FMO DATABASE

FMODB ID: 5YN5Z

Calculation Name: 3NER-B-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NER

Chain ID: B

ChEMBL ID:

UniProt ID: O43169

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-627986.797189
FMO2-HF: Nuclear repulsion	591834.223982
FMO2-HF: Total energy	-36152.573207
FMO2-MP2: Total energy	-36259.573265

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:LYS)

Summations of interaction energy for fragment #1(A:-4:LYS)

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.
-242.562	-239.796	0.006	-1.45	-1.322	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.820 / q_NPA : 1.893

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	-2	GLN	0	0.004	-0.002	3.197	-12.448	-9.881	0.007	-1.433	-1.141	-0.006
4	A	-1	GLU	-1	-0.940	-0.958	4.399	-87.093	-86.894	-0.001	-0.017	-0.181	0.000
5	A	0	VAL	0	-0.039	-0.022	6.904	3.197	3.197	0.000	0.000	0.000	0.000
6	A	1	GLU	-1	-0.921	-0.949	10.593	-39.265	-39.265	0.000	0.000	0.000	0.000
7	A	2	THR	0	-0.040	-0.032	12.418	1.068	1.068	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.022	-0.011	15.929	-0.191	-0.191	0.000	0.000	0.000	0.000
9	A	4	VAL	0	-0.004	0.010	19.071	0.890	0.890	0.000	0.000	0.000	0.000
10	A	5	THR	0	0.008	0.012	18.451	-1.850	-1.850	0.000	0.000	0.000	0.000
11	A	6	TYR	0	-0.012	-0.012	17.516	0.722	0.722	0.000	0.000	0.000	0.000
12	A	7	TYR	0	0.028	0.011	19.592	-1.298	-1.298	0.000	0.000	0.000	0.000
13	A	8	ARG	1	0.919	0.949	16.940	30.588	30.588	0.000	0.000	0.000	0.000
14	A	9	LEU	0	0.051	0.022	22.898	0.339	0.339	0.000	0.000	0.000	0.000
15	A	10	GLU	-1	-0.957	-0.977	24.017	-24.207	-24.207	0.000	0.000	0.000	0.000
16	A	11	GLU	-1	-0.897	-0.949	21.780	-25.532	-25.532	0.000	0.000	0.000	0.000
17	A	12	VAL	0	0.000	0.006	25.131	0.509	0.509	0.000	0.000	0.000	0.000
18	A	13	ALA	0	0.024	0.006	28.133	0.651	0.651	0.000	0.000	0.000	0.000
19	A	14	LYS	1	0.833	0.934	24.386	24.273	24.273	0.000	0.000	0.000	0.000
20	A	15	ARG	1	0.729	0.865	24.625	23.251	23.251	0.000	0.000	0.000	0.000
21	A	16	ASN	0	0.057	0.013	31.599	0.315	0.315	0.000	0.000	0.000	0.000
22	A	17	SER	0	-0.008	-0.008	35.145	0.625	0.625	0.000	0.000	0.000	0.000
23	A	18	LEU	0	0.072	0.017	36.858	-0.292	-0.292	0.000	0.000	0.000	0.000
24	A	19	LYS	1	0.865	0.938	35.253	16.385	16.385	0.000	0.000	0.000	0.000
25	A	20	GLU	-1	-0.844	-0.928	28.720	-21.473	-21.473	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.052	-0.003	33.568	0.043	0.043	0.000	0.000	0.000	0.000
