FMO DATABASE

FMODB ID: 2MZYR

Calculation Name: 6KPP-E-Xray547

Preferred Name:

Target Type:

Ligand 3-letter code: GTP | GDP | DO6 | MES | GOL | CA | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6KPP

Chain ID: E

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-628259.121163
FMO2-HF: Nuclear repulsion	576838.448372
FMO2-HF: Total energy	-51420.672792
FMO2-MP2: Total energy	-51568.699496

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-59.434	-51.716	11.161	-8.217	-10.665	-0.077

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.773 / q_NPA : 0.882

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	6	VAL	0	-0.027	-0.011	3.832	1.995	3.592	-0.023	-0.629	-0.945	-0.002
17	A	20	VAL	0	-0.031	-0.032	2.523	-3.289	-3.111	1.891	-0.392	-1.678	-0.004
18	A	21	ILE	0	0.071	0.059	4.438	-0.612	-0.056	-0.001	-0.206	-0.350	-0.001
19	A	22	LEU	0	-0.026	-0.037	2.127	-28.754	-25.736	9.049	-5.992	-6.076	-0.052
20	A	23	LYS	1	0.916	0.942	2.723	20.326	22.695	0.245	-0.998	-1.616	-0.018
4	A	7	ILE	0	0.042	0.013	6.288	1.982	1.982	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.891	-0.950	9.505	-19.573	-19.573	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.054	-0.019	10.956	0.959	0.959	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.002	0.012	12.918	1.591	1.591	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.882	0.917	15.369	16.866	16.866	0.000	0.000	0.000	0.000
9	A	12	CYS	0	-0.012	0.016	17.653	0.743	0.743	0.000	0.000	0.000	0.000
10	A	13	THR	0	0.029	-0.007	20.433	-0.314	-0.314	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.003	-0.006	22.163	0.313	0.313	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.019	0.014	18.099	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	16	GLN	0	-0.003	-0.007	13.601	-0.251	-0.251	0.000	0.000	0.000	0.000
14	A	17	SER	0	-0.017	0.005	12.854	0.211	0.211	0.000	0.000	0.000	0.000
15	A	18	PHE	0	-0.001	-0.002	5.874	0.373	0.373	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.881	-0.924	8.163	-27.463	-27.463	0.000	0.000	0.000	0.000
21	A	24	PRO	0	0.036	0.022	5.434	1.643	1.643	0.000	0.000	0.000	0.000
22	A	25	PRO	0	-0.007	0.006	8.525	0.307	0.307	0.000	0.000	0.000	0.000
23	A	26	SER	-1	-0.943	-0.964	12.094	-19.568	-19.568	0.000	0.000	0.000	0.000
24	A	42	ASP	0	-0.088	-0.047	37.508	-0.430	-0.430	0.000	0.000	0.000	0.000
25	A	43	PRO	0	0.030	0.005	40.465	0.036	0.036	0.000	0.000	0.000	0.000
26	A	44	SER	0	0.036	0.021	44.139	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	45	LEU	0	0.039	0.009	46.875	0.003	0.003	0.000	0.000	0.000	0.000
28	A	46	GLU	-1	-0.846	-0.909	48.463	-5.957	-5.957	0.000	0.000	0.000	0.000
29	A	47	GLU	-1	-0.834	-0.916	47.193	-6.743	-6.743	0.000	0.000	0.000	0.000
30	A	48	ILE	0	-0.021	-0.015	44.361	0.022	0.022	0.000	0.000	0.000	0.000
31	A	49	GLN	0	-0.018	-0.011	48.415	-0.046	-0.046	0.000	0.000	0.000	0.000
32	A	50	LYS	1	0.903	0.947	52.080	5.996	5.996	0.000	0.000	0.000	0.000
33	A	51	LYS	1	0.892	0.938	47.123	6.664	6.664	0.000	0.000	0.000	0.000
34	A	52	LEU	0	-0.001	0.004	48.198	0.023	0.023	0.000	0.000	0.000	0.000
35	A	53	GLU	-1	-0.849	-0.920	52.012	-5.530	-5.530	0.000	0.000	0.000	0.000
36	A	54	ALA	0	-0.008	-0.008	54.259	0.098	0.098	0.000	0.000	0.000	0.000
