FMO DATABASE

FMODB ID: 74ZNK

Calculation Name: 1KSH-B-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | phosphate ion | s,s-(2-hydroxyethyl)thiocysteine | magnesium ion

Ligand 3-letter code: GDP | PO4 | CME | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KSH

Chain ID: B

ChEMBL ID:

UniProt ID: Q9D0J4

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1470131.966689
FMO2-HF: Nuclear repulsion	1409345.024387
FMO2-HF: Total energy	-60786.942302
FMO2-MP2: Total energy	-60963.602741

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(B:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
-117.423	-116.825	28.426	-16.418	-12.607	-0.114

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.778 / q_NPA : 0.859

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	B	4	LYS	1	0.997	1.006	2.859	36.063	38.796	0.572	-1.356	-1.949	0.006
4	B	5	ASP	-1	-0.819	-0.888	1.680	-127.424	-130.463	27.838	-14.736	-10.064	-0.120
5	B	6	GLU	-1	-0.929	-0.965	3.744	-42.068	-41.164	0.016	-0.326	-0.594	0.000
6	B	7	ARG	1	0.856	0.916	5.452	29.746	29.746	0.000	0.000	0.000	0.000
7	B	8	ALA	0	0.005	-0.001	6.637	3.397	3.397	0.000	0.000	0.000	0.000
8	B	9	ARG	1	0.848	0.917	5.090	48.540	48.540	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.897	-0.932	9.217	-25.970	-25.970	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.022	0.000	11.039	1.697	1.697	0.000	0.000	0.000	0.000
11	B	12	LEU	0	-0.047	-0.026	11.151	1.222	1.222	0.000	0.000	0.000	0.000
12	B	13	ARG	1	0.849	0.930	10.036	27.380	27.380	0.000	0.000	0.000	0.000
13	B	14	GLY	0	0.042	0.027	15.210	1.036	1.036	0.000	0.000	0.000	0.000
14	B	15	PHE	0	-0.026	-0.006	17.344	1.140	1.140	0.000	0.000	0.000	0.000
15	B	16	LYS	1	0.908	0.953	19.309	12.398	12.398	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.001	0.006	22.568	0.377	0.377	0.000	0.000	0.000	0.000
17	B	18	ASN	0	-0.094	-0.070	25.326	-0.184	-0.184	0.000	0.000	0.000	0.000
18	B	19	TRP	0	0.016	-0.001	28.276	0.314	0.314	0.000	0.000	0.000	0.000
19	B	20	MET	0	-0.019	0.005	29.750	-0.113	-0.113	0.000	0.000	0.000	0.000
20	B	21	ASN	0	-0.124	-0.071	32.456	0.283	0.283	0.000	0.000	0.000	0.000
21	B	22	LEU	0	0.053	0.028	35.920	-0.115	-0.115	0.000	0.000	0.000	0.000
22	B	23	ARG	1	0.841	0.905	37.975	8.269	8.269	0.000	0.000	0.000	0.000
23	B	24	ASP	-1	-0.764	-0.864	41.839	-6.729	-6.729	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.020	-0.028	42.776	-0.008	-0.008	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.884	-0.921	44.634	-6.295	-6.295	0.000	0.000	0.000	0.000
26	B	27	THR	0	-0.092	-0.066	48.054	0.083	0.083	0.000	0.000	0.000	0.000
27	B	28	GLY	0	0.026	0.023	44.677	0.027	0.027	0.000	0.000	0.000	0.000
28	B	29	LYS	1	0.885	0.944	44.574	6.508	6.508	0.000	0.000	0.000	0.000
29	B	30	ILE	0	0.021	0.012	40.129	-0.011	-0.011	0.000	0.000	0.000	0.000
30	B	31	LEU	0	-0.075	-0.046	42.233	0.217	0.217	0.000	0.000	0.000	0.000
31	B	32	TRP	0	0.053	0.001	33.670	0.087	0.087	0.000	0.000	0.000	0.000
