FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: XM9LZ

Calculation Name: 1Z3E-A-Xray31

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z3E

Chain ID: A

ChEMBL ID:

UniProt ID: P20429

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1275771.169022
FMO2-HF: Nuclear repulsion 1219102.230299
FMO2-HF: Total energy -56668.938723
FMO2-MP2: Total energy -56828.306327


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)


Summations of interaction energy for fragment #1(A:0: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.
-276.469-265.43919.744-14.608-16.165-0.158
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.745 / q_NPA : 0.846
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   
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].
3A2VAL00.0260.0263.781-0.4501.272-0.024-0.698-0.999-0.002
4A3THR00.011-0.0035.6184.8844.8840.0000.0000.0000.000
5A4LEU0-0.048-0.0178.6670.3060.3060.0000.0000.0000.000
6A5TYR00.010-0.01611.9101.1321.1320.0000.0000.0000.000
7A6THR0-0.011-0.02014.4420.9120.9120.0000.0000.0000.000
8A7SER00.0590.00017.7490.2860.2860.0000.0000.0000.000
9A8PRO0-0.041-0.01421.3770.0390.0390.0000.0000.0000.000
10A9SER0-0.056-0.03924.6170.0650.0650.0000.0000.0000.000
11A13CYS00.0580.06118.191-0.653-0.6530.0000.0000.0000.000
12A11THR0-0.049-0.03122.764-0.235-0.2350.0000.0000.0000.000
13A12SER00.0400.00820.339-0.464-0.4640.0000.0000.0000.000
14A14ARG10.8900.94118.32711.29011.2900.0000.0000.0000.000
15A15LYS10.9430.98420.11012.27012.2700.0000.0000.0000.000
16A16ALA00.0690.03814.873-0.232-0.2320.0000.0000.0000.000
17A17ARG10.8150.88015.47914.70114.7010.0000.0000.0000.000
18A18ALA00.0040.00816.516-0.349-0.3490.0000.0000.0000.000
19A19TRP00.0810.04011.429-0.651-0.6510.0000.0000.0000.000
20A20LEU00.000-0.01210.229-0.390-0.3900.0000.0000.0000.000
21A21GLU-1-0.956-0.96913.641-16.252-16.2520.0000.0000.0000.000
22A22GLU-1-0.880-0.92616.005-13.867-13.8670.0000.0000.0000.000
23A23HIS0-0.125-0.06313.9250.8060.8060.0000.0000.0000.000
24A24GLU-1-1.014-0.99913.538-17.176-17.1760.0000.0000.0000.000
25A25ILE0-0.058-0.0158.001-1.409-1.4090.0000.0000.0000.000
26A26PRO0-0.017-0.0147.1110.6790.6790.0000.0000.0000.000
27A27PHE00.0110.0038.008-3.052-3.0520.0000.0000.0000.000
28A28VAL00.0380.0408.9982.5492.5490.0000.0000.0000.000
29A29GLU-1-0.781-0.87611.120-17.370-17.3700.0000.0000.0000.000
30A30ARG10.7750.86513.81619.77719.7770.0000.0000.0000.000
31A31ASN00.0400.02615.906-0.002-0.0020.0000.0000.0000.000
32A32ILE00.0520.01516.9710.3410.3410.0000.0000.0000.000
33A33PHE0-0.013-0.01419.4750.4910.4910.0000.0000.0000.000
34A34SER0-0.064-0.02121.9570.8040.8040.0000.0000.0000.000
35A35GLU-1-0.849-0.89618.216-15.939-15.9390.0000.0000.0000.000
36A36PRO00.0080.01319.228-0.893-0.8930.0000.0000.0000.000
37A37LEU00.0210.02615.380-0.376-0.3760.0000.0000.0000.000
38A38SER00.032-0.00817.2110.8760.8760.0000.0000.0000.000
39A39ILE00.0420.00818.267-0.579-0.5790.0000.0000.0000.000