37	A	55	ALA	0	-0.090	-0.053	52.511	0.034	0.034	0.000	0.000	0.000	0.000
38	A	56	GLU	-1	-0.852	-0.914	54.649	-5.308	-5.308	0.000	0.000	0.000	0.000
39	A	57	GLU	-1	-0.851	-0.937	57.277	-5.008	-5.008	0.000	0.000	0.000	0.000
40	A	58	ARG	1	0.904	0.955	52.952	5.838	5.838	0.000	0.000	0.000	0.000
41	A	59	ARG	1	0.858	0.927	56.124	5.469	5.469	0.000	0.000	0.000	0.000
42	A	60	LYS	1	0.964	0.978	59.165	5.102	5.102	0.000	0.000	0.000	0.000
43	A	61	TYR	0	-0.022	0.004	62.274	0.058	0.058	0.000	0.000	0.000	0.000
44	A	62	GLN	0	-0.008	-0.014	57.840	0.050	0.050	0.000	0.000	0.000	0.000
45	A	63	GLU	-1	-0.959	-0.972	63.089	-4.871	-4.871	0.000	0.000	0.000	0.000
46	A	64	ALA	0	0.013	0.001	64.718	0.084	0.084	0.000	0.000	0.000	0.000
47	A	65	GLU	-1	-0.821	-0.899	66.140	-4.513	-4.513	0.000	0.000	0.000	0.000
48	A	66	LEU	0	-0.021	0.001	65.222	0.071	0.071	0.000	0.000	0.000	0.000
49	A	67	LEU	0	-0.011	-0.023	68.052	0.078	0.078	0.000	0.000	0.000	0.000
50	A	68	LYS	1	0.843	0.916	70.223	4.548	4.548	0.000	0.000	0.000	0.000
51	A	69	HIS	0	0.058	0.033	70.622	0.070	0.070	0.000	0.000	0.000	0.000
52	A	70	LEU	0	-0.046	-0.032	69.945	0.063	0.063	0.000	0.000	0.000	0.000
53	A	71	ALA	0	-0.037	-0.014	73.714	0.066	0.066	0.000	0.000	0.000	0.000
54	A	72	GLU	-1	-0.864	-0.933	75.665	-4.138	-4.138	0.000	0.000	0.000	0.000
55	A	73	LYS	1	0.849	0.919	75.095	4.123	4.123	0.000	0.000	0.000	0.000
56	A	74	ARG	1	0.797	0.855	75.251	4.127	4.127	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.962	-0.962	79.945	-3.800	-3.800	0.000	0.000	0.000	0.000
58	A	76	HIS	0	0.079	0.032	80.768	0.053	0.053	0.000	0.000	0.000	0.000
59	A	77	GLU	-1	-0.838	-0.887	78.870	-3.956	-3.956	0.000	0.000	0.000	0.000
60	A	78	ARG	1	0.906	0.962	83.222	3.778	3.778	0.000	0.000	0.000	0.000
61	A	79	GLU	-1	-0.885	-0.938	85.787	-3.619	-3.619	0.000	0.000	0.000	0.000
62	A	80	VAL	0	-0.014	-0.008	84.846	0.053	0.053	0.000	0.000	0.000	0.000
63	A	81	ILE	0	-0.032	-0.015	87.708	0.046	0.046	0.000	0.000	0.000	0.000
64	A	82	GLN	0	-0.004	-0.014	89.573	0.021	0.021	0.000	0.000	0.000	0.000
65	A	83	LYS	1	0.932	0.983	90.674	3.517	3.517	0.000	0.000	0.000	0.000
66	A	84	ALA	0	0.004	0.003	91.537	0.041	0.041	0.000	0.000	0.000	0.000
67	A	85	ILE	0	-0.049	-0.023	93.427	0.043	0.043	0.000	0.000	0.000	0.000
68	A	86	GLU	-1	-0.897	-0.943	95.661	-3.171	-3.171	0.000	0.000	0.000	0.000
69	A	87	GLU	-1	-0.912	-0.974	94.512	-3.330	-3.330	0.000	0.000	0.000	0.000
70	A	88	ASN	0	-0.026	-0.004	97.763	0.046	0.046	0.000	0.000	0.000	0.000
71	A	89	ASN	0	0.004	-0.008	99.527	0.052	0.052	0.000	0.000	0.000	0.000
72	A	90	ASN	0	0.028	0.001	101.203	0.068	0.068	0.000	0.000	0.000	0.000
73	A	91	PHE	0	-0.001	0.011	102.159	0.041	0.041	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.004	-0.003	103.047	0.042	0.042	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.885	0.959	105.647	3.038	3.038	0.000	0.000	0.000	0.000
76	A	94	MET	0	0.021	0.000	105.817	0.028	0.028	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.033	-0.001	108.057	0.033	0.033	0.000	0.000	0.000	0.000
78	A	96	LYS	1	0.951	0.963	109.796	2.895	2.895	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.868	-0.935	109.895	-2.889	-2.889	0.000	0.000	0.000	0.000
80	A	98	LYS	1	0.963	0.980	109.810	2.926	2.926	0.000	0.000	0.000	0.000
