FMO DATABASE

FMODB ID: 4635N

Calculation Name: 3A0B-e-Xray547

Preferred Name:

Target Type:

Ligand 3-letter code: CLA | PHO | HEM | DGD | PQ9 | BCR | MGE | LHG | OEC | FE2 | BR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A0B

Chain ID: e

ChEMBL ID:

UniProt ID: P0A387

Base Structure: X-ray

Registration Date: 2025-10-04

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-415199.748974
FMO2-HF: Nuclear repulsion	383219.796263
FMO2-HF: Total energy	-31979.952711
FMO2-MP2: Total energy	-32076.066746

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:5003:GLY)

Summations of interaction energy for fragment #1(A:5003:GLY)

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.
-43.086	-39.4	0.782	-2.443	-2.025	-0.029

Interaction energy analysis for fragmet #1(A:5003:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.911

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

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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	5005	THR	0	-0.018	-0.047	2.440	-25.437	-21.824	0.783	-2.435	-1.961	-0.029
4	A	5006	GLY	0	0.018	0.023	5.010	5.565	5.638	-0.001	-0.008	-0.064	0.000
5	A	5007	GLU	-1	-0.865	-0.894	7.090	-36.498	-36.498	0.000	0.000	0.000	0.000
6	A	5008	ARG	1	0.893	0.927	9.904	25.568	25.568	0.000	0.000	0.000	0.000
7	A	5009	PRO	0	0.017	0.004	13.146	-0.779	-0.779	0.000	0.000	0.000	0.000
8	A	5010	PHE	0	0.030	0.016	13.813	-0.758	-0.758	0.000	0.000	0.000	0.000
9	A	5011	SER	0	0.038	0.002	12.595	1.259	1.259	0.000	0.000	0.000	0.000
10	A	5012	ASP	-1	-0.843	-0.907	15.736	-14.654	-14.654	0.000	0.000	0.000	0.000
11	A	5013	ILE	0	-0.096	-0.042	18.813	0.901	0.901	0.000	0.000	0.000	0.000
12	A	5014	ILE	0	0.030	-0.001	20.744	0.655	0.655	0.000	0.000	0.000	0.000
13	A	5015	THR	0	0.009	-0.002	22.106	0.751	0.751	0.000	0.000	0.000	0.000
14	A	5016	SER	0	-0.060	-0.011	23.340	0.759	0.759	0.000	0.000	0.000	0.000
15	A	5017	VAL	0	0.080	0.030	25.117	0.272	0.272	0.000	0.000	0.000	0.000
16	A	5018	ARG	1	0.964	0.969	26.192	11.932	11.932	0.000	0.000	0.000	0.000
17	A	5019	TYR	0	-0.022	0.007	24.722	0.169	0.169	0.000	0.000	0.000	0.000
18	A	5020	TRP	0	0.102	0.024	27.192	0.376	0.376	0.000	0.000	0.000	0.000
19	A	5021	VAL	0	-0.007	0.016	29.656	0.348	0.348	0.000	0.000	0.000	0.000
20	A	5022	ILE	0	-0.033	-0.018	29.179	0.232	0.232	0.000	0.000	0.000	0.000
21	A	5023	HIS	0	-0.035	-0.024	26.893	-0.121	-0.121	0.000	0.000	0.000	0.000
22	A	5024	SER	0	0.000	0.005	30.971	0.186	0.186	0.000	0.000	0.000	0.000
23	A	5025	ILE	0	-0.037	-0.003	34.027	0.309	0.309	0.000	0.000	0.000	0.000
24	A	5026	THR	0	0.015	-0.006	30.470	0.166	0.166	0.000	0.000	0.000	0.000
25	A	5027	ILE	0	0.016	0.012	29.257	0.087	0.087	0.000	0.000	0.000	0.000
26	A	5028	PRO	0	0.011	0.001	33.321	0.131	0.131	0.000	0.000	0.000	0.000
27	A	5029	ALA	0	0.026	0.013	36.482	0.191	0.191	0.000	0.000	0.000	0.000
28	A	5030	LEU	0	-0.012	0.002	32.284	0.101	0.101	0.000	0.000	0.000	0.000
29	A	5031	PHE	0	-0.015	-0.005	35.590	0.124	0.124	0.000	0.000	0.000	0.000
30	A	5032	ILE	0	0.011	-0.007	37.083	0.168	0.168	0.000	0.000	0.000	0.000
31	A	5033	ALA	0	0.011	0.020	37.880	0.203	0.203	0.000	0.000	0.000	0.000
32	A	5034	GLY	0	0.016	0.004	38.192	0.126	0.126	0.000	0.000	0.000	0.000
33	A	5035	TRP	0	0.007	0.001	39.059	0.087	0.087	0.000	0.000	0.000	0.000
34	A	5036	LEU	0	-0.001	-0.009	42.040	0.201	0.201	0.000	0.000	0.000	0.000
35	A	5037	PHE	0	-0.002	0.023	41.378	0.181	0.181	0.000	0.000	0.000	0.000
36	A	5038	VAL	0	0.013	0.006	42.019	0.107	0.107	0.000	0.000	0.000	0.000