40A40ASP-1-0.827-0.90315.272-18.009-18.0090.0000.0000.0000.000
41A41GLU-1-0.762-0.83713.438-21.177-21.1770.0000.0000.0000.000
42A42ILE00.0260.02113.943-1.161-1.1610.0000.0000.0000.000
43A43LYS10.8360.90715.04817.79817.7980.0000.0000.0000.000
44A44GLN00.0220.02510.110-1.242-1.2420.0000.0000.0000.000
45A45ILE00.0210.01811.379-1.386-1.3860.0000.0000.0000.000
46A46LEU0-0.015-0.00713.047-0.053-0.0530.0000.0000.0000.000
47A47ARG10.7090.8327.81833.43033.4300.0000.0000.0000.000
48A48MET0-0.043-0.0027.252-0.835-0.8350.0000.0000.0000.000
49A49THR0-0.110-0.04111.2940.3050.3050.0000.0000.0000.000
50A50GLU-1-0.931-0.97614.533-22.297-22.2970.0000.0000.0000.000
51A51ASP-1-0.902-0.96816.405-15.004-15.0040.0000.0000.0000.000
52A52GLY0-0.0050.01618.5370.9970.9970.0000.0000.0000.000
53A53THR0-0.044-0.07719.657-0.409-0.4090.0000.0000.0000.000
54A54ASP-1-0.839-0.91021.523-12.726-12.7260.0000.0000.0000.000
55A55GLU-1-0.791-0.87416.280-19.156-19.1560.0000.0000.0000.000
56A56ILE00.0300.00016.342-0.276-0.2760.0000.0000.0000.000
57A57ILE0-0.0040.02119.3170.2540.2540.0000.0000.0000.000
58A58SER00.007-0.00922.9200.4390.4390.0000.0000.0000.000
59A59THR00.005-0.00524.7880.3700.3700.0000.0000.0000.000
60A60ARG10.8530.94125.86612.34012.3400.0000.0000.0000.000
61A61SER00.0110.01626.6960.4410.4410.0000.0000.0000.000
62A62LYS10.8910.91428.8109.3959.3950.0000.0000.0000.000
63A63VAL00.0340.00127.6070.3590.3590.0000.0000.0000.000
64A64PHE00.0970.05828.1020.1920.1920.0000.0000.0000.000
65A65GLN00.0420.02530.3280.3910.3910.0000.0000.0000.000
66A66LYS10.8700.93933.6758.8728.8720.0000.0000.0000.000
67A67LEU00.0160.02729.9050.3060.3060.0000.0000.0000.000
68A68ASN0-0.067-0.01434.0370.1030.1030.0000.0000.0000.000
69A69VAL00.0480.02430.6020.2170.2170.0000.0000.0000.000
70A70ASN00.0050.01532.664-0.102-0.1020.0000.0000.0000.000
71A71VAL00.0600.00326.3340.0470.0470.0000.0000.0000.000
72A72GLU-1-0.824-0.86928.104-11.792-11.7920.0000.0000.0000.000
73A73SER0-0.071-0.02529.967-0.033-0.0330.0000.0000.0000.000
74A74MET0-0.0460.01728.0480.1540.1540.0000.0000.0000.000
75A75PRO00.0170.01128.610-0.379-0.3790.0000.0000.0000.000
76A76LEU00.0760.03320.655-0.067-0.0670.0000.0000.0000.000
77A77GLN00.0090.00921.591-0.472-0.4720.0000.0000.0000.000
78A78ASP-1-0.723-0.86124.639-10.880-10.8800.0000.0000.0000.000
79A79LEU00.0160.01822.9540.0870.0870.0000.0000.0000.000
80A80TYR0-0.015-0.02018.805-0.229-0.2290.0000.0000.0000.000
81A81ARG10.9100.93922.53211.51711.5170.0000.0000.0000.000
82A82LEU0-0.0110.01325.4580.1200.1200.0000.0000.0000.000
83A83ILE0-0.004-0.01220.5460.1410.1410.0000.0000.0000.000
84A84ASN0-0.067-0.02821.8990.4950.4950.0000.0000.0000.000
85A85GLU-1-0.837-0.89923.416-10.664-10.6640.0000.0000.0000.000
86A86HIS0-0.074-0.02926.1320.3400.3400.0000.0000.0000.000
87A87PRO00.0840.03421.613-0.121-0.1210.0000.0000.0000.000
88A88GLY0-0.023-0.00122.280-0.483-0.4830.0000.0000.0000.000
89A89LEU0-0.052-0.02524.2940.1650.1650.0000.0000.0000.000
90A90LEU0-0.0330.01017.775-0.085-0.0850.0000.0000.0000.000
