FMO DATABASE

FMODB ID: R4L28

Calculation Name: 5XJC-v-Other547

Preferred Name:

Target Type:

Ligand 3-letter code: IHP | GTP | ATP | ADP | SEP | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XJC

Chain ID: v

ChEMBL ID:

UniProt ID: O60306

Base Structure: ElectronMicroscopy

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1396411.648684
FMO2-HF: Nuclear repulsion	1337858.766156
FMO2-HF: Total energy	-58552.882529
FMO2-MP2: Total energy	-58726.177469

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:5:SER)

Summations of interaction energy for fragment #1(A:5: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.
-79.959	-78.149	0.059	-0.803	-1.066	-0.003

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.776 / q_NPA : 0.864

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	7	PHE	0	0.041	0.014	3.399	3.011	4.415	-0.007	-0.563	-0.834	-0.001
91	A	95	GLY	0	-0.024	-0.007	3.001	1.170	1.444	0.066	-0.145	-0.195	-0.001
92	A	96	ASP	-1	-0.980	-0.997	3.991	-41.012	-40.880	0.000	-0.095	-0.037	-0.001
4	A	8	TYR	0	-0.088	-0.059	6.996	2.396	2.396	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.035	0.031	9.968	0.351	0.351	0.000	0.000	0.000	0.000
6	A	10	ARG	1	0.756	0.872	13.498	17.060	17.060	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.004	-0.008	16.689	0.391	0.391	0.000	0.000	0.000	0.000
8	A	12	TYR	0	-0.036	-0.036	20.161	0.537	0.537	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.009	0.006	23.517	0.185	0.185	0.000	0.000	0.000	0.000
10	A	14	GLY	0	0.038	0.015	27.076	0.156	0.156	0.000	0.000	0.000	0.000
11	A	15	HIS	0	-0.018	0.001	30.167	-0.186	-0.186	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.937	0.961	31.207	9.979	9.979	0.000	0.000	0.000	0.000
13	A	17	GLY	0	0.020	0.007	35.817	0.142	0.142	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.926	0.963	39.410	6.942	6.942	0.000	0.000	0.000	0.000
15	A	19	PHE	0	0.003	0.005	39.037	0.265	0.265	0.000	0.000	0.000	0.000
16	A	20	GLY	0	0.089	0.065	37.445	-0.153	-0.153	0.000	0.000	0.000	0.000
17	A	21	HIS	0	-0.027	-0.015	28.481	-0.080	-0.080	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.790	-0.855	32.913	-8.874	-8.874	0.000	0.000	0.000	0.000
19	A	23	PHE	0	-0.032	-0.022	25.867	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	24	LEU	0	0.002	0.012	25.559	0.192	0.192	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.884	-0.947	21.485	-14.443	-14.443	0.000	0.000	0.000	0.000
22	A	26	PHE	0	-0.026	-0.018	18.597	0.526	0.526	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.752	-0.840	15.163	-19.679	-19.679	0.000	0.000	0.000	0.000
24	A	28	PHE	0	0.033	0.009	13.442	0.823	0.823	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.850	0.906	11.356	19.817	19.817	0.000	0.000	0.000	0.000
26	A	30	PRO	0	0.058	0.023	6.487	0.887	0.887	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.907	-0.959	8.532	-23.850	-23.850	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.030	0.009	11.330	2.055	2.055	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.815	0.925	13.139	18.416	18.416	0.000	0.000	0.000	0.000
30	A	34	LEU	0	0.008	0.014	15.104	-0.793	-0.793	0.000	0.000	0.000	0.000
31	A	35	ARG	1	0.838	0.897	17.752	16.501	16.501	0.000	0.000	0.000	0.000
32	A	36	TYR	0	0.029	0.012	20.137	-0.078	-0.078	0.000	0.000	0.000	0.000
33	A	37	ALA	0	-0.015	-0.021	23.231	0.400	0.400	0.000	0.000	0.000	0.000
34	A	38	ASN	0	-0.018	0.002	25.908	0.051	0.051	0.000	0.000	0.000	0.000
35	A	39	ASN	0	0.016	-0.008	29.223	0.267	0.267	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.036	-0.022	31.883	0.073	0.073	0.000	0.000	0.000	0.000
37	A	41	ASN	0	-0.033	-0.012	35.422	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	42	TYR	0	0.014	-0.002	38.711	0.402	0.402	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.860	0.929	40.860	7.057	7.057	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.029	-0.015	41.793	0.056	0.056	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.859	-0.895	38.135	-8.580	-8.580	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.021	-0.025	35.585	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	47	MET	0	-0.041	-0.006	29.298	-0.341	-0.341	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.007	0.004	29.839	0.024	0.024	0.000	0.000	0.000	0.000
