASP	-1	-0.800	-0.885	20.344	-13.665	-13.665	0.000	0.000	0.000	0.000
68	A	109	VAL	0	-0.071	-0.026	15.210	-0.977	-0.977	0.000	0.000	0.000	0.000
69	A	110	LYS	1	0.929	0.955	14.492	16.878	16.878	0.000	0.000	0.000	0.000
70	A	111	ILE	0	0.041	0.024	11.966	-1.450	-1.450	0.000	0.000	0.000	0.000
71	A	112	SER	0	-0.095	-0.059	10.351	1.367	1.367	0.000	0.000	0.000	0.000
72	A	113	VAL	0	0.013	0.009	8.792	-1.155	-1.155	0.000	0.000	0.000	0.000
73	A	114	GLU	-1	-0.862	-0.914	5.801	-29.925	-29.925	0.000	0.000	0.000	0.000
75	A	116	ASN	0	-0.068	-0.045	6.324	-0.194	-0.194	0.000	0.000	0.000	0.000
78	A	119	VAL	0	-0.052	-0.031	5.521	-5.850	-5.850	0.000	0.000	0.000	0.000
79	A	120	ILE	0	0.034	0.011	7.495	3.494	3.494	0.000	0.000	0.000	0.000
80	A	121	LYS	1	0.887	0.940	9.361	21.008	21.008	0.000	0.000	0.000	0.000
81	A	122	GLY	0	0.037	0.018	11.933	1.240	1.240	0.000	0.000	0.000	0.000
82	A	123	GLU	-1	-0.899	-0.962	15.329	-17.577	-17.577	0.000	0.000	0.000	0.000
83	A	124	GLN	0	0.003	0.006	18.146	0.450	0.450	0.000	0.000	0.000	0.000
84	A	125	LYS	1	0.843	0.918	21.516	10.921	10.921	0.000	0.000	0.000	0.000
85	A	126	LYS	1	0.795	0.892	24.598	10.496	10.496	0.000	0.000	0.000	0.000
86	A	127	GLU	-1	-0.840	-0.901	26.229	-9.846	-9.846	0.000	0.000	0.000	0.000
87	A	128	ASP	-1	-0.835	-0.909	29.598	-9.991	-9.991	0.000	0.000	0.000	0.000
88	A	129	SER	0	-0.043	-0.039	32.728	0.083	0.083	0.000	0.000	0.000	0.000
89	A	130	ASP	-1	-0.939	-0.967	36.077	-8.200	-8.200	0.000	0.000	0.000	0.000
90	A	131	ASP	-1	-0.879	-0.929	30.606	-10.078	-10.078	0.000	0.000	0.000	0.000
91	A	132	SER	0	-0.013	0.004	33.594	0.102	0.102	0.000	0.000	0.000	0.000
92	A	133	TRP	0	-0.057	-0.048	29.516	-0.314	-0.314	0.000	0.000	0.000	0.000
93	A	134	SER	0	-0.060	-0.034	28.685	-0.176	-0.176	0.000	0.000	0.000	0.000
94	A	135	GLY	0	0.022	0.010	26.342	-0.355	-0.355	0.000	0.000	0.000	0.000
95	A	136	ARG	1	0.897	0.954	24.088	12.341	12.341	0.000	0.000	0.000	0.000
96	A	137	SER	0	0.019	-0.010	22.691	0.087	0.087	0.000	0.000	0.000	0.000
97	A	138	VAL	0	0.029	0.051	19.083	-0.663	-0.663	0.000	0.000	0.000	0.000
98	A	139	SER	0	-0.081	-0.044	18.525	0.321	0.321	0.000	0.000	0.000	0.000
99	A	140	SER	0	0.004	0.008	15.318	-1.347	-1.347	0.000	0.000	0.000	0.000
100	A	141	TYR	0	-0.011	-0.001	10.585	-1.770	-1.770	0.000	0.000	0.000	0.000
101	A	142	GLY	0	0.024	0.000	9.175	1.045	1.045	0.000	0.000	0.000	0.000
102	A	143	THR	0	-0.088	-0.035	5.616	-2.974	-2.974	0.000	0.000	0.000	0.000
107	A	148	PRO	0	-0.037	-0.028	7.450	-0.131	-0.131	0.000	0.000	0.000	0.000
108	A	149	ASP	-1	-0.856	-0.918	10.061	-17.033	-17.033	0.000	0.000	0.000	0.000
109	A	150	ASN	0	-0.017	-0.008	10.157	-2.809	-2.809	0.000	0.000	0.000	0.000