91A91ARG10.9250.99119.39714.63314.6330.0000.0000.0000.000
92A92ARG10.8110.91018.17711.94011.9400.0000.0000.0000.000
93A93PRO00.017-0.01815.5370.6550.6550.0000.0000.0000.000
94A94ILE00.0260.01611.9470.0750.0750.0000.0000.0000.000
95A95ILE0-0.023-0.0108.913-0.023-0.0230.0000.0000.0000.000
96A96ILE0-0.006-0.0087.6730.5200.5200.0000.0000.0000.000
97A97ASP-1-0.679-0.8172.460-62.194-60.4910.601-0.872-1.432-0.008
98A98GLU-1-0.772-0.8522.386-38.936-37.4680.810-0.787-1.492-0.005
99A99LYS10.8190.9532.94746.58248.4880.800-0.545-2.1610.003
100A100ARG10.9110.9424.92042.12242.3440.000-0.027-0.1960.000
101A101LEU00.0680.0447.137-2.053-2.0530.0000.0000.0000.000
102A102GLN0-0.072-0.0089.9540.8250.8250.0000.0000.0000.000
103A103VAL0-0.003-0.00912.450-0.188-0.1880.0000.0000.0000.000
104A104GLY00.0360.03015.6340.7710.7710.0000.0000.0000.000
105A105TYR0-0.105-0.08916.554-1.163-1.1630.0000.0000.0000.000
106A106ASN00.0140.00417.4760.9270.9270.0000.0000.0000.000
107A107GLU-1-0.866-0.92117.435-14.830-14.8300.0000.0000.0000.000
108A108ASP-1-0.926-0.96718.047-14.404-14.4040.0000.0000.0000.000
109A109GLU-1-0.963-0.99315.757-17.580-17.5800.0000.0000.0000.000
110A110ILE00.0340.02612.704-1.710-1.7100.0000.0000.0000.000
111A111ARG10.9590.97812.07315.11715.1170.0000.0000.0000.000
112A112ARG10.8530.92310.71720.07520.0750.0000.0000.0000.000
113A113PHE0-0.027-0.0166.394-2.004-2.0040.0000.0000.0000.000
114A114LEU0-0.0200.0158.133-1.180-1.1800.0000.0000.0000.000
115A115PRO00.0090.0228.789-1.237-1.2370.0000.0000.0000.000
116A116ARG10.9490.9599.91724.97924.9790.0000.0000.0000.000
117A117LYS10.9800.99012.20416.97716.9770.0000.0000.0000.000
118A118VAL0-0.030-0.03515.6990.2990.2990.0000.0000.0000.000
119A119NME00.0280.03718.4480.6640.6640.0000.0000.0000.000
120A400SO4-2-1.606-1.7761.725-195.272-193.16616.453-10.281-8.277-0.130
121A401SO4-2-1.706-1.82823.983-24.707-24.7070.0000.0000.0000.000
122A403SO4-2-1.649-1.77222.179-26.282-26.2820.0000.0000.0000.000
123A404HOH0-0.028-0.01930.9090.1510.1510.0000.0000.0000.000
124A405HOH00.0100.00610.8040.3230.3230.0000.0000.0000.000
125A406HOH0-0.001-0.00629.5700.0470.0470.0000.0000.0000.000
126A407HOH0-0.022-0.01417.6700.3980.3980.0000.0000.0000.000
127A409HOH00.0320.02226.988-0.188-0.1880.0000.0000.0000.000
128A410HOH0-0.010-0.0065.6272.9932.9930.0000.0000.0000.000
129A412HOH00.009-0.00721.391-0.089-0.0890.0000.0000.0000.000
130A413HOH00.0250.01614.443-0.577-0.5770.0000.0000.0000.000
131A414HOH0-0.036-0.03019.7550.2230.2230.0000.0000.0000.000
132A415HOH00.0150.00420.612-0.349-0.3490.0000.0000.0000.000
133A416HOH0-0.018-0.00922.900-0.067-0.0670.0000.0000.0000.000
134A417HOH0-0.055-0.03726.346-0.065-0.0650.0000.0000.0000.000
135A418HOH0-0.005-0.0115.055-2.248-2.2480.0000.0000.0000.000
136A419HOH00.0050.00031.3110.0340.0340.0000.0000.0000.000
137A421HOH00.0350.01712.345-0.181-0.1810.0000.0000.0000.000
138A422HOH0-0.025-0.01620.9720.1310.1310.0000.0000.0000.000