45	A	49	ARG	1	0.941	0.954	25.456	11.372	11.372	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.901	0.968	25.605	11.292	11.292	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.804	-0.891	20.972	-15.188	-15.188	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.010	0.008	20.700	0.682	0.682	0.000	0.000	0.000	0.000
49	A	53	TYR	0	-0.015	0.002	15.497	0.090	0.090	0.000	0.000	0.000	0.000
50	A	54	VAL	0	-0.004	0.004	14.982	1.013	1.013	0.000	0.000	0.000	0.000
51	A	55	HIS	0	0.033	0.030	15.133	-1.738	-1.738	0.000	0.000	0.000	0.000
52	A	56	LYS	1	1.016	0.994	10.209	22.961	22.961	0.000	0.000	0.000	0.000
53	A	57	SER	0	0.013	-0.015	11.793	-0.852	-0.852	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.013	0.008	14.190	0.166	0.166	0.000	0.000	0.000	0.000
55	A	59	MET	0	0.000	0.008	10.110	0.913	0.913	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.877	-0.919	7.973	-35.321	-35.321	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.821	-0.872	10.942	-17.166	-17.166	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.036	-0.018	12.854	0.617	0.617	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.839	0.901	5.400	40.206	40.206	0.000	0.000	0.000	0.000
60	A	64	ARG	1	0.816	0.881	10.756	17.848	17.848	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.031	-0.014	13.092	0.897	0.897	0.000	0.000	0.000	0.000
62	A	66	ILE	0	-0.009	-0.008	12.416	0.876	0.876	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.898	-0.940	10.316	-26.539	-26.539	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.883	-0.952	13.526	-16.096	-16.096	0.000	0.000	0.000	0.000
65	A	69	SER	0	-0.108	-0.064	16.716	1.037	1.037	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.944	-0.978	16.425	-14.924	-14.924	0.000	0.000	0.000	0.000
67	A	71	ILE	0	0.004	-0.006	15.399	0.114	0.114	0.000	0.000	0.000	0.000
68	A	72	THR	0	-0.082	-0.061	11.926	1.041	1.041	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.890	0.955	14.880	18.742	18.742	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.919	-0.938	17.975	-13.015	-13.015	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.895	-0.968	18.923	-14.713	-14.713	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.830	-0.910	21.348	-13.195	-13.195	0.000	0.000	0.000	0.000
73	A	77	ALA	0	-0.001	0.017	23.828	0.688	0.688	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.067	-0.045	26.329	0.628	0.628	0.000	0.000	0.000	0.000
75	A	79	TRP	0	-0.044	-0.024	21.735	0.463	0.463	0.000	0.000	0.000	0.000
76	A	80	PRO	0	-0.015	-0.008	28.738	0.189	0.189	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.059	0.043	29.365	-0.366	-0.366	0.000	0.000	0.000	0.000
78	A	82	PRO	0	-0.030	-0.009	27.988	0.237	0.237	0.000	0.000	0.000	0.000
79	A	83	ASP	-1	-0.807	-0.912	30.345	-9.081	-9.081	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.876	0.917	33.888	7.880	7.880	0.000	0.000	0.000	0.000
81	A	85	VAL	0	-0.020	0.002	35.444	0.098	0.098	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.038	-0.041	32.490	-0.043	-0.043	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.851	0.925	25.378	12.076	12.076	0.000	0.000	0.000	0.000
84	A	88	GLN	0	0.004	-0.005	24.848	-0.195	-0.195	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.789	-0.877	21.403	-13.702	-13.702	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.025	-0.007	17.266	0.133	0.133	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.867	-0.921	14.371	-19.487	-19.487	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.004	-0.016	10.840	-0.248	-0.248	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.015	0.004	6.303	0.188	0.188	0.000	0.000	0.000	0.000
