FMO DATABASE

FMODB ID: QKLMY

Calculation Name: 1B0B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | n-acetyl-serine | cyanide ion

Ligand 3-letter code: HEM | SAC | CYN

Ligand of Interest (LOI):

PDB ID: 1B0B

Chain ID: A

ChEMBL ID:

UniProt ID: P41260

Base Structure: X-ray

Registration Date: 2025-09-02

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1157618.03278
FMO2-HF: Nuclear repulsion	1105249.327537
FMO2-HF: Total energy	-52368.705242
FMO2-MP2: Total energy	-52518.742564

3D Structure

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:2:LEU)

Summations of interaction energy for fragment #1(A:2: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.
-32.164	-23.364	15.03	-7.719	-16.113	-0.056

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.925

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	4	ALA	0	0.087	0.034	3.416	-0.816	1.274	0.026	-0.996	-1.121	-0.001
5	A	6	GLN	0	0.015	0.017	2.199	-18.855	-17.898	6.316	-3.249	-4.024	-0.030
6	A	7	LYS	1	0.893	0.921	2.203	47.437	48.669	3.059	-0.800	-3.490	-0.004
7	A	8	ASP	-1	-0.852	-0.917	3.957	-24.227	-24.113	0.004	-0.024	-0.094	0.000
9	A	10	VAL	0	0.029	0.034	4.182	2.376	2.505	-0.001	-0.011	-0.117	0.000
78	A	79	LEU	0	0.000	0.006	2.925	-2.852	-2.093	0.129	-0.165	-0.723	-0.001
79	A	80	ASP	-1	-0.892	-0.929	3.931	-39.400	-39.192	0.004	-0.074	-0.139	0.000
125	A	126	ALA	0	-0.052	-0.035	4.014	-5.845	-5.664	0.000	-0.026	-0.155	0.000
126	A	127	TRP	0	0.010	-0.003	3.724	-5.485	-5.000	0.010	-0.144	-0.351	-0.001
128	A	129	ALA	0	-0.055	-0.026	2.615	-3.400	-2.597	1.326	-0.703	-1.426	-0.001
129	A	130	VAL	0	-0.017	-0.011	2.418	-8.659	-7.279	4.036	-1.608	-3.807	-0.016
130	A	131	ALA	0	0.030	0.023	3.417	2.631	2.583	0.039	0.206	-0.198	-0.001
132	A	133	ALA	0	-0.043	-0.021	3.152	1.519	1.982	0.083	-0.122	-0.425	-0.001
133	A	134	LEU	0	0.033	0.016	5.028	3.781	3.828	-0.001	-0.003	-0.043	0.000
4	A	5	ALA	0	0.087	0.040	5.615	0.878	0.878	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.003	0.014	6.800	1.965	1.965	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.925	0.950	6.780	29.039	29.039	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.042	-0.030	9.084	2.376	2.376	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.025	-0.024	9.530	1.389	1.389	0.000	0.000	0.000	0.000
13	A	14	TRP	0	0.015	-0.008	10.373	1.216	1.216	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.015	0.008	12.158	1.264	1.264	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.909	0.960	14.817	16.475	16.475	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.047	0.024	14.728	0.809	0.809	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.000	-0.002	15.757	1.064	1.064	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.015	-0.002	17.490	0.700	0.700	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.026	0.017	19.838	0.558	0.558	0.000	0.000	0.000	0.000
20	A	21	TRP	0	-0.033	-0.008	16.759	0.288	0.288	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.005	0.002	21.096	0.139	0.139	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.042	-0.015	24.053	0.305	0.305	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.033	0.003	19.841	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.036	0.011	20.311	-0.390	-0.390	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.019	-0.009	21.324	-0.193	-0.193	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.809	-0.881	22.553	-10.724	-10.724	0.000	0.000	0.000	0.000
27	A	28	PHE	0	-0.029	-0.007	16.107	-0.191	-0.191	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.015	-0.008	20.186	-0.253	-0.253	0.000	0.000	0.000	0.000
29	A	30	MET	0	-0.021	0.004	22.201	0.193	0.193	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.024	0.016	20.644	0.091	0.091	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.045	-0.013	18.574	-0.201	-0.201	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.017	-0.017	21.162	0.119	0.119	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.909	-0.951	24.859	-10.228	-10.228	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.080	-0.024	21.761	0.166	0.166	0.000	0.000	0.000	0.000
35	A	36	HIS	0	-0.019	-0.006	19.456	0.103	0.103	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.811	-0.896	24.001	-9.852	-9.852	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.821	-0.906	24.211	-12.021	-12.021	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.019	-0.018	21.174	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.003	0.003	24.392	0.120	0.120	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.027	0.009	26.992	0.221	0.221	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.860	0.956	25.083	11.245	11.245	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.012	-0.002	22.026	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.014	-0.011	28.046	0.327	0.327	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.004	0.002	31.398	0.272	0.272	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.032	-0.001	27.239	0.147	0.147	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.007	-0.022	27.314	0.150	0.150	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.008	0.007	32.803	0.266	0.266	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.011	-0.003	35.042	0.235	0.235	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.035	-0.003	34.967	0.107	0.107	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.038	0.010	34.320	-0.239	-0.239	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.851	0.911	27.981	10.348	10.348	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.002	-0.003	31.447	-0.140	-0.140	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.074	-0.048	33.387	0.120	0.120	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.016	0.011	28.985	0.033	0.033	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.859	0.920	27.736	10.131	10.131	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.031	-0.021	29.295	-0.422	-0.422	0.000	0.000	0.000	0.000