32	B	33	GLN	0	0.032	0.010	35.715	0.095	0.095	0.000	0.000	0.000	0.000
33	B	34	GLY	0	-0.012	0.020	34.154	0.141	0.141	0.000	0.000	0.000	0.000
34	B	35	THR	0	-0.032	-0.049	32.533	-0.190	-0.190	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.867	-0.931	30.859	-10.260	-10.260	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.875	-0.934	27.178	-11.778	-11.778	0.000	0.000	0.000	0.000
37	B	38	LEU	0	0.015	0.009	27.756	-0.122	-0.122	0.000	0.000	0.000	0.000
38	B	39	SER	0	-0.022	-0.018	22.646	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	40	VAL	0	-0.020	0.015	22.811	-0.763	-0.763	0.000	0.000	0.000	0.000
40	B	41	PRO	0	0.005	-0.010	21.636	0.275	0.275	0.000	0.000	0.000	0.000
41	B	42	GLY	0	-0.013	-0.018	24.074	0.289	0.289	0.000	0.000	0.000	0.000
42	B	43	VAL	0	-0.010	0.004	27.251	0.474	0.474	0.000	0.000	0.000	0.000
43	B	44	GLU	-1	-0.968	-0.973	28.628	-10.073	-10.073	0.000	0.000	0.000	0.000
44	B	45	HIS	0	-0.005	0.003	26.798	0.672	0.672	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.854	-0.937	31.596	-8.562	-8.562	0.000	0.000	0.000	0.000
46	B	47	ALA	0	-0.018	-0.001	35.184	0.003	0.003	0.000	0.000	0.000	0.000
47	B	48	ARG	1	0.875	0.945	37.459	8.011	8.011	0.000	0.000	0.000	0.000
48	B	49	VAL	0	0.038	0.015	40.474	0.052	0.052	0.000	0.000	0.000	0.000
49	B	50	PRO	0	0.000	-0.006	42.514	0.144	0.144	0.000	0.000	0.000	0.000
50	B	51	LYS	1	1.012	0.998	45.920	6.353	6.353	0.000	0.000	0.000	0.000
51	B	52	LYS	1	0.916	0.974	47.188	6.558	6.558	0.000	0.000	0.000	0.000
52	B	53	ILE	0	0.086	0.027	40.921	0.073	0.073	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.042	-0.015	43.645	-0.024	-0.024	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.875	0.922	46.313	6.291	6.291	0.000	0.000	0.000	0.000
55	B	56	CYS	0	-0.053	0.000	45.672	0.093	0.093	0.000	0.000	0.000	0.000
56	B	57	LYS	1	0.865	0.927	46.376	6.249	6.249	0.000	0.000	0.000	0.000
57	B	58	ALA	0	0.050	0.037	44.373	-0.089	-0.089	0.000	0.000	0.000	0.000
58	B	59	VAL	0	-0.011	0.000	39.843	0.075	0.075	0.000	0.000	0.000	0.000
59	B	60	SER	0	-0.023	-0.020	38.913	-0.062	-0.062	0.000	0.000	0.000	0.000
60	B	61	ARG	1	0.816	0.877	33.032	9.126	9.126	0.000	0.000	0.000	0.000
61	B	62	GLU	-1	-0.829	-0.883	33.768	-8.901	-8.901	0.000	0.000	0.000	0.000
62	B	63	LEU	0	-0.020	-0.013	27.457	-0.104	-0.104	0.000	0.000	0.000	0.000
63	B	64	ASN	0	0.030	0.019	29.670	-0.197	-0.197	0.000	0.000	0.000	0.000
64	B	65	PHE	0	0.038	0.013	23.339	-0.117	-0.117	0.000	0.000	0.000	0.000
65	B	66	SER	0	0.047	0.033	24.252	0.426	0.426	0.000	0.000	0.000	0.000
66	B	67	SER	0	-0.012	-0.013	18.935	-0.749	-0.749	0.000	0.000	0.000	0.000
67	B	68	THR	0	-0.005	-0.020	17.287	0.450	0.450	0.000	0.000	0.000	0.000
68	B	69	GLU	-1	-0.839	-0.882	14.223	-20.154	-20.154	0.000	0.000	0.000	0.000
69	B	70	GLN	0	-0.050	-0.013	16.944	1.062	1.062	0.000	0.000	0.000	0.000
70	B	71	MET	0	-0.046	-0.007	15.289	-1.719	-1.719	0.000	0.000	0.000	0.000