90	A	94	ILE	0	0.026	0.002	6.449	-2.789	-2.789	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.832	-0.896	6.267	-21.998	-21.998	0.000	0.000	0.000	0.000
94	A	98	HIS	0	-0.059	-0.028	9.136	-1.104	-1.104	0.000	0.000	0.000	0.000
95	A	99	ILE	0	0.053	0.032	10.825	1.788	1.788	0.000	0.000	0.000	0.000
96	A	100	SER	0	-0.057	-0.056	14.207	-0.401	-0.401	0.000	0.000	0.000	0.000
97	A	101	PHE	0	0.032	0.042	16.744	0.604	0.604	0.000	0.000	0.000	0.000
98	A	102	THR	0	-0.078	-0.059	20.554	0.031	0.031	0.000	0.000	0.000	0.000
99	A	103	THR	0	-0.009	-0.011	23.886	0.372	0.372	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.004	0.000	26.991	-0.072	-0.072	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.795	0.896	28.842	9.399	9.399	0.000	0.000	0.000	0.000
102	A	106	ILE	0	0.027	0.031	27.323	0.227	0.227	0.000	0.000	0.000	0.000
103	A	107	GLY	0	-0.028	-0.009	31.343	-0.097	-0.097	0.000	0.000	0.000	0.000
104	A	108	SER	0	-0.045	-0.033	33.718	0.111	0.111	0.000	0.000	0.000	0.000
105	A	109	LEU	0	0.065	0.020	31.319	-0.053	-0.053	0.000	0.000	0.000	0.000
106	A	110	ILE	0	-0.048	-0.003	34.038	0.032	0.032	0.000	0.000	0.000	0.000
107	A	111	ASP	-1	-0.814	-0.924	33.654	-8.953	-8.953	0.000	0.000	0.000	0.000
108	A	112	VAL	0	-0.006	0.009	29.677	-0.085	-0.085	0.000	0.000	0.000	0.000
109	A	113	ASN	0	0.017	0.002	32.126	-0.292	-0.292	0.000	0.000	0.000	0.000
110	A	114	GLN	0	-0.032	-0.010	34.728	0.165	0.165	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.077	-0.026	31.603	0.031	0.031	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.886	0.931	32.081	9.811	9.811	0.000	0.000	0.000	0.000
113	A	117	ASP	-1	-0.744	-0.871	26.219	-11.961	-11.961	0.000	0.000	0.000	0.000
114	A	118	PRO	0	-0.030	-0.014	28.755	-0.251	-0.251	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.825	-0.883	27.944	-10.363	-10.363	0.000	0.000	0.000	0.000
116	A	120	GLY	0	0.112	0.046	24.172	-0.304	-0.304	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.056	-0.023	24.149	-0.344	-0.344	0.000	0.000	0.000	0.000
118	A	122	ARG	1	0.728	0.827	26.450	10.328	10.328	0.000	0.000	0.000	0.000
119	A	123	VAL	0	0.043	0.038	20.603	0.055	0.055	0.000	0.000	0.000	0.000
120	A	124	PHE	0	0.013	0.003	21.158	-0.266	-0.266	0.000	0.000	0.000	0.000
121	A	125	TYR	0	-0.015	-0.022	22.884	0.019	0.019	0.000	0.000	0.000	0.000
122	A	126	TYR	0	-0.010	-0.002	24.909	0.424	0.424	0.000	0.000	0.000	0.000
123	A	127	LEU	0	0.119	0.077	17.209	0.011	0.011	0.000	0.000	0.000	0.000
124	A	128	VAL	0	-0.001	-0.003	21.381	-0.273	-0.273	0.000	0.000	0.000	0.000
125	A	129	GLN	0	-0.138	-0.086	22.936	0.501	0.501	0.000	0.000	0.000	0.000
126	A	130	ASP	-1	-0.863	-0.922	21.227	-13.355	-13.355	0.000	0.000	0.000	0.000
127	A	131	LEU	0	0.006	-0.002	16.731	-0.163	-0.163	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.899	0.961	20.581	12.018	12.018	0.000	0.000	0.000	0.000
129	A	133	CYS	0	-0.033	-0.001	23.924	0.346	0.346	0.000	0.000	0.000	0.000
130	A	134	LEU	0	0.061	0.043	17.273	0.344	0.344	0.000	0.000	0.000	0.000
131	A	135	VAL	0	0.017	0.003	20.122	0.115	0.115	0.000	0.000	0.000	0.000
132	A	136	PHE	0	-0.046	-0.042	22.224	0.340	0.340	0.000	0.000	0.000	0.000
133	A	137	SER	0	-0.018	-0.007	23.884	0.604	0.604	0.000	0.000	0.000	0.000
134	A	138	LEU	0	-0.026	-0.009	18.908	0.291	0.291	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.029	-0.020	22.540	0.380	0.380	0.000	0.000	0.000	0.000
136	A	140	GLY	0	-0.013	-0.010	25.458	0.486	0.486	0.000	0.000	0.000	0.000
137	A	141	LEU	0	-0.029	-0.030	25.623	0.419	0.419	0.000	0.000	0.000	0.000
138	A	142	HIS	0	-0.011	0.011	24.663	0.097	0.097	0.000	0.000	0.000	0.000
139	A	143	PHE	0	-0.027	-0.023	25.002	0.213	0.213	0.000	0.000	0.000	0.000
140	A	144	LYS	1	0.875	0.955	30.098	9.686	9.686	0.000	0.000	0.000	0.000
141	A	145	ILE	0	0.030	0.017	32.813	0.008	0.008	0.000	0.000	0.000	0.000
142	A	146	LYS	1	0.932	0.960	34.389	9.094	9.094	0.000	0.000	0.000	0.000
143	A	147	PRO	0	-0.041	-0.036	37.226	0.100	0.100	0.000	0.000	0.000	0.000
144	A	148	ILE	-1	-0.898	-0.923	39.773	-7.829	-7.829	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)