81	A	99	LEU	0	-0.035	-0.013	113.984	0.026	0.026	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.020	0.005	115.909	0.029	0.029	0.000	0.000	0.000	0.000
83	A	101	GLN	0	0.026	0.015	116.980	0.009	0.009	0.000	0.000	0.000	0.000
84	A	102	LYS	1	0.937	0.965	116.044	2.770	2.770	0.000	0.000	0.000	0.000
85	A	103	MET	0	-0.041	-0.020	119.640	0.020	0.020	0.000	0.000	0.000	0.000
86	A	104	GLU	-1	-0.786	-0.879	121.865	-2.539	-2.539	0.000	0.000	0.000	0.000
87	A	105	SER	0	-0.038	-0.021	122.653	0.019	0.019	0.000	0.000	0.000	0.000
88	A	106	ASN	0	-0.070	-0.046	124.052	0.032	0.032	0.000	0.000	0.000	0.000
89	A	107	LYS	1	0.829	0.909	125.823	2.545	2.545	0.000	0.000	0.000	0.000
90	A	108	GLU	-1	-0.822	-0.897	125.775	-2.539	-2.539	0.000	0.000	0.000	0.000
91	A	109	ASN	0	-0.016	-0.007	126.342	0.034	0.034	0.000	0.000	0.000	0.000
92	A	110	ARG	1	0.922	0.962	130.070	2.446	2.446	0.000	0.000	0.000	0.000
93	A	111	GLU	-1	-0.908	-0.966	131.498	-2.428	-2.428	0.000	0.000	0.000	0.000
94	A	112	ALA	0	0.025	0.016	133.082	0.024	0.024	0.000	0.000	0.000	0.000
95	A	113	HIS	0	-0.028	-0.013	134.018	0.019	0.019	0.000	0.000	0.000	0.000
96	A	114	LEU	0	-0.036	-0.024	135.676	0.020	0.020	0.000	0.000	0.000	0.000
97	A	115	ALA	0	0.018	0.014	137.677	0.022	0.022	0.000	0.000	0.000	0.000
98	A	116	ALA	0	0.076	0.029	138.727	0.020	0.020	0.000	0.000	0.000	0.000
99	A	117	MET	0	-0.114	-0.058	139.087	0.019	0.019	0.000	0.000	0.000	0.000
100	A	118	LEU	0	0.011	-0.002	141.970	0.019	0.019	0.000	0.000	0.000	0.000
101	A	119	GLU	-1	-0.922	-0.948	142.223	-2.246	-2.246	0.000	0.000	0.000	0.000
102	A	120	ARG	1	0.928	0.955	140.252	2.293	2.293	0.000	0.000	0.000	0.000
103	A	121	LEU	0	-0.050	-0.019	146.377	0.016	0.016	0.000	0.000	0.000	0.000
104	A	122	GLN	0	0.014	0.013	147.126	0.014	0.014	0.000	0.000	0.000	0.000
105	A	123	GLU	-1	-0.792	-0.876	149.388	-2.112	-2.112	0.000	0.000	0.000	0.000
106	A	124	LYS	1	0.930	0.965	151.162	2.120	2.120	0.000	0.000	0.000	0.000
107	A	125	ASP	-1	-0.884	-0.945	152.906	-2.086	-2.086	0.000	0.000	0.000	0.000
108	A	126	LYS	1	0.816	0.897	152.531	2.131	2.131	0.000	0.000	0.000	0.000
109	A	127	HIS	0	-0.002	-0.002	155.241	0.011	0.011	0.000	0.000	0.000	0.000
110	A	128	ALA	0	-0.012	-0.008	157.062	0.016	0.016	0.000	0.000	0.000	0.000
111	A	129	GLU	-1	-0.857	-0.912	158.732	-1.993	-1.993	0.000	0.000	0.000	0.000
112	A	130	GLU	-1	-0.949	-0.967	158.912	-2.027	-2.027	0.000	0.000	0.000	0.000
113	A	131	VAL	0	-0.016	-0.015	160.790	0.017	0.017	0.000	0.000	0.000	0.000
114	A	132	ARG	1	0.808	0.887	159.293	2.025	2.025	0.000	0.000	0.000	0.000
115	A	133	LYS	1	0.834	0.898	164.383	1.960	1.960	0.000	0.000	0.000	0.000
116	A	134	ASN	0	-0.039	-0.018	165.067	0.018	0.018	0.000	0.000	0.000	0.000
117	A	135	LYS	1	0.828	0.898	167.019	1.901	1.901	0.000	0.000	0.000	0.000
118	A	136	GLU	-1	-0.788	-0.892	168.367	-1.915	-1.915	0.000	0.000	0.000	0.000
119	A	137	LEU	0	0.001	-0.003	168.223	0.011	0.011	0.000	0.000	0.000	0.000
120	A	138	LYS	1	0.874	0.942	169.328	1.910	1.910	0.000	0.000	0.000	0.000
121	A	139	GLU	-1	-0.902	-0.930	173.383	-1.862	-1.862	0.000	0.000	0.000	0.000
122	A	140	GLU	-1	-0.984	-0.983	175.043	-1.811	-1.811	0.000	0.000	0.000	0.000
123	A	141	ALA	-1	-0.998	-0.979	175.354	-1.825	-1.825	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)