FMO DATABASE

FMODB ID: N6VYQ

Calculation Name: 4U8U-D-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | 2-acetamido-2-deoxy-beta-d-glucopyranose | calcium ion | cyanide ion | zinc ion

Ligand 3-letter code: HEM | NAG | CA | CYN | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4U8U

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0M3

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1343300.739877
FMO2-HF: Nuclear repulsion	1287483.937723
FMO2-HF: Total energy	-55816.802154
FMO2-MP2: Total energy	-55982.244179

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(D:1:ASP)

Summations of interaction energy for fragment #1(D:1:ASP)

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.
-9.164	-3.276	1.604	-2.905	-4.587	0.027

Interaction energy analysis for fragmet #1(D:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.047

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	D	3	SER	0	0.002	-0.017	3.757	-6.231	-4.864	0.004	-0.645	-0.726	0.002
130	D	130	LYS	1	0.866	0.943	2.699	-17.362	-13.850	1.397	-1.879	-3.030	0.025
133	D	134	THR	0	-0.047	-0.030	2.853	-4.557	-3.548	0.203	-0.381	-0.831	0.000
4	D	4	ILE	0	0.055	0.011	5.421	1.925	1.925	0.000	0.000	0.000	0.000
5	D	5	LEU	0	0.007	-0.001	8.746	0.806	0.806	0.000	0.000	0.000	0.000
6	D	6	GLU	-1	-0.799	-0.866	5.877	1.066	1.066	0.000	0.000	0.000	0.000
7	D	7	LEU	0	0.055	0.018	7.342	0.900	0.900	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.022	-0.009	9.536	0.471	0.471	0.000	0.000	0.000	0.000
9	D	9	LYS	1	0.781	0.888	12.119	-0.781	-0.781	0.000	0.000	0.000	0.000
10	D	10	VAL	0	0.027	0.011	9.855	0.112	0.112	0.000	0.000	0.000	0.000
11	D	11	LYS	1	0.864	0.929	12.246	1.717	1.717	0.000	0.000	0.000	0.000
12	D	12	ASN	0	-0.042	-0.019	15.181	0.008	0.008	0.000	0.000	0.000	0.000
13	D	13	GLN	0	0.002	-0.016	15.613	0.264	0.264	0.000	0.000	0.000	0.000
14	D	14	TRP	0	-0.014	-0.030	16.034	0.171	0.171	0.000	0.000	0.000	0.000
15	D	15	ARG	1	0.884	0.949	17.949	0.166	0.166	0.000	0.000	0.000	0.000
16	D	16	GLU	-1	-0.745	-0.849	20.855	0.528	0.528	0.000	0.000	0.000	0.000
17	D	17	ALA	0	0.037	0.030	20.011	-0.003	-0.003	0.000	0.000	0.000	0.000
18	D	18	PHE	0	-0.041	-0.026	21.127	0.012	0.012	0.000	0.000	0.000	0.000
19	D	19	GLY	0	0.001	0.001	22.922	-0.053	-0.053	0.000	0.000	0.000	0.000
20	D	20	GLU	-1	-0.882	-0.940	24.887	0.093	0.093	0.000	0.000	0.000	0.000
21	D	21	GLY	0	-0.024	-0.023	27.658	0.044	0.044	0.000	0.000	0.000	0.000
22	D	22	HIS	0	-0.045	-0.032	29.322	-0.013	-0.013	0.000	0.000	0.000	0.000
23	D	23	HIS	0	-0.074	-0.046	25.365	0.020	0.020	0.000	0.000	0.000	0.000
24	D	24	ARG	1	0.876	0.956	24.947	-0.115	-0.115	0.000	0.000	0.000	0.000
25	D	25	VAL	0	0.017	0.010	26.091	0.041	0.041	0.000	0.000	0.000	0.000