57	A	58	THR	0	0.006	0.006	31.014	0.187	0.187	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.014	-0.005	30.835	-0.284	-0.284	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.852	-0.928	30.042	-9.047	-9.047	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.035	0.005	25.881	-0.541	-0.541	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.006	0.009	25.848	-0.471	-0.471	0.000	0.000	0.000	0.000
62	A	63	ALA	0	0.034	0.016	25.502	-0.401	-0.401	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.000	0.012	21.932	-0.114	-0.114	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.018	0.007	21.558	-0.684	-0.684	0.000	0.000	0.000	0.000
65	A	66	GLN	0	-0.020	-0.011	20.542	-0.544	-0.544	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.033	-0.032	20.504	-0.402	-0.402	0.000	0.000	0.000	0.000
67	A	68	PHE	0	-0.028	-0.011	14.794	-0.539	-0.539	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.906	0.942	16.148	12.583	12.583	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.018	0.024	15.763	-0.637	-0.637	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.004	0.008	13.642	-0.338	-0.338	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.013	0.006	10.819	-1.207	-1.207	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.017	-0.019	10.698	-1.381	-1.381	0.000	0.000	0.000	0.000
73	A	74	ASN	0	0.025	0.027	11.371	-1.470	-1.470	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.064	0.006	7.873	-0.964	-0.964	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.039	-0.022	6.915	-2.332	-2.332	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.919	-0.960	7.681	-19.946	-19.946	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.071	-0.042	8.547	0.476	0.476	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.052	-0.023	6.575	0.915	0.915	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.033	0.017	7.788	0.629	0.629	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.117	0.058	8.585	0.658	0.658	0.000	0.000	0.000	0.000
83	A	84	ALA	0	-0.020	-0.006	11.314	1.128	1.128	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.030	-0.007	5.628	0.701	0.701	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.862	-0.939	9.950	-20.913	-20.913	0.000	0.000	0.000	0.000
86	A	87	GLY	0	-0.008	0.008	12.237	1.010	1.010	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.020	-0.005	12.337	1.336	1.336	0.000	0.000	0.000	0.000
88	A	89	CYS	0	-0.072	-0.035	10.277	0.297	0.297	0.000	0.000	0.000	0.000
89	A	90	LYS	1	1.027	1.021	13.201	14.679	14.679	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.049	-0.032	16.580	1.016	1.016	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.003	-0.007	14.166	0.680	0.680	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.060	0.025	16.065	0.592	0.592	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.040	0.020	17.747	0.639	0.639	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.043	-0.030	20.689	1.003	1.003	0.000	0.000	0.000	0.000
95	A	96	HIS	0	-0.075	-0.052	18.949	0.693	0.693	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.904	0.944	21.347	13.286	13.286	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.018	-0.007	22.997	0.462	0.462	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.898	0.960	22.365	12.220	12.220	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.024	0.013	26.219	0.189	0.189	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.071	-0.037	20.611	0.053	0.053	0.000	0.000	0.000	0.000
101	A	102	SER	0	0.024	0.011	21.573	-0.467	-0.467	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.082	0.025	16.599	-0.348	-0.348	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.032	0.016	16.567	-0.869	-0.869	0.000	0.000	0.000	0.000
104	A	105	GLN	0	-0.031	-0.030	18.203	-0.231	-0.231	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.004	0.005	15.075	-0.144	-0.144	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.868	-0.923	12.905	-21.422	-21.422	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.009	0.000	13.989	-0.807	-0.807	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.027	0.012	15.980	-0.095	-0.095	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.007	-0.012	9.468	-0.628	-0.628	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.946	0.978	11.623	17.554	17.554	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.003	-0.002	13.195	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.004	0.007	11.226	0.287	0.287	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.012	-0.015	9.740	-0.040	-0.040	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.029	0.016	11.176	0.029	0.029	0.000	0.000	0.000	0.000
115	A	116	PHE	0	-0.020	-0.008	14.552	0.550	0.550	0.000	0.000	0.000	0.000
116	A	117	MET	0	-0.013	-0.015	11.276	1.138	1.138	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.862	0.944	13.640	18.124	18.124	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.039	-0.015	14.801	0.511	0.511	0.000	0.000	0.000	0.000
119	A	120	TYR	0	-0.031	-0.016	14.676	0.878	0.878	0.000	0.000	0.000	0.000
120	A	121	GLY	0	-0.012	-0.003	14.427	-0.305	-0.305	0.000	0.000	0.000	0.000
121	A	122	GLY	0	-0.020	-0.007	10.420	-1.133	-1.133	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.848	-0.941	7.762	-29.458	-29.458	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.794	-0.897	8.473	-21.676	-21.676	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.008	0.015	7.901	-1.084	-1.084	0.000	0.000	0.000	0.000
127	A	128	THR	0	-0.022	-0.017	6.064	0.520	0.520	0.000	0.000	0.000	0.000
131	A	132	GLY	0	-0.006	-0.002	6.098	2.538	2.538	0.000	0.000	0.000	0.000
134	A	135	MET	0	-0.022	-0.018	7.255	2.864	2.864	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.051	-0.020	8.471	1.999	1.999	0.000	0.000	0.000	0.000
136	A	137	MET	0	-0.033	-0.015	7.136	1.688	1.688	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.008	-0.005	10.817	1.680	1.680	0.000	0.000	0.000	0.000
138	A	139	ARG	1	0.844	0.903	11.662	23.545	23.545	0.000	0.000	0.000	0.000
139	A	140	PRO	0	-0.027	-0.017	14.051	0.994	0.994	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.878	-0.934	16.690	-14.903	-14.903	0.000	0.000	0.000	0.000
141	A	142	MET	-1	-0.983	-0.944	17.056	-12.799	-12.799	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)