FMO DATABASE

FMODB ID: 5GZ8Z

Calculation Name: 1X9F-C-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | phosphate ion | carbon monoxide

Ligand 3-letter code: HEM | PO4 | CMO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X9F

Chain ID: C

ChEMBL ID:

UniProt ID: P02218

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	-1424975.80403
FMO2-HF: Nuclear repulsion	1366514.308741
FMO2-HF: Total energy	-58461.495289
FMO2-MP2: Total energy	-58634.595046

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(C:3:HIS)

Summations of interaction energy for fragment #1(C:3:HIS)

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.
-112.718	-112.187	3.975	0.297	-4.803	-0.046

Interaction energy analysis for fragmet #1(C:3:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / 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

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	C	5	HIS	0	-0.001	-0.045	2.297	-19.503	-21.636	3.912	1.528	-3.307	-0.036
4	C	6	CYS	-1	-0.905	-0.934	4.908	-23.783	-23.642	-0.001	-0.013	-0.127	0.000
6	C	8	SER	0	-0.010	-0.026	3.393	-5.270	-4.959	0.010	-0.091	-0.230	0.000
7	C	9	GLU	-1	-0.858	-0.946	2.954	-58.509	-56.314	0.055	-1.127	-1.123	-0.010
8	C	10	GLU	-1	-0.814	-0.871	5.382	-20.885	-20.868	-0.001	0.000	-0.016	0.000
5	C	7	CYS	0	-0.050	-0.016	6.182	-1.961	-1.961	0.000	0.000	0.000	0.000
9	C	11	ASP	-1	-0.814	-0.874	7.206	-32.211	-32.211	0.000	0.000	0.000	0.000
10	C	12	HIS	1	0.882	0.923	6.510	39.901	39.901	0.000	0.000	0.000	0.000
11	C	13	ARG	1	0.812	0.888	9.574	28.115	28.115	0.000	0.000	0.000	0.000
12	C	14	ILE	0	-0.074	-0.036	11.478	2.610	2.610	0.000	0.000	0.000	0.000
13	C	15	VAL	0	0.025	0.008	12.778	1.664	1.664	0.000	0.000	0.000	0.000
14	C	16	GLN	0	0.023	-0.001	12.311	0.329	0.329	0.000	0.000	0.000	0.000
15	C	17	LYS	1	0.928	0.970	15.646	18.916	18.916	0.000	0.000	0.000	0.000
16	C	18	GLN	0	0.028	0.000	17.351	0.411	0.411	0.000	0.000	0.000	0.000
17	C	19	TRP	0	-0.027	-0.031	18.521	0.999	0.999	0.000	0.000	0.000	0.000
18	C	20	ASP	-1	-0.926	-0.960	19.994	-13.635	-13.635	0.000	0.000	0.000	0.000
19	C	21	ILE	0	-0.038	-0.013	21.904	0.764	0.764	0.000	0.000	0.000	0.000
20	C	22	LEU	0	-0.022	-0.010	24.180	0.663	0.663	0.000	0.000	0.000	0.000
21	C	23	TRP	0	-0.036	-0.037	22.537	1.010	1.010	0.000	0.000	0.000	0.000
22	C	24	ARG	1	0.931	0.975	26.034	11.808	11.808	0.000	0.000	0.000	0.000
23	C	25	ASP	-1	-0.909	-0.950	28.606	-9.474	-9.474	0.000	0.000	0.000	0.000
24	C	26	THR	0	0.040	0.008	31.192	-0.178	-0.178	0.000	0.000	0.000	0.000
25	C	27	GLU	-1	-0.971	-0.975	33.511	-8.562	-8.562	0.000	0.000	0.000	0.000
26	C	28	SER	0	0.053	0.026	29.112	-0.045	-0.045	0.000	0.000	0.000	0.000
27	C	29	SER	0	0.004	-0.004	30.755	-0.168	-0.168	0.000	0.000	0.000	0.000
28	C	30	LYS	1	0.956	0.972	33.017	8.206	8.206	0.000	0.000	0.000	0.000
29	C	31	ILE	0	0.055	0.039	28.919	0.088	0.088	0.000	0.000	0.000	0.000