27	A	22	TRP	0	-0.021	-0.021	24.575	-0.459	-0.459	0.000	0.000	0.000	0.000
28	A	23	LEU	0	0.006	0.009	31.737	0.207	0.207	0.000	0.000	0.000	0.000
29	A	24	VAL	0	0.014	0.002	29.439	-0.584	-0.584	0.000	0.000	0.000	0.000
30	A	25	ILE	0	0.003	0.006	31.685	0.582	0.582	0.000	0.000	0.000	0.000
31	A	26	HIS	0	-0.039	-0.050	32.350	-0.707	-0.707	0.000	0.000	0.000	0.000
32	A	27	GLY	0	0.026	0.022	29.470	-0.326	-0.326	0.000	0.000	0.000	0.000
33	A	28	ARG	1	0.785	0.889	26.689	19.760	19.760	0.000	0.000	0.000	0.000
34	A	29	VAL	0	0.023	0.009	25.896	0.564	0.564	0.000	0.000	0.000	0.000
35	A	30	TYR	0	-0.009	-0.016	28.460	-0.233	-0.233	0.000	0.000	0.000	0.000
36	A	31	ASP	-1	-0.833	-0.889	29.740	-18.823	-18.823	0.000	0.000	0.000	0.000
37	A	32	VAL	0	0.015	-0.008	31.558	0.328	0.328	0.000	0.000	0.000	0.000
38	A	33	THR	0	0.014	-0.006	33.119	0.552	0.552	0.000	0.000	0.000	0.000
39	A	34	ARG	1	0.854	0.918	32.376	18.214	18.214	0.000	0.000	0.000	0.000
40	A	35	PHE	0	0.025	0.012	37.556	0.329	0.329	0.000	0.000	0.000	0.000
41	A	36	LEU	0	-0.008	0.006	38.067	0.364	0.364	0.000	0.000	0.000	0.000
42	A	37	ASN	0	0.025	0.003	41.349	0.438	0.438	0.000	0.000	0.000	0.000
43	A	38	GLU	-1	-0.980	-0.986	41.955	-14.142	-14.142	0.000	0.000	0.000	0.000
44	A	39	HIS	0	-0.071	-0.019	42.319	0.194	0.194	0.000	0.000	0.000	0.000
45	A	40	PRO	0	-0.019	-0.027	44.258	0.203	0.203	0.000	0.000	0.000	0.000
46	A	41	GLY	0	-0.019	-0.002	46.120	0.287	0.287	0.000	0.000	0.000	0.000
47	A	42	GLY	0	-0.011	0.001	46.756	0.093	0.093	0.000	0.000	0.000	0.000
48	A	43	GLU	-1	-0.881	-0.955	43.166	-14.287	-14.287	0.000	0.000	0.000	0.000
49	A	44	GLU	-1	-0.896	-0.956	42.588	-14.157	-14.157	0.000	0.000	0.000	0.000
50	A	45	VAL	0	-0.002	0.007	43.192	-0.270	-0.270	0.000	0.000	0.000	0.000
51	A	46	LEU	0	-0.050	-0.018	39.047	-0.296	-0.296	0.000	0.000	0.000	0.000
52	A	47	LEU	0	0.003	-0.008	38.747	-0.492	-0.492	0.000	0.000	0.000	0.000
53	A	48	GLU	-1	-0.950	-0.986	39.241	-14.066	-14.066	0.000	0.000	0.000	0.000
54	A	49	GLN	0	-0.018	0.003	37.745	-0.306	-0.306	0.000	0.000	0.000	0.000
55	A	50	ALA	0	0.021	0.013	34.884	-0.538	-0.538	0.000	0.000	0.000	0.000
56	A	51	GLY	0	-0.038	-0.022	31.498	0.088	0.088	0.000	0.000	0.000	0.000
57	A	52	VAL	0	-0.046	-0.005	32.226	-0.312	-0.312	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.898	-0.917	33.123	-18.034	-18.034	0.000	0.000	0.000	0.000
59	A	54	ALA	0	0.052	0.026	34.275	0.461	0.461	0.000	0.000	0.000	0.000
