FMO DATABASE

FMODB ID: 3G8RL

Calculation Name: 1PDK-B-Xray547

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PDK

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1260642.769253
FMO2-HF: Nuclear repulsion	1205255.618834
FMO2-HF: Total energy	-55387.150419
FMO2-MP2: Total energy	-55551.347295

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:9:LEU)

Summations of interaction energy for fragment #1(B:9:LEU)

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.
-4.037	-0.74	0.959	-1.293	-2.963	-0.009

Interaction energy analysis for fragmet #1(B:9:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.914

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	11	ASP	-1	-0.839	-0.922	2.252	-37.969	-34.751	0.958	-1.283	-2.893	-0.009
4	B	12	ARG	1	0.878	0.950	3.969	24.947	25.026	0.001	-0.010	-0.070	0.000
5	B	13	PRO	0	0.052	0.030	7.251	-1.646	-1.646	0.000	0.000	0.000	0.000
6	B	14	CYS	0	-0.058	-0.026	7.269	5.727	5.727	0.000	0.000	0.000	0.000
7	B	15	HIS	0	-0.024	0.002	4.882	2.083	2.083	0.000	0.000	0.000	0.000
8	B	16	VAL	0	0.016	0.003	10.109	-0.835	-0.835	0.000	0.000	0.000	0.000
9	B	17	SER	0	-0.019	-0.027	9.482	-2.632	-2.632	0.000	0.000	0.000	0.000
10	B	18	GLY	0	0.037	0.002	9.819	2.139	2.139	0.000	0.000	0.000	0.000
11	B	19	ASP	-1	-0.801	-0.866	11.589	-20.937	-20.937	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.114	-0.057	13.501	1.624	1.624	0.000	0.000	0.000	0.000
13	B	21	LEU	0	0.009	0.001	12.516	0.797	0.797	0.000	0.000	0.000	0.000
14	B	22	ASN	0	-0.008	0.003	15.698	1.273	1.273	0.000	0.000	0.000	0.000
15	B	23	LYS	1	0.854	0.936	18.167	16.719	16.719	0.000	0.000	0.000	0.000
16	B	24	HIS	0	0.019	0.013	21.338	0.569	0.569	0.000	0.000	0.000	0.000
17	B	25	VAL	0	0.001	0.001	25.143	-0.162	-0.162	0.000	0.000	0.000	0.000
18	B	26	VAL	0	0.064	0.039	28.049	0.228	0.228	0.000	0.000	0.000	0.000
19	B	27	PHE	0	0.041	0.018	31.291	0.091	0.091	0.000	0.000	0.000	0.000
20	B	28	LYS	1	0.823	0.907	31.644	9.970	9.970	0.000	0.000	0.000	0.000
21	B	29	THR	0	-0.010	0.021	37.155	0.162	0.162	0.000	0.000	0.000	0.000
22	B	30	ARG	1	0.846	0.895	40.102	7.520	7.520	0.000	0.000	0.000	0.000
23	B	31	ALA	0	0.029	0.019	43.881	0.047	0.047	0.000	0.000	0.000	0.000
24	B	32	SER	0	0.038	0.011	45.745	-0.046	-0.046	0.000	0.000	0.000	0.000
25	B	33	ARG	1	0.900	0.943	46.161	6.763	6.763	0.000	0.000	0.000	0.000
26	B	34	ASP	-1	-0.781	-0.866	42.125	-7.580	-7.580	0.000	0.000	0.000	0.000
27	B	35	PHE	0	-0.016	-0.016	39.523	-0.030	-0.030	0.000	0.000	0.000	0.000
28	B	36	TRP	0	-0.036	-0.011	45.411	0.149	0.149	0.000	0.000	0.000	0.000
29	B	37	TYR	0	0.013	-0.015	48.191	0.203	0.203	0.000	0.000	0.000	0.000
30	B	38	PRO	0	0.028	0.022	47.096	-0.158	-0.158	0.000	0.000	0.000	0.000
31	B	39	PRO	0	-0.011	-0.010	42.857	0.083	0.083	0.000	0.000	0.000	0.000
32	B	40	GLY	0	0.026	0.015	43.905	-0.063	-0.063	0.000	0.000	0.000	0.000