71	B	72	GLU	-1	-0.845	-0.923	15.780	-15.307	-15.307	0.000	0.000	0.000	0.000
72	B	73	LYS	1	0.784	0.893	15.340	18.128	18.128	0.000	0.000	0.000	0.000
73	B	74	PHE	0	0.044	0.022	18.036	-0.263	-0.263	0.000	0.000	0.000	0.000
74	B	75	ARG	1	0.881	0.926	18.305	15.867	15.867	0.000	0.000	0.000	0.000
75	B	76	LEU	0	-0.040	-0.017	21.022	-0.569	-0.569	0.000	0.000	0.000	0.000
76	B	77	GLU	-1	-0.871	-0.930	22.248	-12.777	-12.777	0.000	0.000	0.000	0.000
77	B	78	GLN	0	-0.019	-0.024	25.216	0.117	0.117	0.000	0.000	0.000	0.000
78	B	79	LYS	1	0.920	0.980	25.493	11.910	11.910	0.000	0.000	0.000	0.000
79	B	80	VAL	0	0.007	0.004	29.911	-0.164	-0.164	0.000	0.000	0.000	0.000
80	B	81	TYR	0	0.031	0.011	27.498	0.191	0.191	0.000	0.000	0.000	0.000
81	B	82	PHE	0	0.038	0.012	34.300	0.115	0.115	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.899	0.943	36.084	7.788	7.788	0.000	0.000	0.000	0.000
83	B	84	GLY	0	0.019	0.018	33.860	-0.282	-0.282	0.000	0.000	0.000	0.000
84	B	85	GLN	0	-0.046	-0.011	34.582	-0.030	-0.030	0.000	0.000	0.000	0.000
85	B	86	CYS	0	-0.070	-0.040	33.209	-0.053	-0.053	0.000	0.000	0.000	0.000
86	B	87	LEU	0	-0.053	-0.025	35.234	0.264	0.264	0.000	0.000	0.000	0.000
87	B	88	GLU	-1	-0.733	-0.846	34.680	-8.549	-8.549	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-0.906	-0.955	30.610	-10.090	-10.090	0.000	0.000	0.000	0.000
89	B	90	TRP	0	-0.054	-0.023	30.538	0.196	0.196	0.000	0.000	0.000	0.000
90	B	91	PHE	0	0.006	-0.010	25.826	-0.489	-0.489	0.000	0.000	0.000	0.000
91	B	92	PHE	0	-0.023	-0.015	26.228	0.503	0.503	0.000	0.000	0.000	0.000
92	B	93	GLU	-1	-0.866	-0.931	22.078	-13.953	-13.953	0.000	0.000	0.000	0.000
93	B	94	PHE	0	-0.045	-0.044	23.344	0.571	0.571	0.000	0.000	0.000	0.000
94	B	95	GLY	0	0.017	0.025	21.685	0.289	0.289	0.000	0.000	0.000	0.000
95	B	96	PHE	0	-0.042	-0.009	20.245	-0.538	-0.538	0.000	0.000	0.000	0.000
96	B	97	VAL	0	-0.027	-0.011	20.147	0.585	0.585	0.000	0.000	0.000	0.000
97	B	98	ILE	0	0.040	0.010	20.587	-0.572	-0.572	0.000	0.000	0.000	0.000
98	B	99	PRO	0	-0.001	0.021	19.498	-0.079	-0.079	0.000	0.000	0.000	0.000
99	B	100	ASN	0	-0.049	-0.044	21.188	0.511	0.511	0.000	0.000	0.000	0.000
100	B	101	SER	0	-0.001	0.013	23.281	0.696	0.696	0.000	0.000	0.000	0.000
101	B	102	THR	0	-0.032	-0.037	24.906	-0.281	-0.281	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.054	-0.020	24.596	0.577	0.577	0.000	0.000	0.000	0.000
103	B	104	THR	0	-0.011	-0.016	28.253	-0.023	-0.023	0.000	0.000	0.000	0.000
104	B	105	TRP	0	0.021	0.011	28.900	-0.060	-0.060	0.000	0.000	0.000	0.000
105	B	106	GLN	0	0.017	0.008	30.936	0.201	0.201	0.000	0.000	0.000	0.000
106	B	107	SER	0	-0.007	0.023	33.359	0.072	0.072	0.000	0.000	0.000	0.000
107	B	108	LEU	0	-0.012	-0.024	35.319	0.117	0.117	0.000	0.000	0.000	0.000
108	B	109	ILE	0	-0.017	-0.005	36.087	-0.081	-0.081	0.000	0.000	0.000	0.000
109	B	110	GLU	-1	-0.851	-0.941	39.691	-6.990	-6.990	0.000	0.000	0.000	0.000
110	B	111	ALA	0	0.027	0.010	41.599	0.072	0.072	0.000	0.000	0.000	0.000