60	A	55	SER	0	-0.044	-0.069	35.062	0.302	0.302	0.000	0.000	0.000	0.000
61	A	56	GLU	-1	-0.977	-0.973	37.490	-14.329	-14.329	0.000	0.000	0.000	0.000
62	A	57	SER	0	0.038	-0.002	40.569	0.383	0.383	0.000	0.000	0.000	0.000
63	A	58	PHE	0	-0.065	-0.025	39.114	0.305	0.305	0.000	0.000	0.000	0.000
64	A	59	GLU	-1	-0.867	-0.951	40.218	-14.597	-14.597	0.000	0.000	0.000	0.000
65	A	60	ASP	-1	-0.886	-0.928	42.825	-13.168	-13.168	0.000	0.000	0.000	0.000
66	A	61	VAL	0	-0.101	-0.042	44.946	0.339	0.339	0.000	0.000	0.000	0.000
67	A	62	GLY	0	-0.006	0.006	46.192	0.243	0.243	0.000	0.000	0.000	0.000
68	A	63	HIS	1	0.850	0.941	42.529	14.345	14.345	0.000	0.000	0.000	0.000
69	A	64	SER	0	0.067	0.020	45.322	-0.105	-0.105	0.000	0.000	0.000	0.000
70	A	65	SER	0	0.004	-0.025	43.488	-0.268	-0.268	0.000	0.000	0.000	0.000
71	A	66	ASP	-1	-0.910	-0.945	42.474	-13.876	-13.876	0.000	0.000	0.000	0.000
72	A	67	ALA	0	0.045	0.018	42.163	-0.323	-0.323	0.000	0.000	0.000	0.000
73	A	68	ARG	1	0.921	0.962	39.213	13.941	13.941	0.000	0.000	0.000	0.000
74	A	69	GLU	-1	-0.855	-0.910	37.822	-16.241	-16.241	0.000	0.000	0.000	0.000
75	A	70	MET	0	-0.029	-0.011	37.516	-0.474	-0.474	0.000	0.000	0.000	0.000
76	A	71	LEU	0	0.011	0.012	34.983	-0.283	-0.283	0.000	0.000	0.000	0.000
77	A	72	LYS	1	0.823	0.892	33.283	15.890	15.890	0.000	0.000	0.000	0.000
78	A	73	GLN	0	-0.051	-0.016	32.486	-0.391	-0.391	0.000	0.000	0.000	0.000
79	A	74	TYR	0	-0.006	-0.006	32.850	-0.304	-0.304	0.000	0.000	0.000	0.000
80	A	75	TYR	0	-0.089	-0.048	25.470	-0.526	-0.526	0.000	0.000	0.000	0.000
81	A	76	ILE	0	-0.024	-0.010	25.661	-0.181	-0.181	0.000	0.000	0.000	0.000
82	A	77	GLY	0	0.004	0.000	23.582	-1.186	-1.186	0.000	0.000	0.000	0.000
83	A	78	ASP	-1	-0.790	-0.847	23.251	-21.685	-21.685	0.000	0.000	0.000	0.000
84	A	79	ILE	0	0.029	0.005	23.491	-0.826	-0.826	0.000	0.000	0.000	0.000
85	A	80	HIS	0	0.001	0.015	16.796	0.519	0.519	0.000	0.000	0.000	0.000
86	A	81	PRO	0	0.019	-0.002	19.752	0.756	0.756	0.000	0.000	0.000	0.000
87	A	82	SER	0	-0.073	-0.047	20.677	0.344	0.344	0.000	0.000	0.000	0.000
88	A	83	ASP	-1	-0.837	-0.920	22.590	-24.361	-24.361	0.000	0.000	0.000	0.000
89	A	84	LEU	0	-0.050	-0.012	25.358	0.893	0.893	0.000	0.000	0.000	0.000
90	A	85	LYS	1	0.929	0.960	27.660	17.158	17.158	0.000	0.000	0.000	0.000
91	A	86	PRO	-1	-0.928	-0.952	29.924	-18.695	-18.695	0.000	0.000	0.000	0.000

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