33	B	41	ARG	1	0.846	0.912	35.368	8.567	8.567	0.000	0.000	0.000	0.000
34	B	42	SER	0	0.006	0.011	35.741	0.097	0.097	0.000	0.000	0.000	0.000
35	B	43	PRO	0	0.041	0.015	35.571	-0.038	-0.038	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.010	0.008	30.550	0.088	0.088	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.836	-0.892	29.427	-10.122	-10.122	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.050	-0.036	25.578	-0.179	-0.179	0.000	0.000	0.000	0.000
39	B	47	PHE	0	-0.010	-0.014	21.916	-0.191	-0.191	0.000	0.000	0.000	0.000
40	B	48	VAL	0	0.009	0.015	17.787	-0.054	-0.054	0.000	0.000	0.000	0.000
41	B	49	ILE	0	0.001	0.008	16.083	-0.459	-0.459	0.000	0.000	0.000	0.000
42	B	50	ARG	1	0.826	0.885	11.309	23.863	23.863	0.000	0.000	0.000	0.000
43	B	51	LEU	0	-0.021	-0.002	11.688	-0.698	-0.698	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.815	-0.933	6.219	-35.725	-35.725	0.000	0.000	0.000	0.000
45	B	53	ASN	0	-0.037	-0.027	5.228	-6.932	-6.932	0.000	0.000	0.000	0.000
46	B	55	HIS	0	0.073	0.032	9.691	2.000	2.000	0.000	0.000	0.000	0.000
47	B	56	ALA	0	0.072	0.035	14.102	0.847	0.847	0.000	0.000	0.000	0.000
48	B	57	THR	0	-0.029	-0.027	17.825	0.814	0.814	0.000	0.000	0.000	0.000
49	B	58	ALA	0	-0.015	0.002	15.081	0.675	0.675	0.000	0.000	0.000	0.000
50	B	59	VAL	0	0.073	0.030	16.044	0.248	0.248	0.000	0.000	0.000	0.000
51	B	60	GLY	0	0.048	0.030	17.299	-0.095	-0.095	0.000	0.000	0.000	0.000
52	B	61	LYS	1	0.893	0.952	18.376	15.678	15.678	0.000	0.000	0.000	0.000
53	B	62	ILE	0	0.006	0.011	12.785	0.018	0.018	0.000	0.000	0.000	0.000
54	B	63	VAL	0	-0.005	-0.011	15.599	-0.119	-0.119	0.000	0.000	0.000	0.000
55	B	64	THR	0	-0.051	-0.017	17.751	0.759	0.759	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.025	0.001	17.003	-0.325	-0.325	0.000	0.000	0.000	0.000
57	B	66	THR	0	0.040	0.023	21.032	0.543	0.543	0.000	0.000	0.000	0.000
58	B	67	PHE	0	0.033	0.035	22.761	-0.523	-0.523	0.000	0.000	0.000	0.000
59	B	68	LYS	1	0.843	0.902	25.699	12.406	12.406	0.000	0.000	0.000	0.000
60	B	69	GLY	0	0.061	0.016	27.774	-0.257	-0.257	0.000	0.000	0.000	0.000
61	B	70	THR	0	-0.017	-0.004	30.569	0.063	0.063	0.000	0.000	0.000	0.000
62	B	71	GLU	-1	-0.803	-0.881	34.401	-8.756	-8.756	0.000	0.000	0.000	0.000
63	B	72	GLU	-1	-0.807	-0.898	36.209	-7.558	-7.558	0.000	0.000	0.000	0.000
64	B	73	ALA	0	0.023	0.007	39.196	0.044	0.044	0.000	0.000	0.000	0.000
65	B	74	ALA	0	-0.022	-0.009	42.122	0.141	0.141	0.000	0.000	0.000	0.000
66	B	75	LEU	0	-0.068	-0.033	39.694	0.120	0.120	0.000	0.000	0.000	0.000
67	B	76	PRO	0	0.054	0.023	38.856	-0.254	-0.254	0.000	0.000	0.000	0.000
68	B	77	GLY	0	-0.054	-0.040	35.251	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	78	HIS	0	-0.047	-0.026	34.306	-0.284	-0.284	0.000	0.000	0.000	0.000
70	B	79	LEU	0	0.012	0.007	29.514	0.093	0.093	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.799	0.882	34.163	8.045	8.045	0.000	0.000	0.000	0.000