110	A	151	CYS	0	-0.001	0.006	10.695	1.416	1.416	0.000	0.000	0.000	0.000
111	A	152	GLU	-1	-0.819	-0.900	12.614	-13.743	-13.743	0.000	0.000	0.000	0.000
112	A	153	LYS	1	0.894	0.937	13.658	17.477	17.477	0.000	0.000	0.000	0.000
113	A	154	ASP	-1	-0.860	-0.925	15.740	-12.785	-12.785	0.000	0.000	0.000	0.000
114	A	155	LYS	1	0.837	0.908	18.012	13.360	13.360	0.000	0.000	0.000	0.000
115	A	156	ILE	0	-0.020	-0.009	13.015	0.252	0.252	0.000	0.000	0.000	0.000
116	A	157	LYS	1	0.868	0.944	17.100	14.260	14.260	0.000	0.000	0.000	0.000
117	A	158	ALA	0	0.006	0.005	17.019	-0.660	-0.660	0.000	0.000	0.000	0.000
118	A	159	GLU	-1	-0.915	-0.952	18.755	-11.551	-11.551	0.000	0.000	0.000	0.000
119	A	160	LEU	0	0.026	0.005	19.600	-0.693	-0.693	0.000	0.000	0.000	0.000
120	A	161	LYS	1	0.871	0.933	22.075	12.284	12.284	0.000	0.000	0.000	0.000
121	A	162	ASN	0	-0.013	-0.009	24.083	-0.174	-0.174	0.000	0.000	0.000	0.000
122	A	163	GLY	0	0.041	0.035	23.282	0.046	0.046	0.000	0.000	0.000	0.000
123	A	164	VAL	0	-0.015	-0.005	19.522	-0.565	-0.565	0.000	0.000	0.000	0.000
124	A	165	LEU	0	-0.034	0.003	14.975	0.456	0.456	0.000	0.000	0.000	0.000
125	A	166	PHE	0	-0.008	-0.018	17.634	-0.444	-0.444	0.000	0.000	0.000	0.000
126	A	167	ILE	0	0.009	-0.009	13.129	0.170	0.170	0.000	0.000	0.000	0.000
127	A	168	THR	0	-0.010	-0.005	15.411	-0.898	-0.898	0.000	0.000	0.000	0.000
128	A	169	ILE	0	0.012	-0.018	11.335	-0.114	-0.114	0.000	0.000	0.000	0.000
129	A	170	PRO	0	-0.012	-0.015	15.422	-0.039	-0.039	0.000	0.000	0.000	0.000
130	A	171	LYS	1	0.860	0.964	15.120	14.384	14.384	0.000	0.000	0.000	0.000
131	A	172	THR	0	0.038	0.016	16.994	0.973	0.973	0.000	0.000	0.000	0.000
132	A	173	LYS	1	0.852	0.933	19.285	12.795	12.795	0.000	0.000	0.000	0.000
133	A	174	VAL	0	0.003	-0.009	19.756	0.083	0.083	0.000	0.000	0.000	0.000
134	A	175	GLU	-1	-0.912	-0.950	22.846	-10.609	-10.609	0.000	0.000	0.000	0.000
135	A	176	ARG	1	0.763	0.884	20.763	13.287	13.287	0.000	0.000	0.000	0.000
136	A	177	LYS	1	0.936	0.964	19.201	14.950	14.950	0.000	0.000	0.000	0.000
137	A	178	VAL	0	0.063	0.029	23.965	-0.232	-0.232	0.000	0.000	0.000	0.000
138	A	179	ILE	0	-0.037	-0.013	25.158	-0.153	-0.153	0.000	0.000	0.000	0.000
139	A	180	ASP	-1	-0.891	-0.936	27.837	-9.647	-9.647	0.000	0.000	0.000	0.000
140	A	181	VAL	0	-0.052	-0.034	30.718	-0.197	-0.197	0.000	0.000	0.000	0.000
141	A	182	GLN	0	-0.026	-0.002	33.315	-0.025	-0.025	0.000	0.000	0.000	0.000
142	A	183	ILE	0	-0.065	-0.038	35.191	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	184	GLN	-1	-0.917	-0.955	38.103	-7.979	-7.979	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:LEU)