139A423HOH0-0.033-0.02221.887-0.089-0.0890.0000.0000.0000.000
140A424HOH0-0.041-0.02826.3920.1240.1240.0000.0000.0000.000
141A425HOH0-0.011-0.01815.776-0.342-0.3420.0000.0000.0000.000
142A426HOH0-0.081-0.0553.5930.2280.4260.004-0.080-0.1220.000
143A427HOH0-0.068-0.05323.8460.2520.2520.0000.0000.0000.000
144A428HOH0-0.021-0.02419.188-0.072-0.0720.0000.0000.0000.000
145A429HOH0-0.069-0.0635.3462.1372.1370.0000.0000.0000.000
146A430HOH0-0.043-0.0406.3272.1452.1450.0000.0000.0000.000
147A431HOH0-0.057-0.04018.4570.1430.1430.0000.0000.0000.000
148A432HOH00.0040.02425.553-0.145-0.1450.0000.0000.0000.000
149A433HOH00.0090.00921.259-0.268-0.2680.0000.0000.0000.000
150A434HOH0-0.049-0.04032.280-0.026-0.0260.0000.0000.0000.000
151A435HOH0-0.036-0.02615.803-0.542-0.5420.0000.0000.0000.000
152A436HOH0-0.001-0.00715.182-0.139-0.1390.0000.0000.0000.000
153A437HOH0-0.0120.00414.9970.3290.3290.0000.0000.0000.000
154A438HOH0-0.008-0.00231.4230.0310.0310.0000.0000.0000.000
155A441HOH0-0.007-0.00218.524-0.262-0.2620.0000.0000.0000.000
156A442HOH0-0.064-0.05623.0930.2020.2020.0000.0000.0000.000
157A443HOH0-0.020-0.02322.2740.2840.2840.0000.0000.0000.000
158A447HOH0-0.008-0.0075.188-1.159-1.1590.0000.0000.0000.000
159A449HOH0-0.032-0.0302.247-9.090-7.3851.100-1.318-1.486-0.016
160A457HOH0-0.027-0.02119.6860.3270.3270.0000.0000.0000.000
161A459HOH0-0.045-0.04018.2120.4100.4100.0000.0000.0000.000
162A461HOH0-0.068-0.08027.3050.0410.0410.0000.0000.0000.000
163A462HOH0-0.021-0.00813.2010.3250.3250.0000.0000.0000.000
164A463HOH0-0.043-0.03537.9200.0630.0630.0000.0000.0000.000
165A464HOH0-0.033-0.02712.737-0.141-0.1410.0000.0000.0000.000
166A466HOH0-0.036-0.03223.7470.0700.0700.0000.0000.0000.000
167A467HOH0-0.023-0.01612.7550.0370.0370.0000.0000.0000.000
168A468HOH0-0.031-0.01617.8170.3320.3320.0000.0000.0000.000
169A469HOH0-0.025-0.01831.355-0.059-0.0590.0000.0000.0000.000
170A471HOH0-0.018-0.02623.9800.1060.1060.0000.0000.0000.000
171A473HOH0-0.016-0.02521.6940.0190.0190.0000.0000.0000.000
172A474HOH0-0.046-0.01912.914-0.500-0.5000.0000.0000.0000.000
173A476HOH0-0.022-0.01512.4690.3300.3300.0000.0000.0000.000
174A477HOH00.0190.02116.4460.1110.1110.0000.0000.0000.000
175A480HOH00.0320.0208.8250.5330.5330.0000.0000.0000.000
176A481HOH0-0.043-0.03133.425-0.030-0.0300.0000.0000.0000.000
177A482HOH0-0.002-0.00516.4440.1920.1920.0000.0000.0000.000
178A483HOH0-0.025-0.01323.9920.1260.1260.0000.0000.0000.000
179A484HOH0-0.014-0.02122.9840.1530.1530.0000.0000.0000.000
180A488HOH0-0.008-0.02315.635-0.070-0.0700.0000.0000.0000.000
181A490HOH0-0.035-0.02512.1950.1930.1930.0000.0000.0000.000
182A494HOH0-0.005-0.00325.509-0.094-0.0940.0000.0000.0000.000
183A495HOH00.0420.03312.362-0.090-0.0900.0000.0000.0000.000
184A498HOH0-0.041-0.02520.616-0.018-0.0180.0000.0000.0000.000
185A499HOH0-0.021-0.01613.2860.4580.4580.0000.0000.0000.000
186A500HOH0-0.021-0.0158.9640.6110.6110.0000.0000.0000.000
187B45HOH0-0.045-0.01821.6190.3150.3150.0000.0000.0000.000