30	C	32	LYS	1	0.843	0.916	25.692	11.837	11.837	0.000	0.000	0.000	0.000
31	C	33	ILE	0	-0.037	-0.021	29.899	-0.033	-0.033	0.000	0.000	0.000	0.000
32	C	34	GLY	0	0.002	-0.005	33.076	0.034	0.034	0.000	0.000	0.000	0.000
33	C	35	PHE	0	0.042	0.019	24.504	0.115	0.115	0.000	0.000	0.000	0.000
34	C	36	GLY	0	0.058	0.012	28.784	-0.123	-0.123	0.000	0.000	0.000	0.000
35	C	37	ARG	1	0.903	0.957	29.725	8.357	8.357	0.000	0.000	0.000	0.000
36	C	38	LEU	0	-0.008	0.014	30.077	0.225	0.225	0.000	0.000	0.000	0.000
37	C	39	LEU	0	0.007	0.011	25.671	0.126	0.126	0.000	0.000	0.000	0.000
38	C	40	LEU	0	-0.004	-0.006	28.746	0.041	0.041	0.000	0.000	0.000	0.000
39	C	41	THR	0	-0.040	-0.025	31.379	0.308	0.308	0.000	0.000	0.000	0.000
40	C	42	LYS	1	0.818	0.888	30.970	9.917	9.917	0.000	0.000	0.000	0.000
41	C	43	LEU	0	0.006	-0.002	28.300	0.081	0.081	0.000	0.000	0.000	0.000
42	C	44	ALA	0	0.012	0.006	31.328	0.094	0.094	0.000	0.000	0.000	0.000
43	C	45	LYS	1	0.865	0.939	34.875	8.314	8.314	0.000	0.000	0.000	0.000
44	C	46	ASP	-1	-0.799	-0.895	31.690	-9.534	-9.534	0.000	0.000	0.000	0.000
45	C	47	ILE	0	-0.013	-0.006	30.265	0.016	0.016	0.000	0.000	0.000	0.000
46	C	48	PRO	0	0.023	0.018	34.452	-0.033	-0.033	0.000	0.000	0.000	0.000
47	C	49	GLU	-1	-0.776	-0.886	34.348	-9.037	-9.037	0.000	0.000	0.000	0.000
48	C	50	VAL	0	0.009	-0.004	31.993	0.001	0.001	0.000	0.000	0.000	0.000
49	C	51	ASN	0	-0.084	-0.056	34.880	-0.043	-0.043	0.000	0.000	0.000	0.000
50	C	52	ASP	-1	-0.906	-0.944	37.984	-7.683	-7.683	0.000	0.000	0.000	0.000
51	C	53	LEU	0	-0.035	-0.004	32.505	0.043	0.043	0.000	0.000	0.000	0.000
52	C	54	PHE	0	0.009	-0.008	30.066	-0.099	-0.099	0.000	0.000	0.000	0.000
53	C	55	LYS	1	1.046	1.029	36.178	7.264	7.264	0.000	0.000	0.000	0.000
54	C	56	ARG	1	0.888	0.940	35.700	8.647	8.647	0.000	0.000	0.000	0.000
55	C	57	VAL	0	-0.095	-0.061	34.569	0.071	0.071	0.000	0.000	0.000	0.000
56	C	58	ASP	-1	-0.821	-0.900	37.891	-7.390	-7.390	0.000	0.000	0.000	0.000
57	C	59	ILE	0	-0.001	0.016	35.261	0.038	0.038	0.000	0.000	0.000	0.000
58	C	60	GLU	-1	-0.935	-0.961	38.848	-6.895	-6.895	0.000	0.000	0.000	0.000
59	C	61	HIS	1	0.788	0.879	41.915	7.209	7.209	0.000	0.000	0.000	0.000
60	C	62	ALA	0	0.047	0.032	37.899	-0.079	-0.079	0.000	0.000	0.000	0.000
61	C	63	GLU	-1	-0.885	-0.962	38.302	-7.703	-7.703	0.000	0.000	0.000	0.000
62	C	64	GLY	0	0.036	0.023	40.751	0.034	0.034	0.000	0.000	0.000	0.000
63	C	65	PRO	0	-0.007	-0.013	39.960	-0.226	-0.226	0.000	0.000	0.000	0.000
64	C	66	LYS	1	0.914	0.956	38.859	7.252	7.252	0.000	0.000	0.000	0.000
65	C	67	PHE	0	0.048	0.044	33.959	-0.266	-0.266	0.000	0.000	0.000	0.000
66	C	68	SER	0	0.029	0.011	35.171	-0.356	-0.356	0.000	0.000	0.000	0.000
67	C	69	ALA	0	0.000	-0.013	34.441	-0.285	-0.285	0.000	0.000	0.000	0.000
68	C	70	HIS	0	-0.021	-0.012	31.139	-0.125	-0.125	0.000	0.000	0.000	0.000
69	C	71	ALA	0	0.001	0.012	30.914	-0.369	-0.369	0.000	0.000	0.000	0.000
70	C	72	LEU	0	0.018	0.004	29.573	-0.365	-0.365	0.000	0.000	0.000	0.000
