FMO DATABASE

FMODB ID: 1YZKZ

Calculation Name: 7APD-G-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7APD

Chain ID: G

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1524745.579226
FMO2-HF: Nuclear repulsion	1463946.913661
FMO2-HF: Total energy	-60798.665566
FMO2-MP2: Total energy	-60972.992658

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:156:GLY)

Summations of interaction energy for fragment #1(A:156:GLY)

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.
64.621	66.9	15.722	-10.372	-7.631	-0.121

Interaction energy analysis for fragmet #1(A:156:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.893

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	158	ARG	1	0.897	0.963	3.855	34.254	34.935	-0.004	-0.258	-0.420	0.000
30	A	185	ASP	-1	-0.815	-0.907	4.048	-52.407	-52.300	0.000	-0.046	-0.060	0.000
92	A	247	ARG	1	0.863	0.934	3.054	72.867	73.994	0.081	-0.395	-0.814	-0.004
103	A	258	GLU	-1	-0.767	-0.905	1.956	-138.530	-138.166	15.645	-9.673	-6.337	-0.117
4	A	159	ALA	0	0.078	0.020	6.063	3.316	3.316	0.000	0.000	0.000	0.000
5	A	160	THR	0	-0.052	-0.025	7.198	0.183	0.183	0.000	0.000	0.000	0.000
6	A	161	VAL	0	0.102	0.037	10.015	0.759	0.759	0.000	0.000	0.000	0.000
7	A	162	PHE	0	0.039	0.022	10.623	0.794	0.794	0.000	0.000	0.000	0.000
8	A	163	LYS	1	0.789	0.922	7.347	39.001	39.001	0.000	0.000	0.000	0.000
9	A	164	LEU	0	-0.017	-0.017	12.761	1.098	1.098	0.000	0.000	0.000	0.000
10	A	165	GLY	0	0.047	0.032	15.444	1.118	1.118	0.000	0.000	0.000	0.000
11	A	166	LEU	0	-0.003	0.005	17.076	0.807	0.807	0.000	0.000	0.000	0.000
12	A	167	PHE	0	0.017	-0.005	16.608	0.388	0.388	0.000	0.000	0.000	0.000
13	A	168	LYS	0	0.016	0.016	18.608	1.009	1.009	0.000	0.000	0.000	0.000
14	A	169	SER	0	-0.040	-0.024	21.176	0.970	0.970	0.000	0.000	0.000	0.000
15	A	170	LEU	0	-0.001	0.009	20.406	0.555	0.555	0.000	0.000	0.000	0.000
16	A	171	PHE	0	-0.060	-0.049	20.958	0.630	0.630	0.000	0.000	0.000	0.000
17	A	172	LEU	0	-0.033	-0.011	24.230	0.374	0.374	0.000	0.000	0.000	0.000
18	A	173	CYS	-1	-0.790	-0.781	23.277	-13.347	-13.347	0.000	0.000	0.000	0.000
19	A	174	SER	0	-0.033	-0.056	19.555	-1.169	-1.169	0.000	0.000	0.000	0.000
20	A	175	PHE	0	0.076	-0.002	12.205	-0.286	-0.286	0.000	0.000	0.000	0.000
21	A	176	HIS	0	-0.062	-0.031	13.517	-0.775	-0.775	0.000	0.000	0.000	0.000
22	A	177	ASP	-1	-0.819	-0.883	17.819	-13.966	-13.966	0.000	0.000	0.000	0.000
23	A	178	ILE	0	-0.020	-0.008	18.164	0.590	0.590	0.000	0.000	0.000	0.000
24	A	179	THR	0	-0.075	-0.045	15.494	-0.387	-0.387	0.000	0.000	0.000	0.000
25	A	180	ARG	1	0.965	0.969	16.502	15.533	15.533	0.000	0.000	0.000	0.000
26	A	181	LEU	0	0.004	0.005	13.648	-1.231	-1.231	0.000	0.000	0.000	0.000
27	A	182	PHE	0	0.017	0.011	11.745	0.725	0.725	0.000	0.000	0.000	0.000
28	A	183	LYS	1	0.991	0.982	5.933	33.955	33.955	0.000	0.000	0.000	0.000
29	A	184	ASN	0	0.022	0.016	8.167	-3.061	-3.061	0.000	0.000	0.000	0.000
31	A	186	LYS	1	0.878	0.924	7.752	32.081	32.081	0.000	0.000	0.000	0.000
