FMO DATABASE

FMODB ID: 3MRKL

Calculation Name: 4II2-C-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | 2-(2-methoxyethoxy)ethanol | 1,2-ethanediol

Ligand 3-letter code: ATP | PG0 | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4II2

Chain ID: C

ChEMBL ID:

UniProt ID: P0CH07

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1379620.386639
FMO2-HF: Nuclear repulsion	1321860.941742
FMO2-HF: Total energy	-57759.444897
FMO2-MP2: Total energy	-57930.274558

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:1:MET)

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

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.
60.972	64.944	2.308	-1.602	-4.68	-0.005

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.906

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	3	LEU	0	0.104	0.069	3.855	-0.095	1.138	-0.006	-0.450	-0.777	-0.001
4	A	4	LYS	1	0.965	0.957	2.228	47.334	48.943	2.311	-0.883	-3.039	-0.003
5	A	5	ARG	1	0.698	0.840	3.736	35.823	36.402	0.002	-0.182	-0.399	-0.001
6	A	6	ILE	0	0.069	0.042	4.930	4.317	4.518	-0.001	-0.019	-0.181	0.000
8	A	8	ARG	1	0.887	0.964	3.134	56.464	56.814	0.002	-0.068	-0.284	0.000
7	A	7	ASN	0	0.020	0.000	6.908	4.871	4.871	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.666	-0.802	8.876	-26.109	-26.109	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.013	0.011	11.215	1.854	1.854	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.020	-0.009	11.827	1.649	1.649	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.920	-0.978	11.756	-23.104	-23.104	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.023	0.013	14.599	1.178	1.178	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.028	0.002	16.687	1.017	1.017	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.765	0.880	14.468	20.376	20.376	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.891	-0.934	18.018	-16.611	-16.611	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.052	-0.023	20.537	0.452	0.452	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.020	-0.028	24.105	-0.179	-0.179	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.001	0.008	23.171	0.274	0.274	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.027	-0.012	25.347	0.175	0.175	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.003	0.004	23.443	0.214	0.214	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.013	0.018	22.177	-0.509	-0.509	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.005	-0.017	18.496	0.195	0.195	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.027	0.023	16.377	-0.409	-0.409	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.034	-0.016	13.570	0.502	0.502	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.013	0.015	16.175	1.037	1.037	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.014	-0.006	18.254	-0.240	-0.240	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.928	-0.966	15.415	-16.749	-16.749	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.851	-0.915	13.881	-21.965	-21.965	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.021	-0.040	8.230	-0.811	-0.811	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.084	-0.050	6.448	-3.598	-3.598	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.017	-0.002	12.080	1.094	1.094	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.020	0.005	11.838	0.392	0.392	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.013	0.010	16.968	0.815	0.815	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.035	-0.025	20.076	-0.539	-0.539	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.021	-0.008	21.873	0.677	0.677	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.019	-0.012	24.408	-0.434	-0.434	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.013	0.014	27.234	0.355	0.355	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.015	-0.002	30.581	-0.163	-0.163	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.010	0.010	31.186	0.230	0.230	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.018	0.004	33.724	0.239	0.239	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.911	-0.951	35.278	-8.965	-8.965	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.041	0.016	35.617	0.090	0.090	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.077	-0.045	37.713	0.119	0.119	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.021	-0.049	34.831	0.072	0.072	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.010	0.011	36.044	-0.171	-0.171	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.022	-0.013	36.284	0.217	0.217	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.013	0.006	35.287	0.030	0.030	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.028	-0.017	29.937	-0.267	-0.267	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.027	-0.023	29.494	0.102	0.102	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.057	0.018	26.171	-0.507	-0.507	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.005	-0.002	23.196	0.176	0.176	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.018	0.022	21.234	-0.131	-0.131	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.017	-0.024	15.683	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	HIS	0	0.031	0.025	15.904	-0.660	-0.660	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.000	-0.009	10.670	-0.370	-0.370	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.002	0.010	10.947	0.314	0.314	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.064	0.010	8.962	-2.045	-2.045	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.884	-0.934	6.821	-30.982	-30.982	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.015	0.001	7.645	0.483	0.483	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.056	-0.043	5.041	-8.594	-8.594	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.017	-0.027	5.423	2.520	2.520	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.864	0.936	9.955	26.856	26.856	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.045	0.032	12.214	-1.657	-1.657	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.033	-0.020	13.521	0.041	0.041	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.902	0.954	15.212	18.673	18.673	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.005	0.004	18.604	-0.335	-0.335	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.049	-0.032	20.815	0.464	0.464	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.021	0.002	24.252	-0.228	-0.228	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.018	-0.021	25.812	0.107	0.107	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.001	0.032	