71	C	73	ARG	1	0.866	0.958	28.752	9.270	9.270	0.000	0.000	0.000	0.000
72	C	74	ILE	0	0.010	0.008	25.560	-0.346	-0.346	0.000	0.000	0.000	0.000
73	C	75	LEU	0	0.012	0.017	24.680	-0.566	-0.566	0.000	0.000	0.000	0.000
74	C	76	ASN	0	0.029	0.010	24.050	-0.612	-0.612	0.000	0.000	0.000	0.000
75	C	77	GLY	0	0.012	0.022	23.105	-0.387	-0.387	0.000	0.000	0.000	0.000
76	C	78	LEU	0	-0.006	-0.004	18.729	-0.670	-0.670	0.000	0.000	0.000	0.000
77	C	79	ASP	-1	-0.802	-0.889	19.248	-14.564	-14.564	0.000	0.000	0.000	0.000
78	C	80	LEU	0	-0.029	0.003	19.544	-0.634	-0.634	0.000	0.000	0.000	0.000
79	C	81	ALA	0	0.003	-0.003	16.467	-0.784	-0.784	0.000	0.000	0.000	0.000
80	C	82	ILE	0	0.025	0.002	15.095	-1.453	-1.453	0.000	0.000	0.000	0.000
81	C	83	ASN	0	-0.050	-0.040	14.869	-1.308	-1.308	0.000	0.000	0.000	0.000
82	C	84	LEU	0	-0.016	-0.005	14.924	-0.371	-0.371	0.000	0.000	0.000	0.000
83	C	85	LEU	0	-0.049	-0.030	10.525	-1.342	-1.342	0.000	0.000	0.000	0.000
84	C	86	ASP	-1	-0.926	-0.956	9.361	-31.581	-31.581	0.000	0.000	0.000	0.000
85	C	87	ASP	-1	-0.885	-0.941	10.573	-21.802	-21.802	0.000	0.000	0.000	0.000
86	C	88	PRO	0	0.037	0.011	7.658	1.541	1.541	0.000	0.000	0.000	0.000
87	C	89	PRO	0	-0.022	-0.007	10.540	1.354	1.354	0.000	0.000	0.000	0.000
88	C	90	ALA	0	0.029	0.018	13.220	1.525	1.525	0.000	0.000	0.000	0.000
89	C	91	LEU	0	-0.032	-0.006	11.067	1.372	1.372	0.000	0.000	0.000	0.000
90	C	92	ASP	-1	-0.829	-0.926	12.506	-21.855	-21.855	0.000	0.000	0.000	0.000
91	C	93	ALA	0	-0.006	0.008	15.111	1.192	1.192	0.000	0.000	0.000	0.000
92	C	94	ALA	0	0.004	0.002	17.894	1.039	1.039	0.000	0.000	0.000	0.000
93	C	95	LEU	0	-0.040	-0.029	14.251	0.881	0.881	0.000	0.000	0.000	0.000
94	C	96	ASP	-1	-0.778	-0.884	18.336	-13.681	-13.681	0.000	0.000	0.000	0.000
95	C	97	HIS	0	-0.023	0.010	20.244	0.796	0.796	0.000	0.000	0.000	0.000
96	C	98	LEU	0	-0.012	-0.026	20.215	0.676	0.676	0.000	0.000	0.000	0.000
97	C	99	ALA	0	0.025	0.031	20.969	0.533	0.533	0.000	0.000	0.000	0.000
98	C	100	HIS	0	-0.030	-0.016	23.021	0.822	0.822	0.000	0.000	0.000	0.000
99	C	101	GLN	0	-0.067	-0.040	25.923	0.311	0.311	0.000	0.000	0.000	0.000
100	C	102	HIS	0	-0.115	-0.073	24.927	0.654	0.654	0.000	0.000	0.000	0.000
101	C	103	GLU	-1	-0.814	-0.892	26.822	-11.090	-11.090	0.000	0.000	0.000	0.000
102	C	104	VAL	0	-0.065	-0.023	28.539	0.419	0.419	0.000	0.000	0.000	0.000
103	C	105	ARG	1	0.827	0.914	30.600	9.699	9.699	0.000	0.000	0.000	0.000
104	C	106	GLU	-1	-0.863	-0.919	32.151	-8.306	-8.306	0.000	0.000	0.000	0.000
105	C	107	GLY	0	0.019	0.004	34.421	0.027	0.027	0.000	0.000	0.000	0.000
106	C	108	VAL	0	-0.032	-0.023	28.219	-0.156	-0.156	0.000	0.000	0.000	0.000
107	C	109	GLN	0	0.020	0.015	28.379	-0.183	-0.183	0.000	0.000	0.000	0.000
108	C	110	LYS	1	0.870	0.917	22.444	12.686	12.686	0.000	0.000	0.000	0.000
109	C	111	ALA	0	-0.014	0.000	24.966	-0.346	-0.346	0.000	0.000	0.000	0.000