32	A	187	THR	0	0.010	0.025	11.188	1.358	1.358	0.000	0.000	0.000	0.000
33	A	188	THR	0	-0.021	-0.011	12.234	-1.619	-1.619	0.000	0.000	0.000	0.000
34	A	189	ASN	0	0.066	0.038	14.748	1.561	1.561	0.000	0.000	0.000	0.000
35	A	190	GLN	0	0.021	0.022	16.339	-0.699	-0.699	0.000	0.000	0.000	0.000
36	A	191	GLN	0	-0.029	-0.021	18.427	-0.272	-0.272	0.000	0.000	0.000	0.000
37	A	192	TRP	0	-0.061	-0.048	10.913	-2.117	-2.117	0.000	0.000	0.000	0.000
38	A	193	VAL	0	0.018	0.016	15.331	1.049	1.049	0.000	0.000	0.000	0.000
39	A	194	LEU	0	-0.056	-0.019	10.870	-2.253	-2.253	0.000	0.000	0.000	0.000
40	A	195	ALA	0	0.016	-0.001	13.057	1.848	1.848	0.000	0.000	0.000	0.000
41	A	196	VAL	0	0.012	0.011	11.931	-2.490	-2.490	0.000	0.000	0.000	0.000
42	A	197	PHE	0	-0.021	-0.029	12.346	1.475	1.475	0.000	0.000	0.000	0.000
43	A	198	GLY	0	0.024	0.013	14.027	-1.057	-1.057	0.000	0.000	0.000	0.000
44	A	199	LEU	0	0.000	0.017	16.386	0.064	0.064	0.000	0.000	0.000	0.000
45	A	200	ALA	0	0.040	0.009	17.935	0.779	0.779	0.000	0.000	0.000	0.000
46	A	201	GLU	-1	-0.793	-0.908	21.512	-13.758	-13.758	0.000	0.000	0.000	0.000
47	A	202	VAL	0	0.071	0.040	24.145	-0.195	-0.195	0.000	0.000	0.000	0.000
48	A	203	PHE	0	0.012	-0.007	19.929	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	204	PHE	0	-0.006	0.003	19.752	-0.799	-0.799	0.000	0.000	0.000	0.000
50	A	205	GLU	-1	-0.885	-0.926	21.532	-11.637	-11.637	0.000	0.000	0.000	0.000
51	A	206	ALA	0	0.029	0.002	23.000	0.067	0.067	0.000	0.000	0.000	0.000
52	A	207	SER	0	-0.059	-0.055	18.571	-0.612	-0.612	0.000	0.000	0.000	0.000
53	A	208	PHE	0	0.041	-0.007	20.592	-0.283	-0.283	0.000	0.000	0.000	0.000
54	A	209	GLU	-1	-0.945	-0.965	23.094	-11.472	-11.472	0.000	0.000	0.000	0.000
55	A	210	LEU	0	-0.038	-0.016	20.075	0.094	0.094	0.000	0.000	0.000	0.000
56	A	211	LEU	0	-0.004	-0.012	16.666	-0.237	-0.237	0.000	0.000	0.000	0.000
57	A	212	LYS	1	0.945	1.000	20.783	11.298	11.298	0.000	0.000	0.000	0.000
58	A	213	LYS	1	0.924	0.961	23.439	13.371	13.371	0.000	0.000	0.000	0.000
59	A	214	GLN	0	-0.010	-0.013	18.266	0.220	0.220	0.000	0.000	0.000	0.000
60	A	215	CYS	0	-0.077	-0.039	20.585	-0.834	-0.834	0.000	0.000	0.000	0.000
61	A	216	SER	0	0.012	0.001	22.825	0.414	0.414	0.000	0.000	0.000	0.000
62	A	217	PHE	0	0.008	0.001	23.645	0.376	0.376	0.000	0.000	0.000	0.000
63	A	218	LEU	0	-0.047	-0.013	19.987	-0.838	-0.838	0.000	0.000	0.000	0.000
64	A	219	GLN	0	-0.004	-0.006	22.005	0.513	0.513	0.000	0.000	0.000	0.000
65	A	220	MET	0	-0.035	-0.004	19.128	-0.924	-0.924	0.000	0.000	0.000	0.000
66	A	221	GLN	0	0.024	0.003	21.710	0.598	0.598	0.000	0.000	0.000	0.000
67	A	222	LYS	1	0.834	0.933	20.648	13.970	13.970	0.000	0.000	0.000	0.000
68	A	223	ARG	1	0.851	0.929	21.961	13.098	13.098	0.000	0.000	0.000	0.000
69	A	224	SER	0	-0.002	-0.045	22.229	-0.160	-0.160	0.000	0.000	0.000	0.000
70	A	225	HIS	0	0.045	0.027	24.593	0.206	0.206	0.000	0.000	0.000	0.000