26	D	26	GLN	0	-0.005	-0.003	28.302	0.030	0.030	0.000	0.000	0.000	0.000
27	D	27	PHE	0	0.040	0.033	18.992	0.063	0.063	0.000	0.000	0.000	0.000
28	D	28	GLY	0	0.031	0.019	23.807	0.081	0.081	0.000	0.000	0.000	0.000
29	D	29	LEU	0	-0.010	-0.024	24.863	0.046	0.046	0.000	0.000	0.000	0.000
30	D	30	GLU	-1	-0.841	-0.906	25.806	0.780	0.780	0.000	0.000	0.000	0.000
31	D	31	LEU	0	0.017	0.022	19.156	0.071	0.071	0.000	0.000	0.000	0.000
32	D	32	TRP	0	0.043	0.003	22.059	0.103	0.103	0.000	0.000	0.000	0.000
33	D	33	LYS	1	0.920	0.974	24.922	-0.543	-0.543	0.000	0.000	0.000	0.000
34	D	34	ARG	1	0.937	0.984	22.236	-1.187	-1.187	0.000	0.000	0.000	0.000
35	D	35	PHE	0	0.023	0.012	20.323	0.068	0.068	0.000	0.000	0.000	0.000
36	D	36	PHE	0	-0.013	-0.027	23.331	0.009	0.009	0.000	0.000	0.000	0.000
37	D	37	ASP	-1	-0.992	-0.978	26.754	0.745	0.745	0.000	0.000	0.000	0.000
38	D	38	THR	0	-0.059	-0.047	23.427	0.048	0.048	0.000	0.000	0.000	0.000
39	D	39	HIS	1	0.856	0.942	21.345	-1.250	-1.250	0.000	0.000	0.000	0.000
40	D	40	PRO	0	0.035	0.030	25.432	-0.042	-0.042	0.000	0.000	0.000	0.000
41	D	41	GLU	-1	-0.872	-0.960	24.985	0.914	0.914	0.000	0.000	0.000	0.000
42	D	42	VAL	0	-0.003	0.010	22.698	-0.058	-0.058	0.000	0.000	0.000	0.000
43	D	43	LYS	1	0.955	0.976	25.802	-0.570	-0.570	0.000	0.000	0.000	0.000
44	D	44	GLY	0	-0.052	-0.019	28.808	-0.053	-0.053	0.000	0.000	0.000	0.000
45	D	45	LEU	0	-0.004	-0.002	23.652	-0.050	-0.050	0.000	0.000	0.000	0.000
46	D	46	PHE	0	0.019	0.000	22.968	-0.041	-0.041	0.000	0.000	0.000	0.000
47	D	47	LYS	1	0.983	0.993	29.044	-0.373	-0.373	0.000	0.000	0.000	0.000
48	D	48	GLY	0	-0.016	0.000	31.867	-0.019	-0.019	0.000	0.000	0.000	0.000
49	D	49	VAL	0	-0.055	-0.026	28.530	-0.028	-0.028	0.000	0.000	0.000	0.000
50	D	50	ASN	0	0.029	0.015	32.018	0.011	0.011	0.000	0.000	0.000	0.000
51	D	51	GLY	0	0.025	0.002	29.980	0.013	0.013	0.000	0.000	0.000	0.000
52	D	52	ASP	-1	-1.015	-1.005	30.790	0.390	0.390	0.000	0.000	0.000	0.000
53	D	53	ASN	0	0.017	-0.004	33.598	0.024	0.024	0.000	0.000	0.000	0.000
54	D	54	ILE	0	0.043	0.019	29.048	-0.024	-0.024	0.000	0.000	0.000	0.000
55	D	55	TYR	0	-0.005	-0.008	31.799	0.009	0.009	0.000	0.000	0.000	0.000
56	D	56	SER	0	-0.017	0.009	34.201	-0.031	-0.031	0.000	0.000	0.000	0.000
57	D	57	PRO	0	0.018	-0.003	34.162	0.011	0.011	0.000	0.000	0.000	0.000
58	D	58	GLU	-1	-0.861	-0.933	33.868	0.208	0.208	0.000	0.000	0.000	0.000
59	D	59	PHE	0	0.010	0.017	26.359	0.007	0.007	0.000	0.000	0.000	0.000
60	D	60	ALA	0	0.011	0.009	29.403	0.024	0.024	0.000	0.000	0.000	0.000
61	D	61	ALA	0	0.012	-0.003	29.476	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	62	HIS	0	-0.016	-0.010	24.621	-0.081	-0.081	0.000	0.000	0.000	0.000
63	D	63	ALA	0	-0.002	-0.007	25.068	0.009	0.009	0.000	0.000	0.000	0.000