110	C	112	HIS	0	-0.022	-0.027	27.290	-0.307	-0.307	0.000	0.000	0.000	0.000
111	C	113	PHE	0	0.049	0.021	22.067	-0.126	-0.126	0.000	0.000	0.000	0.000
112	C	114	LYS	1	0.923	0.976	22.560	12.113	12.113	0.000	0.000	0.000	0.000
113	C	115	LYS	1	0.874	0.934	23.626	10.562	10.562	0.000	0.000	0.000	0.000
114	C	116	PHE	0	0.035	0.011	22.813	0.100	0.100	0.000	0.000	0.000	0.000
115	C	117	GLY	0	0.055	0.019	21.263	-0.171	-0.171	0.000	0.000	0.000	0.000
116	C	118	GLU	-1	-0.918	-0.956	21.920	-12.122	-12.122	0.000	0.000	0.000	0.000
117	C	119	ILE	0	-0.041	-0.007	24.067	0.146	0.146	0.000	0.000	0.000	0.000
118	C	120	LEU	0	-0.008	0.000	20.546	0.198	0.198	0.000	0.000	0.000	0.000
119	C	121	ALA	0	-0.014	-0.013	20.593	-0.139	-0.139	0.000	0.000	0.000	0.000
120	C	122	THR	0	-0.062	-0.025	22.010	0.132	0.132	0.000	0.000	0.000	0.000
121	C	123	GLY	0	-0.003	-0.012	25.607	0.248	0.248	0.000	0.000	0.000	0.000
122	C	124	LEU	0	0.002	-0.004	19.952	0.264	0.264	0.000	0.000	0.000	0.000
123	C	125	PRO	0	0.033	0.022	22.548	0.176	0.176	0.000	0.000	0.000	0.000
124	C	126	GLN	0	-0.083	-0.037	24.677	0.410	0.410	0.000	0.000	0.000	0.000
125	C	127	VAL	0	-0.081	-0.042	25.605	0.457	0.457	0.000	0.000	0.000	0.000
126	C	128	LEU	0	-0.062	-0.010	21.119	-0.005	-0.005	0.000	0.000	0.000	0.000
127	C	129	ASP	-1	-0.897	-0.952	24.975	-11.787	-11.787	0.000	0.000	0.000	0.000
128	C	130	ASP	-1	-0.909	-0.940	19.979	-15.664	-15.664	0.000	0.000	0.000	0.000
129	C	131	TYR	0	0.006	-0.022	19.398	-0.370	-0.370	0.000	0.000	0.000	0.000
130	C	132	ASP	-1	-0.854	-0.913	14.576	-19.986	-19.986	0.000	0.000	0.000	0.000
131	C	133	ALA	0	0.012	-0.014	16.195	-0.609	-0.609	0.000	0.000	0.000	0.000
132	C	134	LEU	0	-0.077	-0.038	13.089	0.168	0.168	0.000	0.000	0.000	0.000
133	C	135	ALA	0	0.037	0.024	11.068	-0.894	-0.894	0.000	0.000	0.000	0.000
134	C	136	TRP	0	0.007	-0.009	12.081	-0.837	-0.837	0.000	0.000	0.000	0.000
135	C	137	LYS	1	0.914	0.968	14.945	16.930	16.930	0.000	0.000	0.000	0.000
136	C	138	SER	0	0.017	0.003	9.849	0.629	0.629	0.000	0.000	0.000	0.000
137	C	140	LEU	0	0.022	0.014	11.671	0.943	0.943	0.000	0.000	0.000	0.000
138	C	141	LYS	1	0.932	0.975	13.464	21.616	21.616	0.000	0.000	0.000	0.000
139	C	142	GLY	0	0.029	0.025	11.517	0.767	0.767	0.000	0.000	0.000	0.000
140	C	143	ILE	0	0.027	0.008	12.460	0.882	0.882	0.000	0.000	0.000	0.000
141	C	144	LEU	0	-0.007	-0.004	15.198	0.957	0.957	0.000	0.000	0.000	0.000
142	C	145	THR	0	-0.073	-0.036	15.313	1.094	1.094	0.000	0.000	0.000	0.000
143	C	146	LYS	1	0.865	0.937	11.503	23.677	23.677	0.000	0.000	0.000	0.000
144	C	147	ILE	0	-0.022	0.009	16.955	0.802	0.802	0.000	0.000	0.000	0.000
145	C	148	SER	0	-0.054	-0.055	20.276	0.699	0.699	0.000	0.000	0.000	0.000
146	C	149	SER	0	-0.011	-0.026	19.172	0.699	0.699	0.000	0.000	0.000	0.000
147	C	150	ARG	1	0.757	0.856	21.240	13.303	13.303	0.000	0.000	0.000	0.000
148	C	151	LEU	-1	-0.871	-0.903	24.558	-11.113	-11.113	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3:HIS)