71	A	226	GLU	-1	-0.901	-0.950	26.337	-10.771	-10.771	0.000	0.000	0.000	0.000
72	A	227	GLY	0	0.006	0.014	23.569	-0.073	-0.073	0.000	0.000	0.000	0.000
73	A	228	GLY	0	-0.004	0.001	19.668	-0.707	-0.707	0.000	0.000	0.000	0.000
74	A	229	THR	0	-0.033	0.003	18.640	0.015	0.015	0.000	0.000	0.000	0.000
75	A	230	CYS	0	-0.038	-0.014	16.121	-1.140	-1.140	0.000	0.000	0.000	0.000
76	A	231	ALA	0	0.012	0.021	17.388	1.024	1.024	0.000	0.000	0.000	0.000
77	A	232	VAL	0	-0.020	-0.012	16.967	-1.562	-1.562	0.000	0.000	0.000	0.000
78	A	233	TYR	0	0.058	0.006	16.145	0.512	0.512	0.000	0.000	0.000	0.000
79	A	234	LEU	0	-0.007	-0.003	17.804	-0.686	-0.686	0.000	0.000	0.000	0.000
80	A	235	ILE	0	0.029	0.019	14.721	0.641	0.641	0.000	0.000	0.000	0.000
81	A	236	CYS	0	-0.057	-0.016	18.268	-0.456	-0.456	0.000	0.000	0.000	0.000
82	A	237	PHE	0	0.052	0.017	14.738	0.613	0.613	0.000	0.000	0.000	0.000
83	A	238	ASN	0	0.073	0.031	20.206	0.259	0.259	0.000	0.000	0.000	0.000
84	A	239	THR	0	0.008	0.004	20.396	0.082	0.082	0.000	0.000	0.000	0.000
85	A	240	ALA	0	0.000	-0.009	18.169	-0.805	-0.805	0.000	0.000	0.000	0.000
86	A	241	LYS	1	0.898	0.967	13.698	18.568	18.568	0.000	0.000	0.000	0.000
87	A	242	SER	0	0.069	0.033	10.966	-0.361	-0.361	0.000	0.000	0.000	0.000
88	A	243	ARG	1	0.785	0.876	6.005	34.978	34.978	0.000	0.000	0.000	0.000
89	A	244	GLU	-1	-0.878	-0.926	5.769	-40.046	-40.046	0.000	0.000	0.000	0.000
90	A	245	THR	0	0.018	-0.004	7.144	0.063	0.063	0.000	0.000	0.000	0.000
91	A	246	VAL	0	0.016	0.010	10.328	0.818	0.818	0.000	0.000	0.000	0.000
93	A	248	ASN	0	0.005	0.002	7.401	0.306	0.306	0.000	0.000	0.000	0.000
94	A	249	LEU	0	0.001	0.002	8.654	1.772	1.772	0.000	0.000	0.000	0.000
95	A	250	MET	0	0.008	-0.005	9.900	1.872	1.872	0.000	0.000	0.000	0.000
96	A	251	ALA	0	-0.032	-0.025	7.548	0.971	0.971	0.000	0.000	0.000	0.000
97	A	252	ASN	0	-0.027	-0.002	9.698	1.098	1.098	0.000	0.000	0.000	0.000
98	A	253	MET	0	-0.063	-0.003	12.890	1.546	1.546	0.000	0.000	0.000	0.000
99	A	254	LEU	0	-0.028	-0.026	12.825	1.310	1.310	0.000	0.000	0.000	0.000
100	A	255	ASN	0	-0.016	0.004	14.647	-0.225	-0.225	0.000	0.000	0.000	0.000
101	A	256	VAL	0	0.051	0.034	10.559	0.397	0.397	0.000	0.000	0.000	0.000
102	A	257	ARG	1	0.985	0.984	7.471	31.405	31.405	0.000	0.000	0.000	0.000
104	A	259	GLU	-1	-0.854	-0.927	5.266	-45.943	-45.943	0.000	0.000	0.000	0.000
105	A	260	CYS	0	-0.057	-0.002	6.060	0.533	0.533	0.000	0.000	0.000	0.000
106	A	261	LEU	0	0.067	0.047	6.271	2.905	2.905	0.000	0.000	0.000	0.000
107	A	262	MET	0	-0.038	-0.023	8.212	-1.847	-1.847	0.000	0.000	0.000	0.000
108	A	263	LEU	0	0.056	0.043	7.719	2.452	2.452	0.000	0.000	0.000	0.000
109	A	264	GLN	0	0.034	0.014	9.820	-2.268	-2.268	0.000	0.000	0.000	0.000
110	A	265	PRO	0	0.050	0.039	12.628	0.592	0.592	0.000	0.000	0.000	0.000
111	A	266	PRO	0	0.054	0.036	15.941	-0.125	-0.125	0.000	0.000	0.000	0.000
112	A	267	LYS	1	0.822	0.904	19.093	13.859	13.859	0.000	0.000	0.000	0.000
113	A	268	ILE	0	0.059	0.024	21.666	0.462	0.462	0.000	0.000	0.000	0.000