72	B	81	VAL	0	-0.036	0.007	35.554	-0.237	-0.237	0.000	0.000	0.000	0.000
73	B	82	THR	0	-0.056	-0.047	36.428	0.245	0.245	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.101	0.041	38.749	-0.042	-0.042	0.000	0.000	0.000	0.000
75	B	84	VAL	0	0.007	-0.013	41.325	0.081	0.081	0.000	0.000	0.000	0.000
76	B	85	ASN	0	0.008	-0.006	42.439	0.341	0.341	0.000	0.000	0.000	0.000
77	B	86	ALA	0	0.064	0.045	41.375	-0.077	-0.077	0.000	0.000	0.000	0.000
78	B	87	GLY	0	-0.027	-0.008	41.908	0.201	0.201	0.000	0.000	0.000	0.000
79	B	88	ARG	1	0.840	0.929	43.825	6.846	6.846	0.000	0.000	0.000	0.000
80	B	89	LEU	0	0.001	0.004	39.886	0.074	0.074	0.000	0.000	0.000	0.000
81	B	90	GLY	0	0.036	0.024	37.698	-0.024	-0.024	0.000	0.000	0.000	0.000
82	B	91	ILE	0	-0.040	-0.023	31.587	0.050	0.050	0.000	0.000	0.000	0.000
83	B	92	ALA	0	0.034	0.025	33.652	-0.097	-0.097	0.000	0.000	0.000	0.000
84	B	93	LEU	0	-0.001	-0.004	26.914	-0.204	-0.204	0.000	0.000	0.000	0.000
85	B	94	LEU	0	-0.050	-0.017	29.130	0.263	0.263	0.000	0.000	0.000	0.000
86	B	95	ASP	-1	-0.658	-0.827	25.507	-12.848	-12.848	0.000	0.000	0.000	0.000
87	B	96	THR	0	-0.045	-0.035	21.795	0.004	0.004	0.000	0.000	0.000	0.000
88	B	97	ASP	-1	-0.809	-0.863	25.120	-10.603	-10.603	0.000	0.000	0.000	0.000
89	B	98	GLY	0	-0.010	-0.001	28.161	0.342	0.342	0.000	0.000	0.000	0.000
90	B	99	SER	0	-0.082	-0.047	29.784	0.442	0.442	0.000	0.000	0.000	0.000
91	B	100	SER	0	-0.056	-0.064	30.539	0.409	0.409	0.000	0.000	0.000	0.000
92	B	101	LEU	0	-0.059	-0.026	31.014	-0.282	-0.282	0.000	0.000	0.000	0.000
93	B	102	LEU	0	-0.042	-0.017	25.318	0.068	0.068	0.000	0.000	0.000	0.000
94	B	103	LYS	1	0.966	0.993	30.014	9.010	9.010	0.000	0.000	0.000	0.000
95	B	104	PRO	0	0.034	0.025	30.042	-0.354	-0.354	0.000	0.000	0.000	0.000
96	B	105	GLY	0	-0.029	-0.011	29.267	0.275	0.275	0.000	0.000	0.000	0.000
97	B	106	THR	0	-0.085	-0.050	29.462	-0.028	-0.028	0.000	0.000	0.000	0.000
98	B	107	SER	0	0.010	-0.012	24.868	-0.142	-0.142	0.000	0.000	0.000	0.000
99	B	108	HIS	1	0.780	0.858	21.644	14.120	14.120	0.000	0.000	0.000	0.000
100	B	109	ASN	0	-0.039	-0.024	24.662	-0.102	-0.102	0.000	0.000	0.000	0.000
101	B	110	LYS	1	0.752	0.853	20.294	14.835	14.835	0.000	0.000	0.000	0.000
102	B	111	GLY	0	-0.016	-0.012	23.187	0.513	0.513	0.000	0.000	0.000	0.000
103	B	112	GLN	0	0.013	-0.001	23.843	-0.210	-0.210	0.000	0.000	0.000	0.000
104	B	113	GLY	0	0.073	0.044	24.821	0.029	0.029	0.000	0.000	0.000	0.000
105	B	114	GLU	-1	-0.786	-0.851	19.693	-15.668	-15.668	0.000	0.000	0.000	0.000
106	B	115	LYS	1	0.938	0.977	18.469	16.701	16.701	0.000	0.000	0.000	0.000
107	B	116	VAL	0	-0.009	0.003	14.844	-0.942	-0.942	0.000	0.000	0.000	0.000
108	B	117	THR	0	-0.026	-0.032	13.408	1.681	1.681	0.000	0.000	0.000	0.000
109	B	118	GLY	0	0.025	0.030	11.544	-1.918	-1.918	0.000	0.000	0.000	0.000
110	B	119	ASN	0	-0.030	-0.018	5.647	4.684	4.684	0.000	0.000	0.000	0.000