111	B	112	ALA	0	0.007	-0.006	42.923	0.064	0.064	0.000	0.000	0.000	0.000
112	B	113	PRO	0	-0.035	-0.013	45.250	0.105	0.105	0.000	0.000	0.000	0.000
113	B	114	GLU	-1	-0.780	-0.876	40.889	-7.545	-7.545	0.000	0.000	0.000	0.000
114	B	115	SER	0	-0.036	-0.040	42.805	0.088	0.088	0.000	0.000	0.000	0.000
115	B	116	GLN	0	-0.059	-0.024	45.104	0.169	0.169	0.000	0.000	0.000	0.000
116	B	117	MET	0	-0.038	-0.016	46.966	0.174	0.174	0.000	0.000	0.000	0.000
117	B	118	MET	0	-0.044	-0.006	41.814	-0.007	-0.007	0.000	0.000	0.000	0.000
118	B	119	PRO	0	0.005	-0.001	46.150	-0.088	-0.088	0.000	0.000	0.000	0.000
119	B	120	ALA	0	0.030	-0.007	46.610	0.050	0.050	0.000	0.000	0.000	0.000
120	B	121	SER	0	-0.047	-0.018	45.628	-0.177	-0.177	0.000	0.000	0.000	0.000
121	B	122	VAL	0	0.018	0.017	44.496	-0.081	-0.081	0.000	0.000	0.000	0.000
122	B	123	LEU	0	0.059	0.031	41.210	-0.186	-0.186	0.000	0.000	0.000	0.000
123	B	124	THR	0	0.002	0.009	40.923	-0.291	-0.291	0.000	0.000	0.000	0.000
124	B	125	GLY	0	0.024	0.013	39.034	0.062	0.062	0.000	0.000	0.000	0.000
125	B	126	ASN	0	-0.090	-0.059	37.923	-0.328	-0.328	0.000	0.000	0.000	0.000
126	B	127	VAL	0	0.013	0.017	36.350	-0.110	-0.110	0.000	0.000	0.000	0.000
127	B	128	ILE	0	-0.049	-0.020	30.276	-0.099	-0.099	0.000	0.000	0.000	0.000
128	B	129	ILE	0	0.041	0.030	30.271	0.039	0.039	0.000	0.000	0.000	0.000
129	B	130	GLU	-1	-0.849	-0.928	25.580	-12.432	-12.432	0.000	0.000	0.000	0.000
130	B	131	THR	0	-0.017	-0.004	25.100	0.305	0.305	0.000	0.000	0.000	0.000
131	B	132	LYS	1	0.864	0.928	21.003	13.053	13.053	0.000	0.000	0.000	0.000
132	B	133	PHE	0	0.042	0.013	19.757	0.592	0.592	0.000	0.000	0.000	0.000
133	B	134	PHE	0	0.003	-0.010	16.077	-0.851	-0.851	0.000	0.000	0.000	0.000
134	B	135	ASP	-1	-0.757	-0.891	13.963	-18.337	-18.337	0.000	0.000	0.000	0.000
135	B	136	ASP	-1	-0.852	-0.924	13.851	-19.565	-19.565	0.000	0.000	0.000	0.000
136	B	137	ASP	-1	-0.878	-0.923	14.015	-16.098	-16.098	0.000	0.000	0.000	0.000
137	B	138	LEU	0	-0.105	-0.043	9.175	-1.316	-1.316	0.000	0.000	0.000	0.000
138	B	139	LEU	0	-0.021	-0.013	12.355	1.087	1.087	0.000	0.000	0.000	0.000
139	B	140	VAL	0	-0.007	-0.004	14.109	-1.137	-1.137	0.000	0.000	0.000	0.000
140	B	141	SER	0	0.010	0.004	15.552	0.248	0.248	0.000	0.000	0.000	0.000
141	B	142	THR	0	-0.029	-0.036	18.679	0.289	0.289	0.000	0.000	0.000	0.000
142	B	143	SER	0	-0.011	0.020	21.505	0.089	0.089	0.000	0.000	0.000	0.000
143	B	144	ARG	1	0.903	0.939	25.138	11.445	11.445	0.000	0.000	0.000	0.000
144	B	145	VAL	0	0.028	0.024	28.082	0.051	0.051	0.000	0.000	0.000	0.000
145	B	146	ARG	1	0.885	0.945	31.670	9.356	9.356	0.000	0.000	0.000	0.000
146	B	147	LEU	0	-0.001	0.001	34.678	0.120	0.120	0.000	0.000	0.000	0.000
147	B	148	PHE	0	-0.014	-0.001	37.542	0.190	0.190	0.000	0.000	0.000	0.000
148	B	149	TYR	0	0.003	-0.008	40.102	0.029	0.029	0.000	0.000	0.000	0.000
149	B	150	VAL	-1	-0.951	-0.979	44.372	-6.908	-6.908	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)