114	A	269	ARG	1	0.960	1.000	24.923	11.173	11.173	0.000	0.000	0.000	0.000
115	A	270	GLY	0	0.000	-0.009	25.377	-0.525	-0.525	0.000	0.000	0.000	0.000
116	A	271	LEU	0	0.070	0.055	26.781	0.043	0.043	0.000	0.000	0.000	0.000
117	A	272	SER	0	0.031	-0.069	25.028	0.213	0.213	0.000	0.000	0.000	0.000
118	A	273	ALA	0	-0.047	-0.018	23.369	-0.193	-0.193	0.000	0.000	0.000	0.000
119	A	274	ALA	0	0.043	0.034	24.139	-0.360	-0.360	0.000	0.000	0.000	0.000
120	A	275	LEU	0	0.015	0.015	26.909	0.072	0.072	0.000	0.000	0.000	0.000
121	A	276	PHE	0	0.068	0.030	21.411	0.212	0.212	0.000	0.000	0.000	0.000
122	A	277	TRP	0	0.030	0.009	19.169	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	278	PHE	0	0.030	0.031	26.117	0.166	0.166	0.000	0.000	0.000	0.000
124	A	279	LYS	1	0.997	0.992	28.992	11.158	11.158	0.000	0.000	0.000	0.000
125	A	280	SER	0	-0.021	-0.020	25.844	0.091	0.091	0.000	0.000	0.000	0.000
126	A	281	SER	0	-0.054	-0.030	27.896	-0.017	-0.017	0.000	0.000	0.000	0.000
127	A	282	LEU	0	0.026	0.023	29.798	0.184	0.184	0.000	0.000	0.000	0.000
128	A	283	SER	0	-0.058	-0.016	28.825	0.162	0.162	0.000	0.000	0.000	0.000
129	A	284	PRO	0	0.026	0.007	30.642	-0.171	-0.171	0.000	0.000	0.000	0.000
130	A	285	ALA	0	0.013	0.008	27.209	0.050	0.050	0.000	0.000	0.000	0.000
131	A	286	THR	0	-0.077	-0.042	26.141	-0.606	-0.606	0.000	0.000	0.000	0.000
132	A	287	LEU	0	0.003	0.017	25.423	0.447	0.447	0.000	0.000	0.000	0.000
133	A	288	LYS	1	0.877	0.922	25.671	10.176	10.176	0.000	0.000	0.000	0.000
134	A	289	HIS	0	0.005	0.006	26.168	0.526	0.526	0.000	0.000	0.000	0.000
135	A	290	GLY	0	0.032	0.022	27.500	-0.336	-0.336	0.000	0.000	0.000	0.000
136	A	291	ALA	0	0.002	0.002	30.086	0.129	0.129	0.000	0.000	0.000	0.000
137	A	292	LEU	0	0.019	0.002	26.669	-0.365	-0.365	0.000	0.000	0.000	0.000
138	A	293	PRO	0	0.028	0.016	23.610	0.201	0.201	0.000	0.000	0.000	0.000
139	A	294	GLU	-1	-0.843	-0.933	26.311	-10.341	-10.341	0.000	0.000	0.000	0.000
140	A	295	TRP	0	-0.023	-0.008	21.370	0.187	0.187	0.000	0.000	0.000	0.000
141	A	296	ILE	0	0.033	0.000	23.861	0.410	0.410	0.000	0.000	0.000	0.000
142	A	297	ARG	1	0.836	0.916	27.819	10.116	10.116	0.000	0.000	0.000	0.000
143	A	298	ALA	0	0.034	0.027	30.112	0.356	0.356	0.000	0.000	0.000	0.000
144	A	299	GLN	0	-0.139	-0.082	25.542	0.095	0.095	0.000	0.000	0.000	0.000
145	A	300	THR	0	-0.004	-0.014	30.413	0.119	0.119	0.000	0.000	0.000	0.000
146	A	301	THR	0	-0.016	0.004	32.534	0.190	0.190	0.000	0.000	0.000	0.000
147	A	302	LEU	0	-0.019	-0.014	34.563	-0.107	-0.107	0.000	0.000	0.000	0.000
148	A	303	ASN	0	-0.018	-0.005	36.623	0.002	0.002	0.000	0.000	0.000	0.000
149	A	304	ALA	0	0.041	0.028	39.708	-0.090	-0.090	0.000	0.000	0.000	0.000
150	A	305	ALA	0	-0.033	-0.028	41.449	0.012	0.012	0.000	0.000	0.000	0.000
151	A	306	ALA	0	-0.053	-0.030	42.940	0.008	0.008	0.000	0.000	0.000	0.000
152	A	307	ALA	-1	-0.906	-0.929	46.088	-6.733	-6.733	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:156:GLY)