111	B	120	SER	0	0.027	0.020	8.966	-1.673	-1.673	0.000	0.000	0.000	0.000
112	B	121	LEU	0	-0.015	-0.007	10.869	1.923	1.923	0.000	0.000	0.000	0.000
113	B	122	GLU	-1	-0.840	-0.922	14.243	-18.891	-18.891	0.000	0.000	0.000	0.000
114	B	123	LEU	0	0.004	-0.007	16.571	0.815	0.815	0.000	0.000	0.000	0.000
115	B	124	PRO	0	-0.002	-0.005	19.465	-0.047	-0.047	0.000	0.000	0.000	0.000
116	B	125	PHE	0	0.041	0.031	20.210	0.459	0.459	0.000	0.000	0.000	0.000
117	B	126	GLY	0	0.026	0.012	24.425	0.039	0.039	0.000	0.000	0.000	0.000
118	B	127	ALA	0	0.009	0.003	27.874	-0.052	-0.052	0.000	0.000	0.000	0.000
119	B	128	TYR	0	-0.021	-0.018	30.229	0.086	0.086	0.000	0.000	0.000	0.000
120	B	129	VAL	0	0.026	0.033	33.968	0.008	0.008	0.000	0.000	0.000	0.000
121	B	130	VAL	0	0.008	-0.017	36.703	0.137	0.137	0.000	0.000	0.000	0.000
122	B	131	ALA	0	0.032	0.014	39.824	-0.026	-0.026	0.000	0.000	0.000	0.000
123	B	132	THR	0	0.003	-0.010	43.188	-0.050	-0.050	0.000	0.000	0.000	0.000
124	B	133	PRO	0	0.032	0.012	44.708	0.141	0.141	0.000	0.000	0.000	0.000
125	B	134	GLU	-1	-0.760	-0.858	47.585	-6.015	-6.015	0.000	0.000	0.000	0.000
126	B	135	ALA	0	-0.022	0.017	46.567	0.131	0.131	0.000	0.000	0.000	0.000
127	B	136	LEU	0	-0.007	0.007	46.507	0.068	0.068	0.000	0.000	0.000	0.000
128	B	137	ARG	1	0.786	0.864	48.848	6.023	6.023	0.000	0.000	0.000	0.000
129	B	138	THR	0	-0.047	-0.060	51.779	0.099	0.099	0.000	0.000	0.000	0.000
130	B	139	LYS	1	0.901	0.970	50.757	6.130	6.130	0.000	0.000	0.000	0.000
131	B	140	SER	0	-0.009	0.004	50.186	-0.053	-0.053	0.000	0.000	0.000	0.000
132	B	141	VAL	0	-0.025	-0.008	44.499	-0.059	-0.059	0.000	0.000	0.000	0.000
133	B	142	VAL	0	0.035	0.021	47.214	0.094	0.094	0.000	0.000	0.000	0.000
134	B	143	PRO	0	-0.033	-0.027	45.900	-0.181	-0.181	0.000	0.000	0.000	0.000
135	B	144	GLY	0	0.027	0.012	44.264	0.137	0.137	0.000	0.000	0.000	0.000
136	B	145	ASP	-1	-0.912	-0.939	39.089	-7.989	-7.989	0.000	0.000	0.000	0.000
137	B	146	TYR	0	-0.087	-0.083	36.132	0.092	0.092	0.000	0.000	0.000	0.000
138	B	147	GLU	-1	-0.851	-0.914	33.204	-9.730	-9.730	0.000	0.000	0.000	0.000
139	B	148	ALA	0	-0.011	-0.007	32.572	0.223	0.223	0.000	0.000	0.000	0.000
140	B	149	THR	0	-0.013	0.000	28.939	-0.299	-0.299	0.000	0.000	0.000	0.000
141	B	150	ALA	0	0.009	-0.002	26.595	0.246	0.246	0.000	0.000	0.000	0.000
142	B	151	THR	0	-0.032	-0.009	22.693	-0.348	-0.348	0.000	0.000	0.000	0.000
143	B	152	PHE	0	0.018	0.008	17.158	0.180	0.180	0.000	0.000	0.000	0.000
144	B	153	GLU	-1	-0.821	-0.902	20.142	-13.308	-13.308	0.000	0.000	0.000	0.000
145	B	154	LEU	0	-0.011	-0.010	14.750	0.119	0.119	0.000	0.000	0.000	0.000
146	B	155	THR	0	0.003	-0.001	17.816	-0.038	-0.038	0.000	0.000	0.000	0.000
147	B	156	TYR	0	-0.039	-0.028	11.750	-0.104	-0.104	0.000	0.000	0.000	0.000
148	B	157	ARG	0	-0.019	0.015	17.496	-1.332	-1.332	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:LEU)