64	D	64	GLU	-1	-0.804	-0.894	24.493	0.230	0.230	0.000	0.000	0.000	0.000
65	D	65	ARG	1	0.895	0.957	24.920	-0.207	-0.207	0.000	0.000	0.000	0.000
66	D	66	VAL	0	-0.045	-0.010	20.194	-0.031	-0.031	0.000	0.000	0.000	0.000
67	D	67	LEU	0	0.006	0.005	20.195	0.018	0.018	0.000	0.000	0.000	0.000
68	D	68	SER	0	0.005	0.007	20.371	-0.063	-0.063	0.000	0.000	0.000	0.000
69	D	69	GLY	0	0.023	0.004	19.817	-0.092	-0.092	0.000	0.000	0.000	0.000
70	D	70	LEU	0	-0.001	0.005	13.965	-0.072	-0.072	0.000	0.000	0.000	0.000
71	D	71	ASP	-1	-0.828	-0.900	15.937	-0.288	-0.288	0.000	0.000	0.000	0.000
72	D	72	MET	0	-0.020	0.002	16.922	-0.144	-0.144	0.000	0.000	0.000	0.000
73	D	73	THR	0	-0.053	-0.033	12.604	-0.146	-0.146	0.000	0.000	0.000	0.000
74	D	74	ILE	0	0.039	0.013	12.200	-0.339	-0.339	0.000	0.000	0.000	0.000
75	D	75	GLY	0	-0.003	-0.002	13.234	-0.289	-0.289	0.000	0.000	0.000	0.000
76	D	76	LEU	0	-0.030	-0.030	13.935	-0.196	-0.196	0.000	0.000	0.000	0.000
77	D	77	LEU	0	-0.035	-0.011	7.834	-0.295	-0.295	0.000	0.000	0.000	0.000
78	D	78	ASP	-1	-0.900	-0.947	8.508	-3.356	-3.356	0.000	0.000	0.000	0.000
79	D	79	ASP	-1	-0.828	-0.909	10.687	-2.369	-2.369	0.000	0.000	0.000	0.000
80	D	80	THR	0	-0.022	-0.033	8.088	0.140	0.140	0.000	0.000	0.000	0.000
81	D	81	ASN	0	-0.046	-0.017	10.761	-0.132	-0.132	0.000	0.000	0.000	0.000
82	D	82	ALA	0	0.026	0.011	14.281	0.179	0.179	0.000	0.000	0.000	0.000
83	D	83	PHE	0	-0.013	0.007	8.205	0.107	0.107	0.000	0.000	0.000	0.000
84	D	84	LYS	1	0.983	0.988	10.010	4.175	4.175	0.000	0.000	0.000	0.000
85	D	85	ALA	0	0.000	0.025	13.130	0.289	0.289	0.000	0.000	0.000	0.000
86	D	86	GLN	0	0.047	0.018	15.324	0.152	0.152	0.000	0.000	0.000	0.000
87	D	87	VAL	0	-0.014	-0.001	11.219	0.255	0.255	0.000	0.000	0.000	0.000
88	D	88	THR	0	-0.015	-0.026	14.555	0.256	0.256	0.000	0.000	0.000	0.000
89	D	89	HIS	0	-0.003	0.012	16.918	0.127	0.127	0.000	0.000	0.000	0.000
90	D	90	LEU	0	0.007	0.006	15.695	0.135	0.135	0.000	0.000	0.000	0.000
91	D	91	HIS	0	-0.015	0.010	16.611	0.096	0.096	0.000	0.000	0.000	0.000
92	D	92	SER	0	-0.056	-0.033	18.410	0.097	0.097	0.000	0.000	0.000	0.000
93	D	93	GLN	0	-0.022	-0.007	21.492	0.072	0.072	0.000	0.000	0.000	0.000
94	D	94	HIS	0	-0.074	-0.066	19.722	0.181	0.181	0.000	0.000	0.000	0.000
95	D	95	VAL	0	0.030	0.023	21.025	0.072	0.072	0.000	0.000	0.000	0.000
96	D	96	GLU	-1	-0.949	-0.963	22.484	0.018	0.018	0.000	0.000	0.000	0.000
97	D	97	ARG	1	0.802	0.897	24.214	-0.191	-0.191	0.000	0.000	0.000	0.000
98	D	98	SER	0	0.007	0.005	23.930	0.022	0.022	0.000	0.000	0.000	0.000
99	D	99	ILE	0	-0.046	-0.027	19.781	0.044	0.044	0.000	0.000	0.000	0.000
100	D	100	ASN	0	-0.013	-0.013	20.237	0.050	0.050	0.000	0.000	0.000	0.000
101	D	101	PRO	0	0.060	0.020	15.893	0.085	0.085	0.000	0.000	0.000	0.000
102	D	102	GLU	-1	-0.878	-0.922	15.403	1.754	1.754	0.000	0.000	0.000	0.000