37	A	5039	SER	0	-0.041	-0.030	44.762	0.169	0.169	0.000	0.000	0.000	0.000
38	A	5040	THR	0	-0.059	-0.035	47.079	0.178	0.178	0.000	0.000	0.000	0.000
39	A	5041	GLY	0	-0.012	0.004	48.420	0.147	0.147	0.000	0.000	0.000	0.000
40	A	5042	LEU	0	0.018	0.001	44.432	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	5043	ALA	0	0.006	-0.006	43.823	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	5044	TYR	0	-0.041	-0.019	44.970	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	5045	ASP	-1	-0.846	-0.917	48.032	-6.347	-6.347	0.000	0.000	0.000	0.000
44	A	5046	VAL	0	-0.080	-0.022	42.265	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	5047	PHE	0	-0.059	-0.037	39.912	-0.147	-0.147	0.000	0.000	0.000	0.000
46	A	5048	GLY	0	0.022	0.026	45.221	0.017	0.017	0.000	0.000	0.000	0.000
47	A	5049	THR	0	-0.059	-0.026	45.549	0.088	0.088	0.000	0.000	0.000	0.000
48	A	5050	PRO	0	0.017	0.002	48.627	0.032	0.032	0.000	0.000	0.000	0.000
49	A	5051	ARG	1	0.907	0.945	50.851	6.058	6.058	0.000	0.000	0.000	0.000
50	A	5052	PRO	0	-0.034	-0.029	52.161	0.030	0.030	0.000	0.000	0.000	0.000
51	A	5053	ASP	-1	-0.856	-0.918	54.242	-5.655	-5.655	0.000	0.000	0.000	0.000
52	A	5054	SER	0	-0.043	-0.026	54.956	0.055	0.055	0.000	0.000	0.000	0.000
53	A	5055	TYR	0	-0.055	-0.022	49.567	-0.085	-0.085	0.000	0.000	0.000	0.000
54	A	5056	TYR	0	-0.043	-0.019	55.949	-0.034	-0.034	0.000	0.000	0.000	0.000
55	A	5057	ALA	0	0.046	0.023	59.563	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	5058	GLN	0	-0.031	-0.015	62.494	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	5059	GLU	-1	-0.941	-0.964	64.747	-4.662	-4.662	0.000	0.000	0.000	0.000
58	A	5060	GLN	0	-0.022	-0.009	62.249	-0.073	-0.073	0.000	0.000	0.000	0.000
59	A	5061	ARG	1	0.970	0.981	62.520	4.972	4.972	0.000	0.000	0.000	0.000
60	A	5062	SER	0	-0.013	-0.013	61.673	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	5063	ILE	0	0.023	0.014	55.027	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	5064	PRO	0	0.036	0.019	54.719	0.056	0.056	0.000	0.000	0.000	0.000
63	A	5065	LEU	0	-0.045	-0.028	53.612	-0.132	-0.132	0.000	0.000	0.000	0.000
64	A	5066	VAL	0	0.011	0.011	52.237	0.108	0.108	0.000	0.000	0.000	0.000
65	A	5067	THR	0	-0.011	-0.011	54.843	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	5068	ASP	-1	-0.738	-0.842	56.358	-5.742	-5.742	0.000	0.000	0.000	0.000
67	A	5069	ARG	1	0.811	0.875	51.962	5.619	5.619	0.000	0.000	0.000	0.000
68	A	5070	PHE	0	-0.043	-0.029	52.194	-0.098	-0.098	0.000	0.000	0.000	0.000
69	A	5071	GLU	-1	-0.872	-0.941	54.396	-5.622	-5.622	0.000	0.000	0.000	0.000
70	A	5072	ALA	0	-0.035	-0.010	52.463	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	5073	LYS	1	0.950	0.973	51.814	5.978	5.978	0.000	0.000	0.000	0.000
72	A	5074	GLN	0	-0.002	0.012	53.834	0.053	0.053	0.000	0.000	0.000	0.000
73	A	5075	GLN	0	0.009	0.015	56.573	0.015	0.015	0.000	0.000	0.000	0.000
74	A	5076	VAL	0	0.006	0.000	51.984	0.036	0.036	0.000	0.000	0.000	0.000
75	A	5077	GLU	-1	-0.875	-0.944	55.251	-5.826	-5.826	0.000	0.000	0.000	0.000
76	A	5078	THR	0	-0.022	-0.027	57.381	0.067	0.067	0.000	0.000	0.000	0.000
77	A	5079	PHE	0	-0.059	-0.037	57.550	0.092	0.092	0.000	0.000	0.000	0.000
78	A	5080	LEU	0	-0.018	0.001	53.225	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	5081	GLU	-1	-0.995	-1.003	57.723	-5.029	-5.029	0.000	0.000	0.000	0.000
80	A	5082	GLN	0	-0.048	-0.028	60.996	0.121	0.121	0.000	0.000	0.000	0.000
81	A	5083	LEU	0	-0.072	-0.030	57.752	0.081	0.081	0.000	0.000	0.000	0.000
82	A	5084	LYS	0	0.029	0.032	62.009	-0.209	-0.209	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5003:GLY)