28.584	0.245	0.245	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.885	0.949	31.440	8.367	8.367	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.051	0.022	31.773	0.168	0.168	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.025	0.022	34.921	0.097	0.097	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.053	0.015	32.272	0.143	0.143	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.028	0.021	35.302	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.017	-0.003	30.490	0.131	0.131	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.003	0.005	29.251	-0.441	-0.441	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.049	0.029	30.328	0.302	0.302	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.004	-0.013	32.467	-0.197	-0.197	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.042	-0.016	30.211	0.176	0.176	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.041	0.045	28.722	-0.351	-0.351	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.001	-0.003	26.567	-0.333	-0.333	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.000	-0.005	24.021	0.427	0.427	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.044	0.003	25.928	-0.426	-0.426	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.060	0.008	23.581	0.174	0.174	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.789	-0.890	23.487	-12.762	-12.762	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.038	-0.023	18.589	-0.589	-0.589	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.021	-0.012	18.599	-1.172	-1.172	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.815	0.877	19.606	13.138	13.138	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.835	-0.900	19.193	-14.248	-14.248	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.036	-0.008	20.427	-0.412	-0.412	0.000	0.000	0.000	0.000
93	A	93	TRP	0	-0.035	-0.025	11.209	-0.100	-0.100	0.000	0.000	0.000	0.000
94	A	94	SER	0	0.027	-0.001	14.078	-0.140	-0.140	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.003	-0.011	8.716	-0.470	-0.470	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.002	0.012	9.932	-2.518	-2.518	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.047	0.011	12.480	0.739	0.739	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.006	-0.018	11.915	-1.781	-1.781	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.066	0.027	13.535	1.585	1.585	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.048	0.024	15.860	0.789	0.789	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.914	0.962	16.288	19.295	19.295	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.014	0.013	16.963	0.862	0.862	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.021	0.007	19.615	0.820	0.820	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.015	0.011	21.710	0.720	0.720	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.012	0.019	22.558	0.860	0.860	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.021	0.000	22.349	0.510	0.510	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.009	-0.006	25.605	0.632	0.632	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.016	-0.012	26.932	0.477	0.477	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.008	0.015	27.662	0.376	0.376	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.043	-0.013	29.403	0.363	0.363	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.072	-0.033	31.890	0.354	0.354	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.905	-0.946	32.868	-8.831	-8.831	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.070	-0.036	32.825	-0.270	-0.270	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.043	0.017	31.191	0.488	0.488	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.052	-0.024	34.212	-0.066	-0.066	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.854	-0.929	36.365	-8.012	-8.012	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.938	-0.958	30.304	-10.403	-10.403	0.000	0.000	0.000	0.000
118	A	118	PRO	0	-0.056	-0.024	33.120	-0.184	-0.184	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.007	-0.005	29.934	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.042	-0.027	33.800	0.159	0.159	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.033	0.002	37.072	0.147	0.147	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.942	-0.959	39.883	-7.213	-7.213	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.014	-0.009	37.600	0.159	0.159	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.015	0.013	38.007	0.056	0.056	0.000	0.000	0.000	0.000
125	A	125	HIS	0	0.016	0.009	39.773	0.014	0.014	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.013	0.007	43.520	0.136	0.136	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.027	0.007	37.747	0.173	0.173	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.870	0.926	40.858	7.760	7.760	0.000	0.000	0.000	0.000
129	A	129	THR	0	-0.083	-0.044	43.850	0.168	0.168	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.825	-0.901	46.655	-6.409	-6.409	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.933	0.972	41.003	7.643	7.643	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.004	-0.008	44.868	-0.084	-0.084	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.965	0.981	45.008	6.908	6.908	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.022	-0.016	37.174	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.889	-0.956	41.962	-7.559	-7.559	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.036	-0.021	43.177	-0.074	-0.074	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.053	-0.041	43.145	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.005	0.007	38.897	-0.102	-0.102	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.999	1.029	39.790	7.080	7.080	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.838	-0.896	41.921	-7.019	-7.019	0.000	0.000	0.000	0.000
141	A	141	TRP	0	-0.032	-0.033	37.139	-0.072	-0.072	0.000	0.000	0.000	0.000
142	A	142	THR	0	0.035	0.006	36.772	-0.232	-0.232	0.000	0.000	0.000	0.000
143	A	143	ARG	1	0.852	0.896	38.673	6.995	6.995	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.834	0.932	41.424	7.197	7.197	0.000	0.000	0.000	0.000
145	A	145	TYR	0	-0.049	-0.034	36.573	0.080	0.080	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.026	0.017	34.499	-0.210	-0.210	0.000	0.000	0.000	0.000
147	A	147	ILE	0	-0.030	-0.001	35.163	-0.144	-0.144	0.000	0.000	0.000	0.000
148	A	148	HIS	0	-0.078	-0.022	34.226	-0.209	-0.209	0.000	0.000	0.000	0.000
149	A	149	GLY	-1	-0.891	-0.942	36.352	-8.261	-8.261	0.000	0.000	0.000	0.000

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