103	D	103	PHE	0	-0.004	-0.024	16.979	0.107	0.107	0.000	0.000	0.000	0.000
104	D	104	TYR	0	0.009	0.006	13.412	-0.003	-0.003	0.000	0.000	0.000	0.000
105	D	105	GLU	-1	-0.820	-0.896	11.828	4.807	4.807	0.000	0.000	0.000	0.000
106	D	106	HIS	0	-0.040	-0.026	14.492	-0.112	-0.112	0.000	0.000	0.000	0.000
107	D	107	PHE	0	-0.008	0.010	15.412	-0.106	-0.106	0.000	0.000	0.000	0.000
108	D	108	LEU	0	0.006	0.018	10.259	-0.117	-0.117	0.000	0.000	0.000	0.000
109	D	109	GLY	0	0.033	0.009	14.530	-0.018	-0.018	0.000	0.000	0.000	0.000
110	D	110	ALA	0	-0.072	-0.037	16.750	-0.160	-0.160	0.000	0.000	0.000	0.000
111	D	111	LEU	0	0.036	0.005	13.958	-0.132	-0.132	0.000	0.000	0.000	0.000
112	D	112	LEU	0	-0.018	-0.013	12.176	-0.139	-0.139	0.000	0.000	0.000	0.000
113	D	113	HIS	0	-0.038	-0.016	16.494	-0.248	-0.248	0.000	0.000	0.000	0.000
114	D	114	VAL	0	-0.009	-0.009	20.077	-0.129	-0.129	0.000	0.000	0.000	0.000
115	D	115	LEU	0	0.054	0.026	15.816	-0.112	-0.112	0.000	0.000	0.000	0.000
116	D	116	PRO	0	-0.049	-0.022	18.887	-0.126	-0.126	0.000	0.000	0.000	0.000
117	D	117	LYS	1	0.765	0.889	21.291	-0.978	-0.978	0.000	0.000	0.000	0.000
118	D	118	TYR	0	-0.040	-0.045	22.966	-0.105	-0.105	0.000	0.000	0.000	0.000
119	D	119	LEU	0	-0.051	-0.003	18.016	-0.024	-0.024	0.000	0.000	0.000	0.000
120	D	120	GLY	0	0.005	0.011	22.703	0.000	0.000	0.000	0.000	0.000	0.000
121	D	121	THR	0	-0.117	-0.080	19.970	0.056	0.056	0.000	0.000	0.000	0.000
122	D	122	LYS	1	0.960	0.970	18.539	-1.167	-1.167	0.000	0.000	0.000	0.000
123	D	123	LEU	0	0.029	0.025	14.933	-0.004	-0.004	0.000	0.000	0.000	0.000
124	D	124	ASP	-1	-0.822	-0.894	11.108	2.484	2.484	0.000	0.000	0.000	0.000
125	D	125	GLN	0	0.020	0.005	11.379	0.042	0.042	0.000	0.000	0.000	0.000
126	D	126	ASP	-1	-0.838	-0.901	7.562	7.910	7.910	0.000	0.000	0.000	0.000
127	D	127	ALA	0	-0.011	-0.014	6.664	2.277	2.277	0.000	0.000	0.000	0.000
128	D	128	TRP	0	-0.008	-0.033	7.824	0.452	0.452	0.000	0.000	0.000	0.000
129	D	129	THR	0	-0.036	-0.022	7.383	0.576	0.576	0.000	0.000	0.000	0.000
131	D	132	PHE	0	0.045	0.028	6.349	-1.742	-1.742	0.000	0.000	0.000	0.000
132	D	133	HIS	0	-0.016	-0.025	5.338	0.368	0.368	0.000	0.000	0.000	0.000
134	D	135	ILE	0	-0.037	-0.007	5.932	-1.905	-1.905	0.000	0.000	0.000	0.000
135	D	136	ALA	0	0.009	-0.011	9.674	-0.391	-0.391	0.000	0.000	0.000	0.000
136	D	137	ASP	-1	-0.903	-0.967	7.359	3.609	3.609	0.000	0.000	0.000	0.000
137	D	138	GLY	0	-0.006	0.005	10.257	-0.380	-0.380	0.000	0.000	0.000	0.000
138	D	139	ILE	0	-0.056	-0.030	11.893	-0.097	-0.097	0.000	0.000	0.000	0.000
139	D	140	LYS	1	0.811	0.912	10.691	-2.441	-2.441	0.000	0.000	0.000	0.000
140	D	141	GLY	-1	-0.904	-0.939	15.254	-0.102	-0.102	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:ASP)